@article {pmid37749660,
year = {2023},
author = {Wegner, CE and Stahl, R and Velsko, I and Hübner, A and Fagernäs, Z and Warinner, C and Lehmann, R and Ritschel, T and Totsche, KU and Küsel, K},
title = {A glimpse of the paleome in endolithic microbial communities.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {210},
pmid = {37749660},
issn = {2049-2618},
support = {CRC 1076 AquaDiva - Project-ID 218627073//Deutsche Forschungsgemeinschaft/ ; CRC 1076 AquaDiva - Project-ID 218627073//Deutsche Forschungsgemeinschaft/ ; CRC 1076 AquaDiva - Project-ID 218627073//Deutsche Forschungsgemeinschaft/ ; CRC 1076 AquaDiva - Project-ID 218627073//Deutsche Forschungsgemeinschaft/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Genomics ; Paleontology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; },
abstract = {BACKGROUND: The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.<br><br>RESULTS: By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25&#x2009;&#xd7;&#x2009;10[5] cells&#x2009;&#xd7;&#x2009;g[-1] rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.<br><br>CONCLUSIONS: Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.},
}
@article {pmid37749192,
year = {2023},
author = {Akter, S and Rahman, MS and Ali, H and Minch, B and Mehzabin, K and Siddique, MM and Galib, SM and Yesmin, F and Azmuda, N and Adnan, N and Hasan, NA and Rahman, SR and Moniruzzaman, M and Ahmed, MF},
title = {Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15976},
pmid = {37749192},
issn = {2045-2322},
mesh = {Bays ; Phylogeny ; *Microbiota ; *Alteromonas ; *Dinoflagellida ; },
abstract = {The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.},
}
@article {pmid37743871,
year = {2023},
author = {Liu, Y and Chan, MTV and Chan, FKL and Wu, WKK and Ng, SC and Zhang, L},
title = {Lower gut abundance of Eubacterium rectale is linked to COVID-19 mortality.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1249069},
pmid = {37743871},
issn = {2235-2988},
mesh = {Adult ; Humans ; Eubacterium ; *COVID-19 ; Butyrates ; *Gastrointestinal Microbiome ; Metagenome ; },
abstract = {INTRODUCTION: Emerging preclinical and clinical studies suggest that altered gut microbiome composition and functions are associated with coronavirus 2019 (COVID- 19) severity and its long-term complications. We hypothesize that COVID-19 outcome is associated with gut microbiome status in population-based settings.<br><br>METHODS: Gut metagenomic data of the adult population consisting of 2871 subjects from 16 countries were obtained from ExperimentHub through R, while the dynamic death data of COVID-19 patients between January 22, 2020 and December 8, 2020 in each country was acquired from Johns Hopkins Coronavirus Resource Center. An adjusted stable mortality rate (SMR) was used to represent these countries' mortality and correlated with the mean relative abundance (mRA) of healthy adult gut microbiome species.<br><br>RESULTS: After excluding bacterial species with low prevalence (prevalence <0.2 in the included countries), the &#x3b2;-diversity was significantly higher in the countries with high SMR when compared with those with median or low SMR (p <0.001). We then identified the mRA of two butyrate producers, Eubacterium rectale and Roseburia intestinalis, that were negatively correlated with SMR during the study period. And the reduction of these species was associated with severer COVID-19 manifestation.<br><br>CONCLUSION: Population-based microbiome signatures with the stable mortality rate of COVID-19 in different countries suggest that altered gut microbiome composition and functions are associated with mortality of COVID-19.},
}
@article {pmid37741805,
year = {2023},
author = {Wicaksono, WA and Cernava, T and Wassermann, B and Abdelfattah, A and Soto-Giron, MJ and Toledo, GV and Virtanen, SM and Knip, M and Hyöty, H and Berg, G},
title = {The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2258565},
pmid = {37741805},
issn = {1949-0984},
mesh = {Humans ; Vegetables ; Plants, Edible ; Fruit ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria/genetics ; },
abstract = {Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.},
}
@article {pmid37740058,
year = {2023},
author = {Komori, E and Kato-Kogoe, N and Imai, Y and Sakaguchi, S and Taniguchi, K and Omori, M and Ohmichi, M and Nakamura, S and Nakano, T and Lee, SW and Ueno, T},
title = {Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15863},
pmid = {37740058},
issn = {2045-2322},
mesh = {Humans ; *Stomach Neoplasms/surgery ; RNA, Ribosomal, 16S/genetics ; Gastrectomy ; *Microbiota/genetics ; },
abstract = {Gastric cancer is one of the leading causes of death worldwide, and resections are performed to cure the disease. We have previously reported the changes in the gastric microbiota after gastric cancer resection, which may be associated with the oral microbiota; however, the changes in the oral microbiota remain uncharacterized. This study aimed to characterize the changes in the salivary microbiota caused by gastric cancer resection and to evaluate their association with the gastric fluid microbiota. Saliva and gastric fluid samples were collected from 63 patients who underwent gastrectomy before and after surgery, and a 16S rRNA metagenomic analysis was performed to compare the microbiota composition. The number of bacterial species in the salivary microbiota decreased, and the bacterial composition changed after the resection of gastric cancer. In addition, we identified several bacterial genera that varied significantly in the salivary microbiota, some of which also showed similar changes in the gastric fluid microbiota. These findings indicate that changes in the gastric environment affect the oral microbiota, emphasizing the close association between the oral and gastric fluid microbiota. Our study signifies the importance of focusing on the oral microbiota in the perioperative period of gastrectomy in patients with gastric cancer.},
}
@article {pmid37499616,
year = {2023},
author = {Xiong, X and Rao, Y and Ma, J and Wang, Z and He, Q and Gong, J and Sheng, W and Xu, J and Zhu, X and Tan, Y and Yang, Y},
title = {A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome.},
journal = {Poultry science},
volume = {102},
number = {10},
pages = {102931},
pmid = {37499616},
issn = {1525-3171},
mesh = {Animals ; *Metagenome ; *Gastrointestinal Microbiome ; Quail/genetics ; Chickens/genetics ; Genes, Microbial ; },
abstract = {The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.},
}
@article {pmid37739268,
year = {2023},
author = {Ge, F and Guo, R and Liang, Y and Chen, Y and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M},
title = {Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus.},
journal = {Virus research},
volume = {336},
number = {},
pages = {199226},
doi = {10.1016/j.virusres.2023.199226},
pmid = {37739268},
issn = {1872-7492},
abstract = {Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.},
}
@article {pmid37737154,
year = {2023},
author = {Luan, M and Niu, M and Yang, P and Han, D and Zhang, Y and Li, W and He, Q and Zhao, Y and Mao, B and Chen, J and Mou, K and Li, P},
title = {Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {265},
pmid = {37737154},
issn = {1471-2180},
support = {2020QN-31//Institutional Foundation of The First Affiliated Hospital of Xi'an Jiaotong University/ ; 2022SF-248//the Science and Technology Research and Development Program of Shaanxi Province of China/ ; 81972935//National Natural Sciences Foundation of China/ ; 2023-JC-YB-665//the Natural Science Basis Research Plan in Shaanxi Province of China/ ; },
mesh = {Humans ; *Vitiligo/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Bacteroides fragilis ; Clostridiales ; },
abstract = {BACKGROUND: Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo.<br><br>METHODS: Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases.<br><br>RESULTS: Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs.<br><br>CONCLUSIONS: The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.},
}
@article {pmid37737001,
year = {2023},
author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE},
title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).},
journal = {Infectious disease reports},
volume = {15},
number = {5},
pages = {549-563},
pmid = {37737001},
issn = {2036-7430},
abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.},
}
@article {pmid37736746,
year = {2023},
author = {Li, S and Lian, WH and Han, JR and Ali, M and Lin, ZL and Liu, YH and Li, L and Zhang, DY and Jiang, XZ and Li, WJ and Dong, L},
title = {Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {67},
pmid = {37736746},
issn = {2055-5008},
support = {32061143043//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270076//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32000005//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Metagenome ; Soil ; },
abstract = {Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.},
}
@article {pmid37735195,
year = {2023},
author = {Malukiewicz, J and D'arc, M and Dias, CA and Cartwright, RA and Grativol, AD and Moreira, SB and Souza, AR and Tavares, MCH and Pissinatti, A and Ruiz-Miranda, CR and Santos, AFA},
title = {Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15679},
pmid = {37735195},
issn = {2045-2322},
mesh = {Humans ; Animals ; *Callithrix ; *Gastrointestinal Microbiome ; Bifidobacterium ; Callitrichinae ; },
abstract = {Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.},
}
@article {pmid37699793,
year = {2023},
author = {Chakraborty, M and Acharya, D and Dutta, TK},
title = {Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches.},
journal = {Journal of applied microbiology},
volume = {134},
number = {9},
pages = {},
doi = {10.1093/jambio/lxad208},
pmid = {37699793},
issn = {1365-2672},
support = {760/CSIR-UGC NET/June 2017//University Grants Commission/ ; //Department of Science and Technology, Government of West Bengal/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Fishes ; Firmicutes/genetics ; Bacteroidetes/genetics ; Bangladesh ; Proteobacteria/genetics ; },
abstract = {AIMS: The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota.<br><br>METHODS AND RESULTS: Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively.<br><br>CONCLUSIONS: A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential.<br><br>IMPACT STATEMENT: The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.},
}
@article {pmid37679294,
year = {2023},
author = {Umar, M and Bowman, JP and Asis, C and McConchie, C and Eyles, A and Stanley, R and Gracie, A},
title = {Microbial communities associated with resin canal discoloration in mango fruit.},
journal = {Letters in applied microbiology},
volume = {76},
number = {9},
pages = {},
doi = {10.1093/lambio/ovad104},
pmid = {37679294},
issn = {1472-765X},
support = {IC140100024//Australian Research Council/ ; },
mesh = {*Mangifera ; Fruit ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Enterobacteriaceae ; },
abstract = {Resin canal discoloration (RCD) severely impacts the fruit quality of mango, diminishes consumer confidence, and reduces sales, but the biological cause is still unclear. Using next-generation sequencing, the overall microbial community composition of RCD+ and visually healthy mango fruits was determined for the first time to examine the possible role of bacterial and fungal pathogens in RCD. The diversity profile of bacterial and fungal communities was determined using primers targeting the 16S rRNA gene and Internal Transcribed Spacer (ITS) regions. Results showed that bacterial communities in healthy fruits are clustered together and significantly different from those in RCD+ fruits. Tatumella and Pantoea species were the most abundant bacterial taxa on RCD+ fruit, and both have been linked to disease outbreaks in a variety of fruit crops. Fungal communities were generally similar between RCD+ and normal samples, though non-pathogenic yeasts Meyerozyma and Naganishia tended to dominate the fungal communities on RCD+ fruit. The study indicates that bacteria rather than fungal organisms are more likely to be associated with RCD in mango. This finding will facilitate the isolation and confirmation of RCD-causing organisms and the development of control strategies to manage RCD problem in mango.},
}
@article {pmid37666133,
year = {2023},
author = {Ahmed, B and Gahlot, P and Balasundaram, G and Tyagi, VK and Banu J, R and Vivekanand, V and Kazmi, AA},
title = {Semi-continuous anaerobic co-digestion of thermal and thermal-alkali processed organic fraction of municipal solid waste: Methane yield, energy analysis, anaerobic microbiome.},
journal = {Journal of environmental management},
volume = {345},
number = {},
pages = {118907},
doi = {10.1016/j.jenvman.2023.118907},
pmid = {37666133},
issn = {1095-8630},
mesh = {Anaerobiosis ; *Solid Waste ; *Microbiota ; Alkalies ; Methane ; Digestion ; },
abstract = {The semi-continuous anaerobic co-digestion (AcoD) of thermal and thermal-alkali pretreated organic fraction of municipal solid waste (OFMSW) and sewage sludge (SS) was studied under varying hydraulic retention times (HRT) and organic loading rates (OLR Three semi-continuous digesters were operated under control (non-pre-treated), thermally pretreated (125 °C), and thermal-alkali pretreated (125°C-3g/L NaOH) conditions at variable OLRs at 2.5, 4.0, 5.1, and 7.6 kgVS/m[3].d and corresponding HRTs of 30, 20, 15, and 10 days. The 10 and 43% higher methane yield (0.445 m[3]/kgVS) and 11 and 57% higher VS removal (52%) was achieved for thermal-alkali pretreated digester at 5.1 kgVS/m[3].d OLR over thermally pretreated (0.408 m[3]/kgVS, 45% VS removal) and control digesters (0.310 m[3]/kgVS, 33% VS removal), respectively. Thermal and thermal-alkali digesters failed on increasing the OLR to 7.6 kgVS/m[3].d, whereas the control digester becomes upset at 5.1 kgVS/m[3].d OLR. The metagenomic study revealed that Firmicutes, Bacteroidetes, Chloroflexi, Euryarchaeota, Proteobacteria, and Actinobacteria were the predominant bacterial population, whereas Methanosarcina and Methanothrix dominated the archaeal community. Energy balance analysis revealed that thermal alkali pretreatment showed the highest positive energy balance of 114.6 MJ/ton with an energy ratio of 1.25 compared with thermally pretreated (81.5 MJ/ton) and control samples (-46.9 MJ/ton). This work pave the way for scaleup of both thermal and thermal-alkali pre-treatment at 125 °C to realize the techno-economic and energy potential of the process.},
}
@article {pmid37604017,
year = {2023},
author = {Xu, N and Qiu, D and Zhang, Z and Wang, Y and Chen, B and Zhang, Q and Wang, T and Hong, W and Zhou, NY and Penuelas, J and Gillings, M and Zhu, YG and Qian, H},
title = {A global atlas of marine antibiotic resistance genes and their expression.},
journal = {Water research},
volume = {244},
number = {},
pages = {120488},
doi = {10.1016/j.watres.2023.120488},
pmid = {37604017},
issn = {1879-2448},
mesh = {Humans ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Drug Resistance, Microbial/genetics ; *Microbiota ; },
abstract = {Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.},
}
@article {pmid37429473,
year = {2023},
author = {Yue, Y and Zhang, H and Deng, P and Tan, M and Chen, C and Tang, B and Li, J and Chen, F and Zhao, Q and Li, L and Hao, R and Wang, H and Luo, Y and Tian, L and Xie, J and Chen, M and Yu, Z and Zhou, Z and Pi, H},
title = {Environmental cadmium exposure facilitates mammary tumorigenesis via reprogramming gut microbiota-mediated glutamine metabolism in MMTV-Erbb2 mice.},
journal = {The Science of the total environment},
volume = {897},
number = {},
pages = {165348},
doi = {10.1016/j.scitotenv.2023.165348},
pmid = {37429473},
issn = {1879-1026},
mesh = {Mice ; Animals ; Cadmium/toxicity ; Glutamine ; *Gastrointestinal Microbiome ; Ki-67 Antigen ; *Mammary Neoplasms, Experimental/chemically induced/metabolism/pathology ; Cell Transformation, Neoplastic/metabolism ; Mice, Transgenic ; Carcinogenesis/chemically induced ; Necrosis ; },
abstract = {Cadmium (Cd) is a heavy metal that has been widely reported to be linked to the onset and progression of breast cancer (BC). However, the mechanism of Cd-induced mammary tumorigenesis remains elusive. In our study, a transgenic mouse model that spontaneously develops tumors through overexpression of wild-type Erbb2 (MMTV-Erbb2) was constructed to investigate the effects of Cd exposure on BC tumorigenesis. The results showed that oral exposure to 3.6 mg/L Cd for 23 weeks dramatically accelerated tumor appearance and growth, increased Ki67 density and enhanced focal necrosis and neovascularization in the tumor tissue of MMTV-Erbb2 mice. Notably, Cd exposure enhanced glutamine (Gln) metabolism in tumor tissue, and 6-diazo-5-oxo-l-norleucine (DON), a Gln metabolism antagonist, inhibited Cd-induced breast carcinogenesis. Then our metagenomic sequencing and mass spectrometry-based metabolomics confirmed that Cd exposure disturbed gut microbiota homeostasis, especially Helicobacter and Campylobacter abundance remodeling, which altered the gut metabolic homeostasis of Gln. Moreover, intratumoral Gln metabolism profoundly increased under Cd-elevated gut permeability. Importantly, depletion of microbiota with an antibiotic cocktail (AbX) treatment led to a significant delay in the appearance of palpable tumors, inhibition of tumor growth, decrease in tumor weight, reduction in Ki67 expression and low-grade pathology in Cd-exposed MMTV-Erbb2 mice. Also, transplantation of Cd-modulated microbiota decreased tumor latency, accelerated tumor growth, increased tumor weight, upregulated Ki67 expression and exacerbated neovascularization as well as focal necrosis in MMTV-Erbb2 mice. In summary, Cd exposure induced gut microbiota dysbiosis, elevated gut permeability and increased intratumoral Gln metabolism, leading to the promotion of mammary tumorigenesis. This study provides novel insights into environmental Cd exposure-mediated carcinogenesis.},
}
@article {pmid37385198,
year = {2023},
author = {Tian, Z and Li, G and Xiong, Y and Cao, X and Pang, H and Tang, W and Liu, Y and Bai, M and Zhu, Q and Du, C and Li, M and Zhang, L},
title = {Step-feeding food waste fermentation liquid as supplementary carbon source for low C/N municipal wastewater treatment: Bench scale performance and response of microbial community.},
journal = {Journal of environmental management},
volume = {345},
number = {},
pages = {118434},
doi = {10.1016/j.jenvman.2023.118434},
pmid = {37385198},
issn = {1095-8630},
mesh = {Humans ; Wastewater ; Fermentation ; Food ; Waste Disposal, Fluid/methods ; Carbon ; Sewage ; *Severe Fever with Thrombocytopenia Syndrome ; Bioreactors ; *Refuse Disposal ; *Microbiota ; Nitrogen ; Denitrification ; },
abstract = {Municipal wastewater treatment often lacks carbon source, while carbon-rich organics in food waste are deficiently utilized. In this study, the food waste fermentation liquid (FWFL) was step-fed into a bench-scale step-feed three-stage anoxic/aerobic system (SFTS-A/O), to investigate its performance in nutrients removal and the response of microbial community as a supplementary carbon source. The results showed that the total nitrogen (TN) removal rate increased by 21.8-109.3% after step-feeding FWFL. However, the biomass of the SFTS-A/O system was increased by 14.6% and 11.9% in the two phases of the experiment, respectively. Proteobacteria was found to be the dominant functional phyla induced by FWFL, and the increase of its abundance attributed to the enrichment of denitrifying bacteria and carbohydrate-metabolizing bacteria was responsible for the biomass increase. Azospira belonged to Proteobacteria phylum was the dominant denitrifying genera when step-fed with FWFL, its abundance was increased from 2.7% in series 1 (S1) to 18.6% in series 2 (S2) and became the keystone species in the microbial networks. Metagenomics analysis revealed that step-feeding FWFL enhanced the abundance of denitrification and carbohydrates-metabolism genes, which were encode mainly by Proteobacteria. This study constitutes a key step towards the application of FWFL as a supplementary carbon source for low C/N municipal wastewater treatment.},
}
@article {pmid36995238,
year = {2023},
author = {Zhao, X and Sun, C and Jin, M and Chen, J and Xing, L and Yan, J and Wang, H and Liu, Z and Chen, WH},
title = {Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0434022},
pmid = {36995238},
issn = {2165-0497},
mesh = {Humans ; *Bacteriophages/classification/genetics/isolation &amp; purification ; *Feces/microbiology/virology ; *Lactobacillus plantarum/virology ; Metagenomics ; Culture Techniques ; Genome, Viral/genetics ; Biodiversity ; },
abstract = {Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.},
}
@article {pmid35118437,
year = {2022},
author = {Pryszlak, A and Wenzel, T and Seitz, KW and Hildebrand, F and Kartal, E and Cosenza, MR and Benes, V and Bork, P and Merten, CA},
title = {Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.},
journal = {Cell reports methods},
volume = {2},
number = {1},
pages = {None},
pmid = {35118437},
issn = {2667-2375},
support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Microfluidics/methods ; Genomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by successfully enriching endogenous Bacteroides vulgatus to the level required for de novo assembly of high-quality genomes. Although microbiome strains are increasingly demanded for biomedical applications, a vast majority of species and strains are uncultivated and without reference genomes. We address this shortcoming by encapsulating complex microbiome samples directly into microfluidic droplets and amplifying a target-specific genomic fragment using a custom molecular TaqMan probe. We separate those positive droplets by droplet sorting, selectively enriching single target strain cells. Finally, we present a protocol to purify the genomic DNA while specifically removing amplicons and cell debris for high-quality genome sequencing.},
}
@article {pmid37734616,
year = {2023},
author = {Sang, Y and Mo, S and Zeng, S and Wu, X and Kashif, M and Song, J and Yu, D and Bai, L and Jiang, C},
title = {Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {167199},
doi = {10.1016/j.scitotenv.2023.167199},
pmid = {37734616},
issn = {1879-1026},
abstract = {Aquacultures are the main reason for the environmental selection of antibiotic resistance genes (ARGs), resulting in the enrichment of ARGs. As a filter, a marine mangrove ecosystem can reduce antimicrobial resistance (AMR) or eliminate ARGs; however, its elimination mechanism remains unclear. This study investigated the spatiotemporal dynamic distribution of ARGs in two different types of mangrove habitats (shrimp ponds and virgin forests), within a subtropical gulf located in the Beibu Gulf, China, during dry and wet seasons by using metagenomics and real time quantitative polymerase chain reaction (RT-qPCR) analysis. As the key environmental factors, sulfide, salinity, and mobile genetic elements significantly were found to contribute to ARGs distribution, respectively. Wet and dry seasons influenced the dispersal of ARGs but did not affect the microbial community structure. Three potential biomarkers, TEM-116, smeD, and smeE, played key roles in seasonal differences. The key different genes in the biological relevance of absolute abundance were demonstrated by RT-qPCR. Co-occurrence network analysis indicated that high-abundance ARGs were distributed in a modular manner. For the first time, a risk index weighted by risk rank (RIR) was proposed and used to quantify the human risk of ARGs in the mangrove metagenome. The shrimp ponds during the wet season showed the highest RIR detected. In addition to offering a perspective on reducing AMR in mangrove wetlands, this study constructed the first spatiotemporal dynamic model of ARGs in the Beibu Gulf, China and contributed to revealing the global spread of ARGs. Meanwhile, this study proposes a new pipeline for assessing the risk of ARGs, while also exploring the concept of "One Health."},
}
@article {pmid37732776,
year = {2023},
author = {Mujakić, I and Cabello-Yeves, PJ and Villena-Alemany, C and Piwosz, K and Rodriguez-Valera, F and Picazo, A and Camacho, A and Koblížek, M},
title = {Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0111223},
doi = {10.1128/spectrum.01112-23},
pmid = {37732776},
issn = {2165-0497},
abstract = {Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.},
}
@article {pmid37727808,
year = {2023},
author = {Herzog, EL and Kreuzer, M and Zinkernagel, MS and Zysset-Burri, DC},
title = {Challenges and insights in the exploration of the low abundance human ocular surface microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1232147},
pmid = {37727808},
issn = {2235-2988},
mesh = {Humans ; *Nylons ; Reproducibility of Results ; Face ; Conjunctiva ; *Microbiota ; },
abstract = {PURPOSE: The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes.<br><br>METHODS: Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2.<br><br>RESULTS: The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied.<br><br>CONCLUSION: The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.},
}
@article {pmid37657622,
year = {2023},
author = {Dong, Z and Xie, Q and Yuan, Y and Shen, X and Hao, Y and Li, J and Xu, H and Kuang, W},
title = {Strain-level structure of gut microbiome showed potential association with cognitive function in major depressive disorder: A pilot study.},
journal = {Journal of affective disorders},
volume = {341},
number = {},
pages = {236-247},
doi = {10.1016/j.jad.2023.08.129},
pmid = {37657622},
issn = {1573-2517},
mesh = {Animals ; Humans ; *Depressive Disorder, Major ; *Gastrointestinal Microbiome/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Cognition ; },
abstract = {BACKGROUND: Although the association between gut microbiota and the pathogenesis of major depressive disorder (MDD) has been well studied, it is unclear whether gut microbiota affects cognitive function in patients with MDD. In this study, we explored the association between gut microbiota and cognitive function in MDD and its possible mechanisms.<br><br>METHODS: We enrolled 57 patients with MDD and 30 healthy controls (HCs) and used 16S rRNA gene sequencing analysis and shotgun metagenomic sequencing analysis to determine gut microbial composition.<br><br>RESULTS: The richness and diversity of gut microbiota in patients with MDD were the same as those in HCs, but there were differences in the abundance of Bifidobacterium and Blautia. Compared with HCs, two strains (bin_32 and bin_55) were significantly increased, and one strain (bin_31) was significantly decreased in patients with MDD based on the strain-level meta-analysis. Time to complete the Stroop-C had significant negative correlations with bin_31 and bin_32. Bin_55 had significant negative correlations with time to complete the Stroop-C, time to complete the Stroop-CW, and repeated animal words in 60&#xa0;s but significant positive correlations with correct answers in 120&#xa0;s on the Stroop-CW.<br><br>LIMITATIONS: This study only tested the cognitive function of MDD in a small sample, which may have caused some bias.<br><br>CONCLUSIONS: Based on our strain-level analysis, we found that gut microbiota may be associated with the pathogenesis of MDD and may have potential effects on cognitive function.},
}
@article {pmid37505986,
year = {2023},
author = {Shetty, P and Shetty, S and Rai, P and Kumar, BK and Bhat, R},
title = {Role of oral microbiota in irreversible pulpitis - Current strategies and future perspectives.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {70},
number = {3},
pages = {177-186},
doi = {10.1556/030.2023.02082},
pmid = {37505986},
issn = {1588-2640},
mesh = {Humans ; *Pulpitis/microbiology ; Bacteria/genetics ; *Microbiota ; Inflammation ; },
abstract = {Irreversible pulpitis is an inflammation of the tooth pulp caused by an opportunity-driven invasion of the pulp space by oral microbiota typically prevalent in the oral cavity. Microbial organisms are extensively recognised to be the fundamental cause of endodontic infections and treatment failures. Previously, bacterial species responsible for these infections were largely recognised using conventional microbial culture techniques, lending credence to the widely held belief that anaerobic Gram-negative bacteria frequently enter the pulp space and trigger endodontic infections. The advent of novel technologies grants the advantage of detecting and studying microbial populations via an amalgamation of the modern "Omics" techniques and meticulous bioinformatics analysis, additionally detecting the metatranscriptome, metaproteome and metabolome along with the metagenome. Amongst these analytical strategies, metagenomic analyses are essentially pragmatic for investigating the oral microbiome. Metagenomics favor not only assessment of microbial composition in diseased conditions, but also contributes to detection of novel, potentially pathogenic species inclusive of non-viable bacteria. The present review describes current knowledge of root canal microbiome, including its composition and functional attributes, the novel strategies available for detection of microbiome as well as challenges associated and provides some crucial pointers for areas of future research.},
}
@article {pmid37488221,
year = {2023},
author = {Sun, J and Germain, A and Kaglan, G and Servant, F and Lelouvier, B and Federici, M and Fernandez-Real, JM and Sala, DT and Neagoe, RM and Bouloumié, A and Burcelin, R},
title = {The visceral adipose tissue bacterial microbiota provides a signature of obesity based on inferred metagenomic functions.},
journal = {International journal of obesity (2005)},
volume = {47},
number = {10},
pages = {1008-1022},
pmid = {37488221},
issn = {1476-5497},
mesh = {Animals ; Humans ; *Intra-Abdominal Fat/metabolism ; Obesity/metabolism ; *Microbiota ; Obesity, Abdominal/metabolism ; Inflammation/metabolism ; Adipose Tissue/metabolism ; },
abstract = {BACKGROUND: Metabolic inflammation mediated obesity requires bacterial molecules to trigger immune and adipose cells leading to inflammation and adipose depot development. In addition to the well-established gut microbiota dysbiosis, a leaky gut has been identified in patients with obesity and animal models, characterized by the presence of a tissue microbiota in the adipose fat pads.<br><br>METHODS: To determine its potential role, we sequenced the bacterial 16&#x2009;S rRNA genes in the visceral adipose depot of patients with obesity. Taking great care (surgical, biochemical, and bioinformatic) to avoid environmental contaminants. We performed statistical discriminant analyses to identify specific signatures and constructed network of interactions between variables.<br><br>RESULTS: The data showed that a specific 16SrRNA gene signature was composed of numerous bacterial families discriminating between lean versus patients with obesity and people with severe obesity. The main discriminant families were Burkholderiaceae, Yearsiniaceae, and Xanthomonadaceae, all of which were gram-negative. Interestingly, the Morganellaceae were totally absent from people without obesity while preponderant in all in patients with obesity. To generate hypotheses regarding their potential role, we inferred metabolic pathways from the 16SrRNA gene signatures. We identified several pathways associated with adenosyl-cobalamine previously described to be linked with adipose tissue development. We further identified chorismate biosynthesis, which is involved in aromatic amino-acid metabolism and could play a role in fat pad development. This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis.<br><br>CONCLUSIONS: This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis in obesity and notably the potential role of tissue microbiota.},
}
@article {pmid37487417,
year = {2023},
author = {Armstrong, AJS and Horton, DB and Andrews, T and Greenberg, P and Roy, J and Gennaro, ML and Carson, JL and Panettieri, RA and Barrett, ES and Blaser, MJ},
title = {Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults.},
journal = {EBioMedicine},
volume = {94},
number = {},
pages = {104731},
pmid = {37487417},
issn = {2352-3964},
support = {R01 AI158911/AI/NIAID NIH HHS/United States ; R33 HD105619/HD/NICHD NIH HHS/United States ; R61 HD105619/HD/NICHD NIH HHS/United States ; UL1 TR003017/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Adult ; *COVID-19 ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Saliva ; *Microbiota ; },
abstract = {BACKGROUND: The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease.<br><br>METHODS: In early 2020, a cohort of 831 adults without known SARS-CoV-2 infection was followed over a six-month period to assess the occurrence and natural history of SARS-CoV-2 infection. From this cohort, 81 participants with a SARS-CoV-2 infection, along with 57 unexposed counterparts were selected with a total of 748 serial saliva samples were collected for analysis. Total bacterial abundance, composition, population structure, and gene function of the salivary microbiome were measured using 16S rRNA gene and shotgun metagenomic sequencing.<br><br>FINDINGS: The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection. However, there were significant reductions in microbiome diversity among SARS-CoV-2-positive participants with severe symptoms early after infection. Over time, the microbiome diversity in these participants showed signs of recovery.<br><br>INTERPRETATION: These findings demonstrate the resilience of the salivary microbiome in relation to SARS-CoV-2 infection. Mild to moderate infections did not significantly disrupt the stability of the salivary microbiome, suggesting its ability to maintain its composition and function. However, severe SARS-CoV-2 infection was associated with temporary reductions in microbiome diversity, indicating the limits of microbiome resilience in the face of severe infection.<br><br>FUNDING: This project was supported in part by Danone North America and grants from the National Institutes of Health, United States.},
}
@article {pmid37369278,
year = {2023},
author = {Hazime, H and Ducasa, GM and Santander, AM and Brito, N and González, EE and Ban, Y and Kaunitz, J and Akiba, Y and Fernández, I and Burgueño, JF and Abreu, MT},
title = {Intestinal Epithelial Inactivity of Dual Oxidase 2 Results in Microbiome-Mediated Metabolic Syndrome.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {16},
number = {4},
pages = {557-572},
pmid = {37369278},
issn = {2352-345X},
mesh = {Male ; Female ; Mice ; Animals ; *Metabolic Syndrome ; Dual Oxidases ; *Glucose Intolerance ; Hydrogen Peroxide ; Obesity/metabolism ; Lipopolysaccharides ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents ; },
abstract = {BACKGROUND &amp; AIMS: Metabolic syndrome (MetS) is characterized by obesity, glucose intolerance, and hepatic steatosis. Alterations in the gut microbiome play important roles in the development of MetS. However, the mechanisms by which this occurs are poorly understood. Dual oxidase 2 (DUOX2) is an antimicrobial reduced nicotinamide adenine dinucleotide phosphate oxidase expressed in the gut epithelium. Here, we posit that epithelial DUOX2 activity provides a mechanistic link between the gut microbiome and the development of MetS.<br><br>METHODS: Mice carrying an intestinal epithelial-specific deletion of dual oxidase maturation factor 1/2 (DA IEC-KO), and wild-type littermates were fed a standard diet and killed at 24 weeks. Metabolic alterations were determined by glucose tolerance, lipid tests, and body and organ weight measurements. DUOX2 activity was determined by Amplex Red. Intestinal permeability was determined by fluorescein isothiocyanate-dextran, microbial translocation assessments, and portal vein lipopolysaccharide measurements. Metagenomic analysis of the stool microbiome was performed. The role of the microbiome was assessed in antibiotic-treated mice.<br><br>RESULTS: DA IEC-KO males showed increased body and organ weights accompanied by glucose intolerance and increased plasma lipid and liver enzyme levels, and increased adiposity in the liver and adipose tissue. Expression of F4/80, CD68, uncoupling protein 1, carbohydrate response element binding protein, leptin, and adiponectin was altered in the liver and adipose tissue of DA IEC-KO males. DA IEC-KO males produced less epithelial H2O2, had altered relative abundance of Akkermansiaceae and Lachnospiraceae in stool, and showed increased portal vein lipopolysaccharides and intestinal permeability. Females were protected from barrier defects and MetS, despite producing less H2O2. Antibiotic depletion abrogated all MetS phenotypes observed.<br><br>CONCLUSIONS: Intestinal epithelial inactivity of DUOX2 promotes MetS in a microbiome-dependent manner.},
}
@article {pmid37726374,
year = {2023},
author = {Hansen, ZA and Vasco, K and Rudrik, JT and Scribner, KT and Zhang, L and Manning, SD},
title = {Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15524},
pmid = {37726374},
issn = {2045-2322},
support = {U19AI090872/NH/NIH HHS/United States ; U19AI090872/NH/NIH HHS/United States ; },
mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Aminoglycosides ; },
abstract = {Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.},
}
@article {pmid37726348,
year = {2023},
author = {Warner, BB and Rosa, BA and Ndao, IM and Tarr, PI and Miller, JP and England, SK and Luby, JL and Rogers, CE and Hall-Moore, C and Bryant, RE and Wang, JD and Linneman, LA and Smyser, TA and Smyser, CD and Barch, DM and Miller, GE and Chen, E and Martin, J and Mitreva, M},
title = {Social and psychological adversity are associated with distinct mother and infant gut microbiome variations.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5824},
pmid = {37726348},
issn = {2041-1723},
support = {R01 MH113883/MH/NIMH NIH HHS/United States ; },
mesh = {Female ; Pregnancy ; Humans ; Infant ; *Gastrointestinal Microbiome/genetics ; Mothers ; Case-Control Studies ; Bifidobacterium/genetics ; Cytokines ; Vitamins ; },
abstract = {Health disparities are driven by underlying social disadvantage and psychosocial stressors. However, how social disadvantage and psychosocial stressors lead to adverse health outcomes is unclear, particularly when exposure begins prenatally. Variations in the gut microbiome and circulating proinflammatory cytokines offer potential mechanistic pathways. Here, we interrogate the gut microbiome of mother-child dyads to compare high-versus-low prenatal social disadvantage, psychosocial stressors and maternal circulating cytokine cohorts (prospective case-control study design using gut microbiomes from 121 dyads profiled with 16 S rRNA sequencing and 89 dyads with shotgun metagenomic sequencing). Gut microbiome characteristics significantly predictive of social disadvantage and psychosocial stressors in the mothers and children indicate that different discriminatory taxa and related pathways are involved, including many species of Bifidobacterium and related pathways across several comparisons. The lowest inter-individual gut microbiome similarity was observed among high-social disadvantage/high-psychosocial stressors mothers, suggesting distinct environmental exposures driving a diverging gut microbiome assembly compared to low-social disadvantage/low-psychosocial stressors controls (P = 3.5 × 10[-5] for social disadvantage, P = 2.7 × 10[-15] for psychosocial stressors). Children's gut metagenome profiles at 4 months also significantly predicted high/low maternal prenatal IL-6 (P = 0.029), with many bacterial species overlapping those identified by social disadvantage and psychosocial stressors. These differences, based on maternal social and psychological status during a critical developmental window early in life, offer potentially modifiable targets to mitigate health inequities.},
}
@article {pmid37724520,
year = {2023},
author = {Yan, Z and Wang, Y and Zeng, W and Xia, R and Liu, Y and Wu, Z and Deng, W and Zhu, M and Xu, J and Deng, H and Miao, Y},
title = {Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis.},
journal = {Renal failure},
volume = {45},
number = {2},
pages = {2256421},
doi = {10.1080/0886022X.2023.2256421},
pmid = {37724520},
issn = {1525-6049},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Cross-Sectional Studies ; Catheters, Indwelling/adverse effects ; *Microbiota ; *Catheter-Related Infections/diagnosis ; Renal Dialysis/adverse effects ; },
abstract = {Background: Catheter-related infection (CRI) is a major complication in patients undergoing hemodialysis. The lack of high-throughput research on catheter-related microbiota makes it difficult to predict the occurrence of CRI. Thus, this study aimed to delineate the microbial structure and diversity landscape of hemodialysis catheter tips among patients during the perioperative period of kidney transplantation (KTx) and provide insights into predicting the occurrence of CRI.Methods: Forty patients at the Department of Transplantation undergoing hemodialysis catheter removal were prospectively included. Samples, including catheter tip, catheter outlet skin swab, catheter blood, peripheral blood, oropharynx swab, and midstream urine, from the separate pre- and post-KTx groups were collected and analyzed using metagenomic next-generation sequencing (mNGS). All the catheter tips and blood samples were cultured conventionally.Results: The positive detection rates for bacteria using mNGS and traditional culture were 97.09% (200/206) and 2.65% (3/113), respectively. Low antibiotic-sensitivity biofilms with colonized bacteria were detected at the catheter tip. In asymptomatic patients, no statistically significant difference was observed in the catheter tip microbial composition and diversity between the pre- and post-KTx group. The catheter tip microbial composition and diversity were associated with fasting blood glucose levels. Microorganisms at the catheter tip most likely originated from catheter outlet skin and peripheral blood.Conclusions: The long-term colonization microbiota at the catheter tip is in a relatively stable state and is not readily influenced by KTx. It does not act as the source of infection in all CRIs, but could reflect hematogenous infection to some extent.},
}
@article {pmid37723422,
year = {2023},
author = {Hess, MK and Hodgkinson, HE and Hess, AS and Zetouni, L and Budel, JCC and Henry, H and Donaldson, A and Bilton, TP and van Stijn, TC and Kirk, MR and Dodds, KG and Brauning, R and McCulloch, AF and Hickey, SM and Johnson, PL and Jonker, A and Morton, N and Hendy, S and Oddy, VH and Janssen, PH and McEwan, JC and Rowe, SJ},
title = {Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {551},
pmid = {37723422},
issn = {1471-2164},
support = {SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; Curiosity Fund//AgResearch/ ; Curiosity Fund//AgResearch/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; C10X1306//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Sheep/genetics ; *Metagenome ; Rumen ; *Microbiota ; Livestock ; Methane ; },
abstract = {BACKGROUND: Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.<br><br>RESULTS: Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.<br><br>CONCLUSIONS: Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.},
}
@article {pmid37705113,
year = {2023},
author = {De Filippis, F and Bonelli, M and Bruno, D and Sequino, G and Montali, A and Reguzzoni, M and Pasolli, E and Savy, D and Cangemi, S and Cozzolino, V and Tettamanti, G and Ercolini, D and Casartelli, M and Caccia, S},
title = {Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {205},
pmid = {37705113},
issn = {2049-2618},
mesh = {Animals ; Larva ; *Gastrointestinal Microbiome/genetics ; Plastics ; RNA, Ribosomal, 16S/genetics ; *Diptera ; },
abstract = {BACKGROUND: In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking.<br><br>RESULTS: In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and [1]H nuclear magnetic resonance analyses&#xa0;on plastics.<br><br>CONCLUSIONS: In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.},
}
@article {pmid37704738,
year = {2023},
author = {Chang, YH and Yanckello, LM and Chlipala, GE and Green, SJ and Aware, C and Runge, A and Xing, X and Chen, A and Wenger, K and Flemister, A and Wan, C and Lin, AL},
title = {Prebiotic inulin enhances gut microbial metabolism and anti-inflammation in apolipoprotein E4 mice with sex-specific implications.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15116},
pmid = {37704738},
issn = {2045-2322},
support = {RF1 AG062480/AG/NIA NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; },
mesh = {Female ; Male ; Animals ; Mice ; Apolipoprotein E4/genetics ; Apolipoprotein E3 ; Dysbiosis ; *Gastrointestinal Microbiome ; Inulin/pharmacology ; *Alzheimer Disease ; Anti-Inflammatory Agents ; Escherichia coli ; },
abstract = {Gut dysbiosis has been identified as a crucial factor of Alzheimer's disease (AD) development for apolipoprotein E4 (APOE4) carriers. Inulin has shown the potential to mitigate dysbiosis. However, it remains unclear whether the dietary response varies depending on sex. In the study, we fed 4-month-old APOE4 mice with inulin for 16 weeks and performed shotgun metagenomic sequencing to determine changes in microbiome diversity, taxonomy, and functional gene pathways. We also formed the same experiments with APOE3 mice to identify whether there are APOE-genotype dependent responses to inulin. We found that APOE4 female mice fed with inulin had restored alpha diversity, significantly reduced Escherichia coli and inflammation-associated pathway responses. However, compared with APOE4 male mice, they had less metabolic responses, including the levels of short-chain fatty acids-producing bacteria and the associated kinases, especially those related to acetate and Erysipelotrichaceae. These diet- and sex- effects were less pronounced in the APOE3 mice, indicating that different APOE variants also play a significant role. The findings provide insights into the higher susceptibility of APOE4 females to AD, potentially due to inefficient energy production, and imply the importance of considering precision nutrition for mitigating dysbiosis and AD risk in the future.},
}
@article {pmid37702461,
year = {2023},
author = {Hussan, H and Clinton, SK and Grainger, EM and Webb, M and Wang, C and Webb, A and Needleman, B and Noria, S and Zhu, J and Choueiry, F and Pietrzak, M and Bailey, MT},
title = {Distinctive patterns of sulfide- and butyrate-metabolizing bacteria after bariatric surgery: potential implications for colorectal cancer risk.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2255345},
pmid = {37702461},
issn = {1949-0984},
support = {R35 GM133510/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Female ; Middle Aged ; Aged ; Male ; Butyrates ; Cross-Sectional Studies ; Escherichia coli ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Bacteria/genetics ; *Colorectal Neoplasms/surgery ; },
abstract = {Despite improved cardiometabolic outcomes following bariatric surgery, its long-term impact on colorectal cancer (CRC) risk remains uncertain. In parallel, the influence of bariatric surgery on the host microbiome and relationships with disease outcomes is beginning to be appreciated. Therefore, we investigated the impact of Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) on the patterns of sulfide-reducing and butyrate-producing bacteria, which are hypothesized to modulate CRC risk after bariatric surgery. In this single-center, cross-sectional study, we included 15 pre-surgery subjects with severe obesity and patients who are at a median (range) of 25.6 (9.9-46.5) months after RYGB (n = 16) or VSG (n = 10). The DNA abundance of fecal bacteria and enzymes involved in butyrate and sulfide metabolism were identified using metagenomic sequencing. Differences between pre-surgery and post-RYGB or post-VSG cohorts were quantified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Our sample was predominantly female (87%) with a median (range) age of 46 (23-71) years. Post-RYGB and post-VSG patients had a higher DNA abundance of fecal sulfide-reducing bacteria than pre-surgery controls (LDA = 1.3-4.4, p < .05). The most significant enrichments were for fecal E. coli, Acidaminococcus and A. finegoldii after RYGB, and for A. finegoldii, S. vestibularis, V. parvula after VSG. As for butyrate-producing bacteria, R. faecis was more abundant, whereas B. dentium and A. hardus were lower post-RYGB vs. pre-surgery. B. dentium was also lower in post-VSG vs. pre-surgery. Consistent with these findings, our analysis showed a greater enrichment of sulfide-reducing enzymes after bariatric surgery, especially RYGB, vs. pre-surgery. The DNA abundance of butyrate-producing enzymes was lower post-RYGB. In conclusion, the two most used bariatric surgeries, RYGB and VSG, are associated with microbiome patterns that are potentially implicated in CRC risk. Future studies are needed to validate and understand the impact of these microbiome changes on CRC risk after bariatric surgery.},
}
@article {pmid37701837,
year = {2023},
author = {Bulygin, I and Shatov, V and Rykachevskiy, A and Raiko, A and Bernstein, A and Burnaev, E and Gelfand, MS},
title = {Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15838},
pmid = {37701837},
issn = {2167-8359},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Metagenome ; Algorithms ; },
abstract = {Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.},
}
@article {pmid37606634,
year = {2023},
author = {Liu, D and Wang, S and Liu, Y and Luo, Y and Wen, B and Wu, W and Zeng, H and Huang, J and Liu, Z},
title = {Fuzhuan brick tea ameliorates hepatic steatosis and steatohepatitis through gut microbiota-derived aryl hydrocarbon receptor ligands in high-fat diet-induced obese mice.},
journal = {Food &amp; function},
volume = {14},
number = {18},
pages = {8351-8368},
doi = {10.1039/d3fo01782f},
pmid = {37606634},
issn = {2042-650X},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Diet, High-Fat/adverse effects ; Ligands ; Mice, Obese ; Receptors, Aryl Hydrocarbon/genetics ; *Fatty Liver/drug therapy ; Escherichia coli ; Tea ; },
abstract = {High-fat diet (HFD) induced obesity and its associated conditions, such as hepatic steatosis and steatohepatitis, are major health concerns worldwide. Previous studies have reported the excellent efficiency of Fuzhuan brick tea (FBT) in attenuating HFD-induced obesity and metabolic disorders. In this study, we investigated the effects of FBT on hepatic steatosis and simple steatohepatitis in HFD-induced obese mice, as well as the metabolic function of the gut microbiome using metagenomics and metabolomics. The results showed that FBT ameliorated dyslipidemia, hepatic steatosis and steatohepatitis in HFD-induced obese mice by normalizing the gut microbiota structure and tryptophan metabolism. FBT increased the cecal abundance of aryl hydrocarbon receptor (AhR)-ligand producing bacteria such as Lactobacillus_reuteri and Lactobacillus_johnsonii, at the expense of AhR-ligand consuming bacteria, such as Faecalibaculum_rodentium and Escherichia_coli, and elevated the cecal contents of AhR-ligands such as IAA, IPA, and KYNA. Furthermore, FBT regulated the expressions of AhR and its targeted lipometabolic genes such as Pemt, Fasn, and SREBP-1c, as well as other inflammatory genes including TNF-α, IL-6, and IL-1β in the liver of mice. Overall, these findings highlight the beneficial effects of FBT on obesity-related hepatic steatosis and steatohepatitis via microbiota-derived AhR signaling.},
}
@article {pmid37478939,
year = {2023},
author = {Jin, L and Wu, H and Li, G and Yang, S and Wei, R and Huang, Y and Penttinen, P and Deng, W and Chen, J and Han, X and Li, C and Hu, L and Li, T and Zhang, H and Zhao, K and Zou, L},
title = {Gastrointestinal microbiome, resistance genes, and risk assessment of heavy metals in wild giant pandas.},
journal = {The Science of the total environment},
volume = {899},
number = {},
pages = {165671},
doi = {10.1016/j.scitotenv.2023.165671},
pmid = {37478939},
issn = {1879-1026},
mesh = {Animals ; *Ursidae ; *Gastrointestinal Microbiome ; *Metals, Heavy/analysis ; Anti-Bacterial Agents ; Risk Assessment ; Soil ; Genes, Bacterial ; },
abstract = {The gastrointestinal microbiome (GM) of giant panda (GP) plays an important role in food utilization and health and is also an essential reservoir of resistance genes. Currently, little knowledge is available on the GM, acid resistance genes (AcRGs), antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in wild GPs. We sampled the gastrointestinal tract of a dead GP and explored the composition and function of GM and resistance genes through cryo-scanning electron microscopy, metagenomic sequencing, and genome-resolved metagenomics. The concentration of metals in the gastrointestinal lumen, feces, bamboo, and soil was measured by inductively coupled plasma mass spectrometry. Results showed that the composition of the microbiota varied in different gastrointestinal regions. Fecal microbiota was highly associated with small intestinal and colonic microbes. The lignocellulosic cross-linked structure of bamboo was destroyed in the stomach initially and destroying degree increased from stomach to anus. Reconstruction of metagenome-assembled-genomes confirmed that core GM, e.g., Streptococcus, Clostridium, Lactococcus, Leuconostoc, and Enterococcus, carried genes encoding the lignocellulose degradation enzyme. There were no significant differences of resistance genes between gastrointestinal and fecal samples, except MGEs. Multidrug and multi-metal resistance genes were predominant in all samples, while the transposase gene tnpA was the major type of MGE. Significant correlations were observed among the abundance of GM, resistance genes, and MGEs. Gastrointestinal and fecal mercury and chromium were the main metals influencing GM and resistance genes. The content of gastrointestinal and fecal metals was significantly associated with the presence of the same metals in bamboo, which could pose a threat to the health of wild GPs. This study characterized the gastrointestinal microbiome of wild GPs, providing new evidence for the role of the gastrointestinal microbiome in degrading lignocellulose from bamboo and highlighting the urgent need to monitor metal levels in soil and bamboo.},
}
@article {pmid37478933,
year = {2023},
author = {Yan, Q and Xu, Y and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Feng, G},
title = {Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater.},
journal = {The Science of the total environment},
volume = {900},
number = {},
pages = {165672},
doi = {10.1016/j.scitotenv.2023.165672},
pmid = {37478933},
issn = {1879-1026},
mesh = {*Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; *Microbiota ; Drug Resistance, Microbial/genetics ; },
abstract = {Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.},
}
@article {pmid37459997,
year = {2023},
author = {Liu, M and Wei, Y and Lian, L and Wei, B and Bi, Y and Liu, N and Yang, G and Zhang, Y},
title = {Macrofungi promote SOC decomposition and weaken sequestration by modulating soil microbial function in temperate steppe.},
journal = {The Science of the total environment},
volume = {899},
number = {},
pages = {165556},
doi = {10.1016/j.scitotenv.2023.165556},
pmid = {37459997},
issn = {1879-1026},
mesh = {*Soil/chemistry ; Carbon/metabolism ; Soil Microbiology ; Biomass ; *Microbiota ; Carbon Sequestration ; },
abstract = {Soil organic carbon (SOC) sequestration is a key grassland ecosystem function, and the magnitude of SOC reservoirs depends on microbial involvement, especially that of fungi. Mycelia developed by macrofungi potentially influence carbon (C) fixation and decomposition; however, the mechanisms underlying their effects on SOC storage in grassland ecosystems remain poorly understood. The fairy rings formed by macrofungi in grasslands are natural platform for exploring macrofungal effects on SOC. In this study, we collected topsoil (0-10 cm) from four different fairy ring zones in a temperate steppe to reveal the macrofungal effects on SOC fractions, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the SOC storage microbial mechanism using metagenomic sequencing technology. Both POC and MAOC decreased after macrofungal passage, resulting in a 7.37 % reduction in SOC. Macrofungal presence reduced microbial biomass carbon (MBC), but significantly enhanced the β-1,4-glucosidase (BG) activity, which increased dissolved organic carbon (DOC). In addition, the abundance of copiotrophs (Proteobacteria and Bacteroidetes) with lower C metabolic rates increased, and that of oligotrophs (Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia) with higher substrate utilization efficiency decreased in the presence of macrofungi. This may further promote SOC decomposition. Correspondingly, there was a lower abundance of C-fixation genes but more C-degradation genes (especially hemicellulosic degradation genes) during macrofungal passage. Our results indicate that the presence of macrofungi can modulate the soil microbial community and functional genes to reduce SOC storage by inhibiting microbial C sequestration while promoting C decomposition in grassland ecosystems. These findings refine our mechanistic understanding of SOC persistence through the interactions between macrofungi and other microbes.},
}
@article {pmid37392873,
year = {2023},
author = {Li, ZT and Yang, SY and Zhao, HP},
title = {The effects of arsenic on dechlorination of trichloroethene by consortium DH: Microbial response and resistance.},
journal = {The Science of the total environment},
volume = {896},
number = {},
pages = {165219},
doi = {10.1016/j.scitotenv.2023.165219},
pmid = {37392873},
issn = {1879-1026},
mesh = {*Chloroflexi/metabolism ; *Trichloroethylene/metabolism ; *Arsenic/metabolism ; Bacteria/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Vinyl Chloride ; },
abstract = {Inorganic arsenic and organochlorines are frequently co-occurring contaminants in anoxic groundwater environments, and the bioremediation of their composite pollution has long been a rigorous predicament. Currently, the dechlorination behaviors and stress responses of microbial dechlorination consortia to arsenic are not yet fully understood. This study assessed the reductive dechlorination performance of a Dehalococcoides-bearing microcosm DH under gradient concentrations of arsenate [As(V)] or arsenite [As(III)] and investigated the response patterns of different functional microorganisms. Our results demonstrated that although the dechlorination rates declined with increasing arsenic concentrations in both As(III/V) scenarios, the inhibitory impact was more pronounced in As(III)-amended groups compared to As(V)-amended groups. Moreover, the vinyl chloride (VC)-to-ethene step was more susceptible to arsenic exposure compared to the trichloroethene (TCE)-to-dichloroethane (DCE) step, while high levels of arsenic exposure [e.g. As(III) > 75 μM] can induce significant accumulation of VC. Functional gene variations and microbial community analyses revealed that As(III/V) affected reductive dechlorination by directly inhibiting organohalide-respiring bacteria (OHRB) and indirectly inhibiting synergistic populations such as acetogens. Metagenomic results indicated that arsenic metabolic and efflux mechanisms were identical among different Dhc strains, and variations in arsenic uptake pathways were possibly responsible for their differential responses to arsenic exposures. By comparison, fermentative bacteria showed high potential for arsenic resistance due to their inherent advantages in arsenic detoxification and efflux mechanisms. Collectively, our findings expanded the understanding of the response patterns of different functional populations to arsenic stress in the dechlorinating consortium and provided insights into modifying bioremediation strategies at co-contaminated sites for furtherance.},
}
@article {pmid37667515,
year = {2023},
author = {Baker, JL},
title = {Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.},
journal = {FEMS microbiology reviews},
volume = {47},
number = {5},
pages = {},
pmid = {37667515},
issn = {1574-6976},
support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; K99-DE029228/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Quality of Life ; Computational Biology ; Genomics ; Metabolomics ; *Microbiota/genetics ; },
abstract = {The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.},
}
@article {pmid37647765,
year = {2023},
author = {Young, GR and Nelson, A and Stewart, CJ and Smith, DL},
title = {Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease.},
journal = {Current opinion in microbiology},
volume = {75},
number = {},
pages = {102379},
doi = {10.1016/j.mib.2023.102379},
pmid = {37647765},
issn = {1879-0364},
mesh = {Infant, Newborn ; Infant ; Humans ; Infant Health ; Infant, Premature ; *Microbiota ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome ; },
abstract = {Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.},
}
@article {pmid37598984,
year = {2023},
author = {Jian, J and Yuan, Y and Vilatersana, R and Li, L and Wang, Y and Zhang, W and Song, Z and Kong, H and Peter Comes, H and Yang, J},
title = {Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago.},
journal = {Molecular phylogenetics and evolution},
volume = {188},
number = {},
pages = {107908},
doi = {10.1016/j.ympev.2023.107908},
pmid = {37598984},
issn = {1095-9513},
mesh = {*Ranunculaceae ; *Nigella ; Phylogeny ; Metagenomics ; Genomics ; },
abstract = {The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial-temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a 'mixing-isolation-mixing (MIM)' mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of 'non-adaptive' radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.},
}
@article {pmid37490989,
year = {2024},
author = {Deng, Z and Ouyang, Z and Mei, S and Zhang, X and Li, Q and Meng, F and Hu, Y and Dai, X and Zhou, S and Mao, K and Huang, C and Dai, J and Yi, C and Tan, N and Feng, T and Long, H and Tian, X},
title = {Enhancing NKT cell-mediated immunity against hepatocellular carcinoma: Role of XYXD in promoting primary bile acid synthesis and improving gut microbiota.},
journal = {Journal of ethnopharmacology},
volume = {318},
number = {Pt B},
pages = {116945},
doi = {10.1016/j.jep.2023.116945},
pmid = {37490989},
issn = {1872-7573},
mesh = {Animals ; *Carcinoma, Hepatocellular/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/drug therapy ; Bile Acids and Salts ; Immunity, Cellular ; },
abstract = {'Xiayuxue decoction' (XYXD) is a traditional Chinese medicine compound, composing of three natural medicines: Rheum officinale Baill., Prunus persica (L.) Batsch and Eupolyphaga sinensis Walker. It is derived from the famous traditional Chinese medical classics 'Jingui Yaolue' and has been used for thousands of years. In the Guidelines for the Diagnosis and Treatment of Primary liver Cancer issued by China's Health Commission, XYXD was applied in the treatment of primary liver cancer.<br><br>AIM OF THE STUDY: To clarify the pharmacodynamic material basis and mechanism of XYXD in the treatment of hepatocellular carcinoma (HCC).<br><br>MATERIALS AND METHODS: Firstly, the active components of XYXD and its distribution in vivo were identified by Ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Then, the effective components and mechanism of XYXD against HCC were explored by network pharmacology combined with cell experiments in vitro. Furthermore, the anti-HCC effect of XYXD was determined by animal experiments in vivo. Metagenomic sequencing was used to detect its effect in gut microbiota, and targeted metabolism was used to detect the changes of bile acids in the liver. Finally, the related targets of NKT cell immune function activation were detected by RT-qPCR and Elisa.<br><br>RESULTS: A total of 113 active ingredients in XYXD were identified, and the distribution of active ingredients in blood, liver, tumor, cecum, intestinal contents and feces was clarified. The circulation process and active ingredient group of XYXD were preliminarily clarified. In addition, we found five anti-HCC active ingredients in XYXD through network pharmacology combined with cell experiments in vitro, among which aloe emodin had the most significant effect, and predicted the potential mechanism of XYXD against HCC through NKT cell pathway. Moreover, the inhibitory effect of XYXD on liver tumor growth was clarified by animal experiments in vivo. The mechanism was mainly to promote the production of bile salt hydrolase (BSH) by increasing the abundance of Bacteroides and Lactobacillus, BSH converts conjugated bile acids into primary bile acids, and reduces the conversion of primary bile acids to secondary bile acids by reducing the abundance of Eubacterium, thereby increasing the content of primary bile acids. Primary bile acids trigger NKT cells in the liver to produce interferon-&#x3b3; to exert anti-HCC immune effects.<br><br>CONCLUSION: This study found that the traditional Chinese herbal formula XYXD can trigger the immune effect of NKT cells against HCC by regulating the interaction between gut microbiota and bile acids.},
}
@article {pmid37454234,
year = {2023},
author = {Ustick, LJ and Larkin, AA and Martiny, AC},
title = {Global scale phylogeography of functional traits and microdiversity in Prochlorococcus.},
journal = {The ISME journal},
volume = {17},
number = {10},
pages = {1671-1679},
pmid = {37454234},
issn = {1751-7370},
support = {T32 AI141346/AI/NIAID NIH HHS/United States ; },
mesh = {Phylogeography ; Phylogeny ; *Prochlorococcus/genetics ; Seawater ; Ecotype ; },
abstract = {Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.},
}
@article {pmid37700504,
year = {2023},
author = {Bender, SF and Schulz, S and Martínez-Cuesta, R and Laughlin, RJ and Kublik, S and Pfeiffer-Zakharova, K and Vestergaard, G and Hartman, K and Parladé, E and Römbke, J and Watson, CJ and Schloter, M and van der Heijden, MGA},
title = {Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19252},
pmid = {37700504},
issn = {1469-8137},
support = {31003A-166079//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
abstract = {Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.},
}
@article {pmid37698879,
year = {2023},
author = {Danhof, HA and Lee, J and Thapa, A and Britton, RA and Di Rienzi, SC},
title = {Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2256043},
pmid = {37698879},
issn = {1949-0984},
support = {R01 DK056388/DK/NIDDK NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; Secretin ; Oxytocin ; *Gastrointestinal Microbiome ; *Gastrointestinal Hormones ; Intestinal Mucosa ; *Limosilactobacillus reuteri ; },
abstract = {Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for L. reuteri-mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We find that L. reuteri facilitates oxytocin secretion from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells, while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri. This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.},
}
@article {pmid37660237,
year = {2023},
author = {Li, R and Hu, M and Jiang, X and Xu, C},
title = {Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage.},
journal = {Journal of applied microbiology},
volume = {134},
number = {9},
pages = {},
doi = {10.1093/jambio/lxad197},
pmid = {37660237},
issn = {1365-2672},
support = {31872420//National Natural Science Foundation of China/ ; },
mesh = {*Lactic Acid ; Medicago sativa/genetics ; Butyrates ; L-Lactate Dehydrogenase/genetics ; Silage ; *Microbiota/genetics ; Escherichia coli ; },
abstract = {AIMS: Lactate and butyrate are important indicators of silage quality. However, the microorganisms and mechanisms responsible for lactate and butyrate production in silage are not well documented.<br><br>METHODS AND RESULTS: whole-metagenomic sequencing was used to analyse metabolic pathways, microbiota composition, functional genes, and their contributions to lactate and butyrate production in alfalfa silage with (SA) and without (CK) sucrose addition. Carbon metabolism was the most abundant metabolic pathway. We identified 11 and 2 functional genes associated with lactate and butyrate metabolism, respectively. Among them, D-lactate dehydrogenase (ldhA) and L-lactate dehydrogenase (ldhB) were most important for the transition between D/L-lactate and pyruvate and were primarily related to Lactobacillus in the SA group. The genes encoding L-lactate dehydrogenase (lldD), which decomposes lactate, were the most abundant and primarily associated with Enterobacter cloacae. Butyrate-related genes, mainly encoding butyryl-CoA: acetate CoA-transferase (but), were predominantly associated with Klebsiella oxytoca and Escherichia coli in the CK group.<br><br>CONCLUSIONS: Enterobacteriaceae and Lactobacillaceae were mainly responsible for butyrate and lactate formation, respectively.},
}
@article {pmid37648852,
year = {2023},
author = {Takeuchi, T and Kubota, T and Nakanishi, Y and Tsugawa, H and Suda, W and Kwon, AT and Yazaki, J and Ikeda, K and Nemoto, S and Mochizuki, Y and Kitami, T and Yugi, K and Mizuno, Y and Yamamichi, N and Yamazaki, T and Takamoto, I and Kubota, N and Kadowaki, T and Arner, E and Carninci, P and Ohara, O and Arita, M and Hattori, M and Koyasu, S and Ohno, H},
title = {Gut microbial carbohydrate metabolism contributes to insulin resistance.},
journal = {Nature},
volume = {621},
number = {7978},
pages = {389-395},
pmid = {37648852},
issn = {1476-4687},
mesh = {Animals ; Mice ; Humans ; *Insulin Resistance ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome ; Carbohydrate Metabolism ; Monosaccharides ; },
abstract = {Insulin resistance is the primary pathophysiology underlying metabolic syndrome and type 2 diabetes[1,2]. Previous metagenomic studies have described the characteristics of gut microbiota and their roles in metabolizing major nutrients in insulin resistance[3-9]. In particular, carbohydrate metabolism of commensals has been proposed to contribute up to 10% of the host's overall energy extraction[10], thereby playing a role in the pathogenesis of obesity and prediabetes[3,4,6]. Nevertheless, the underlying mechanism remains unclear. Here we investigate this relationship using a comprehensive multi-omics strategy in humans. We combine unbiased faecal metabolomics with metagenomics, host metabolomics and transcriptomics data to profile the involvement of the microbiome in insulin resistance. These data reveal that faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines. We identify gut bacteria associated with insulin resistance and insulin sensitivity that show a distinct pattern of carbohydrate metabolism, and demonstrate that insulin-sensitivity-associated bacteria ameliorate host phenotypes of insulin resistance in a mouse model. Our study, which provides a comprehensive view of the host-microorganism relationships in insulin resistance, reveals the impact of carbohydrate metabolism by microbiota, suggesting a potential therapeutic target for ameliorating insulin resistance.},
}
@article {pmid37437419,
year = {2023},
author = {Gundogdu, A and Nalbantoglu, OU},
title = {The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {114},
number = {},
pages = {112118},
doi = {10.1016/j.nut.2023.112118},
pmid = {37437419},
issn = {1873-1244},
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; Nutrients ; Nutritional Status ; Micronutrients ; },
abstract = {The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, Alzheimer's disease, depression, and onset of inflammatory bowel disease; and more generally low-grade inflammation and mortality risks. Beyond being an input source of beneficial micronutrients, it recently has been discovered that the MedDiet plays a role in a more complex human microbiome-mediated mechanism. An interesting hypothesis suggests a bidirectional relationship between the MedDiet and the gut microbiome, where gut microbiota assembly and biosynthetic capacity are responsive to the diet; in return, the microbiome-reachable nutrients shape and modulate the microbiome toward a characteristic probiotic state. It can be speculated that that primary health benefits of the MedDiet exerted via the gut microbiome are mediated by the bioactive compounds transformed by the microbiome. Furthermore, it is possible that additional probiotic properties of the organisms promoted by diet adherence have secondary benefits. As more detailed omic-based studies take place, more evidence on the MedDiet as a core generic probiotic microbiome modulation strategy surface. However, individual-specific microbiome compositions might impose personal variations on the diet outcome. Therefore, a prospective strategy of a fine-tuned precision nutrition approach might deliver optimized benefits of the MedDiet.},
}
@article {pmid37697305,
year = {2023},
author = {Magnuson, E and Altshuler, I and Freyria, NJ and Leveille, RJ and Whyte, LG},
title = {Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {203},
pmid = {37697305},
issn = {2049-2618},
mesh = {Calcium Sulfate ; Canada ; *Microbiota/genetics ; Oxygen ; Sulfates ; *Gammaproteobacteria ; },
abstract = {BACKGROUND: Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L[-1]) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars.<br><br>RESULTS: Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination.<br><br>CONCLUSIONS: We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.},
}
@article {pmid37695063,
year = {2023},
author = {Cerri, A and Bolatti, EM and Zorec, TM and Montani, ME and Rimondi, A and Hosnjak, L and Casal, PE and Di Domenica, V and Barquez, RM and Poljak, M and Giri, AA},
title = {Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0204723},
doi = {10.1128/spectrum.02047-23},
pmid = {37695063},
issn = {2165-0497},
abstract = {Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.},
}
@article {pmid37692394,
year = {2023},
author = {Nemchinov, LG and Irish, BM and Uschapovsky, IV and Grinstead, S and Shao, J and Postnikova, OA},
title = {Composition of the alfalfa pathobiome in commercial fields.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1225781},
pmid = {37692394},
issn = {1664-302X},
abstract = {Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.},
}
@article {pmid37689857,
year = {2023},
author = {Zhu, C and Cheng, Y and Shi, Q and Ge, X and Yang, Y and Huang, Y},
title = {Metagenomic analyses reveal microbial communities and functional differences between Daqu from seven provinces.},
journal = {Food research international (Ottawa, Ont.)},
volume = {172},
number = {},
pages = {113076},
doi = {10.1016/j.foodres.2023.113076},
pmid = {37689857},
issn = {1873-7145},
mesh = {Metagenome ; *Microbiota ; *Bacillus ; Amino Acids ; Lactic Acid ; *Lactobacillales/genetics ; },
abstract = {Microbial communities perform the brewing function in Daqu. Macrogenomics and PICRUST II analyses revealed the differences in microbes and metabolic functions among Daqu from the seven Baijiu-producing provinces. Jiang-flavored Daqu (Guizhou, Shandong, and Hubei provinces) generally forms an aroma-producing functional microbiota with Kroppenstedtia, Bacillus, Thermoascus, Virgibacillus, and Thermomyces as the core, which promotes the metabolism of various amino acids and aroma compounds. Light-flavored Daqu (Shanxi Province) enriched the Saccharomycopsis, Saccharomyces, and lactic acid bacteria (LAB) microbiota through low-temperature fermentation. These microbes can synthesize alcohol and lactic acid but inhibit amino acid metabolism within the Light-flavored Daqu. Bifidobacterium and Saccharomycopsis were dominant in the Tao-flavored Daqu (Henan province). This unique microbial structure is beneficial for pyruvate fermentation to lactate. Research also found that Strong-flavored Daqu from Jiangsu and Sichuan provinces differed significantly. The microbial communities and metabolic pathways within Jiangsu Daqu were similar to those within Jiang-flavored Daqu, but Sichuan Daqu was dominated by Thermoascus, LAB, and Thermoactinomyces. In addition, Spearman correlation analysis indicated that Kroppenstedtia, Bacillus, and Thermomyces were not only positively related to flavor metabolism but also negatively correlated with Saccharomycopsis. This research will help establish a systematic understanding of the microbial community and functional characteristics in Daqu.},
}
@article {pmid37688597,
year = {2023},
author = {Wang, L and Lian, C and Wan, W and Qiu, Z and Luo, X and Huang, Q and Deng, Y and Zhang, T and Yu, K},
title = {Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37688597},
issn = {1432-0614},
abstract = {Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na[+] or Li[+] in exchange for H[+]. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na[+]/H[+] antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.},
}
@article {pmid37643149,
year = {2023},
author = {Song, Y and Finkelstein, R and Rhoads, W and Edwards, MA and Pruden, A},
title = {Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {36},
pages = {13612-13624},
doi = {10.1021/acs.est.3c03568},
pmid = {37643149},
issn = {1520-5851},
mesh = {*Water ; Copper ; Metagenomics ; Sanitary Engineering ; *Microbiota ; Electrodes ; Phosphates ; },
abstract = {Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.},
}
@article {pmid37485738,
year = {2023},
author = {Wuyts, S and Alves, R and Zimmermann-Kogadeeva, M and Nishijima, S and Blasche, S and Driessen, M and Geyer, PE and Hercog, R and Kartal, E and Maier, L and Müller, JB and Garcia Santamarina, S and Schmidt, TSB and Sevin, DC and Telzerow, A and Treit, PV and Wenzel, T and Typas, A and Patil, KR and Mann, M and Kuhn, M and Bork, P},
title = {Consistency across multi-omics layers in a drug-perturbed gut microbial community.},
journal = {Molecular systems biology},
volume = {19},
number = {9},
pages = {e11525},
pmid = {37485738},
issn = {1744-4292},
support = {P400PB_186795/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Humans ; *Multiomics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metabolomics/methods ; Bacteria/genetics ; Metagenomics/methods ; },
abstract = {Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.},
}
@article {pmid37133495,
year = {2023},
author = {Saikrishna, K and Talukdar, D and Das, S and Bakshi, S and Chakravarti, P and Jana, P and Karmakar, S and Wig, N and Das, B and Ray, A},
title = {Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1814-1828},
pmid = {37133495},
issn = {1432-184X},
support = {5/9/1208/2019-Nut, Dt. 16.09.2019//Indian Council of Medical Research/ ; No. BT/PR30159/MED/15/188/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Probiotics/therapeutic use ; Critical Care ; Disease Progression ; },
abstract = {Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.},
}
@article {pmid37099155,
year = {2023},
author = {Wang, B and Qi, M and Ma, Y and Zhang, B and Hu, Y},
title = {Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2109-2119},
pmid = {37099155},
issn = {1432-184X},
mesh = {Humans ; *Cellulose/metabolism ; Rivers ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; Wood/microbiology ; },
abstract = {Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.},
}
@article {pmid37093231,
year = {2023},
author = {Ichige, R and Urabe, J},
title = {Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2097-2108},
pmid = {37093231},
issn = {1432-184X},
support = {JPMJSP2114//Japan Science and Technology Agency/ ; KAKENHI:20H03315//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research/ ; },
mesh = {Animals ; *Daphnia/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Genotype ; },
abstract = {The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.},
}
@article {pmid37017718,
year = {2023},
author = {Thompson, CC and Tschoeke, D and Coutinho, FH and Leomil, L and Garcia, GD and Otsuki, K and Turcq, BJ and Moreira, LS and Turcq, PFM and Cordeiro, RC and Asp, NE and Thompson, FL},
title = {Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2202-2209},
pmid = {37017718},
issn = {1432-184X},
mesh = {*Microbiota/genetics ; Bacteria ; Metagenome ; Rivers/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; },
abstract = {The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.},
}
@article {pmid37442053,
year = {2023},
author = {Durand, M and Touchette, D and Chen, YJ and Magnuson, E and Wasserscheid, J and Greer, CW and Whyte, LG and Altshuler, I},
title = {Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments.},
journal = {Marine pollution bulletin},
volume = {194},
number = {Pt A},
pages = {115226},
doi = {10.1016/j.marpolbul.2023.115226},
pmid = {37442053},
issn = {1879-3363},
mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/metabolism ; Arctic Regions ; *Microbiota ; Hydrocarbons/metabolism ; },
abstract = {Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.},
}
@article {pmid37399986,
year = {2023},
author = {Magnuson, JT and Monticelli, G and Schlenk, D and Bisesi, JH and Pampanin, DM},
title = {Connecting gut microbiome changes with fish health conditions in juvenile Atlantic cod (Gadus morhua) exposed to dispersed crude oil.},
journal = {Environmental research},
volume = {234},
number = {},
pages = {116516},
doi = {10.1016/j.envres.2023.116516},
pmid = {37399986},
issn = {1096-0953},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Gadus morhua/metabolism ; *Petroleum/analysis/metabolism/toxicity ; Fishes ; *Microbiota/genetics ; *Water Pollutants, Chemical/analysis ; },
abstract = {Polycyclic aromatic hydrocarbons found in crude oil can impair fish health following sublethal exposure. However, the dysbiosis of microbial communities within the fish host and influence it has on the toxic response of fish following exposure has been less characterized, particularly in marine species. To better understand the effect of dispersed crude oil (DCO) on juvenile Atlantic cod (Gadus morhua) microbiota composition and potential targets of exposure within the gut, fish were exposed to 0.05 ppm DCO for 1, 3, 7, or 28 days and 16 S metagenomic and metatranscriptomic sequencing on the gut and RNA sequencing on intestinal content were conducted. In addition to assessing species composition, richness, and diversity from microbial gut community analysis and transcriptomic profiling, the functional capacity of the microbiome was determined. Mycoplasma and Aliivibrio were the two most abundant genera after DCO exposure and Photobacterium the most abundant genus in controls, after 28 days. Metagenomic profiles were only significantly different between treatments after a 28-day exposure. The top identified pathways were involved in energy and the biosynthesis of carbohydrates, fatty acids, amino acids, and cellular structure. Biological processes following fish transcriptomic profiling shared common pathways with microbial functional annotations such as energy, translation, amide biosynthetic process, and proteolysis. There were 58 differently expressed genes determined from metatranscriptomic profiling after 7 days of exposure. Predicted pathways that were altered included those involved in translation, signal transduction, and Wnt signaling. EIF2 signaling was consistently dysregulated following exposure to DCO, regardless of exposure duration, with impairments in IL-22 signaling and spermine and spermidine biosynthesis in fish after 28 days. Data were consistent with predictions of a potentially reduced immune response related to gastrointestinal disease. Herein, transcriptomic-level responses helped explain the relevance of differences in gut microbial communities in fish following DCO exposure.},
}
@article {pmid37209986,
year = {2023},
author = {Zhang, M and Tang, H and Chen, Y and Chen, Z and Xu, Y and Fu, X and Sun, Y and Zhao, Z},
title = {Impact of environmental characteristics on children's gut microbiota - A pilot study in assessing the role of indoor microbiome and metabolites.},
journal = {Environmental research},
volume = {234},
number = {},
pages = {116114},
doi = {10.1016/j.envres.2023.116114},
pmid = {37209986},
issn = {1096-0953},
mesh = {Humans ; Child ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; Tryptophan/metabolism ; China ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Indoles ; },
abstract = {BACKGROUND: A diverse and balanced human gut microbiota is crucial for maintaining normal human physiological functions. However, the impact of indoor microbiome and metabolites on gut microbiota is not well understood.<br><br>METHODS: A self-administered questionnaire was used to collect information on more than 40 personal and environmental characteristics and dietary habits from 56 children in Shanghai, China. Shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS) were used to characterize the indoor microbiome and metabolomic/chemical exposure in children's living rooms. PacBio full-length 16&#xa0;S rRNA sequencing was used to characterize children's gut microbiota. Associations between environmental characteristics and gut microbiota diversity/composition were assessed using PERMANOVA and regression.<br><br>RESULTS: In total, 6247 and 318 indoor and gut microbial species and 1442 indoor metabolites were characterized. Age of children (R[2]&#xa0;=&#xa0;0.033, p&#xa0;=&#xa0;0.008), age start kindergarten (R[2]&#xa0;=&#xa0;0.029, p&#xa0;=&#xa0;0.03), living adjacent to heavy traffic (R[2]&#xa0;=&#xa0;0.031, p&#xa0;=&#xa0;0.01) and drinking soft drinks (R[2]&#xa0;=&#xa0;0.028, p&#xa0;=&#xa0;0.04) significantly impacted overall gut microbial composition, consistent with previous studies. Having pets/plants and frequent vegetable intake were positively associated with gut microbiota diversity and the Gut Microbiome Health Index (GMHI), while frequent juice and fries intake decreased gut microbiota diversity (p&#xa0;<&#xa0;0.05). The abundance of indoor Clostridia and Bacilli was positively associated with gut microbial diversity and GMHI (p&#xa0;<&#xa0;0.01). Total indoor indole derivatives and 6 indole metabolites (L-tryptophan, indole, 3-methylindole, indole-3-acetate, 5-hydroxy-L-tryptophan and indolelactic acid, p&#xa0;<&#xa0;0.05) were positively associated with the abundance of total protective gut bacteria, suggesting a potential role in promoting gut health. Neural network analysis revealed that these indole derivatives were derived from indoor microorganisms.<br><br>CONCLUSIONS: The study is the first to report associations between indoor microbiome/metabolites and gut microbiota, highlighting the potential role of indoor microbiome in shaping human gut microbiota.},
}
@article {pmid37086309,
year = {2023},
author = {Sasaki, T and Matsumoto, Y and Murakami, K and Endo, S and Toyozumi, T and Otsuka, R and Kinoshita, K and Hu, J and Iida, S and Morishita, H and Nishioka, Y and Nakano, A and Uesato, M and Matsubara, H},
title = {Gut microbiome can predict chemoradiotherapy efficacy in patients with esophageal squamous cell carcinoma.},
journal = {Esophagus : official journal of the Japan Esophageal Society},
volume = {20},
number = {4},
pages = {691-703},
pmid = {37086309},
issn = {1612-9067},
support = {JP 20H03749//JSPS KAKENHI/ ; },
mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/therapy ; *Esophageal Neoplasms/therapy/pathology ; *Carcinoma, Squamous Cell/therapy/pathology ; *Gastrointestinal Microbiome ; Chemoradiotherapy ; },
abstract = {PURPOSE: The gut microbiome plays an important role in cancer pathogenesis and therapy. Some studies have reported that specific bacteria in tumor tissues may contribute to the prognosis and treatment of esophageal squamous cell carcinoma (ESCC). However, there is limited evidence that the gut microbiome is associated with ESCC. This study assessed the utility of the gut microbiome as a predictive marker of the therapeutic effect in patients with ESCC undergoing chemo-radiotherapy (CRT).<br><br>PATIENTS AND METHODS: Fecal samples were collected from 51 patients with ESCC who had never undergone treatment between April 2021 and May 2022 in the Department of Frontier Surgery, Chiba University. The gut microbiome was analyzed using 16S metagenomics sequencing. The association between the gut microbiome composition and stage according to the TNM classification (American Joint Committee on Cancer 7.0) and CRT response according to the RECIST criteria was evaluated.<br><br>RESULTS: The relative abundance of Fusobacteriaceae was enriched in cStage III-IVb group. Among the 27 patients who received CRT, the relative abundance of Lactobacillaceae was enriched in those with a partial and complete response. Lactobacillaceae also did not correlate with any clinical data, but the high Lactobacillales group had a higher LMR (P&#x2009;=&#x2009;0.032) and lower PLR (P&#x2009;=&#x2009;0.045) than in the low Lactobacillales group.<br><br>CONCLUSIONS: In conclusion, we found that the relative abundance of Lactobacillaceae was enriched in patients with a partial or complete response among CRT those with ESCC, thus suggesting that the relative abundance of Lactobacillaceae can predict the effect of CRT.},
}
@article {pmid37684694,
year = {2023},
author = {Liu, S and Men, X and Guo, Y and Cai, W and Wu, R and Gao, R and Zhong, W and Guo, H and Ruan, H and Chou, S and Mai, J and Ping, S and Jiang, C and Zhou, H and Mou, X and Zhao, W and Lu, Z},
title = {Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {202},
pmid = {37684694},
issn = {2049-2618},
mesh = {Animals ; Mice ; *CADASIL ; *Gastrointestinal Microbiome ; *Mental Disorders ; Cytokines ; gamma-Aminobutyric Acid ; },
abstract = {BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3. The clinical manifestations are influenced by genetic and environmental factors that may include gut microbiome.<br><br>RESULTS: We investigated the fecal metagenome, fecal metabolome, serum metabolome, neurotransmitters, and cytokines in a cohort of 24 CADASIL patients with 28 healthy household controls. The integrated-omics study showed CADASIL patients harbored an altered microbiota composition and functions. The abundance of bacterial coenzyme A, thiamin, and flavin-synthesizing pathways was depleted in patients. Neurotransmitter balance, represented by the glutamate/GABA (4-aminobutanoate) ratio, was disrupted in patients, which was consistent with the increased abundance of two major GABA-consuming bacteria, Megasphaera elsdenii and Eubacterium siraeum. Essential inflammatory cytokines were significantly elevated in patients, accompanied by an increased abundance of bacterial virulence gene homologs. The abundance of patient-enriched Fusobacterium varium positively correlated with the levels of IL-1&#x3b2; and IL-6. Random forest classification based on gut microbial species, serum cytokines, and neurotransmitters showed high predictivity for CADASIL with AUC&#x2009;=&#x2009;0.89. Targeted culturomics and mechanisms study further showed that patient-derived F. varium infection caused systemic inflammation and behavior disorder in Notch3[R170C/+] mice potentially via induction of caspase-8-dependent noncanonical inflammasome activation in macrophages.<br><br>CONCLUSION: These findings suggested the potential linkage among the brain-gut-microbe axis in CADASIL. Video Abstract.},
}
@article {pmid37680093,
year = {2023},
author = {de la Cuesta-Zuluaga, J and Huus, KE and Youngblut, ND and Escobar, JS and Ley, RE},
title = {Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2246634},
pmid = {37680093},
issn = {1949-0984},
mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Obesity ; Adipose Tissue ; Anthropometry ; },
abstract = {Obesity (OB) and cardiometabolic disease are major public health issues linked to changes in the gut microbiome. OB and poor cardiometabolic health status (CHS) are often comorbid, which hinders efforts to identify components of the microbiome uniquely linked to either one. Here, we used a deeply phenotyped cohort of 408 adults from Colombia, including subjects with OB, unhealthy CHS, or both, to validate previously reported features of gut microbiome function and diversity independently correlated with OB or CHS using fecal metagenomes. OB was defined by body mass index, waist circumference, and body fat; CHS as healthy or unhealthy according to blood biochemistry and anthropometric data. We found that OB, more so than metabolic status, drove associations with gut microbiome structure and functions. The microbiome of obese individuals with and without co-existing unhealthy CHS was characterized by reduced metagenomic diversity, reduced fermentative potential and elevated capacity to respond to oxidative stress and produce bacterial antigens. Disease-linked features were correlated with increased host blood pressure and inflammatory markers, and were mainly contributed by members of the family Enterobacteriaceae. Our results link OB with a microbiome able to tolerate an inflammatory and oxygenated gut state, and suggest that OB is the main driver of microbiome functional differences when poor CHS is a comorbidity.},
}
@article {pmid37673036,
year = {2023},
author = {Ni, Y and Qian, L and Siliceo, SL and Long, X and Nychas, E and Liu, Y and Ismaiah, MJ and Leung, H and Zhang, L and Gao, Q and Wu, Q and Zhang, Y and Jia, X and Liu, S and Yuan, R and Zhou, L and Wang, X and Li, Q and Zhao, Y and El-Nezami, H and Xu, A and Xu, G and Li, H and Panagiotou, G and Jia, W},
title = {Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations.},
journal = {Cell metabolism},
volume = {35},
number = {9},
pages = {1530-1547.e8},
doi = {10.1016/j.cmet.2023.08.002},
pmid = {37673036},
issn = {1932-7420},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; Resistant Starch ; Triglycerides ; Humans ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a hepatic manifestation of metabolic dysfunction for which effective interventions are lacking. To investigate the effects of resistant starch (RS) as a microbiota-directed dietary supplement for NAFLD treatment, we coupled a 4-month randomized placebo-controlled clinical trial in individuals with NAFLD (ChiCTR-IOR-15007519) with metagenomics and metabolomics analysis. Relative to the control (n = 97), the RS intervention (n = 99) resulted in a 9.08% absolute reduction of intrahepatic triglyceride content (IHTC), which was 5.89% after adjusting for weight loss. Serum branched-chain amino acids (BCAAs) and gut microbial species, in particular Bacteroides stercoris, significantly correlated with IHTC and liver enzymes and were reduced by RS. Multi-omics integrative analyses revealed the interplay among gut microbiota changes, BCAA availability, and hepatic steatosis, with causality supported by fecal microbiota transplantation and monocolonization in mice. Thus, RS dietary supplementation might be a strategy for managing NAFLD by altering gut microbiota composition and functionality.},
}
@article {pmid37672426,
year = {2023},
author = {Prado, T and Magalhães, MGP and Moreira, DA and Brandão, ML and Fumian, TM and Ferreira, FC and Chame, M and Leomil, L and Degrave, WMS and Leite, JPG and Miagostovich, MP},
title = {Microbiome and virome on indoor surfaces of an Antarctic research ship.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {118},
number = {},
pages = {e230084},
pmid = {37672426},
issn = {1678-8060},
mesh = {Humans ; *Virome ; Ships ; Antarctic Regions ; *Microbiota ; Archaea/genetics ; },
abstract = {BACKGROUND: Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods.<br><br>OBJECTIVES AND METHODS: We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity.<br><br>FINDINGS: Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae.<br><br>MAIN CONCLUSIONS: This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.},
}
@article {pmid37670231,
year = {2023},
author = {Guo, R and Zhang, W and Shen, W and Zhang, G and Xie, T and Li, L and Jinmei, J and Liu, Y and Kong, F and Guo, B and Li, B and Sun, Y and Liu, S},
title = {Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {524},
pmid = {37670231},
issn = {1471-2164},
support = {SDAIT-27//Donkey Innovation Team of Shandong Modern Agricultural Industry Technology System/ ; SD2019 XM 008//Major Agricultural Application Technology Innovation Projects of Shandong Province/ ; 225A6601D//Hebei Provincial science and Technology Planning Project/ ; 2022DZ01//Systematic Evaluation and Screening of donkey germplasm Resources in the Yellow River Basin/ ; 2021E02035//Autonomous region science and technology branch Xinjiang project/ ; ZR2022QC091//Shandong Province Natural Science Foundation/ ; 20210021//Experimental Technology Research Pro-gramme of Qingdao Agriculture University/ ; },
mesh = {Bacteroidetes ; China ; Clostridiales ; Firmicutes ; *Gastrointestinal Microbiome ; *Equidae/microbiology ; },
abstract = {BACKGROUND: Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited.<br><br>RESULTS: In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose.<br><br>CONCLUSION: According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.},
}
@article {pmid37639475,
year = {2023},
author = {Rangel-Pineros, G and Almeida, A and Beracochea, M and Sakharova, E and Marz, M and Reyes Muñoz, A and Hölzer, M and Finn, RD},
title = {VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.},
journal = {PLoS computational biology},
volume = {19},
number = {8},
pages = {e1011422},
pmid = {37639475},
issn = {1553-7358},
mesh = {Humans ; *Eukaryota ; Eukaryotic Cells ; Genome, Viral/genetics ; Metagenome/genetics ; *Microbiota ; },
abstract = {The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.},
}
@article {pmid37597572,
year = {2023},
author = {Joslin, GR and Barber, DG and Aston, L and Liu, P and Kuloyo, O and Oentoro, K and Liu, J and Baugh, AV and Fedenko, JR and Melas, I and Hamilton, PG and Allen, DJ and Tennant, RK},
title = {Metagenomic analysis of ethylene glycol contamination in anaerobic digestion.},
journal = {Bioresource technology},
volume = {387},
number = {},
pages = {129683},
doi = {10.1016/j.biortech.2023.129683},
pmid = {37597572},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Metagenome ; *Microbiota ; Biofuels ; Ethylene Glycols ; },
abstract = {Anaerobic digestion is an established method for the biological conversion of waste feedstocks to biogas and biomethane. While anaerobic digestion is an excellent waste management technique, it can be susceptible to toxins and pollutants from contaminated feedstocks, which may have a detrimental impact on a digester's efficiency and productivity. Ethylene glycol (EG) is readily used in the heat-transfer loops of anaerobic digestion facilities to maintain reactor temperature. Failure of the structural integrity of these heat transfer loops can cause EG to leak into the digester, potentially causing a decrease in the resultant gas yields. Batch fermentations were incubated with 0, 10, 100 and 500 ppm (parts per million) of EG, and analysis showed that the EG was completely metabolised by the digester microbiome. The concentrations of EG tested showed significant increases in gas yields, however there were no significant changes to the digester microbiome.},
}
@article {pmid37572887,
year = {2023},
author = {Li, L and Guan, W and Fan, Y and He, Q and Guo, D and Yuan, A and Xing, Q and Wang, Y and Ma, Z and Ni, J and Chen, J and Zhou, Q and Zhong, Y and Li, J and Zhang, H},
title = {Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production.},
journal = {Bioresource technology},
volume = {387},
number = {},
pages = {129648},
doi = {10.1016/j.biortech.2023.129648},
pmid = {37572887},
issn = {1873-2976},
mesh = {Cattle ; Animals ; Manure ; Genes, Bacterial ; Zinc ; Carbon ; Anti-Bacterial Agents/pharmacology ; *Zinc Oxide ; Quorum Sensing/genetics ; Drug Resistance, Microbial/genetics ; *Microbiota ; *Nanostructures ; },
abstract = {This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.},
}
@article {pmid37541802,
year = {2023},
author = {Pfisterer, N and Ammer-Herrmenau, C and Antweiler, K and Küffer, S and Ellenrieder, V and Neesse, A},
title = {Dynamics of intestinal and intratumoral microbiome signatures in genetically engineered mice and human pancreatic ductal adenocarcinoma.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {23},
number = {6},
pages = {663-673},
doi = {10.1016/j.pan.2023.07.008},
pmid = {37541802},
issn = {1424-3911},
mesh = {Humans ; Mice ; Animals ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; Disease Models, Animal ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Emerging evidence has recently revealed a prominent role of the microbiome in pancreatic ductal adenocarcinoma (PDAC). However, while most observations were made in patients, mouse models still require a precise characterization of their disease-related microbiome to employ them for mechanistic and interventional preclinical studies.<br><br>METHODS: To investigate the fecal and tumoral microbiome of LSL-Kras[G12D/+];LSL-Trp53[R172H/+];Pdx-1-Cre (KPC) and control (CTRL) mice, Oxford Nanopore sequencing was applied. Feces were collected from 10 KPC mice and 10 CTRLs at 3 timepoints (6 weeks, 12 weeks, and when tumor-bearing (KPC) or 6 months (CTRL), respectively). Metagenomic sequencing was performed on feces DNA. KPC tumor and healthy pancreas DNA samples were subjected to 16S rRNA gene sequencing. Bacterial marker components were detected in KPC tumor tissue over time by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC).<br><br>RESULTS: Murine fecal samples showed a significantly different microbiome compared to age-matched healthy CTRLs regarding beta diversity (p&#x202f;=&#x202f;0.001, R2&#x202f;=&#x202f;0.2-0.25 for Bray-Curtis). Adjusted human PDAC classifiers predicted disease status from feces of KPC mice achieving area under the receiver operating characteristic (AUROC) values of 80%. Furthermore, KPC tumors harbored significantly more bacterial components than healthy pancreas. Also the microbial composition differs significantly between KPC tumors and healthy pancreas tissue (p&#x202f;=&#x202f;0.042 for Bray-Curtis). Microbiota found highly abundant in human PDAC samples were considerably more abundant in KPC tumors as compared to healthy pancreas samples (p-value <0.001).<br><br>CONCLUSION: KPC fecal samples show similarities with the microbial composition of stool samples from human PDAC patients.},
}
@article {pmid37532062,
year = {2023},
author = {Liu, J and Yu, J and Tan, Y and Dang, R and Zhou, M and Hernández, M and Lichtfouse, E and Xiao, L},
title = {Biomethane is produced by acetate cleavage, not direct interspecies electron transfer: genome-centric view and carbon isotope.},
journal = {Bioresource technology},
volume = {387},
number = {},
pages = {129589},
doi = {10.1016/j.biortech.2023.129589},
pmid = {37532062},
issn = {1873-2976},
mesh = {Electrons ; Carbon Isotopes ; Carbon Dioxide/metabolism ; Bacteria/metabolism ; Acetates ; Anaerobiosis ; *Microbiota ; *Euryarchaeota/metabolism ; Methane/metabolism ; },
abstract = {Understanding the source of methane (CH4) is of great significance for improving the anaerobic fermentation efficiency in bioengineering, and for mitigating the emission potential of natural ecosystems. Microbes involved in the process named direct interspecies electron transfer coupling with CO2 reduction, i.e., electrons released from electroactive bacteria to reduce CO2 into CH4, have attracted considerable attention for wastewater treatment in the past decade. However, how the synergistic effect of microbiota contributes to this anaerobic carbon metabolism accompanied by CH4 production still remains poorly understood, especial for wastewater with antibiotic exposure. Results show that enhancing lower-abundant acetoclastic methanogens and acetogenic bacteria, rather than electroactive bacteria, contributed to CH4 production, based on a metagenome-assembled genomes network analysis. Natural and artificial isotope tracing of CH4 further confirmed that CH4 mainly originated from acetoclastic methanogenesis. These findings reveal the contribution of direct acetate cleavage (acetoclastic methanogenesis) and provide insightsfor further regulation of methanogenic strategies.},
}
@article {pmid37524154,
year = {2023},
author = {Yan, J and Duan, W and Gao, Q and Mao, T and Wang, M and Duan, J and Li, J},
title = {ENPP2 inhibitor improves proliferation in AOM/DSS-induced colorectal cancer mice via remodeling the gut barrier function and gut microbiota composition.},
journal = {Pharmacological research},
volume = {195},
number = {},
pages = {106877},
doi = {10.1016/j.phrs.2023.106877},
pmid = {37524154},
issn = {1096-1186},
mesh = {Animals ; Mice ; *Colorectal Neoplasms/metabolism ; Azoxymethane/adverse effects ; *Gastrointestinal Microbiome ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; Cell Proliferation ; Mice, Inbred C57BL ; *Colitis/chemically induced ; },
abstract = {In our previous multicenter study, we delineated the inherent metabolic features of colorectal cancer (CRC). Therein, we identified a member of the ectonucleotide pyrophosphatase/ phosphodiesterase family (ENPP2) as a significant differential metabolite of CRC. In this study, the role of ENPP2 in CRC has been demonstrated using established in vitro and in vivo models including ENPP2 gene knockdown, and use of the ENPP2 inhibitor, GLPG1690. We found that CRC proliferation was decreased after either ENPP2 gene knockdown or use of ENPP2 inhibitors. We further evaluated the role of GLPG1690 in AOM/DSS-induced CRC mice via intestinal barrier function, macrophage polarization, inflammatory response and microbial homeostasis. Results of immunofluorescence staining and Western blotting showed that GLPG1690 can restore gut-barrier function by increasing the expression of tight junction proteins, claudin-1, occludin and ZO-1. M2 tumor-associated macrophage polarization and colonic inflammation were attenuated after treatment with GLPG1690 using the Azoxymethane/Dextran Sodium Sulfate (AOM/DSS) model. Moreover, 16 S rDNA pyrosequencing and metagenomic analysis showed that GLPG1690 could alleviate gut dysbiosis in mice. Furthermore, administration of GLPG1690 with antibiotics as well as fecal microbiota transplantation assays demonstrated a close link between the efficacy of GLPG1690 and the gut microbiota composition. Finally, results of metabolomic analysis implicated mainly the gut microbiota-derived metabolites of aromatic amino acids in CRC progression. These findings may provide novel insights into the development of small-molecule ENPP2 inhibitors for the treatment of CRC.},
}
@article {pmid37465976,
year = {2023},
author = {White, MG and Damania, A and Alshenaifi, J and Sahasrabhojane, P and Peacock, O and Losh, J and Wong, MC and Lutter-Berkova, Z and Chang, GJ and Futreal, A and Wargo, JA and Ajami, NJ and Kopetz, S and You, YN},
title = {Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy.},
journal = {Annals of surgery},
volume = {278},
number = {4},
pages = {538-548},
pmid = {37465976},
issn = {1528-1140},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Middle Aged ; Neoadjuvant Therapy ; *Rectal Neoplasms/therapy/pathology ; Biopsy ; *Microbiota ; },
abstract = {OBJECTIVE: External exposures, the host, and the microbiome interact in oncology. We aimed to investigate tumoral microbiomes in young-onset rectal cancers (YORCs) for profiles potentially correlative with disease etiology and biology.<br><br>BACKGROUND: YORC is rapidly increasing, with 1 in 4 new rectal cancer cases occurring under the age of 50 years. Its etiology is unknown.<br><br>METHODS: YORC (<50&#xa0;y old) or later-onset rectal cancer (LORC, &#x2265;50&#xa0;y old) patients underwent pretreatment biopsied of tumor and tumor-adjacent normal (TAN) tissue. After whole genome sequencing, metagenomic analysis quantified microbial communities comparing tumors versus TANs and YORCs versus LORCs, controlling for multiple testing. Response to neoadjuvant therapy (NT) was categorized as major pathological response (MPR, &#x2264;10% residual viable tumor) versus non-MPR.<br><br>RESULTS: Our 107 tumors, 75 TANs from 37 (35%) YORCs, and 70 (65%) LORCs recapitulated bacterial species were previously associated with colorectal cancers (all P <0.0001). YORC and LORC tumoral microbiome signatures were distinct. After NT, 13 patients (12.4%) achieved complete pathologic response, whereas MPR occurred in 47 patients (44%). Among YORCs, MPR was associated with Fusobacterium nucleaum , Bacteroides dorei, and Ruminococcus bromii (all P <0.001), but MPR in LORC was associated with R. bromii (P <0.001). Network analysis of non-MPR tumors demonstrated a preponderance of oral bacteria not observed in MPR tumors.<br><br>CONCLUSIONS: Microbial signatures were distinct between YORC and LORC. Failure to achieve an MPR was associated with oral bacteria in tumors. These findings urge further studies to decipher correlative versus mechanistic associations but suggest a potential for microbial modulation to augment current treatments.},
}
@article {pmid37422083,
year = {2023},
author = {Lee, H and Yoon, S and Park, YH and Lee, JS and Rhyu, DY and Kim, KT},
title = {Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {334},
number = {},
pages = {122108},
doi = {10.1016/j.envpol.2023.122108},
pmid = {37422083},
issn = {1873-6424},
mesh = {Animals ; Male ; Female ; *Diabetes Mellitus, Type 2/metabolism ; Zebrafish/metabolism ; Persistent Organic Pollutants/metabolism/pharmacology ; Dysbiosis/chemically induced/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; *Environmental Pollutants/metabolism ; },
abstract = {Mixtures of chlorinated persistent organic pollutants (C-POPs-Mix) are chemically related risk factors for type 2 diabetes mellitus (T2DM); however, the effects of chronic exposure to C-POPs-Mix on microbial dysbiosis remain poorly understood. Herein, male and female zebrafish were exposed to C-POPs-Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02, 0.1, and 0.5 μg/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance and richness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C-POPs-Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 μg/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis, Rhizobium tibeticum, Bifidobacterium catenulatum, Bifidobacterium adolescentis, and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation, which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM-related molecular pathways. Thus, microbial dysbiosis in T2DM-triggered zebrafish occurred as a result of chronic exposure to C-POPs-Mix, indicating strong host-microbiome interactions.},
}
@article {pmid37350224,
year = {2023},
author = {Zhou, W and Fleming, E and Legendre, G and Roux, L and Latreille, J and Gendronneau, G and Forestier, S and Oh, J},
title = {Skin microbiome attributes associate with biophysical skin ageing.},
journal = {Experimental dermatology},
volume = {32},
number = {9},
pages = {1546-1556},
doi = {10.1111/exd.14863},
pmid = {37350224},
issn = {1600-0625},
support = {P30 CA034196/CA/NCI NIH HHS/United States ; R56 AG060746/AG/NIA NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; R01 AR078634/AR/NIAMS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; },
mesh = {*Skin Aging ; *Microbiota/genetics ; Bacteria ; Anti-Bacterial Agents ; Skin/microbiology ; },
abstract = {Two major arms of skin ageing are changes in the skin's biophysical conditions and alterations in the skin microbiome. This work partitioned both arms to study their interaction in detail. Leveraging the resolution provided by shotgun metagenomics, we explored how skin microbial species, strains and gene content interact with the biophysical traits of the skin during ageing. With a dataset well-controlled for confounding factors, we found that skin biophysical traits, especially the collagen diffusion coefficient, are associated with the composition and the functional potential of the skin microbiome, including the abundance of bacterial strains found in nosocomial infections and the abundance of antibiotic resistance genes. Our findings reveal important associations between skin biophysical features and ageing-related changes in the skin microbiome and generate testable hypotheses for the mechanisms of such associations.},
}
@article {pmid37343864,
year = {2023},
author = {Zhao, W and Chen, Z and Yang, X and Sheng, L and Mao, H and Zhu, S},
title = {Metagenomics reveal arbuscular mycorrhizal fungi altering functional gene expression of rhizosphere microbial community to enhance Iris tectorum's resistance to Cr stress.},
journal = {The Science of the total environment},
volume = {895},
number = {},
pages = {164970},
doi = {10.1016/j.scitotenv.2023.164970},
pmid = {37343864},
issn = {1879-1026},
mesh = {*Mycorrhizae/physiology ; *Iris Plant ; Chromium/analysis ; Plant Roots/microbiology ; Rhizosphere ; Metagenomics ; *Metals, Heavy/analysis ; Soil/chemistry ; *Microbiota ; Gene Expression ; Soil Microbiology ; Fungi ; },
abstract = {Chromium (Cr) can disrupt a plant's normal physiological and metabolic functions and severely impact the microenvironment. However, limited studies have investigated the impact of arbuscular mycorrhizal fungi (AMF) inoculation on the rhizosphere microorganisms of Iris tectorum under Cr stress, and the mechanisms of how rhizosphere microorganisms interact with hosts and contaminants. In this study, we investigated the effects of AMF inoculation on the growth, absorption of nutrients and heavy metals, and functional genes of the rhizosphere microbial community of I. tectorum under Cr stress in a greenhouse pot experiment. The results showed that AMF significantly increased the biomass and nutrient levels of I. tectorum, while decreasing the content of Cr in soil. Furthermore, metagenome analysis demonstrated significant changes in the structure and composition of the rhizosphere microbial community after AMF formed a mycorrhizal symbiosis system with the I. tectorum. Specifically, the abundance of functional genes related to nutrient cycling (N, P) and heavy metal resistance (chrA and arsB), as well as the abundance of heavy metal transporter family (P-atPase, MIT, CDF, and ABC) in the rhizosphere microbial community were up-regulated and their expression. Additionally, the synergies between rhizosphere microbial communities were regulated, and the complexity and stability of the rhizosphere microbial ecological network were enhanced. This study provides evidence that AMF can regulate rhizosphere microbial communities to improve plant growth and heavy metal stress tolerance, and helps us to understand the potential mechanism of wetland plant remediation of Cr-contaminated soil under AMF symbiosis.},
}
@article {pmid37119391,
year = {2023},
author = {Di Ciaula, A and Bonfrate, L and Khalil, M and Garruti, G and Portincasa, P},
title = {Contribution of the microbiome for better phenotyping of people living with obesity.},
journal = {Reviews in endocrine &amp; metabolic disorders},
volume = {24},
number = {5},
pages = {839-870},
pmid = {37119391},
issn = {1573-2606},
mesh = {Animals ; Humans ; Overweight/complications ; Obesity/metabolism ; *Microbiota ; *Gastrointestinal Microbiome/physiology ; Diet ; Inflammation/complications ; },
abstract = {Obesity has reached epidemic proportion worldwide and in all ages. Available evidence points to a multifactorial pathogenesis involving gene predisposition and environmental factors. Gut microbiota plays a critical role as a major interface between external factors, i.e., diet, lifestyle, toxic chemicals, and internal mechanisms regulating energy and metabolic homeostasis, fat production and storage. A shift in microbiota composition is linked with overweight and obesity, with pathogenic mechanisms involving bacterial products and metabolites (mainly endocannabinoid-related mediators, short-chain fatty acids, bile acids, catabolites of tryptophan, lipopolysaccharides) and subsequent alterations in gut barrier, altered metabolic homeostasis, insulin resistance and chronic, low-grade inflammation. Although animal studies point to the links between an "obesogenic" microbiota and the development of different obesity phenotypes, the translational value of these results in humans is still limited by the heterogeneity among studies, the high variation of gut microbiota over time and the lack of robust longitudinal studies adequately considering inter-individual confounders. Nevertheless, available evidence underscores the existence of several genera predisposing to obesity or, conversely, to lean and metabolically health phenotype (e.g., Akkermansia muciniphila, species from genera Faecalibacterium, Alistipes, Roseburia). Further longitudinal studies using metagenomics, transcriptomics, proteomics, and metabolomics with exact characterization of confounders are needed in this field. Results must confirm that distinct genera and specific microbial-derived metabolites represent effective and precision interventions against overweight and obesity in the long-term.},
}
@article {pmid37669363,
year = {2023},
author = {Sireci, M and Muñoz, MA and Grilli, J},
title = {Environmental fluctuations explain the universal decay of species-abundance correlations with phylogenetic distance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {37},
pages = {e2217144120},
doi = {10.1073/pnas.2217144120},
pmid = {37669363},
issn = {1091-6490},
support = {PID2020-113681GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; },
mesh = {Phylogeny ; Cross-Sectional Studies ; *Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Multiple ecological forces act together to shape the composition of microbial communities. Phyloecology approaches-which combine phylogenetic relationships between species with community ecology-have the potential to disentangle such forces but are often hard to connect with quantitative predictions from theoretical models. On the other hand, macroecology, which focuses on statistical patterns of abundance and diversity, provides natural connections with theoretical models but often neglects interspecific correlations and interactions. Here, we propose a unified framework combining both such approaches to analyze microbial communities. In particular, by using both cross-sectional and longitudinal metagenomic data for species abundances, we reveal the existence of an empirical macroecological law establishing that correlations in species-abundance fluctuations across communities decay from positive to null values as a function of phylogenetic dissimilarity in a consistent manner across ecologically distinct microbiomes. We formulate three variants of a mechanistic model-each relying on alternative ecological forces-that lead to radically different predictions. From these analyses, we conclude that the empirically observed macroecological pattern can be quantitatively explained as a result of shared population-independent fluctuating resources, i.e., environmental filtering and not as a consequence of, e.g., species competition. Finally, we show that the macroecological law is also valid for temporal data of a single community and that the properties of delayed temporal correlations can be reproduced as well by the model with environmental filtering.},
}
@article {pmid37666802,
year = {2023},
author = {Kieft, B and Finke, N and McLaughlin, RJ and Nallan, AN and Krzywinski, M and Crowe, SA and Hallam, SJ},
title = {Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5380},
pmid = {37666802},
issn = {2041-1723},
mesh = {*Wastewater ; *Metagenome ; Microbial Consortia/genetics ; Sewage ; Methane ; },
abstract = {Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.},
}
@article {pmid37664620,
year = {2023},
author = {Mao, C and Li, Q and Komijani, M and Huang, J and Li, T},
title = {Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes.},
journal = {iScience},
volume = {26},
number = {9},
pages = {107508},
pmid = {37664620},
issn = {2589-0042},
abstract = {Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.},
}
@article {pmid36977954,
year = {2023},
author = {Mahiddine, FY and You, I and Park, H and Kim, MJ},
title = {Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation.},
journal = {Veterinary research communications},
volume = {47},
number = {3},
pages = {1629-1640},
pmid = {36977954},
issn = {1573-7446},
mesh = {Male ; Dogs ; Animals ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; Semen ; Dietary Supplements ; Spermatozoa ; },
abstract = {The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.},
}
@article {pmid37659809,
year = {2023},
author = {Li, Z and Wen, Q and Pi, J and Zhang, D and Nie, J and Wei, W and Li, W and Guo, DA},
title = {An inulin-type fructan isolated from Serratula chinensis alleviated the dextran sulfate sodium-induced colitis in mice through regulation of intestinal barrier and gut microbiota.},
journal = {Carbohydrate polymers},
volume = {320},
number = {},
pages = {121206},
doi = {10.1016/j.carbpol.2023.121206},
pmid = {37659809},
issn = {1879-1344},
mesh = {Animals ; Mice ; Inulin/pharmacology/therapeutic use ; Fructans/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Dextran Sulfate/toxicity ; Spectroscopy, Fourier Transform Infrared ; *Colitis/chemically induced/drug therapy ; *Coleoptera ; },
abstract = {Herein, we aimed to explore the polysaccharide material basis of Serratula chinensis and establish its beneficial effects against colitis. A neutral polysaccharide (SCP) was extracted from S. chinensis in high yield using hot water. The molecular weights were calculated by HPSEC as Mw = 2928 Da, Mn = 2634 Da, and Mw/Mn = 1.11. FT-IR and 1D/2D-NMR spectroscopic analyses confirmed that SCP was an inulin-type fructan with α-D-Glcp-(1 → [1)-β-D-Fruf-(2]17) linkages. Treatment with SCP (200 or 400 mg/kg) alleviated dextran sulfate sodium (DSS)-induced mouse colitis symptoms, including the loss of body weight, increase of disease activity index score, and shortening of colon length. Histopathological and immunofluorescence assessments revealed that SCP could reduce pathological damage to the colon, restore the number of goblet cells, increase the content of glycoproteins in goblet cells and mucins in crypts, and enhance the expression of tight junction proteins ZO-1 and occludin. In addition, metagenomic sequencing revealed that SCP could improve the dysbiosis of gut microbiomes and act on multiple microbial functions. Moreover, SCP treatment increased the content of colonic acetic acid and butanoic acid. Collectively, these results indicated that SCP could alleviate the DSS-induced colitis in mice through regulation of intestinal barrier and gut microbiota.},
}
@article {pmid37658443,
year = {2023},
author = {Paulo, AC and Lança, J and Almeida, ST and Hilty, M and Sá-Leão, R},
title = {The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {199},
pmid = {37658443},
issn = {2049-2618},
support = {UIDB/04612/2020, UIDP/04612/2020, LA/P/0087/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UI/BD/153385/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/108380/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04612/2020, UIDP/04612/2020, LA/P/0087/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Adult ; Child ; Humans ; Streptococcus pneumoniae/genetics ; Smoking ; Nose ; *Microbiota ; Metagenome ; *Bacillus ; Firmicutes ; },
abstract = {BACKGROUND: The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children.<br><br>RESULTS: Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P&#x2009;<&#x2009;0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis.<br><br>CONCLUSIONS: Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract.},
}
@article {pmid37622435,
year = {2023},
author = {Juge, N},
title = {Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {8},
pages = {},
pmid = {37622435},
issn = {1465-2080},
mesh = {Humans ; *Ruminococcus/genetics ; Gastrointestinal Microbiome ; Symbiosis ; },
abstract = {Ruminococcus gnavus is a human gut symbiont, part of the infant and adult gut microbiota and associated with intestinal and extra-intestinal disorders. R. gnavus mechanisms of adaptation to the gut are strain-specific and underpinned by the capacity of R. gnavus strains to utilize mucin and dietary glycans and produce bacteriocins and adhesins. Several potential mediators underpinning the association between R. gnavus strains and diseases have been identified, including the capacity to elicit a pro- or anti-inflammatory host response and modulate host metabolism, secondary bile acids and tryptophan metabolic pathways. Based on increasing evidence from metagenomics studies in humans and functional investigations in vitro and in mouse models, R. gnavus is emerging as a main player in influencing health and disease outcomes from infants to the elderly.},
}
@article {pmid37459963,
year = {2023},
author = {Wang, Y and Guo, Z and Li, J and Sui, F and Dai, W and Zhang, W and Du, H},
title = {Unraveling the differential perturbations of species-level functional profiling of gut microbiota among phases of methamphetamine-induced conditioned place preference.},
journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry},
volume = {127},
number = {},
pages = {110828},
doi = {10.1016/j.pnpbp.2023.110828},
pmid = {37459963},
issn = {1878-4216},
mesh = {*Methamphetamine/pharmacology ; *Central Nervous System Stimulants/pharmacology ; *Gastrointestinal Microbiome ; Conditioning, Classical ; Reward ; },
abstract = {The gut microbiome plays a significant role in methamphetamine addiction. Previous studies using short-read amplicon sequencing have described alterations in microbiota at the genus level and predicted function, in which taxonomic resolution is insufficient for accurate functional measurements. To address this limitation, we employed metagenome sequencing to intuitively associate species to functions of gut microbiota in methamphetamine-induced conditioned place preference. We observed differential perturbations of species-level functional profiling of the gut microbiota across phases of METH-induced CPP, with alterations in SCFA metabolism and bacterial motility at the acquisition phase and substance dependence-alcoholism pathway and amino acid metabolism at the extinction phase. Our findings suggest that reduced beneficial bacteria, i.e., Lactobacillus reuteri, contributed to the alteration of SCFA metabolism, while the increased abundance of Akkermansia muciniphila during the extinction phase may be associated with altered phenylalanine, tyrosine, and tryptophan metabolism and substance dependence pathway. Our study further supports the association between specific microbial taxa and METH-induced rewarding.},
}
@article {pmid37658428,
year = {2023},
author = {Mao, Q and Liu, Y and Zhang, J and Li, W and Zhang, W and Zhou, C},
title = {Blood virome of patients with traumatic sepsis.},
journal = {Virology journal},
volume = {20},
number = {1},
pages = {198},
pmid = {37658428},
issn = {1743-422X},
mesh = {Humans ; Virome ; *Sepsis/diagnosis ; *Anelloviridae/genetics ; Immunocompromised Host ; Metagenome ; },
abstract = {Sepsis is one of the possible outcomes of severe trauma, and it poses a dire threat to human life, particularly in immunocompromised people. The most prevalent pathogens are bacteria and fungi, but viruses should not be overlooked. For viral metagenomic analysis, we collected blood samples from eight patients with post-traumatic sepsis before and seven days after treatment. The results demonstrated that Anellovirus predominated the viral community, followed by Siphoviridae and Myoviridae, and that the variations in viral community and viral load before and after treatment were not statistically significant. This study allows us to investigate methods for establishing NGS-based viral diagnostic instruments for detecting viral infections in the blood of sepsis patients so that antiviral therapy can be administered quickly.},
}
@article {pmid37489282,
year = {2023},
author = {Thorburn, DJ and Sagonas, K and Binzer-Panchal, M and Chain, FJJ and Feulner, PGD and Bornberg-Bauer, E and Reusch, TBH and Samonte-Padilla, IE and Milinski, M and Lenz, TL and Eizaguirre, C},
title = {Origin matters: Using a local reference genome improves measures in population genomics.},
journal = {Molecular ecology resources},
volume = {23},
number = {7},
pages = {1706-1723},
doi = {10.1111/1755-0998.13838},
pmid = {37489282},
issn = {1755-0998},
support = {EI 841/4-1//Deutsche Forschungsgemeinschaft/ ; EI 841/6-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Metagenomics ; Genome/genetics ; Chromosome Mapping ; Genomics/methods ; Sequence Analysis, DNA/methods ; *Smegmamorpha/genetics ; },
abstract = {Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.},
}
@article {pmid37474105,
year = {2023},
author = {Kyaw, TS and Upadhyay, V and Tolstykh, I and Van Loon, K and Laffan, A and Stanfield, D and Gempis, D and Kenfield, SA and Chan, JM and Piawah, S and Atreya, CE and Ng, K and Venook, A and Kidder, W and Turnbaugh, PJ and Van Blarigan, EL},
title = {Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors.},
journal = {The American journal of clinical nutrition},
volume = {118},
number = {3},
pages = {518-529},
doi = {10.1016/j.ajcnut.2023.07.011},
pmid = {37474105},
issn = {1938-3207},
support = {R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 AT011117/AT/NCCIH NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; F30 CA257378/CA/NCI NIH HHS/United States ; R37 CA248774/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Vegetables ; Fruit ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Diet/methods ; Alcohol Drinking ; *Cancer Survivors ; *Colorectal Neoplasms ; },
abstract = {BACKGROUND: Adherence to the American Cancer Society (ACS) guidelines of avoiding obesity, maintaining physical activity, and consuming a diet rich in fruits, vegetables, and whole grains is associated with longer survival in colorectal cancer (CRC) survivors. Dietary components of the ACS guidelines may act in part by changing the microbiome, which is implicated in CRC outcomes.<br><br>OBJECTIVES: We conducted a pilot cross-sectional study to explore associations between ACS guidelines and the gut microbiome.<br><br>METHODS: Stool samples and questionnaires were collected from 28 CRC survivors at the University of California, San Francisco from 2019 to 2020. ACS scores were calculated based on validated questionnaires. Gut microbial community structure from 16S amplicons and gene/pathway abundances from metagenomics were tested for associations with the ACS score and its components using ANOVA and general linear models.<br><br>RESULTS: The overall ACS score was not significantly associated with variations in the fecal microbiota. However, fruit and vegetable intake and alcohol intake accounted for 19% (P = 0.005) and 13% (P = 0.01) of variation in the microbiota, respectively. Fruit/vegetable consumption was associated with increased microbial diversity, increased Firmicutes, decreased Bacteroidota, and changes to multiple genes and metabolic pathways, including enriched pathways for amino acid and short-chain fatty acid biosynthesis and plant-associated sugar degradation. In contrast, alcohol consumption was positively associated with overall microbial diversity, negatively associated with Bacteroidota abundance, and associated with changes to multiple genes and metabolic pathways. The other components of the ACS score were not statistically significantly associated with the fecal microbiota in our sample.<br><br>CONCLUSIONS: These results guide future studies examining the impact of changes in the intake of fruits, vegetables, and alcoholic drinks on the gut microbiome of CRC survivors.},
}
@article {pmid37382302,
year = {2023},
author = {Puente-Sánchez, F and Hoetzinger, M and Buck, M and Bertilsson, S},
title = {Exploring environmental intra-species diversity through non-redundant pangenome assemblies.},
journal = {Molecular ecology resources},
volume = {23},
number = {7},
pages = {1724-1736},
doi = {10.1111/1755-0998.13826},
pmid = {37382302},
issn = {1755-0998},
support = {892961//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 2019-02336//Svenska Forskningsr&#xe5;det Formas/ ; 2017-04422//Vetenskapsr&#xe5;det/ ; 2018-05973//Vetenskapsr&#xe5;det/ ; },
mesh = {Phylogeny ; *Bacteria/genetics ; Metagenome ; Algorithms ; *Microbiota ; Metagenomics/methods ; },
abstract = {At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.},
}
@article {pmid37314861,
year = {2023},
author = {Palacios, N and Wilkinson, J and Bjornevik, K and Schwarzschild, MA and McIver, L and Ascherio, A and Huttenhower, C},
title = {Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes.},
journal = {Annals of neurology},
volume = {94},
number = {3},
pages = {486-501},
doi = {10.1002/ana.26719},
pmid = {37314861},
issn = {1531-8249},
support = {R01NS097723/NS/NINDS NIH HHS/United States ; U01 CA167552/NH/NIH HHS/United States ; UM1 CA186107/NH/NIH HHS/United States ; },
mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Metagenomics ; Follow-Up Studies ; Prodromal Symptoms ; },
abstract = {OBJECTIVE: Prior studies on the gut microbiome in Parkinson's disease (PD) have yielded conflicting results, and few studies have focused on prodromal (premotor) PD or used shotgun metagenomic profiling to assess microbial functional potential. We conducted a nested case-control study within 2 large epidemiological cohorts to examine the role of the gut microbiome in PD.<br><br>METHODS: We profiled the fecal metagenomes of 420 participants in the Nurses' Health Study and the Health Professionals Follow-up Study with recent onset PD (N&#x2009;=&#x2009;75), with features of prodromal PD (N&#x2009;=&#x2009;101), controls with constipation (N&#x2009;=&#x2009;113), and healthy controls (N&#x2009;=&#x2009;131) to identify microbial taxonomic and functional features associated with PD and features suggestive of prodromal PD. Omnibus and feature-wise analyses identified bacterial species and pathways associated with prodromal and recently onset PD.<br><br>RESULTS: We observed depletion of several strict anaerobes associated with reduced inflammation among participants with PD or features of prodromal PD. A microbiome-based classifier had moderate accuracy (area under the curve [AUC]&#x2009;=&#x2009;0.76 for species and 0.74 for pathways) to discriminate between recently onset PD cases and controls. These taxonomic shifts corresponded with functional shifts indicative of carbohydrate source preference. Similar, but less marked, changes were observed in participants with features of prodromal PD, in both microbial features and functions.<br><br>INTERPRETATION: PD and features of prodromal PD were associated with similar changes in the gut microbiome. These findings suggest that changes in the microbiome could represent novel biomarkers for the earliest phases of PD. ANN NEUROL 2023;94:486-501.},
}
@article {pmid37655299,
year = {2023},
author = {Shen, H and Liu, T and Shen, M and Zhang, Y and Chen, W and Chen, H and Wang, Y and Liu, J and Tao, J and He, L and Lu, G and Yan, G},
title = {Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1200806},
pmid = {37655299},
issn = {2235-2988},
mesh = {Humans ; Child ; Bronchoalveolar Lavage Fluid ; Retrospective Studies ; *Pneumonia/diagnosis ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Intensive Care Units, Pediatric ; Lung ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples.<br><br>METHODS: A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data.<br><br>RESULTS: Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the &#x3b1;-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%).<br><br>CONCLUSIONS: mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.},
}
@article {pmid37652953,
year = {2023},
author = {Wu, J and Li, C and Gao, P and Zhang, C and Zhang, P and Zhang, L and Dai, C and Zhang, K and Shi, B and Liu, M and Zheng, J and Pan, B and Chen, Z and Zhang, C and Liao, W and Pan, W and Fang, W and Chen, C},
title = {Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study.},
journal = {Signal transduction and targeted therapy},
volume = {8},
number = {1},
pages = {326},
pmid = {37652953},
issn = {2059-3635},
support = {82072257//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 20DZ2253700, 20DZ2272000, 21410750500 and 22Y21900500//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; *Lung Transplantation ; Cytokines ; Allografts ; },
abstract = {Whether the alternated microbiota in the gut contribute to the risk of allograft rejection (AR) and pulmonary infection (PI) in the setting of lung transplant recipients (LTRs) remains unexplored. A prospective multicenter cohort of LTRs was identified in the four lung transplant centers. Paired fecal and serum specimens were collected and divided into AR, PI, and event-free (EF) groups according to the diagnosis at sampling. Fecal samples were determined by metagenomic sequencing. And metabolites and cytokines were detected in the paired serum to analyze the potential effect of the altered microbiota community. In total, we analyzed 146 paired samples (AR = 25, PI = 43, and EF = 78). Notably, we found that the gut microbiome of AR followed a major depletion pattern with decreased 487 species and compositional diversity. Further multi-omics analysis showed depleted serum metabolites and increased inflammatory cytokines in AR and PI. Bacteroides uniformis, which declined in AR (2.4% vs 0.6%) and was negatively associated with serum IL-1β and IL-12, was identified as a driven specie in the network of gut microbiome of EF. Functionally, the EF specimens were abundant in probiotics related to mannose and cationic antimicrobial peptide metabolism. Furthermore, a support-vector machine classifier based on microbiome, metabolome, and clinical parameters highly predicted AR (AUPRC = 0.801) and PI (AUPRC = 0.855), whereby the microbiome dataset showed a particularly high diagnostic power. In conclusion, a disruptive gut microbiota showed a significant association with allograft rejection and infection and with systemic cytokines and metabolites in LTRs.},
}
@article {pmid37652940,
year = {2023},
author = {Jacobs, JP and Lee, ML and Rechtman, DJ and Sun, AK and Autran, C and Niklas, V},
title = {Human milk oligosaccharides modulate the intestinal microbiome of healthy adults.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14308},
pmid = {37652940},
issn = {2045-2322},
mesh = {Female ; Infant, Newborn ; Humans ; Adult ; Milk, Human ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Oligosaccharides/pharmacology ; },
abstract = {Human milk contains over 200 distinct oligosaccharides, which are critical to shaping the developing neonatal gut microbiome. To investigate whether a complex mixture of human milk oligosaccharides (HMOs) would similarly modulate the adult gut microbiome, HMO-Concentrate derived from pooled donor breast milk was administered orally to 32 healthy adults for 7 days followed by 21 days of monitoring. Fecal samples were collected for 16S rRNA gene sequencing, shotgun metagenomics, and metabolomics analyses. HMO-Concentrate induced dose-dependent Bifidobacterium expansion, reduced microbial diversity, and altered microbial gene content. Following HMO cessation, a microbial succession occurred with diverse taxonomic changes-including Bacteroides expansion-that persisted through day 28. This was associated with altered microbial gene content, shifts in serum metabolite levels, and increased circulating TGFβ and IL-10. Incubation of cultured adult microbiota with HMO-Concentrate induced dose-dependent compositional shifts that were not recapitulated by individual HMOs or defined mixtures of the 10 most abundant HMOs in HMO-Concentrate at their measured concentrations. These findings support that pooled donor HMOs can exert direct effects on adult gut microbiota and that complex mixtures including low abundance HMOs present in donor milk may be required for maximum effect.Registration: ClinicalTrials.gov NCT05516225.},
}
@article {pmid37650395,
year = {2023},
author = {Huang, G and Qi, D and Yang, Z and Hou, R and Shi, W and Zhao, F and Li, Z and Yan, L and Wei, F},
title = {Gut microbiome as a key monitoring indicator for reintroductions of captive animals.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/cobi.14173},
pmid = {37650395},
issn = {1523-1739},
abstract = {Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild. This article is protected by copyright. All rights reserved.},
}
@article {pmid37648982,
year = {2023},
author = {Diba, F and Hoque, MN and Rahman, MS and Haque, F and Rahman, KMJ and Moniruzzaman, M and Khan, M and Hossain, MA and Sultana, M},
title = {Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {241},
pmid = {37648982},
issn = {1471-2180},
mesh = {*Arsenic ; *Arsenites ; Phylogeny ; *Microbiota ; },
abstract = {BACKGROUND: Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.<br><br>RESULTS: Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23&#xa0;mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32&#xa0;mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.<br><br>CONCLUSIONS: Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.},
}
@article {pmid37648570,
year = {2023},
author = {Robinson, JM and Hodgson, R and Krauss, SL and Liddicoat, C and Malik, AA and Martin, BC and Mohr, JJ and Moreno-Mateos, D and Muñoz-Rojas, M and Peddle, SD and Breed, MF},
title = {Opportunities and challenges for microbiomics in ecosystem restoration.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2023.07.009},
pmid = {37648570},
issn = {1872-8383},
abstract = {Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.},
}
@article {pmid37648499,
year = {2023},
author = {Hagihara, M and Kato, H and Shibata, Y and Umemura, T and Ariyoshi, T and Hirai, J and Asai, N and Mori, N and Mikamo, H},
title = {Mycobiome and Mycobiome-Associated Diseases.},
journal = {Medical mycology journal},
volume = {64},
number = {3},
pages = {55-62},
doi = {10.3314/mmj.23-002},
pmid = {37648499},
issn = {1882-0476},
mesh = {Humans ; *Mycobiome ; Carcinogenesis ; Knowledge ; Metagenome ; Metagenomics ; },
abstract = {The human body is host to a large number of commensal microbial species such as bacteria, fungi, and viruses. Among these, the human mycobiome is often neglected as a potential cause of disease, as it is thought to be comparatively much less abundant and less diverse than the human bacteriome. Additionally, most fungi are not easily cultured, even in specific media. Hence, their study has been limited to date, mainly because of the unavailability of methods used for their detection. However, the utilization of a novel metagenomic methodology will enable the identification of well-characterized mycobiomes in several parts of the human body and broaden our knowledge of their contribution to human health and disease. In this article, we review the role of the human mycobiome in the gut, respiratory organs, skin, genital tract, and carcinogenesis, highlighting the correlations between the human mycobiome and mycobiome-associated diseases.},
}
@article {pmid37504575,
year = {2023},
author = {Li, J and Sauers, L and Zhuang, D and Ren, H and Guo, J and Wang, L and Zhuang, M and Guo, Y and Zhang, Z and Wu, J and Yao, J and Yang, H and Huang, J and Wang, C and Lin, Q and Zhang, Z and Sadd, BM},
title = {Divergence and convergence of gut microbiomes of wild insect pollinators.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0127023},
pmid = {37504575},
issn = {2150-7511},
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/physiology ; Phylogeny ; Insecta/physiology ; *Microbiota ; *Wasps ; Pollination ; },
abstract = {Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali. Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales. IMPORTANCE Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.},
}
@article {pmid37404011,
year = {2023},
author = {Rooney, AM and Cochrane, K and Fedsin, S and Yao, S and Anwer, S and Dehmiwal, S and Hota, S and Poutanen, S and Allen-Vercoe, E and Coburn, B and , },
title = {A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0348222},
doi = {10.1128/mbio.03482-22},
pmid = {37404011},
issn = {2150-7511},
support = {//Weston Foundation/ ; //Canadian Foundation for Innovation/ ; //University of Toronto Department of Medicine Integrating Challenge Grant/ ; },
mesh = {Humans ; Microbial Consortia ; Anti-Bacterial Agents/pharmacology ; *Clostridioides difficile ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial ; Fecal Microbiota Transplantation ; *Clostridium Infections/therapy/microbiology ; Feces/microbiology ; *Microbiota ; Treatment Outcome ; },
abstract = {Intestinal colonization with pathogens and antimicrobial-resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonize intestinal AROs. However, FMT has significant practical barriers to safe and broad implementation. Microbial consortia represent a novel strategy for ARO and pathogen decolonization, with practical and safety advantages over FMT. We undertook an investigator-initiated analysis of stool samples collected from previous interventional studies of a microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT for rCDI before and after treatment. Our aim was to assess whether MET-2 was associated with decreased Pseudomonadota (Proteobacteria) and antimicrobial resistance gene (ARG) burden with similar effects to FMT. Participants were selected for inclusion if baseline stool had Pseudomonadota relative abundance ≥10%. Pre- and post-treatment Pseudomonadota relative abundance, total ARGs, and obligate anaerobe and butyrate-producer relative abundances were determined by shotgun metagenomic sequencing. MET-2 administration had similar effects to FMT on microbiome outcomes. The median Pseudomonadota relative abundance decreased by four logs after MET-2 treatment, a greater decrease than that observed after FMT. Total ARGs decreased, while beneficial obligate anaerobe and butyrate-producer relative abundances increased. The observed microbiome response remained stable over 4 months post-administration for all outcomes. IMPORTANCE Overgrowth of intestinal pathogens and AROs is associated with increased risk of infection. With the rise in antimicrobial resistance, new therapeutic strategies that decrease pathogen and ARO colonization in the gut are needed. We evaluated whether a microbial consortium had similar effects to FMT on Pseudomonadota abundances and ARGs as well as obligate anaerobes and beneficial butyrate producers in individuals with high Pseudomonadota relative abundance at baseline. This study provides support for a randomized, controlled clinical trial of microbial consortia (such as MET-2) for ARO decolonization and anaerobe repletion.},
}
@article {pmid37303219,
year = {2023},
author = {Diao, Z and Zhang, Y and Chen, Y and Han, Y and Chang, L and Ma, Y and Feng, L and Huang, T and Zhang, R and Li, J},
title = {Assessing the Quality of Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Infections.},
journal = {Clinical chemistry},
volume = {69},
number = {9},
pages = {1038-1049},
doi = {10.1093/clinchem/hvad072},
pmid = {37303219},
issn = {1530-8561},
mesh = {Humans ; Reproducibility of Results ; *Respiratory Tract Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Biological Assay ; Metagenomics ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Laboratory-developed metagenomic next-generation sequencing (mNGS) assays are increasingly being used for the diagnosis of infectious disease. To ensure comparable results and advance the quality control for the mNGS assay, we initiated a large-scale multicenter quality assessment to scrutinize the ability of mNGS to detect pathogens in lower respiratory infections.<br><br>METHODS: A reference panel containing artificial microbial communities and real clinical samples was used to assess the performance of 122 laboratories. We comprehensively evaluated the reliability, the source of false-positive and false-negative microbes, as well as the ability to interpret the results.<br><br>RESULTS: A wide variety of weighted F1-scores was observed across 122 participants, with a range from 0.20 to 0.97. The majority of false positive microbes (68.56%, 399/582) were introduced from "wet lab." The loss of microbial sequence during wet labs was the chief cause (76.18%, 275/361) of false-negative errors. When the human context is 2 &#xd7; 105 copies/mL, most DNA and RNA viruses at titers above 104 copies/mL could be detected by >80% of the participants, while >90% of the laboratories could detect bacteria and fungi at titers lower than 103 copies/mL. A total of 10.66% (13/122) to 38.52% (47/122) of the participants could detect the target pathogens but failed to reach a correct etiological diagnosis.<br><br>CONCLUSIONS: This study clarified the sources of false-positive and false-negative results and evaluated the performance of interpreting the results. This study was valuable for clinical mNGS laboratories to improve method development, avoid erroneous results being reported, and implement regulatory quality controls in the clinic.},
}
@article {pmid37145100,
year = {2023},
author = {Zhang, Y and Gan, Y and Bao, H and Wang, R},
title = {Perturbations of gut microbiome and metabolome of pigs infected with Mycoplasma hyorhinis.},
journal = {Journal of the science of food and agriculture},
volume = {103},
number = {13},
pages = {6219-6232},
doi = {10.1002/jsfa.12690},
pmid = {37145100},
issn = {1097-0010},
support = {//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; //Jiangsu Province Belt and Road International Cooperation Project/ ; },
mesh = {Swine ; Animals ; *Mycoplasma hyorhinis ; *Mycoplasma Infections ; *Gastrointestinal Microbiome ; *Swine Diseases ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Metabolome ; Amino Acids ; Lipids ; },
abstract = {BACKGROUND: Mycoplasma hyorhinis is a prevalent respiratory pathogen in swine, causing significant economic loss to pig producers. There is growing evidence that respiratory pathogen infections have a large impact on intestinal microecology. To study the effect of M. hyorhinis infection on gut microbial composition and metabolome profile, pigs were infected with M. hyorhinis. Metagenomic sequencing analysis was performed of fecal samples and a liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of gut digesta was made.<br><br>RESULTS: Pigs infected with M. hyorhinis had enriched Sutterella and Mailhella, and depleted Dechloromonas, Succinatimonas, Campylobacter, Blastocystis, Treponema, and Megasphaera. The pigs infected with M. hyorhinis also had greater abundances of bacterium_0_1xD8_71, Ruminococcus_sp__CAG_353, Firmicutes_bacterium_CAG_194, Firmicutes_bacterium_CAG_534, bacterium_1xD42_87, and lower abundances of Chlamydia_suis, Megasphaera_elsdenii, Treponema_porcinum, Bacteroides_sp__CAG_1060, Faecalibacterium_prausnitzii. Metabolomic analysis revealed that some lipids and lipid-like molecules increased in the small intestine, whereas most lipids and lipid-like molecule metabolites decreased in the large intestine. These altered metabolites induce changes in intestinal sphingolipid metabolism, amino acid metabolism, and thiamine metabolism.<br><br>CONCLUSION: These findings demonstrate that infection with M. hyorhinis can alter the gut microbial composition and metabolite structure in pigs, which may further affect amino acid metabolism and lipid metabolism in the intestine. &#xa9; 2023 Society of Chemical Industry.},
}
@article {pmid37057308,
year = {2023},
author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R},
title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.},
journal = {Environmental microbiology reports},
volume = {15},
number = {5},
pages = {383-391},
pmid = {37057308},
issn = {1758-2229},
support = {lzp-2018/1-0395//Latvijas Zin&#x101;tnes Padome/ ; },
mesh = {Animals ; Humans ; Latvia ; *Microbiota/genetics ; DNA ; Burial ; },
abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.},
}
@article {pmid36807446,
year = {2023},
author = {Bartuv, R and Berihu, M and Medina, S and Salim, S and Feygenberg, O and Faigenboim-Doron, A and Zhimo, VY and Abdelfattah, A and Piombo, E and Wisniewski, M and Freilich, S and Droby, S},
title = {Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples.},
journal = {Environmental microbiology},
volume = {25},
number = {9},
pages = {1728-1746},
doi = {10.1111/1462-2920.16353},
pmid = {36807446},
issn = {1462-2920},
support = {IS-5455-21//BARD/ ; },
mesh = {*Malus ; Fruit ; Phylogeny ; *Ascomycota ; *Microbiota/genetics ; },
abstract = {Fruits harbour abundant and diverse microbial communities that protect them from post-harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of 'Golden Delicious' apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high-quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.},
}
@article {pmid37644066,
year = {2023},
author = {Yan, M and Pratama, AA and Somasundaram, S and Li, Z and Jiang, Y and Sullivan, MB and Yu, Z},
title = {Interrogating the viral dark matter of the rumen ecosystem with a global virome database.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5254},
pmid = {37644066},
issn = {2041-1723},
mesh = {Humans ; Animals ; Virome ; Rumen ; *Microbiota ; *Caudovirales ; Databases, Factual ; },
abstract = {The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.},
}
@article {pmid37644001,
year = {2023},
author = {Hoskinson, C and Dai, DLY and Del Bel, KL and Becker, AB and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Petersen, C and Turvey, SE},
title = {Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4785},
pmid = {37644001},
issn = {2041-1723},
support = {274CHI//Genome Canada (G&#xe9;nome Canada)/ ; EC1-144621//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
mesh = {Infant ; Humans ; Child ; *Gastrointestinal Microbiome/genetics ; *Hypersensitivity ; *Microbiota ; *Asthma ; *Dermatitis, Atopic ; },
abstract = {Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune programming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxidative activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (βindirect = -2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.},
}
@article {pmid37404032,
year = {2023},
author = {Deschênes, T and Tohoundjona, FWE and Plante, PL and Di Marzo, V and Raymond, F},
title = {Gene-based microbiome representation enhances host phenotype classification.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0053123},
pmid = {37404032},
issn = {2379-5077},
support = {RGPIN-2020-03922//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Team Grant: Canadian Microbiome Initiative 2: Research Teams - Dissecting host-microbiome modifiers//Gouvernement du Canada | Canadian Institutes of Health Research (IRSC)/ ; RRG2734 RRG3817//Compute Canada (Calcul Canada)/ ; Canada Excellence Research Chair in Microbiome-Endocannabinoidome Axis in Metabolic Health//Canada Excellence Research Chairs, Government of Canada (CERC)/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/genetics ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Phenotype ; },
abstract = {With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining de novo content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data. IMPORTANCE Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data.},
}
@article {pmid37377419,
year = {2023},
author = {Vyshenska, D and Sampara, P and Singh, K and Tomatsu, A and Kauffman, WB and Nuccio, EE and Blazewicz, SJ and Pett-Ridge, J and Louie, KB and Varghese, N and Kellom, M and Clum, A and Riley, R and Roux, S and Eloe-Fadrosh, EA and Ziels, RM and Malmstrom, RR},
title = {A standardized quantitative analysis strategy for stable isotope probing metagenomics.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0128022},
pmid = {37377419},
issn = {2379-5077},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; RGPIN-2018-04585//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; SWC1632//U.S. Department of Energy (DOE)/ ; DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; },
mesh = {Humans ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; DNA/genetics ; Isotopes ; *Microbiota/genetics ; },
abstract = {Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.},
}
@article {pmid37350639,
year = {2023},
author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Deatherage Kaiser, BL and Fredricks, DN},
title = {Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0067822},
pmid = {37350639},
issn = {2379-5077},
support = {R01AI061628//HHS | National Institutes of Health (NIH)/ ; GM103493//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {Female ; Humans ; RNA, Ribosomal, 16S/genetics ; *Proteomics/methods ; *Microbiota/genetics ; Bacterial Proteins/genetics ; Peptides/metabolism ; Bacteria ; },
abstract = {Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions. IMPORTANCE Metaproteomic analysis can provide valuable insights into the functions of microbial and cellular communities by identifying a broad, untargeted set of proteins. The databases used in the analysis of metaproteomic data influence results by defining what proteins can be identified. Moreover, the size of the database impacts the number of identifications after accounting for false discovery rates (FDRs). Few studies have tested the performance of different strategies for building a protein database to identify proteins from metaproteomic data and those that have largely focused on highly diverse microbial communities. We tested a range of databases on CVL samples and found that a hybrid sample-matched approach, using publicly available proteins from organisms present in the samples, as well as proteins translated from metagenomic sequencing of the samples, had the best performance. However, our results also suggest that public sequence databases will continue to improve as more bacterial genomes are published.},
}
@article {pmid37640834,
year = {2023},
author = {van Dijk, B and Buffard, P and Farr, AD and Giersdorf, F and Meijer, J and Dutilh, BE and Rainey, PB},
title = {Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {90},
pmid = {37640834},
issn = {2730-6151},
abstract = {Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.},
}
@article {pmid37635357,
year = {2023},
author = {Gao, W and Gao, X and Zhu, L and Gao, S and Sun, R and Feng, Z and Wu, D and Liu, Z and Zhu, R and Jiao, N},
title = {Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2245562},
pmid = {37635357},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; *Polymorphism, Single Nucleotide ; *Early Detection of Cancer/methods ; Metagenomics ; *Precancerous Conditions/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Genetic Markers ; Feces/microbiology ; Humans ; Fungi/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Archaea/genetics/isolation &amp; purification ; Viruses/genetics/isolation &amp; purification ; Cohort Studies ; },
abstract = {Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.},
}
@article {pmid37633998,
year = {2023},
author = {Odom, AR and Faits, T and Castro-Nallar, E and Crandall, KA and Johnson, WE},
title = {Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13957},
pmid = {37633998},
issn = {2045-2322},
support = {R01 GM127430/GM/NIGMS NIH HHS/United States ; R21 AI154387/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota ; Bone Plates ; *Cercozoa ; *Polyarteritis Nodosa ; },
abstract = {Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon sequencing. However, the most-used bioinformatics tools cannot produce high quality genus-level or species-level taxonomic calls and may underestimate the potential accuracy of these calls. We used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, concentrating on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads. We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq. Profiling tools were compared using publicly available mock community data from several sources, comprising 136 samples with varied species richness and evenness, several different amplified regions within the 16S rRNA gene, and both DNA spike-ins and cDNA from collections of plated cells. PathoScope 2 and Kraken 2, both tools designed for whole-genome metagenomics, outperformed DADA2, QIIME 2 using the DADA2 plugin, and Mothur, which are theoretically specialized for 16S analyses. Evaluations of reference libraries identified the SILVA and RefSeq/Kraken 2 Standard libraries as superior in accuracy compared to Greengenes. These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.},
}
@article {pmid37595469,
year = {2023},
author = {Rolbiecki, D and Paukszto, &#x141; and Krawczyk, K and Korzeniewska, E and Sawicki, J and Harnisz, M},
title = {Chlorine disinfection modifies the microbiome, resistome and mobilome of hospital wastewater - A nanopore long-read metagenomic approach.},
journal = {Journal of hazardous materials},
volume = {459},
number = {},
pages = {132298},
doi = {10.1016/j.jhazmat.2023.132298},
pmid = {37595469},
issn = {1873-3336},
mesh = {Humans ; Chlorine/pharmacology ; Wastewater ; Angiotensin Receptor Antagonists ; Disinfection ; *Nanopores ; Angiotensin-Converting Enzyme Inhibitors ; Halogens ; *Microbiota/genetics ; Chlorides ; Anti-Bacterial Agents ; Hospitals ; },
abstract = {The aim of the present study was to analyze changes in the microbiome, resistome, and mobilome of hospital wastewater (HWW) induced by disinfection with chlorine compounds. Changes in bacterial communities and specific antibiotic resistance genes (ARGs) in HWW were determined with the use of a nanopore long-read metagenomic approach. The main hosts of ARGs in HWW were identified, and the mobility of resistance mechanisms was analyzed. Special attention was paid to the prevalence of critical-priority pathogens in the HWW microbiome, which pose the greatest threat to human health. The results of this study indicate that chlorine disinfection of HWW can induce significant changes in the structure of the total bacterial population and antibiotic resistant bacteria (ARB) communities, and that it can modify the resistome and mobilome of HWW. Disinfection favored the selection of ARGs, decreased their prevalence in HWW, while increasing their diversity. The mobility of the HWW resistome increased after disinfection. Disinfection led to the emergence of new drug resistance mechanisms in previously sensitive bacterial taxa. In conclusion, this study demonstrated that HWW disinfected with low (sublethal) concentrations of free chlorine significantly contributes to the mobility and transfer of drug resistance mechanisms (including critical mechanisms) between bacteria (including pathogens).},
}
@article {pmid37506647,
year = {2023},
author = {Zhou, Y and Zhou, S},
title = {Role of microplastics in microbial community structure and functions in urban soils.},
journal = {Journal of hazardous materials},
volume = {459},
number = {},
pages = {132141},
doi = {10.1016/j.jhazmat.2023.132141},
pmid = {37506647},
issn = {1873-3336},
mesh = {Humans ; *Microplastics/pharmacology ; Plastics ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; },
abstract = {Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.},
}
@article {pmid37482039,
year = {2023},
author = {Yue, Z and Zhang, J and Zhang, J and Wang, X and Li, L and Yu, H and Liu, B and Li, Q and Zhu, D and Zou, Y},
title = {Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting.},
journal = {Journal of hazardous materials},
volume = {459},
number = {},
pages = {132088},
doi = {10.1016/j.jhazmat.2023.132088},
pmid = {37482039},
issn = {1873-3336},
mesh = {Humans ; Animals ; Swine ; *Metagenome ; Genes, Bacterial ; Virome ; *Composting/methods ; Anti-Bacterial Agents/pharmacology ; Biofuels ; Drug Resistance, Microbial/genetics ; Manure/microbiology ; },
abstract = {The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.},
}
@article {pmid37392922,
year = {2023},
author = {Tian, F and Zhou, B and Li, X and Zhang, Y and Qi, D and Qi, H and Jiang, H and Zhao, K and Liu, S},
title = {Population genomics analysis to identify ion and water transporter genes involved in the adaptation of Tibetan naked carps to brackish water.},
journal = {International journal of biological macromolecules},
volume = {247},
number = {},
pages = {125605},
doi = {10.1016/j.ijbiomac.2023.125605},
pmid = {37392922},
issn = {1879-0003},
mesh = {Animals ; *Carps ; Tibet ; Metagenomics ; *Cyprinidae/genetics ; Genomics ; Lakes ; Water ; },
abstract = {Understanding how evolutionary processes shape the genetic variations and influence the response of species to environmental alterations is critical for biodiversity conservation and molecular breeding. Gymnocypris przewalskii przewalskii is the only known cyprinid fish that dwells in the brackish water of Lake Qinghai on the Qinghai-Tibetan Plateau. To reveal the genetic basis of its adaptation to high salinity and alkalinity, whole-genome sequencing was performed in G. p. przewalskii and its freshwater relatives Gymnocypris eckloni and Gymnocypris przewalskii ganzihonensis. Compared with freshwater species, lower genetic diversity and higher linkage disequilibrium were observed in G. p. przewalskii. Selective sweep analysis identified 424 core-selective genes enriched in transport activities. Transfection analysis showed that genetic changes in the positively selected gene aquaporin 3 (AQP3) improved cell viability after salt treatment, suggesting its involvement in brackish water adaptation. Our analysis indicates that ion and water transporter genes experienced intensive selection, which might have contributed to the maintenance of high osmolality and ion content in G. p. przewalskii. The current study identified key molecules involved in the adaptation of fish to brackish water, providing valuable genomic resources for the molecular breeding of salt-tolerant fish.},
}
@article {pmid37632061,
year = {2023},
author = {Richard, JC and Blevins, E and Dunn, CD and Leis, EM and Goldberg, TL},
title = {Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA.},
journal = {Viruses},
volume = {15},
number = {8},
pages = {},
pmid = {37632061},
issn = {1999-4915},
support = {F19AC00507-04//United States Fish and Wildlife Service/ ; Additional Support//University of Wisconsin-Madison/ ; },
mesh = {Animals ; Oregon ; Washington/epidemiology ; *Fresh Water ; *Bivalvia ; Rivers ; },
abstract = {Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.},
}
@article {pmid37631163,
year = {2023},
author = {Aleynova, OA and Nityagovsky, NN and Ananev, AA and Suprun, AR and Ogneva, ZV and Dneprovskaya, AA and Beresh, AA and Tyunin, AP and Dubrovina, AS and Kiselev, KV},
title = {The Endophytic Microbiome of Wild Grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat Growing in the Russian Far East.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {16},
pages = {},
pmid = {37631163},
issn = {2223-7747},
support = {22-74-10001//Russian Science Foundation/ ; 121031000144-5//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61-65%) and Tremellomycetes (10-11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera's bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.},
}
@article {pmid37454444,
year = {2023},
author = {Schettini, F and Fontana, A and Gattazzo, F and Strina, C and Milani, M and Cappelletti, MR and Cervoni, V and Morelli, L and Curigliano, G and Iebba, V and Generali, D},
title = {Faecal microbiota composition is related to response to CDK4/6-inhibitors in metastatic breast cancer: A prospective cross-sectional exploratory study.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {191},
number = {},
pages = {112948},
doi = {10.1016/j.ejca.2023.112948},
pmid = {37454444},
issn = {1879-0852},
mesh = {Humans ; Female ; *Breast Neoplasms/pathology ; Cross-Sectional Studies ; Prospective Studies ; Progression-Free Survival ; Receptor, ErbB-2/metabolism ; *Microbiota ; Protein Kinase Inhibitors/adverse effects ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Cyclin-Dependent Kinase 4 ; },
abstract = {BACKGROUND: Cyclin-dependent kinase (CDK)4/6-inhibitors with endocrine therapy represent the standard of treatment of hormone receptor-positive(HR+)/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC). Gut microbiota seems to predict treatment response in several tumour types, being directly implied in chemotherapy resistance and development of adverse effects. No evidence is available on gut microbiota impact on efficacy of HR+ breast cancer treatment.<br><br>PATIENTS AND METHODS: We assessed the potential association among faecal microbiota and therapeutic efficacy of CDK4/6-inhibitors on 14 MBC patients classified as responders (R) and non-responders (NR) according to progression-free survival. A stool sample was collected at baseline and V3-V4 16S targeted sequencing was employed to assess its bacterial composition. Statistical associations with R and NR were studied.<br><br>RESULTS: No significant differences were observed between R and NR in terms of &#x3b1;-/&#x3b2;-diversity at the phylum and species level. Machine-learning (ML) algorithms evidenced four bacterial species as a discriminant for R (Bifidobacterium longum, Ruminococcus callidus) and NR (Clostridium innocuum, Schaalia odontolytica), and an area under curve (AUC) of 0.946 after Random Forest modelling. Network analysis evidenced two major clusters of bacterial species, named Species Interacting Groups (SIG)1-2, with SIG1 harbouring 75% of NR-related bacterial species, and SIG2 regrouping 76% of R-related species (p&#xa0;<&#xa0;0.001). Cross-correlations among several patients' circulating immune cells&#xa0;or biomarkers and bacterial species' relative abundances showed associations with potential prognostic implications.<br><br>CONCLUSIONS: Our results provide initial insights into the gut microbiota involvement in sensitivity and/or resistance to CDK4/6-inhibitors&#xa0;+&#xa0;endocrine therapy in MBC. If confirmed in larger trials, several microbiota manipulation strategies might be hypothesised to improve response to CDK4/6-inhibitors.},
}
@article {pmid37628701,
year = {2023},
author = {Soriano, B and Hafez, AI and Naya-Català, F and Moroni, F and Moldovan, RA and Toxqui-Rodríguez, S and Piazzon, MC and Arnau, V and Llorens, C and Pérez-Sánchez, J},
title = {SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628701},
issn = {2073-4425},
mesh = {Animals ; Humans ; Bayes Theorem ; RNA, Ribosomal, 16S/genetics ; Learning ; *Microbiota/genetics ; Aquaculture ; *Sea Bream ; },
abstract = {Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to (i) infer information of how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and (ii) predict how the diversity and functional profile of that microbiome would change under other variable conditions. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of Bayesian network scenarios created by SAMBA using data from a microbial synthetic community, and the pan-microbiome of gilthead sea bream (Sparus aurata) in different feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems as it can be used for modelling microbiome-host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem.},
}
@article {pmid37628698,
year = {2023},
author = {Pandey, S and Avuthu, N and Guda, C},
title = {StrainIQ: A Novel n-Gram-Based Method for Taxonomic Profiling of Human Microbiota at the Strain Level.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628698},
issn = {2073-4425},
support = {P20 GM103427/GM/NIGMS NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; U54 GM115458/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; Algorithms ; Computational Biology ; High-Throughput Nucleotide Sequencing ; },
abstract = {The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development of novel bioinformatics tools to deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important to understanding the onset and progression of diseases, host-pathogen interrelationships, and drug resistance, in addition to designing new therapeutic regimens. In this study, we developed a novel tool called StrainIQ (strain identification and quantification) based on a new n-gram-based (series of n number of adjacent nucleotides in the DNA sequence) algorithm for predicting and quantifying strain-level taxa from whole-genome metagenomic sequencing data. We thoroughly evaluated our method using simulated and mock metagenomic datasets and compared its performance with existing methods. On average, it showed 85.8% sensitivity and 78.2% specificity on simulated datasets. It also showed higher specificity and sensitivity using n-gram models built from reduced reference genomes and on models with lower coverage sequencing data. It outperforms alternative approaches in genus- and strain-level prediction and strain abundance estimation. Overall, the results show that StrainIQ achieves high accuracy by implementing customized model-building and is an efficient tool for site-specific microbial community profiling.},
}
@article {pmid37628619,
year = {2023},
author = {Notario, E and Visci, G and Fosso, B and Gissi, C and Tanaskovic, N and Rescigno, M and Marzano, M and Pesole, G},
title = {Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628619},
issn = {2073-4425},
mesh = {RNA, Ribosomal, 16S/genetics ; *Benchmarking ; Computational Biology ; *Microbiota/genetics ; Technology ; },
abstract = {The 16S rRNA amplicon-based sequencing approach represents the most common and cost-effective strategy with great potential for microbiome profiling. The use of second-generation sequencing (NGS) technologies has led to protocols based on the amplification of one or a few hypervariable regions, impacting the outcome of the analysis. Nowadays, comparative studies are necessary to assess different amplicon-based approaches, including the full-locus sequencing currently feasible thanks to third-generation sequencing (TGS) technologies. This study compared three different methods to achieve the deepest microbiome taxonomic characterization: (a) the single-region approach, (b) the multiplex approach, covering several regions of the target gene/region, both based on NGS short reads, and (c) the full-length approach, which analyzes the whole length of the target gene thanks to TGS long reads. Analyses carried out on benchmark microbiome samples, with a known taxonomic composition, highlighted a different classification performance, strongly associated with the type of hypervariable regions and the coverage of the target gene. Indeed, the full-length approach showed the greatest discriminating power, up to species level, also on complex real samples. This study supports the transition from NGS to TGS for the study of the microbiome, even if experimental and bioinformatic improvements are still necessary.},
}
@article {pmid37628582,
year = {2023},
author = {Gagnon, JC and Beauregard-Tousignant, S and Marcil, JS and Lazar, CS},
title = {Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628582},
issn = {2073-4425},
mesh = {Humans ; Quebec ; Canada ; *Groundwater ; *Microbiota/genetics ; },
abstract = {The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.},
}
@article {pmid37626351,
year = {2023},
author = {Ghaly, TM and Focardi, A and Elbourne, LDH and Sutcliffe, B and Humphreys, W and Paulsen, IT and Tetu, SG},
title = {Stratified microbial communities in Australia's only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {190},
pmid = {37626351},
issn = {2049-2618},
support = {FL140100021//Australian Research Council, Australia/ ; },
mesh = {Humans ; *Nitrogen Cycle ; *Microbiota/genetics ; Sulfur ; Nitrification ; Australia ; },
abstract = {BACKGROUND: Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood.<br><br>RESULTS: Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling.<br><br>CONCLUSION: These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments. Video Abstract.},
}
@article {pmid37623326,
year = {2023},
author = {Sun, K and Yu, M and Zhu, XY and Xue, CX and Zhang, Y and Chen, X and Yao, P and Chen, L and Fu, L and Yang, Z and Zhang, XH},
title = {Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0114923},
doi = {10.1128/spectrum.01149-23},
pmid = {37623326},
issn = {2165-0497},
abstract = {The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.},
}
@article {pmid37622724,
year = {2023},
author = {Xia, Y},
title = {Statistical normalization methods in microbiome data with application to microbiome cancer research.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2244139},
doi = {10.1080/19490976.2023.2244139},
pmid = {37622724},
issn = {1949-0984},
mesh = {RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Research Design ; *Neoplasms ; },
abstract = {Mounting evidence has shown that gut microbiome is associated with various cancers, including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have unique characteristics and pose major challenges when using standard statistical methods causing results to be invalid or misleading. Thus, to analyze microbiome data, it not only needs appropriate statistical methods, but also requires microbiome data to be normalized prior to statistical analysis. Here, we first describe the unique characteristics of microbiome data and the challenges in analyzing them (Section 2). Then, we provide an overall review on the available normalization methods of 16S rRNA and shotgun metagenomic data along with examples of their applications in microbiome cancer research (Section 3). In Section 4, we comprehensively investigate how the normalization methods of 16S rRNA and shotgun metagenomic data are evaluated. Finally, we summarize and conclude with remarks on statistical normalization methods (Section 5). Altogether, this review aims to provide a broad and comprehensive view and remarks on the promises and challenges of the statistical normalization methods in microbiome data with microbiome cancer research examples.},
}
@article {pmid37621874,
year = {2023},
author = {Zhou, Q and Tao, X and Guo, F and Zhu, Y and Wu, Y and Xiang, H and Shang, D},
title = {The crosstalk between microbiota and metabolites in AP mice: an analysis based on metagenomics and untargeted metabolomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1134321},
pmid = {37621874},
issn = {2235-2988},
mesh = {Animals ; Mice ; Metagenomics ; Acute Disease ; *Pancreatitis ; *Microbiota ; Signal Transduction ; Bacteroidetes ; Lactobacillus ; },
abstract = {BACKGROUND AND PURPOSE: Microbiome dysfunction is known to aggravate acute pancreatitis (AP); however, the relationship between this dysfunction and metabolite alterations is not fully understood. This study explored the crosstalk between the microbiome and metabolites in AP mice.<br><br>METHODS: Experimental AP models were established by injecting C57/BL mice with seven doses of cerulein and one dose of lipopolysaccharide (LPS). Metagenomics and untargeted metabolomics were used to identify systemic disturbances in the microbiome and metabolites, respectively, during the progression of AP.<br><br>RESULTS: The gut microbiome of AP mice primarily included Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, and "core microbiota" characterized by an increase in Proteobacteria and a decrease in Actinobacteria. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that significantly different microbes were involved in several signaling networks. Untargeted metabolomics identified 872 metabolites, of which lipids and lipid-like molecules were the most impacted. An integrated analysis of metagenomics and metabolomics indicated that acetate kinase (ackA) gene expression was associated with various gut microbiota, including Alistipes, Butyricimonas, and Lactobacillus, and was strongly correlated with the metabolite daphnoretin. The functional gene, O-acetyl-L-serine sulfhydrylase (cysK), was associated with Alistipes, Jeotgalicoccus, and Lactobacillus, and linked to bufalin and phlorobenzophenone metabolite production.<br><br>CONCLUSION: This study identified the relationship between the gut microbiome and metabolite levels during AP, especially the Lactobacillus-, Alistipes-, and Butyricimonas-associated functional genes, ackA and cysK. Expression of these genes was significantly correlated to the production of the anti-inflammatory and antitumor metabolites daphnoretin and bufalin.},
}
@article {pmid37621652,
year = {2023},
author = {Liang, J and Ali, S and Lv, C and Yang, H and Zhao, X and Ni, X and Li, C and Danzeng, B and Wang, Y and Quan, G},
title = {Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1194425},
pmid = {37621652},
issn = {1664-2392},
mesh = {Sheep ; Animals ; Female ; *Gastrointestinal Microbiome ; Lactation ; Feces ; Dietary Proteins ; Sheep, Domestic ; Clostridiales ; },
abstract = {In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.},
}
@article {pmid37620878,
year = {2023},
author = {Abrantes, J and Varsani, A and Pereira, P and Maia, C and Farias, I and Veríssimo, A and Neves, F},
title = {Identification and characterization of a polyomavirus in the thornback skate (Raja clavata).},
journal = {Virology journal},
volume = {20},
number = {1},
pages = {190},
pmid = {37620878},
issn = {1743-422X},
support = {PD/BD/128492/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; EXPL/BIA-EVL/1045/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; *Polyomavirus/genetics ; *Skates, Fish ; Ecosystem ; Phylogeny ; Polyomaviridae ; Mammals ; },
abstract = {Members of the family Polyomaviridae have a circular double-stranded DNA genome that have been identified in various hosts ranging from mammals to arachnids. Here we report the identification and analysis of a complete genome sequence of a novel polyomavirus, Raja clavata polyomavirus (RcPyV1), from a cartilaginous fish, the thornback skate (Raja clavata). The genome sequence was determined using a metagenomics approach with an aim to provide baseline viral data in cartilaginous fish in different ecosystems. The RcPyV1 genome (4,195 nucleotides) had typical organization of polyomavirus, including early antigens (small T; Large T) encoded on one strand and late viral proteins (VP1; VP2) on the complementary strand. Maximum-likelihood phylogenetic analysis of the large T-antigen revealed that RcPyV1 clusters with a polyomavirus obtained from another cartilaginous fish, the guitarfish polyomavirus 1 (GfPyV1). These two share ~ 56% pairwise identity in LT and VP1 protein sequences. These analyses support the hypothesis that cartilaginous fishes have a specific lineage of polyomaviruses.},
}
@article {pmid37620368,
year = {2023},
author = {Mutti, G and Oteo-Garcia, G and Caldon, M and da Silva, MJF and Minhós, T and Cowlishaw, G and Gottelli, D and Huchard, E and Carter, A and Martinez, FI and Raveane, A and Capelli, C},
title = {Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13839},
pmid = {37620368},
issn = {2045-2322},
support = {LCF/BQ/DI22/11940014//"la Caixa" Foundation/ ; The Y chromosome evolutionary history of the genus Papio//Leakey Foundation/ ; PTDC/IVC-ANT/3058/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PRIMACTION//Born Free Foundation, Chester Zoo Conservation Fund, Primate Conservation Incorporated, CAROSI, C&#xe1;psulas do Norte, Camarc, and JA-Rolhas &amp; C&#xe1;psulas/ ; },
mesh = {Humans ; Male ; Animals ; *Metagenomics ; *Theropithecus ; Papio ; Macaca mulatta ; Microsatellite Repeats/genetics ; },
abstract = {Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.},
}
@article {pmid37541570,
year = {2023},
author = {Liu, YC and Chen, TH and Huang, YF and Chen, CL and Nai, YS},
title = {Investigation of the fall armyworm (Spodoptera frugiperda) gut microbiome and entomopathogenic fungus-induced pathobiome.},
journal = {Journal of invertebrate pathology},
volume = {200},
number = {},
pages = {107976},
doi = {10.1016/j.jip.2023.107976},
pmid = {37541570},
issn = {1096-0805},
mesh = {Animals ; Spodoptera ; *Gastrointestinal Microbiome ; Zea mays ; *Beauveria ; Larva ; },
abstract = {The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both cornfield and laboratory-reared populations was investigated using a 16S metagenomic approach. The alpha- and beta-diversity of the cornfield FAW populations varied among sampling sites and were higher than those of the laboratory-reared FAW population, indicating that different diets and environments influence the gut bacterial composition. To better understand the interaction between the microbiome and entomopathogenic fungi (EPF), FAWs from organic and conventionally managed corn fields and from the laboratory-reared colony were inoculated with Beauveria bassiana NCHU-153 (Bb-NCHU-153). A longer median lethal time (LT50) was observed in the Bb-NCHU-153-infected cornfield FAW population than in the laboratory-reared FAWs. In terms of the microbiome, three Bb-NCHU-153-infected FAW groups showed different gut bacterial compositions compared to noninfected FAW. Further investigation of the cooccurrence network and linear discriminant analysis (LDA) of effect size (LEfSe) revealed that the enriched bacterial genera, such as Enterococcus, Serratia, Achromobacter, and Tsukamurella, in the gut might play the role of opportunistic pathogens after fungal infection; in contrast, some gut bacteria of Methylobacterium, Marinomonas, Paenochrobactrum, Pseudomonas, Acinetobacter, Delftia, Dietzia, Gordonia, Leucobacter, Paracoccus, and Stenotrophomonas might be probiotics against EPF infection. These results indicated that EPF infection can change the gut bacterial composition and lead to a pathobiome in the FAW and that some bacterial species might protect the FAW from EPF infection. These findings could be applied to the design of pathobiome-inducing biocontrol strategies.},
}
@article {pmid37331553,
year = {2023},
author = {Zhang, T and Ji, Z and Chen, X and Yu, L},
title = {Shotgun metagenomics reveals a diverse mycobiome in the seawater from a High Arctic fjord (Kongsfjorden, Svalbard).},
journal = {Environmental research},
volume = {233},
number = {},
pages = {116437},
doi = {10.1016/j.envres.2023.116437},
pmid = {37331553},
issn = {1096-0953},
mesh = {Humans ; *Mycobiome ; Estuaries ; Ecosystem ; Svalbard ; Metagenomics ; Seawater ; Arctic Regions ; },
abstract = {In the Arctic fjords, the marine mycobiome experiences significant changes under environmental conditions driven by climate change. However, research on the ecological roles and the adaptive mechanisms of marine mycobiome in the Arctic fjord remains insufficiently explored. The present study employed shotgun metagenomics to comprehensively characterize the mycobiome in 24 seawater samples from Kongsfjorden, a High Arctic fjord situated in Svalbard. It revealed the presence of a diverse mycobiome with eight phyla, 34 classes, 71 orders, 152 families, 214 genera, and 293 species. The taxonomic and functional composition of the mycobiome differed significantly among the three layers, i.e., upper layer (depth of 0 m), middle layer (depths of 30-100 m), and lower layer (depths of 150-200 m). Several taxonomic groups (e.g., phylum Ascomycota, class Eurotiomycetes, order Eurotiales, family Aspergillaceae, and genus Aspergillus) and KOs (e.g., K03236/EIF1A, K03306/TC.PIT, K08852/ERN1, and K03119/tauD) were significantly distinct among the three layers. Among the measured environmental parameters, depth, NO2[-], and PO4[3-] were identified as the key factors influencing the mycobiome composition. Conclusively, our findings revealed that the mycobiome was diverse in the Arctic seawater and significantly impacted by the variability of environmental conditions in the High Arctic fjord. These results will assist future studies in exploring the ecological and adaptive responses towards the changes within the Arctic ecosystems.},
}
@article {pmid37277984,
year = {2023},
author = {Chen, LL and Abbaspour, A and Aspvall, K and Rück, C and Bulik, CM and Pascal, D},
title = {Longitudinal study of gut microbiome in obsessive-compulsive disorder.},
journal = {Brain and behavior},
volume = {13},
number = {8},
pages = {e3115},
pmid = {37277984},
issn = {2162-3279},
mesh = {Humans ; Longitudinal Studies ; *Gastrointestinal Microbiome ; *Obsessive-Compulsive Disorder/diagnosis ; *Cognitive Behavioral Therapy ; Psychiatric Status Rating Scales ; },
abstract = {INTRODUCTION: Patients with obsessive-compulsive disorder (OCD) often have limited exposure to a diverse environment and perform repetitive compulsions such as excessive cleaning and washing, which could lead to altered gut microbiome. Therefore, longitudinal studies that investigate changes in gut microbiome before and after cognitive behavioral therapy based on exposure and response prevention (ERP) are warranted.<br><br>METHODS: All study participants (N&#xa0;=&#xa0;64) underwent a structured psychiatric diagnostic interview prior to inclusion. Nutritional intake was assessed with a comprehensive food frequency questionnaire. Stool samples were collected from OCD patients before ERP (n&#xa0;=&#xa0;32) and 1&#xa0;month after completion of ERP (n&#xa0;=&#xa0;15), as well as from healthy controls (HCs; n&#xa0;=&#xa0;32). Taxonomic and functional analyses were performed using data from microbiome whole genome sequencing.<br><br>RESULTS: Patients with OCD at baseline reported consuming significantly less fiber than HCs (R[2] &#xa0;=&#xa0;.12, F(2,&#xa0;59)&#xa0;=&#xa0;5.2, p&#xa0;&#x2264;&#xa0;.01). There were no significant differences in &#x3b1;- and &#x3b2;-diversity indices, or taxonomic dissimilarities at the species level between patients with OCD and HCs, or within patients before and after ERP. Functional profiling based on gut microbial gene expression was grouped into 56 gut-brain modules with neuroactive potential. None of the gut-brain modules differed significantly in expression between patients with OCD at baseline and HCs or within patients before and after ERP.<br><br>CONCLUSIONS: The diversity, composition, and functional profile of the gut microbiome in patients with OCD did not differ significantly from HCs and remained stable over time, despite behavioral changes.},
}
@article {pmid37612768,
year = {2023},
author = {Zhang, ZF and Liu, LR and Pan, YP and Pan, J and Li, M},
title = {Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {188},
pmid = {37612768},
issn = {2049-2618},
support = {92251306//National Natural Science Foundation of China/ ; 2019FY100700//National Science and Technology Fundamental Resources Investigation Program of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; 2020KCXTD023//Innovation Team Project of Universities in Guangdong Province/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; },
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Metagenomics ; Fermentation ; Carbon ; },
abstract = {BACKGROUND: Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.<br><br>RESULTS: Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.<br><br>CONCLUSIONS: The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.},
}
@article {pmid37608207,
year = {2023},
author = {Russell, AL and McAdams, ZL and Donovan, E and Seilhamer, N and Siegrist, M and Franklin, CL and Ericsson, AC},
title = {The contribution of maternal oral, vaginal, and gut microbiota to the developing offspring gut.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13660},
pmid = {37608207},
issn = {2045-2322},
support = {U42 OD010918/NH/NIH HHS/United States ; },
mesh = {Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Disease Models, Animal ; Feces ; },
abstract = {There is limited understanding of how the microbiota colonizing various maternal tissues contribute to the development of the neonatal gut microbiota (GM). To determine the contribution of various maternal microbiotic sites to the offspring microbiota in the upper and lower gastrointestinal tract (GIT) during early life, litters of mice were sacrificed at 7, 9, 10, 11, 12, 14, and 21 days of age, and fecal and ileal samples were collected. Dams were euthanized alongside their pups, and oral, vaginal, ileal, and fecal samples were collected. This was done in parallel using mice with either a low-richness or high-richness microbiota to assess the consistency of findings across multiple microbial compositions. Samples were analyzed using 16S rRNA amplicon sequencing. The compositional similarity between pup and dam samples were used to determine the contribution of each maternal source to the composition of the neonate fecal and ileal samples at each timepoint. As expected, similarity between neonate and maternal feces increased significantly over time. During earlier time-points however, the offspring fecal and ileal microbiotas were closer in composition to the maternal oral microbiota than other maternal sites. Prominent taxa contributed by the maternal oral microbiota to the neonate GM were supplier-dependent and included Lactobacillus spp., Streptococcus spp., and a member of the Pasteurellaceae family. These findings align with the microbial taxa reported in infant microbiotas, highlighting the translatability of mouse models in this regard, as well as the dynamic nature of the GM during early life.},
}
@article {pmid37607924,
year = {2023},
author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M},
title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5090},
pmid = {37607924},
issn = {2041-1723},
mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; },
abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.},
}
@article {pmid37603566,
year = {2023},
author = {Velasco-Álvarez, JR and Torres Y Torres, N and Chairez, I and Castrejón-Flores, JL},
title = {Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributions.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0290082},
pmid = {37603566},
issn = {1932-6203},
mesh = {Humans ; *Microbiota ; Metagenome ; Algorithms ; Computer Simulation ; Data Analysis ; },
abstract = {The human gut is home to a complex array of microorganisms interacting with the host and each other, forming a community known as the microbiome. This community has been linked to human health and disease, but understanding the underlying interactions is still challenging for researchers. Standard studies typically use high-throughput sequencing to analyze microbiome distribution in patient samples. Recent advancements in meta-omic data analysis have enabled computational modeling strategies to integrate this information into an in silico model. However, there is a need for improved parameter fitting and data integration features in microbial community modeling. This study proposes a novel alternative strategy utilizing state-of-the-art dynamic flux balance analysis (dFBA) to provide a simple protocol enabling accurate replication of abundance data composition through dynamic parameter estimation and integration of metagenomic data. We used a recurrent optimization algorithm to replicate community distributions from three different sources: mock, in vitro, and clinical microbiome. Our results show an accuracy of 98% and 96% when using in vitro and clinical bacterial abundance distributions, respectively. The proposed modeling scheme allowed us to observe the evolution of metabolites. It could provide a deeper understanding of metabolic interactions while taking advantage of the high contextualization features of GEM schemes to fit the study case. The proposed modeling scheme could improve the approach in cases where external factors determine specific bacterial distributions, such as drug intake.},
}
@article {pmid37597851,
year = {2023},
author = {Li, J and Guo, Y and Liu, J and Guo, F and Du, L and Yang, Y and Li, X and Ma, Y},
title = {Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers.},
journal = {Journal for immunotherapy of cancer},
volume = {11},
number = {8},
pages = {},
pmid = {37597851},
issn = {2051-1426},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; CD8-Positive T-Lymphocytes ; DNA Mismatch Repair/genetics ; Succinic Acid ; Lactic Acid ; *Colorectal Neoplasms/genetics ; },
abstract = {BACKGROUND: Accumulating evidence has indicated the role of gut microbiota in remodeling host immune signatures, but various interplays underlying colorectal cancers (CRC) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) remain poorly understood. This study aims to decipher the gut microbiome-host immune interactions between dMMR and pMMR CRC.<br><br>METHOD: We performed metagenomic sequencing and metabolomic analysis of fecal samples from a cohort encompassing 455 participants, including 21 dMMR CRC, 207 pMMR CRC, and 227 healthy controls. Among them, 50 tumor samples collected from 5 dMMR CRC and 45 pMMR CRC were conducted bulk RNA sequencing.<br><br>RESULTS: Pronounced microbiota and metabolic heterogeneity were identified with 211 dMMR-enriched species, such as Fusobacterium nucleatum and Akkermansia muciniphila, 2 dMMR-depleted species, such as Flavonifractor plautii, 13 dMMR-enriched metabolites, such as retinoic acid, and 77 dMMR-depleted metabolites, such as lactic acid, succinic acid, and 2,3-dihydroxyvaleric acid. F. plautii was enriched in pMMR CRC and it was positively associated with fatty acid degradation, which might account for the accumulation of dMMR-depleted metabolites classified as short chain organic acid (lactic acid, succinic acid, and 2,3-dihydroxyvaleric acid) in pMMR CRC. The microbial-metabolic association analysis revealed the characterization of pMMR CRC as the accumulation of lactate induced by the depletion of specific gut microbiota which was negatively associated with antitumor immune, whereas the nucleotide metabolism and peptide degradation mediated by dMMR-enriched species characterized dMMR CRC. MMR-specific metabolic landscapes were related to distinctive immune features, such as CD8[+] T cells, dendritic cells and M2-like macrophages.<br><br>CONCLUSIONS: Our mutiomics results delineate a heterogeneous landscape of microbiome-host immune interactions within dMMR and pMMR CRC from aspects of bacterial communities, metabolic features, and correlation with immunocyte compartment, which infers the underlying mechanism of heterogeneous immune responses.},
}
@article {pmid37597444,
year = {2023},
author = {Heinze, BM and Küsel, K and Jehmlich, N and von Bergen, M and Taubert, M},
title = {Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater.},
journal = {Water research},
volume = {244},
number = {},
pages = {120426},
doi = {10.1016/j.watres.2023.120426},
pmid = {37597444},
issn = {1879-2448},
abstract = {High rates of CO2 fixation and the genetic potential of various groundwater microbes for autotrophic activity have shown that primary production is an important source of organic C in groundwater ecosystems. However, the contribution of specific chemolithoautotrophic groups such as S-oxidizing bacteria (SOB) to groundwater primary production and their adaptation strategies remain largely unknown. Here, we stimulated anoxic groundwater microcosms with reduced S and sampled the microbial community after 1, 3 and 6 weeks. Genome-resolved metaproteomics was combined with 50at-% [13]CO2 stable isotope probing to follow the C flux through the microbial food web and infer traits expressed by active SOB in the groundwater microcosms. Already after 7 days, 90% of the total microbial biomass C in the microcosms was replaced by CO2-derived C, increasing to 97% at the end of incubation. Stable Isotope Cluster Analysis revealed active autotrophs, characterized by a uniform [13]C-incorporation of 45% in their peptides, to dominate the microbial community throughout incubation. Mixo- and heterotrophs, characterized by 10 to 40% [13]C-incorporation, utilized the primarily produced organic C. Interestingly, obligate autotrophs affiliated with Sulfuricella and Sulfuritalea contained traits enabling the storage of elemental S in globules to maintain primary production under energy limitation. Others related to Sulfurimonas seemed to rapidly utilize substrates for fast proliferation, and most autotrophs further maximized their energy yield via efficient denitrification and the potential for H2 oxidation. Mixotrophic SOB, belonging to Curvibacter or Polaromonas, enhanced metabolic flexibility by using organic compounds to satisfy their C requirements. Time series data spanning eight years further revealed that key taxa of our microcosms composed up to 15% of the microbial groundwater community, demonstrating their in-situ importance. This showed that SOB, by using different metabolic strategies, are able to account for high rates of primary production in groundwater, especially at sites limited to geogenic nutrient sources. The widespread presence of SOB with traits such as S storage, H2 oxidation, and organic C utilization in many aquatic habitats further suggested that metabolic versatility governs S-fueled primary production in the environment.},
}
@article {pmid37517669,
year = {2023},
author = {Ozsefil, IC and Miraloglu, IH and Ozbayram, EG and Uzun, O and Ince, B and Ince, O},
title = {Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach.},
journal = {Chemosphere},
volume = {339},
number = {},
pages = {139675},
doi = {10.1016/j.chemosphere.2023.139675},
pmid = {37517669},
issn = {1879-1298},
mesh = {*Lignin/metabolism ; Anaerobiosis ; *Microbiota ; Metagenome ; Microbial Consortia ; Forests ; },
abstract = {Lignin is one of the most substantial obstacles in the evaluation of lignocellulosic compounds. Although there are numerous approaches for the enhancement of lignin digestion in the literature, there has yet to be an optimized system to date. In this study, samples taken from Igneada floodplain forests were enriched anaerobically at 25 °C and 37 °C, with alkali lignin as the sole carbon source. The activity of the anaerobic lignin-degrading microbial consortium was detected more efficiently at 37 °C, where biogas production exceeded 3.5 mLgas/mLmedium. It was observed that the microbial community initially dominated by Proteobacteria (around 60%) changed completely after enrichment and was led by members of the Firmicutes phylum (up to 90%). The dominant species (Sporomusa termitida, Desulfitobacterium hafniense, Citrobacter freundii, Citrobacter portucalensis, Alkalibacter rhizosphaerae, and Gudongella oleilytica) occupying more than 50% in the final enrichment culture were only around 2% in the raw samples. Therefore, this study, one of the few in which enriched environmental samples were sequenced using MinION, demonstrated that longoses are exceptional reservoirs for lignin-digesting anaerobic microorganisms.},
}
@article {pmid37516054,
year = {2023},
author = {He, S and Deng, X and Han, Y and Gong, Z and Wang, J and Tao, X and Tong, H and Chen, Y},
title = {Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head".},
journal = {Food chemistry},
volume = {429},
number = {},
pages = {136992},
doi = {10.1016/j.foodchem.2023.136992},
pmid = {37516054},
issn = {1873-7072},
mesh = {Tea/chemistry ; *Microbiota ; Bacteria/genetics ; *Catechin ; Fermentation ; },
abstract = {Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.},
}
@article {pmid37485826,
year = {2023},
author = {Jaramillo-Jaramillo, AS and Coulson, TJD and Hofacre, C and Jones, M and O'Neill, L and Nguyen, N and Labbe, A},
title = {Effect of in-water administration of quorum system inhibitors in broilers' productive performance and intestinal microbiome in a mild necrotic enteritis challenge.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {52},
number = {5},
pages = {309-322},
doi = {10.1080/03079457.2023.2224260},
pmid = {37485826},
issn = {1465-3338},
mesh = {Animals ; *Bacterial Toxins/metabolism ; Enterotoxins/metabolism ; *Clostridium Infections/veterinary/microbiology ; Chickens/microbiology ; *Enteritis/veterinary/microbiology ; *Gastrointestinal Microbiome ; Clostridium perfringens/genetics ; Water/metabolism ; *Poultry Diseases/microbiology ; },
abstract = {The poultry industry has been facing the impact of necrotic enteritis (NE), a disease caused by the bacterium Clostridium perfringens producing the haemolytic toxin NetB. NE severity may vary from mild clinical to prominent enteric signs causing reduced growth rates and affecting feed conversion ratio. NetB production is controlled by the Agr-like quorum-sensing (QS) system, which coordinates virulence gene expression in response to bacterial cell density. In this study, the peptide-containing cell-free spent media (CFSM) from Enterococcus faecium was tested in NE challenged broilers in two battery cage and one floor pen studies. Results showed a significant reduction of NE mortality. Metagenomic sequencing of the jejunum microbiome revealed no impact of the CFSM on the microbial community, and growth of C. perfringens was unaffected by CFSM in vitro. The expression of QS-controlled virulence genes netB, plc and pfoA was found to be significantly repressed by CFSM during the mid-logarithmic stage of C. perfringens growth and this corresponded with a significant decrease in haemolytic activity. Purified fractions of CFSM containing bioactive peptides were found to cause reduced haemolysis. These results showed that bioactive peptides reduce NE mortality in broilers by interfering with the QS system of C. perfringens and reducing bacterial virulence. Furthermore, the microbiome of C. perfringens-challenged broilers is not affected by quorum sensing inhibitor containing CFSM.},
}
@article {pmid37029236,
year = {2023},
author = {Dreisbach, C and Prescott, S and Siega-Riz, AM and McCulloch, J and Habermeyer, L and Dudley, D and Trinchieri, G and Kelsey, C and Alhusen, J},
title = {Composition of the maternal gastrointestinal microbiome as a predictor of neonatal birth weight.},
journal = {Pediatric research},
volume = {94},
number = {3},
pages = {1158-1165},
pmid = {37029236},
issn = {1530-0447},
mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Birth Weight ; *Gastrointestinal Microbiome ; Blood Glucose ; Retrospective Studies ; Cross-Sectional Studies ; Body Mass Index ; },
abstract = {BACKGROUND: The biological mechanism by which the maternal gastrointestinal microbiota contributes to fetal growth and neonatal birth weight is currently unknown. The purpose of this study was to explore how the composition of the maternal microbiome in varying pre-gravid body mass index (BMI) groups are associated with neonatal birth weight adjusted for gestational age.<br><br>METHODS: Retrospective, cross-sectional metagenomic analysis of bio-banked fecal swab biospecimens (n&#x2009;=&#x2009;102) self-collected by participants in the late second trimester of pregnancy.<br><br>RESULTS: Through high-dimensional regression analysis using principal components (PC) of the microbiome, we found that the best performing multivariate model explained 22.9% of the variation in neonatal weight adjusted for gestational age. Pre-gravid BMI (p&#x2009;=&#x2009;0.05), PC3 (p&#x2009;=&#x2009;0.03), and the interaction of the maternal microbiome with maternal blood glucose on the glucose challenge test (p&#x2009;=&#x2009;0.01) were significant predictors of neonatal birth weight after adjusting for potential confounders including maternal antibiotic use during gestation and total gestational weight gain.<br><br>CONCLUSIONS: Our results indicate a significant association between the maternal gastrointestinal microbiome in the late second trimester and neonatal birth weight adjusted for gestational age. Moderated by blood glucose at the time of the universal glucose screening, the gastrointestinal microbiome may have a role in the regulation of fetal growth.<br><br>IMPACT: Maternal blood glucose in the late second trimester significantly moderates the relationship between the maternal gastrointestinal microbiome and neonatal size adjusted for gestational age. Our findings provide preliminary evidence for fetal programming of neonatal birth weight through the maternal gastrointestinal microbiome during pregnancy.},
}
@article {pmid37596696,
year = {2023},
author = {Pavia, MJ and Chede, A and Wu, Z and Cadillo-Quiroz, H and Zhu, Q},
title = {BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {186},
pmid = {37596696},
issn = {2049-2618},
support = {CSP No 166//Joint Genome Institute/ ; DEB 1749252//National Science Foundation/ ; },
mesh = {Humans ; *Metagenome/genetics ; *Microbiota/genetics ; Algorithms ; Biological Evolution ; Diarrhea ; },
abstract = {BACKGROUND: Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.<br><br>RESULTS: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.<br><br>CONCLUSIONS: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.},
}
@article {pmid37455332,
year = {2023},
author = {Chang, WS and Wille, M},
title = {Winter is coming-The role of seasonality through the lens of the rodent virome.},
journal = {Molecular ecology},
volume = {32},
number = {17},
pages = {4709-4712},
doi = {10.1111/mec.17078},
pmid = {37455332},
issn = {1365-294X},
support = {DE200100977//Australian Research Council/ ; },
mesh = {Animals ; *Virome ; Rodentia ; *Viruses/genetics ; Seasons ; Phylogeny ; Metagenomics ; },
abstract = {Rodent virus communities (viromes) are overrepresented with zoonotic viruses, and as such are a key host system for the study of zoonotic viruses. However, the extent of viral diversity beyond characterized zoonotic viruses, and the factors that modulate the viromes of rodents remain opaque. In this issue of Molecular Ecology, Raghwani et al. (2023) use rodents as a model to understand the role of seasonality in dictating virome abundance and composition-a factor known to play an important role in most animal one-host, one-pathogen systems. These data are not only highly relevant to rodents, but have broad applications across understanding and disentangling animal virome ecology.},
}
@article {pmid37440367,
year = {2023},
author = {Muralitharan, RR and Snelson, M and Meric, G and Coughlan, MT and Marques, FZ},
title = {Guidelines for microbiome studies in renal physiology.},
journal = {American journal of physiology. Renal physiology},
volume = {325},
number = {3},
pages = {F345-F362},
doi = {10.1152/ajprenal.00072.2023},
pmid = {37440367},
issn = {1522-1466},
mesh = {Animals ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents ; },
abstract = {Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and fecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animals and clinical studies assessing renal function, many of which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatization, baseline microbiota and its normalization, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best-practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardizing study designs, methods, and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.},
}
@article {pmid37596536,
year = {2023},
author = {Araújo, V and Fehn, AM and Phiri, A and Wills, J and Rocha, J and Gayà-Vidal, M},
title = {Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {226},
pmid = {37596536},
issn = {1471-2180},
support = {CEECIND/02765/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVF/2907/2012, PTDC/BIA-GEN/29273/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/BIA/50027/2013, POCI-01-0145-FEDER-006821, UID/BIA/50027/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; FCOMP-01-0124-FEDER-028341//FEDER funds through the Operational Programme for Competitiveness Factors-COMPETE/ ; NORTE-01-0145-FEDER-000046, NORTE-01-0246-FEDER-000063//Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)/ ; POCI-01-0145-FEDER-006821//Operational Programme for Competitiveness Factors - COMPETE/ ; },
mesh = {Humans ; Zimbabwe ; Angola ; Africa, Southern ; *Citrobacter ; *Microbiota/genetics ; },
abstract = {BACKGROUND: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).<br><br>RESULTS: Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization.<br><br>CONCLUSIONS: Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.},
}
@article {pmid37596518,
year = {2023},
author = {Galperine, T and Choi, Y and Pagani, JL and Kritikos, A and Papadimitriou-Olivgeris, M and Méan, M and Scherz, V and Opota, O and Greub, G and Guery, B and Bertelli, C and , },
title = {Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort.},
journal = {BMC infectious diseases},
volume = {23},
number = {1},
pages = {537},
pmid = {37596518},
issn = {1471-2334},
mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteroides ; Butyrates ; },
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients.<br><br>METHODS: From March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR.<br><br>RESULTS: Although similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients.<br><br>CONCLUSIONS: Overall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology.<br><br>TRIAL REGISTRATION: CER-VD 2020-00755 (05.05.2020) &amp; 2017-01820 (08.06.2018).},
}
@article {pmid37596370,
year = {2023},
author = {Vigneron, A and Vincent, WF and Lovejoy, C},
title = {Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {82},
pmid = {37596370},
issn = {2730-6151},
support = {Sentinel North//Canada First Research Excellence Fund (Fonds d&apos;excellence en recherche Apog&#xe9;e Canada)/ ; Sentinel North//Canada First Research Excellence Fund (Fonds d&apos;excellence en recherche Apog&#xe9;e Canada)/ ; Sentinel North//Canada First Research Excellence Fund (Fonds d&apos;excellence en recherche Apog&#xe9;e Canada)/ ; ArcticNet//Gouvernement du Canada | R&#xe9;seaux de centres d&apos;excellence | AUTO21 Network of Centres of Excellence (R&#xe9;seau de Centres d&apos;Excellence AUTO21)/ ; Arctic Net//Gouvernement du Canada | R&#xe9;seaux de centres d&apos;excellence | AUTO21 Network of Centres of Excellence (R&#xe9;seau de Centres d&apos;Excellence AUTO21)/ ; },
abstract = {Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.},
}
@article {pmid37594964,
year = {2023},
author = {Li, W and Kari, L and Yu, Y and Hug, LA},
title = {MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenomeassembled genomes.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0283536},
pmid = {37594964},
issn = {1932-6203},
mesh = {Animals ; Cattle ; Female ; Humans ; *Metagenome/genetics ; Benchmarking ; Computational Biology ; *Gastrointestinal Microbiome ; Machine Learning ; },
abstract = {We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is alignment-free, with k-mer frequencies being the only feature used to distinguish a DNA sequence from another (herein k = 7). MT-MAG is capable of classifying large and diverse metagenomic datasets: a total of 245.68 Gbp in the training sets, and 9.6 Gbp in the test sets analyzed in this study. In addition to complete classifications, MT-MAG offers a "partial classification" option, whereby a classification at a higher taxonomic level is provided for MAGs that cannot be classified to the Species level. MT-MAG outputs complete or partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. To assess the performance of MT-MAG, we define a "weighted classification accuracy," with a weighting scheme reflecting the fact that partial classifications at different ranks are not equally informative. For the two benchmarking datasets analyzed (genomes from human gut microbiome species, and bacterial and archaeal genomes assembled from cow rumen metagenomic sequences), MT-MAG achieves an average of 87.32% in weighted classification accuracy. At the Species level, MT-MAG outperforms DeepMicrobes, the only other comparable software tool, by an average of 34.79% in weighted classification accuracy. In addition, MT-MAG is able to completely classify an average of 67.70% of the sequences at the Species level, compared with DeepMicrobes which only classifies 47.45%. Moreover, MT-MAG provides additional information for sequences that it could not classify at the Species level, resulting in the partial or complete classification of 95.13%, of the genomes in the datasets analyzed. Lastly, unlike other taxonomic assignment tools (e.g., GDTB-Tk), MT-MAG is an alignment-free and genetic marker-free tool, able to provide additional bioinformatics analysis to confirm existing or tentative taxonomic assignments.},
}
@article {pmid37593763,
year = {2023},
author = {Cui, S and Pan, M and Tang, X and Liu, G and Mao, B and Zhao, J and Yang, K},
title = {Metagenomic insights into the effects of cosmetics containing complex polysaccharides on the composition of skin microbiota in females.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1210724},
pmid = {37593763},
issn = {2235-2988},
mesh = {Female ; Humans ; Metagenome ; *Microbiota ; *Cosmetics ; Skin ; *Actinobacteria ; Bifidobacterium ; },
abstract = {INTRODUCTION: The use of cosmetics has become a habit for women. However, their influence on the microbial diversity of the skin has rarely been studied.<br><br>METHODS: Herein, the effect of cosmetics containing complex polysaccharides on the skin bacterial microbiota of female forehead and cheek areas was analyzed. Eighty volunteers were recruited and split into two groups (40 people each); one group was treated with cosmetics containing complex polysaccharides and the other with basic cream for 28 days. Skin samples were collected using sterilized cotton swabs, and 16S rDNA high-throughput sequencing was used to analyze the changes in skin bacterial microbiota composition before and after the intervention.<br><br>RESULTS AND DISCUSSION: A total of twenty-four phyla were detected in the forehead and cheek skin samples of 80 volunteers, the top three of which were Proteobacteria, Firmicutes, and Actinobacteria. The main genera of the forehead skin bacterial microbiota were Cutibacterium (11.1%), Acinetobacter (10.4%), Enterococcus (8.9%), Ralstonia (8.8%), and Staphylococcus (8.7%), while those of the cheek skin bacterial microbiota were Staphylococcus (20.0%), Ralstonia (8.7%), Propionibacterium (7.9%), Acinetobacter (7.2%), and Bifidobacterium (6.0%). Compared with basic cream, the use of cosmetics containing complex polysaccharides significantly increased the relative abundance of Staphylococcus and Bacillus in the forehead and cheek and reduced the relative abundance of Propionibacterium and Bifidobacterium. Thus, cosmetics containing complex polysaccharides could modify the composition of skin bacterial microbiota, which may help to maintain stable conditions of the skin.},
}
@article {pmid37593761,
year = {2023},
author = {Fukuoka, H and Tourlousse, DM and Ohashi, A and Suzuki, S and Nakagawa, K and Ozawa, M and Ishibe, A and Endo, I and Sekiguchi, Y},
title = {Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1216024},
pmid = {37593761},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteria/genetics ; *Colorectal Neoplasms ; },
abstract = {Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one-hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients.},
}
@article {pmid37591872,
year = {2023},
author = {Liao, J and Shenhav, L and Urban, JA and Serrano, M and Zhu, B and Buck, GA and Korem, T},
title = {Microdiversity of the vaginal microbiome is associated with preterm birth.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4997},
pmid = {37591872},
issn = {2041-1723},
support = {R01 HD106017/HD/NICHD NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; },
mesh = {Infant, Newborn ; Pregnancy ; Humans ; Female ; *Premature Birth/genetics ; *Microbiota/genetics ; Metagenome/genetics ; Acclimatization ; Biological Evolution ; },
abstract = {Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.},
}
@article {pmid37441819,
year = {2023},
author = {Ren, Z and Jiang, W and Sun, N and Shi, J and Zhang, D and Zhang, J and Wang, Z and Yang, J and Yu, J and Lv, Z},
title = {Responses of the structure and function of microbes in Yellow River Estuary sediments to different levels of mercury.},
journal = {Marine environmental research},
volume = {190},
number = {},
pages = {106097},
doi = {10.1016/j.marenvres.2023.106097},
pmid = {37441819},
issn = {1879-0291},
mesh = {*Mercury/analysis ; Estuaries ; Rivers/chemistry ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/chemistry ; *Water Pollutants, Chemical/toxicity/analysis ; *Methylmercury Compounds ; *Metals, Heavy/analysis ; *Microbiota ; Environmental Monitoring ; },
abstract = {The health and stability of the estuary of the Yellow River ecosystem have come under increasing pressure from land-based inputs of heavy metals. While it is known that heavy metals affect the function and health of the microbial community, there remains little knowledge on the responses of the microbial community to heavy metals, particularly highly toxic mercury. The research aimed to characterize the responses of the sediment microbial community of the estuary of the Yellow River to different levels of mercury stress. Estuary sediment samples were collected for microbial community analysis, measurement of mercury [including total mercury (THg) and methylmercury (MeHg)], and measurement of other physicochemical factors, including pH, total organic carbon (TOC), sulfide, iron ratio (Fe[3+]/Fe[2+]), ammonium salt (NH4[+]), and biochemical oxygen demand (BOD). The application of 16S rRNA sequencing identified 60 phyla of bacteria, dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stations with higher THg or MeHg and lower microbial abundance and diversity were generally distributed further outside of the estuary. Besides mercury, the measured physicochemical factors had impacts on microbial diversities and distribution. Metagenomics assessment of three stations, representative of low, moderate, and high mercury concentrations and measured physicochemical factors, revealed the abundances and functions of predicted genes. The most abundant genes regulating the metabolic pathways were categorized as metabolic, environmental information processing, and genetic information processing, genes. At stations with high levels of mercury, the dominant genes were related to energy metabolism, signal transport, and membrane transport. Functional genes with a mercury-resistance function were generally in the mer system (merA, merC, merT, merR), alkylmercury lyase, and metal-transporting ATPase. These results offer insight into the microbial community structure of the sediments in the Yellow River Estuary and the microbial function of mercury resistance under mercury stress.},
}
@article {pmid37436163,
year = {2023},
author = {Tan, Y and Chen, Z and Zeng, Z and Wu, S and Liu, J and Zou, S and Wang, M and Liang, K},
title = {Microbiomes Detected by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing among HIV-Infected and Uninfected Patients with Pulmonary Infection.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0000523},
pmid = {37436163},
issn = {2165-0497},
support = {PTXM2020008//Medical science and Technology Innovation Platform Support Project of Zhongnan Hospital, Wuhan University/ ; cxpy2017043//Science and Technology Innovation Cultivation Fund of Zhongnan Hospital, Wuhan University/ ; TFJC2018004//Medical Science Advancement Program (Basic Medical Sciences) of Wuhan University/ ; 2020-PT320-004//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *Pneumonia ; *HIV Infections ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {Comparison of lung microbiomes between HIV-infected and uninfected patients with pulmonary infection by metagenomic next-generation sequencing (mNGS) has not been described in China. The lung microbiomes detected in bronchoalveolar fluid (BALF) by mNGS among HIV-infected and uninfected patients with pulmonary infection were reviewed in the First Hospital of Changsha between January 2019 and June 2022. In total, 476 HIV-infected and 280 uninfected patients with pulmonary infection were enrolled. Compared with HIV-uninfected patients, the proportions of Mycobacterium (P = 0.011), fungi (P < 0.001), and viruses (P < 0.001) were significantly higher in HIV-infected patients. The higher positive rate of Mycobacterium tuberculosis (MTB; P = 0.018), higher positive rates of Pneumocystis jirovecii and Talaromyces marneffei (all P < 0.001), and higher positive rate of cytomegalovirus (P < 0.001) contributed to the increased proportions of Mycobacterium, fungi, and viruses among HIV-infected patients, respectively. The constituent ratios of Streptococcus pneumoniae (P = 0.007) and Tropheryma whipplei (P = 0.002) in the bacteria spectrum were significantly higher, while the constituent ratio of Klebsiella pneumoniae (P = 0.005) was significantly lower in HIV-infected patients than in HIV-uninfected patients. Compared with HIV-uninfected patients, the constituent ratios of P. jirovecii and T. marneffei (all P < 0.001) in the fungal spectrum were significantly higher, while the constituent ratios of Candida and Aspergillus (all P < 0.001) were significantly lower in HIV-infected patients. In comparison to HIV-infected patients without antiretroviral therapy (ART), the proportions of T. whipplei (P = 0.001), MTB (P = 0.024), P. jirovecii (P < 0.001), T. marneffei (P < 0.001), and cytomegalovirus (P = 0.008) were significantly lower in HIV-infected patients on ART. Significant differences in lung microbiomes exist between HIV-infected and uninfected patients with pulmonary infection, and ART influences the lung microbiomes among HIV-infected patients with pulmonary infection. IMPORTANCE A better understanding of lung microorganisms is conducive to early diagnosis and treatment and will improve the prognosis of HIV-infected patients with pulmonary infection. Currently, few studies have systematically described the spectrum of pulmonary infection among HIV-infected patients. This study is the first to provide comprehensive information on the lung microbiomes of HIV-infected patients with pulmonary infection (as assessed by more sensitive metagenomic next-generation sequencing of bronchoalveolar fluid) compared with those from HIV-uninfected patients, which could provide a reference for the etiology of pulmonary infection among HIV-infected patients.},
}
@article {pmid37428087,
year = {2023},
author = {Bai, H and Liu, T and Wang, S and Gong, W and Shen, L and Zhang, S and Wang, Z},
title = {Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0059023},
pmid = {37428087},
issn = {2165-0497},
mesh = {Cats ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Feces/microbiology ; Diarrhea/veterinary/microbiology ; Firmicutes/genetics ; },
abstract = {Changes in diet and environment can lead to acute diarrhea in companion animals, but the composition and interactions of the gut microbiome during acute diarrhea remain unclear. In this multicenter case-control study, we investigated the relationship between intestinal flora and acute diarrhea in two breeds of cats. Acutely diarrheic American Shorthair (MD, n = 12) and British Shorthair (BD, n = 12) and healthy American Shorthair (MH, n = 12) and British Shorthair (BH, n = 12) cats were recruited. Gut microbial 16S rRNA sequencing, metagenomic sequencing, and untargeted metabolomic analysis were performed. We observed significant differences in beta-diversity (Adonis, P < 0.05) across breeds and disease state cohorts. Profound differences in gut microbial structure and function were found between the two cat breeds. In comparison to healthy British Shorthair cats, Prevotella, Providencia, and Sutterella were enriched while Blautia, Peptoclostridium, and Tyzzerella were reduced in American Shorthair cats. In the case-control cohort, cats with acute diarrhea exhibited an increased abundance of Bacteroidota, Prevotella, and Prevotella copri and a decreased abundance of Bacilli, Erysipelotrichales, and Erysipelatoclostridiaceae (both MD and BD cats, P < 0.05). Metabolomic analysis identified significant changes in the BD intestine, affecting 45 metabolic pathways. Moreover, using a random forest classifier, we successfully predicted the occurrence of acute diarrhea with an area under the curve of 0.95. Our findings indicate a distinct gut microbiome profile that is associated with the presence of acute diarrhea in cats. However, further investigations using larger cohorts of cats with diverse conditions are required to validate and extend these findings. IMPORTANCE Acute diarrhea is common in cats, and our understanding of the gut microbiome variations across breeds and disease states remains unclear. We investigated the gut microbiome of two cat breeds (British Shorthair and American Shorthair) with acute diarrhea. Our study revealed significant effects of breeds and disease states on the structure and function of the gut microbiota in cats. These findings emphasize the need to consider breed-related factors in animal nutrition and research models. Additionally, we observed an altered gut metabolome in cats with acute diarrhea, closely linked to changes in bacterial genera. We identified a panel of microbial biomarkers with high diagnostic accuracy for feline acute diarrhea. These findings provide novel insights into the diagnosis, classification, and treatment of feline gastrointestinal diseases.},
}
@article {pmid37404183,
year = {2023},
author = {Stege, PB and Hordijk, J and Sandholt, AKS and Zomer, AL and Viveen, MC and Rogers, MRC and Salomons, M and Wagenaar, JA and Mughini-Gras, L and Willems, RJL and Paganelli, FL},
title = {Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0006323},
pmid = {37404183},
issn = {2165-0497},
support = {Metagenome call//Netherlands Center of one Health (NCOH)/ ; AC16/00039//Joint Programming Initiative on Antimicrobial Resistance (JPIAMR)/ ; },
mesh = {Humans ; Dogs ; Animals ; *Escherichia coli Infections/microbiology ; Bacterial Proteins/genetics ; RNA, Ribosomal, 16S/genetics ; Escherichia coli/genetics ; beta-Lactamases/genetics ; Bacteria/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.},
}
@article {pmid37404173,
year = {2023},
author = {Kiledal, EA and Shaw, M and Polson, SW and Maresca, JA},
title = {Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0511222},
pmid = {37404173},
issn = {2165-0497},
support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; *Microbiota/genetics ; Metagenome ; Sewage ; Sequence Analysis, DNA ; Metagenomics/methods ; Bacteria/genetics ; },
abstract = {Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.},
}
@article {pmid37393724,
year = {2023},
author = {He, Y and Pan, J and Huang, D and Sanford, RA and Peng, S and Wei, N and Sun, W and Shi, L and Jiang, Z and Jiang, Y and Hu, Y and Li, S and Li, Y and Li, M and Dong, Y},
title = {Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering.},
journal = {Environment international},
volume = {178},
number = {},
pages = {108067},
doi = {10.1016/j.envint.2023.108067},
pmid = {37393724},
issn = {1873-6750},
mesh = {Humans ; *Bacteria/genetics ; Metagenome ; *Microbiota ; Weather ; Carbon/metabolism ; },
abstract = {Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca[2+] concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H[+] antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.},
}
@article {pmid37310219,
year = {2023},
author = {Riley, R and Bowers, RM and Camargo, AP and Campbell, A and Egan, R and Eloe-Fadrosh, EA and Foster, B and Hofmeyr, S and Huntemann, M and Kellom, M and Kimbrel, JA and Oliker, L and Yelick, K and Pett-Ridge, J and Salamov, A and Varghese, NJ and Clum, A},
title = {Terabase-Scale Coassembly of a Tropical Soil Microbiome.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0020023},
pmid = {37310219},
issn = {2165-0497},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; SCW1478//U.S. Department of Energy (DOE)/ ; SCW1632//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; 17-SC-20-SC//U.S. Department of Energy (DOE)/ ; DE-AC05-00OR22725//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Viral ; Metagenomics/methods ; },
abstract = {Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.},
}
@article {pmid36694290,
year = {2023},
author = {Urana, R and Yadav, J and Panchal, S and Sharma, P and Singh, N},
title = {Phytoremediation of PAH compounds by microbial communities in sodic soil.},
journal = {International journal of phytoremediation},
volume = {25},
number = {11},
pages = {1501-1509},
doi = {10.1080/15226514.2023.2170321},
pmid = {36694290},
issn = {1549-7879},
mesh = {Biodegradation, Environmental ; Soil ; *Polycyclic Aromatic Hydrocarbons ; *Microbiota ; Microbial Consortia ; *Soil Pollutants ; Soil Microbiology ; },
abstract = {The PAH degrading microbial consortium was collected from sodic soil of the nursery of Guru Jambheshwar University of Science and Technology, Hisar, Haryana (India). And the soil was artificially amended with phenanthrene and naphthalene to isolate the PAHs degrading microbial consortium. The diversity of microbial consortium was analyzed using the NGS (Next Generation Sequencing) based metagenomic approach. The result of diversity analysis showed species Tepidanaerobacter syntrophicus, Sphingomonas oliophenolica, Arthrobacter psychrochitinipnius, Bifidobacterium bombi, Nocardiodies islandensis, Rhodovibrio sodomensis, Thiorhodococus pfennigii, Aeromicrobium ponti, Steroidobacter dentrificans, Actinomaduria maheshkhaliensis, Dactylosporangium maewongense, Pelotomaculum isophthalicicum, and Nocardioides islandensis were present in the consortium. Moreover, Sphingomonas, Arthrobacter, Sphingobium, Azospirillium, Thirohodococcus, and Pelotomaculum were the prominent pollutant degrader genera in the microbial consortium. Since the bioremediation of these pollutants occurs with a significant reduction in toxicity, the study's perspective is to use this type of consortium for bioremediation of specifically contaminated soil.},
}
@article {pmid37587527,
year = {2023},
author = {Liao, H and Ji, Y and Sun, Y},
title = {High-resolution strain-level microbiome composition analysis from short reads.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {183},
pmid = {37587527},
issn = {2049-2618},
mesh = {*Microbiota/genetics ; Metagenome/genetics ; Metagenomics ; Software ; },
abstract = {BACKGROUND: Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important step in understanding the dynamics of microbial communities. Metagenomic sequencing has become the major means for probing the microbial composition in host-associated or environmental samples. Although there are a plethora of composition analysis tools, they are not optimized to address the challenges in strain-level analysis: highly similar strain genomes and the presence of multiple strains under one species in a sample. Thus, this work aims to provide a high-resolution and more accurate strain-level analysis tool for short reads.<br><br>RESULTS: In this work, we present a new strain-level composition analysis tool named StrainScan that employs a novel tree-based k-mers indexing structure to strike a balance between the strain identification accuracy and the computational complexity. We tested StrainScan extensively on a large number of simulated and real sequencing data and benchmarked StrainScan with popular strain-level analysis tools including Krakenuniq, StrainSeeker, Pathoscope2, Sigma, StrainGE, and StrainEst. The results show that StrainScan has higher accuracy and resolution than the state-of-the-art tools on strain-level composition analysis. It improves the F1 score by 20% in identifying multiple strains at the strain level.<br><br>CONCLUSIONS: By using a novel k-mer indexing structure, StrainScan is able to provide strain-level analysis with higher resolution than existing tools, enabling it to return more informative strain composition analysis in one sample or across multiple samples. StrainScan takes short reads and a set of reference strains as input and its source codes are freely available at https://github.com/liaoherui/StrainScan . Video Abstract.},
}
@article {pmid37580828,
year = {2023},
author = {Deng, F and Wang, C and Li, D and Peng, Y and Deng, L and Zhao, Y and Zhang, Z and Wei, M and Wu, K and Zhao, J and Li, Y},
title = {The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host's dietary adaption to bamboo.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {180},
pmid = {37580828},
issn = {2049-2618},
mesh = {Animals ; Mice ; *Ursidae ; *Gastrointestinal Microbiome/genetics ; Feces/chemistry ; Metagenome ; Diet ; },
abstract = {BACKGROUND: The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol of conservation, are believed to be involved in the host's dietary switch to a fibrous bamboo diet. However, their exact roles are still largely unknown.<br><br>RESULTS: In this study, we first comprehensively analyzed a large number of gut metagenomes giant pandas (n&#x2009;=&#x2009;322), including 98 pandas sequenced in this study with deep sequencing (Illumina) and third-generation sequencing (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), and 148 of which (36.27%) were near complete. The most abundant MAG was classified as Streptococcus alactolyticus. A pairwise comparison of the metagenomes and meta-transcriptomes in 14 feces revealed genes involved in carbohydrate metabolism were lower, but those involved in protein metabolism were greater in abundance and expression in giant pandas compared to those in herbivores and omnivores. Of note, S. alactolyticus was positively correlated to the KEGG modules of essential amino-acid biosynthesis. After being isolated from pandas and gavaged to mice, S. alactolyticus significantly increased the relative abundance of essential amino acids in mice jejunum.<br><br>CONCLUSIONS: The study highlights the unique protein metabolic profiles in the giant panda's gut microbiome. The findings suggest that S. alactolyticus is an important player in the gut microbiota that contributes to the giant panda's dietary adaptation by more involvement in protein rather than carbohydrate metabolism. Video Abstract.},
}
@article {pmid37580683,
year = {2023},
author = {Józefiak, A and Rawski, M and Kierończyk, B and Józefiak, D and Mazurkiewicz, J},
title = {Effect of two insect meals on the gut commensal microbiome of healthy sea trout (Salmo trutta vr. trutta).},
journal = {BMC veterinary research},
volume = {19},
number = {1},
pages = {124},
pmid = {37580683},
issn = {1746-6148},
support = {POIR 4.4//Narodowe Centrum Nauki/ ; TEAM TECH no. POIR.04.04.00-00-204E/16-00//Narodowe Centrum Bada&#x144; i Rozwoju/ ; },
mesh = {Animals ; *Trout/microbiology ; Diet/veterinary ; Insecta ; Bacteria ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: The balance of the intestinal commensal microbiome of fish and other animals plays an important role in the physiological processes of healthy animals, contributes to the defense against pathogens, stimulates the immune system and facilitates nutrient metabolism. In the last decade, the interest in the application of the insects in fish nutrition increased, although little is known regarding the effects of insect meals on the gastrointenstinal tract microbiome of the sea trout fingerlings. The aim of this study was to evaluate the effect of two diets containing mealworm (MW) and superworm (SW) on the microbiome of the digesta of sea trout fingerlings and the relative abundances of different taxa among communities under controlled conditions.<br><br>RESULTS: The insect meals produced a similar weight gain and survival rate to sea trout fed fishmeal. The most abundant bacterial phylum in all the treatment groups was Firmicutes followed by Proteobacteria and Actinobacteria, and significant differences in the amount of Cyanobacteria were observed in the SW group.<br><br>CONCLUSIONS: The insect meals did not produce differences in the three most abundant phyla in the sea trout digesta. However, the effect of each type of meal on the lower taxonomic levels was evident, particularly in the case of the superworm meal. These microbiome differences indicated that mealworm meal was more related to fishmeal than superworm meal. Our results highlight the potential effects of insect meals, such as mealworm and superworm meals, on the microbiota of sea trout.},
}
@article {pmid37578240,
year = {2023},
author = {Cabrol, L and Capo, E and van Vliet, DM and von Meijenfeldt, FAB and Bertilsson, S and Villanueva, L and Sánchez-Andrea, I and Björn, E and G Bravo, A and Heimburger Boavida, LE},
title = {Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0053723},
doi = {10.1128/msystems.00537-23},
pmid = {37578240},
issn = {2379-5077},
abstract = {In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc [+]) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc [+] microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc [+] microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc [+]) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc [+] microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.},
}
@article {pmid37246304,
year = {2023},
author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R},
title = {Comparative 16S rRNA gene sequencing study of subgingival microbiota of healthy subjects and patients with periodontitis from four different countries.},
journal = {Journal of clinical periodontology},
volume = {50},
number = {9},
pages = {1176-1187},
doi = {10.1111/jcpe.13827},
pmid = {37246304},
issn = {1600-051X},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Healthy Volunteers ; *Dental Plaque/microbiology ; *Periodontitis/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; },
abstract = {AIM: To investigate the differences between the subgingival microbiota of healthy subjects (HS) and periodontitis patients (PP) from four different countries through a metagenomic approach.<br><br>MATERIALS AND METHODS: Subgingival samples were obtained from subjects from four different countries. Microbial composition was analysed through high-throughput sequencing of the V3-V4 region of the 16S rRNA gene. The country of origin, diagnosis and clinical and demographic variables of the subjects were used to analyse the microbial profiles.<br><br>RESULTS: In total, 506 subgingival samples were analysed: 196 from HS and 310 from patients with periodontitis. Differences in richness, diversity and microbial composition were observed when comparing samples pertaining to different countries of origin and different subject diagnoses. Clinical variables, such as bleeding on probing, did not significantly affect the bacterial composition of the samples. A highly conserved core of microbiota associated with periodontitis was detected, while the microbiota associated with periodontally HS was much more diverse.<br><br>CONCLUSIONS: Periodontal diagnosis of the subjects was the main variable explaining the composition of the microbiota in the subgingival niche. Nevertheless, the country of origin also had a significant impact on the microbiota and is therefore an important factor to consider when describing subgingival bacterial communities.},
}
@article {pmid37365103,
year = {2023},
author = {Ojala, T and Häkkinen, AE and Kankuri, E and Kankainen, M},
title = {Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics.},
journal = {Trends in genetics : TIG},
volume = {39},
number = {9},
pages = {686-702},
doi = {10.1016/j.tig.2023.05.004},
pmid = {37365103},
issn = {0168-9525},
mesh = {Humans ; *Metagenomics ; *Microbiota/genetics ; Transcriptome/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.},
}
@article {pmid37577374,
year = {2023},
author = {Avellaneda-Franco, L and Dahlman, S and Barr, JJ},
title = {The gut virome and the relevance of temperate phages in human health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1241058},
pmid = {37577374},
issn = {2235-2988},
mesh = {Humans ; *Bacteriophages/genetics ; Virome ; Bacteria/genetics ; },
abstract = {Alterations in the gut virome impact human health. Bacteriophages, viruses that infect bacteria, dominate the gut virome and are mainly composed by virulent and temperate phages. While virulent phages exclusively replicate within and lyse their bacterial host's cell, temperate phages switch from an integrated state residing within their bacterial host's chromosome to an induced free virion state via an induction event. How often do these induction events occur and what are their implications on gut homeostasis? Here, we summarize the current knowledge of the gut virome based on metagenomics and present how the proportion of induced temperate phages varies amongst individuals, age, and disease states. Finally, we highlight the importance of building upon classical culture-dependent techniques and sequencing approaches to improve our understanding of temperate phages to enable their potential therapeutic use.},
}
@article {pmid37577371,
year = {2023},
author = {Naud, S and Valles, C and Abdillah, A and Abou Chacra, L and Mekhalif, FZ and Ibrahim, A and Caputo, A and Baudoin, JP and Gouriet, F and Bittar, F and Lagier, JC and Ranque, S and Fenollar, F and Tidjani Alou, M and Raoult, D},
title = {Preliminary landscape of Candidatus Saccharibacteria in the human microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1195679},
pmid = {37577371},
issn = {2235-2988},
mesh = {Female ; Humans ; Prospective Studies ; Retrospective Studies ; *Bacteria/genetics ; *Microbiota ; Real-Time Polymerase Chain Reaction ; },
abstract = {INTRODUCTION: Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date.<br><br>METHODS: In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics.<br><br>RESULTS: Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples.<br><br>CONCLUSION: This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.},
}
@article {pmid37575934,
year = {2023},
author = {Kakkar, RA and Haneen, MA and Parida, AC and Sharma, G},
title = {The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1139215},
pmid = {37575934},
issn = {1664-462X},
abstract = {Humanity will always be indebted to plants. In the ongoing scientific era, the 'Herbal Revolution' has helped discover several valuable medicinal plants and associated novel secondary metabolites from the diverse unexplored ecosystems, treating several diseases via phytotherapy. The Aconitum genus comprises several economically-important poisonous mountainous medicinal plant species whose unique biodiversity is on the verge of extinction due to illegal human intervention triggered habitat loss, over-harvesting, and unrestricted trading. Owing to its vast diversity of diterpene alkaloids, most species are extensively used to treat several ailments in rural parts of the world. Irrespective of this, many unexplored and intriguing prospects exist to understand and utilize this critical plant for human benefit. This systematic review tries to fill this gap by compiling information from the sporadically available literature known for ~300 Aconitum spp. regarding its nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies. We also depicted the disparity in the studied model organisms for this diverse genus. The absence of genomic/metagenomic data is becoming a limiting factor in understanding its plant physiology, metabolic pathways, and plant-microbes interactions, and therefore must be promoted. Additionally, government support and public participation are crucial in establishing conservation protocols to save this plant from endangerment.},
}
@article {pmid37348417,
year = {2023},
author = {Peng, Y and Li, L and Yang, P and Liu, H and Ye, W and Xue, Z and Peng, X and Wang, X},
title = {Integrated genome-centric metagenomic and metaproteomic analyses unravel the responses of the microbial community to ammonia stress.},
journal = {Water research},
volume = {242},
number = {},
pages = {120239},
doi = {10.1016/j.watres.2023.120239},
pmid = {37348417},
issn = {1879-2448},
mesh = {*Propionates ; Ammonia/metabolism ; Anaerobiosis ; Metagenome ; Fatty Acids, Volatile/metabolism ; *Microbiota ; Acetates ; Butyrates ; Valerates ; Firmicutes/metabolism ; Methane/metabolism ; Bioreactors/microbiology ; },
abstract = {Ammonia is a major inhibitor in anaerobic digestion of nitrogen-rich organic wastes. In this study, integrated genome-centric metagenomic and metaproteomic analyses were used to identify the key microorganisms and metabolic links causing instability by characterizing the process performance, microbial community, and metabolic responses of key microorganisms during endogenous ammonia accumulation. The identification of 89 metagenome-assembled genomes and analysis of their abundance profile in different operational phases permitted the identification of key taxa (Firmicutes and Proteobacteria) causing poor performance. Metabolic reconstruction indicated that the key taxa had the genetic potential to participate in the metabolism of C2C5 volatile fatty acids (VFAs). Further investigation suggested that during Phase I, the total ammonia nitrogen (TAN) level was maintained below 2000 mg N/L, and the reactor showed a high methane yield (478.30 ± 33.35 mL/g VS) and low VFAs concentration. When the TAN accumulated to > 2000 mg N/L, acid accumulation, mainly of acetate, began to occur, and the methane yield gradually decreased to 330.44 mL/g VS (Phase II). During this phase, the VFA degradation functions of the community were mainly mediated by Firmicutes. Approximately 61.54% of significant differentially expressed proteins (DEPs) related to acetate metabolism in Firmicutes were down-regulated, which led to an increase in acetate concentration to 4897.91 ± 1558.96 mg/L. However, the reactor performance showed spontaneous recovery without any interference (Phase III), during which Firmicutes gradually adapted to the high ammonia conditions. Approximately 75% of the significant DEPs related to acetate metabolism of Proteobacteria were also up-regulated in Phase III compared with Phase II; thus, VFA-related metabolic functions of the community were enhanced, which resulted in a decrease in the total VFA concentration to 195.39 mg/L. When the TAN increased above 4000 mg N/L, the system gradually showed acid accumulation dominated by propionate, accompanied by a second decrease in methane yield (Phase IV). During this phase, the number of up-regulated and down-regulated proteins related to acetate metabolism of Firmicutes and butyrate/valerate metabolism of Proteobacteria was comparable with that of Phase III, indicating that the metabolic functions related to acetate, butyrate, and valerate of the microbial community were not significantly affected. However, for propionate metabolism, the expression activity of fumarate hydratase from Firmicutes and Proteobacteria was severely inhibited by ammonia, as shown by down-regulation ratios of 63.64% and 85.71%, respectively. No protein with the same function that was not inhibited by ammonia could be detected, and the fumarate degradation function of the microbial community was severely damaged, leading to blocked propionate metabolism and irreversible deterioration of reactor performance. This study has provided a new perspective on the microecological mechanisms of ammonia inhibition.},
}
@article {pmid36401059,
year = {2023},
author = {Gao, Y and Wang, H and Hu, Y and Li, J and Xu, W and Zhao, L and Su, X and Han, J and Li, T and Fang, X and Liu, L},
title = {Whole-genome metagenomic analysis of the oral microbiota in patients with obstructive sleep apnea.},
journal = {Sleep &amp; breathing = Schlaf &amp; Atmung},
volume = {27},
number = {4},
pages = {1383-1398},
pmid = {36401059},
issn = {1522-1709},
support = {QNC19054//Youth Program for Military Medicine of Chinese PLA General Hospital/ ; 19BJZ34//Military Health Care Project/ ; LB20211A010013//Army Equipment Construction Applied Research Project/ ; },
mesh = {Humans ; Novobiocin ; *Sleep Apnea, Obstructive/diagnosis/therapy ; Cholesterol, LDL ; Lipids ; Continuous Positive Airway Pressure ; *Microbiota/genetics ; },
abstract = {PURPOSE: The oral microbiota is closely associated with systemic health, but few studies have investigated the oral microbiota in patients with obstructive sleep apnea (OSA). This study aimed to identify the variation of oral microbiota among patients with severe OSA, and the change of oral microbiota after treatment with continuous positive airway pressure (CPAP).<br><br>METHODS: Participants were enrolled in the study&#xa0;from November 2020 to August 2021. Sleep parameters using full nocturnal polysomnography (PSG) were collected on healthy controls, patients with&#xa0;severe OSA, and patients with&#xa0;severe OSA after CPAP treatment for 3&#xa0;months. Oral samples were also collected by rubbing disposable medical sterile swabs on the buccal mucosa. Routine blood tests and biochemical indicators were measured&#xa0;using the fully automated biochemical analyzer. Oral microbial composition of oral samples were determined&#xa0;using whole-genome metagenomic analysis in all participants. Correlations were analyzed&#xa0;between the oral microbiota and blood lipids.<br><br>RESULTS: Study enrollment included 14 participants, 7 healthy controls and 7 patients with severe OSA.&#xa0;At the species level, the relative abundances of Prevotella, Alloprevotella, Bacteroides, Veillonella_tobetsuensis, Candidatus&#xa0;saccharimonas, and Leptotrichia in the groups with&#xa0;severe OSA were significantly lower than those in the healthy controls (P both&#x2009;<&#x2009;0.05). The abundances of Capnocytophaga, Veillonella, Bacillus_anthracis, Eikenella, and Kingella were significantly higher whereas the abundances of Gordonia and Streptococcus were significantly lower in the group with&#xa0;severe OSA compared to the severe OSA-CPAP group (P&#x2009;<&#x2009;0.05 for both). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), 4 pathways changed in the group with&#xa0;severe OSA compared with healthy controls (P both&#x2009;<&#x2009;0.05). Pathways related to Novobiocin biosynthesis, 2-Oxocarboxylic acid metabolism, and Histidine metabolism were enriched in the&#xa0;patients with severe OSA. Nine pathways showed significant differences with regard to the relative abundances of phenylalanine metabolism; alanine, aspartate, and glutamate metabolism; one carbon pool by folate; monobactam biosynthesis; 2-oxocarboxylic acid metabolism; arginine biosynthesis and vitamin B6 metabolism; novobiocin biosynthesis; and arginine and proline metabolism, which were significantly higher in the group with&#xa0;severe OSA compared to the severe OSA-CPAP group (P both&#x2009;<&#x2009;0.05). The Spearman correlation analysis between blood lipid parameters and oral microbiota components showed that negative correlations were observed between total cholesterol and Streptomyces (r&#x2009;=&#x2009;&#x2009;-&#x2009;0.893, P&#x2009;=&#x2009;0.007), and high-density lipoprotein cholesterol (HDL-C) and Gordonia (r&#x2009;= -&#x2009;0.821, P&#x2009;=&#x2009;0.023); positive correlations were observed between HDL-C and Candidatus saccharimonas (r&#x2009;=&#x2009;0.929, P&#x2009;=&#x2009;0.003), and low-density lipoprotein cholesterol (LDL-C) and Capnocytophaga (r&#x2009;=&#x2009;0.893, P&#x2009;=&#x2009;0.007).<br><br>CONCLUSION: There was an apparent discrepancy of the oral microbiota and metabolic pathways between the group with&#xa0;severe OSA and controls, and CPAP significantly changed oral microbial abundance and metabolic pathways in patients with severe OSA. Correlation analysis showed that these oral bacteria were strongly correlated with the blood lipids level.},
}
@article {pmid37573460,
year = {2023},
author = {Dwiyanto, J and Huët, MAL and Hussain, MH and Su, TT and Tan, JBL and Toh, KY and Lee, JWJ and Rahman, S and Chong, CW},
title = {Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {55},
pmid = {37573460},
issn = {2055-5008},
support = {LG-2017-01-SCI//Monash University Malaysia (Monash Malaysia)/ ; },
mesh = {Humans ; Malaysia ; Escherichia coli/genetics ; Saccharomyces cerevisiae ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Demography ; },
abstract = {The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community's health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.},
}
@article {pmid37573429,
year = {2023},
author = {Zhou, Y and Li, J and Huang, F and Ai, H and Gao, J and Chen, C and Huang, L},
title = {Characterization of the pig lower respiratory tract antibiotic resistome.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4868},
pmid = {37573429},
issn = {2041-1723},
support = {CARS-35//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota/genetics ; Respiratory System ; Swine ; },
abstract = {Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.},
}
@article {pmid37570344,
year = {2023},
author = {Yue, L and Wang, C and Meng, B and Xie, B and Cao, H and Su, H and Zhang, M},
title = {The Food Niche Overlap and Interspecific Relationship between the Sympatric Tibetan Macaque and Grey Snub-Nosed Monkey.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {15},
pages = {},
pmid = {37570344},
issn = {2076-2615},
support = {Grant No. 32260331//National Natural Science Foundation of China/ ; },
abstract = {Assessing the trophic niche and interspecific relationships between related species and determining how the species maintain differences in nutritional niches while coexisting in the same area are important topics in ecological research. Therefore, exploring the mechanism of food resource utilization, competition and coexistence among species distributed in the same region is important. In this study, we used fecal samples and metagenome sequencing technology to study the plant feeding habits and coexistence mechanisms of Tibetan macaques (Macaca thibetana) and grey snub-nosed monkeys (Rhinopithecus brelichi) within the same area. In the winter of 2020, we collected a total of 40 fecal samples from Tibetan macaques and grey snub-nosed monkeys; of those, 29 samples were considered valid and were analyzed using DNA metabarcoding. The results showed that in winter, Tibetan macaques consumed plants from 117 families and 184 genera, whereas grey snub-nosed monkeys consumed plants from 109 families and 165 genera. Diversity analysis revealed that there was a significant difference in the food composition of Tibetan macaques and grey snub-nosed monkeys. Tibetan macaques had a broader food niche width than grey snub-nosed monkeys at the family and genus levels. In winter, the food niches of Tibetan macaques and grey snub-nosed monkeys almost entirely overlapped (0.99). Our research provides detailed dietary data for Tibetan macaques and grey snub-nosed monkeys and valuable information that can aid in conservation efforts targeting these species.},
}
@article {pmid37569608,
year = {2023},
author = {Oñate, FP and Chamignon, C and Burz, SD and Lapaque, N and Monnoye, M and Philippe, C and Bredel, M and Chêne, L and Farin, W and Paillarse, JM and Boursier, J and Ratziu, V and Mousset, PY and Doré, J and Gérard, P and Blottière, HM},
title = {Adlercreutzia equolifaciens Is an Anti-Inflammatory Commensal Bacterium with Decreased Abundance in Gut Microbiota of Patients with Metabolic Liver Disease.},
journal = {International journal of molecular sciences},
volume = {24},
number = {15},
pages = {},
pmid = {37569608},
issn = {1422-0067},
support = {MetaGenoPolis ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; FunAMetaGen ANR-15-CE14-0021//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; Mice ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Liver/metabolism ; *Metabolic Diseases/metabolism ; *Liver Neoplasms/metabolism ; Anti-Inflammatory Agents/pharmacology/therapeutic use/metabolism ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD) affects about 20-40% of the adult population in high-income countries and is now a leading indication for liver transplantation and can lead to hepatocellular carcinoma. The link between gut microbiota dysbiosis and NAFLD is now clearly established. Through analyses of the gut microbiota with shotgun metagenomics, we observe that compared to healthy controls, Adlercreutzia equolifaciens is depleted in patients with liver diseases such as NAFLD. Its abundance also decreases as the disease progresses and eventually disappears in the last stages indicating a strong association with disease severity. Moreover, we show that A. equolifaciens possesses anti-inflammatory properties, both in vitro and in vivo in a humanized mouse model of NAFLD. Therefore, our results demonstrate a link between NAFLD and the severity of liver disease and the presence of A. equolifaciens and its anti-inflammatory actions. Counterbalancing dysbiosis with this bacterium may be a promising live biotherapeutic strategy for liver diseases.},
}
@article {pmid37563687,
year = {2023},
author = {Lai, S and Yan, Y and Pu, Y and Lin, S and Qiu, JG and Jiang, BH and Keller, MI and Wang, M and Bork, P and Chen, WH and Zheng, Y and Zhao, XM},
title = {Enterotypes of the human gut mycobiome.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {179},
pmid = {37563687},
issn = {2049-2618},
support = {2020YFA0712403//the National Key Research and Development Program of China/ ; T2225015, 61932008//National Natural Science Foundation of China/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; },
mesh = {Humans ; Aged ; *Mycobiome/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Candida ; Aging ; },
abstract = {BACKGROUND: The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.<br><br>RESULTS: We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.<br><br>CONCLUSIONS: We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.},
}
@article {pmid37563185,
year = {2023},
author = {Xue, Z and Han, Y and Tian, W and Zhang, W},
title = {Metagenome sequencing and 103 microbial genomes from ballast water and sediments.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {536},
pmid = {37563185},
issn = {2052-4463},
mesh = {Archaea/genetics ; Bacteria/genetics ; Genome, Microbial ; *Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {The great threat of microbes carried by ballast water calls for figuring out the species composition of the ballast-tank microbial community, where the dark, cold, and anoxic tank environment might select special taxa. In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea, from four vessels on international voyages. Of these MAGs, 60 were 'near complete' (completeness >90%), 34 were >80% complete, and nine were >75% complete. Phylogenomic analysis revealed that over 70% (n = 74) of these MAGs represented new taxa at different taxonomical levels, including one order, three families, 12 genera, and 58 species. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 69), Bacteroidota (n = 17), and Actinobacteriota (n = 7). These draft genomes provided novel data on species diversity and function in the ballast-tank microbial community, which will facilitate ballast water and sediments management.},
}
@article {pmid37561193,
year = {2023},
author = {Samanta, B and Sharma, S and Budhwar, R},
title = {Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity.},
journal = {Current microbiology},
volume = {80},
number = {10},
pages = {317},
pmid = {37561193},
issn = {1432-0991},
support = {F. No: 2021/0003//Gandhi Institute of Technology and Management/ ; },
mesh = {Caves/microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; Sulfur ; *Bacteria/chemistry/classification/isolation &amp; purification ; },
abstract = {The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.},
}
@article {pmid37556397,
year = {2023},
author = {Hunter, S and Flaten, E and Petersen, C and Gervain, J and Werker, JF and Trainor, LJ and Finlay, BB},
title = {Babies, bugs and brains: How the early microbiome associates with infant brain and behavior development.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0288689},
pmid = {37556397},
issn = {1932-6203},
support = {//CIHR/Canada ; },
mesh = {Humans ; Infant ; Pilot Projects ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria ; Feces/microbiology ; Brain ; },
abstract = {Growing evidence is demonstrating the connection between the microbiota gut-brain axis and neurodevelopment. Microbiota colonization occurs before the maturation of many neural systems and is linked to brain health. Because of this it has been hypothesized that the early microbiome interactions along the gut-brain axis evolved to promote advanced cognitive functions and behaviors. Here, we performed a pilot study with a multidisciplinary approach to test if the microbiota composition of infants is associated with measures of early cognitive development, in particular neural rhythm tracking; language (forward speech) versus non-language (backwards speech) discrimination; and social joint attention. Fecal samples were collected from 56 infants between four and six months of age and sequenced by shotgun metagenomic sequencing. Of these, 44 performed the behavioral Point and Gaze test to measure joint attention. Infants were tested on either language discrimination using functional near-infrared spectroscopy (fNIRS; 25 infants had usable data) or neural rhythm tracking using electroencephalogram (EEG; 15 had usable data). Infants who succeeded at the Point and Gaze test tended to have increased Actinobacteria and reduced Firmicutes at the phylum level; and an increase in Bifidobacterium and Eggerthella along with a reduction in Hungatella and Streptococcus at the genus level. Measurements of neural rhythm tracking associated negatively to the abundance of Bifidobacterium and positively to the abundance of Clostridium and Enterococcus for the bacterial abundances, and associated positively to metabolic pathways that can influence neurodevelopment, including branched chain amino acid biosynthesis and pentose phosphate pathways. No associations were found for the fNIRS language discrimination measurements. Although the tests were underpowered due to the small pilot sample sizes, potential associations were identified between the microbiome and measurements of early cognitive development that are worth exploring further.},
}
@article {pmid37554329,
year = {2023},
author = {Jeong, S and Cho, WK and Jo, Y and Choi, SR and Lee, N and Jeon, K and Park, MJ and Song, W and Lee, KY},
title = {Immune-checkpoint proteins, cytokines, and microbiome impact on patients with cervical insufficiency and preterm birth.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1228647},
pmid = {37554329},
issn = {1664-3224},
mesh = {*Immune Checkpoint Proteins/metabolism ; Humans ; Female ; Pregnancy ; *Microbiota ; *Cytokines/metabolism ; *Premature Birth/diagnosis ; Cerclage, Cervical ; *Cervix Uteri/microbiology ; Prospective Studies ; *Uterine Cervical Incompetence ; },
abstract = {BACKGROUND: Microenvironmental factors, including microbe-induced inflammation and immune-checkpoint proteins that modulate immune cells have been associated with both cervical insufficiency and preterm delivery. These factors are incompletely understood. This study aimed to explore and compare interactions among microbiome and inflammatory factors, such as cytokines and immune-checkpoint proteins, in patients with cervical insufficiency and preterm birth. In particular, factors related to predicting preterm birth were identified and the performance of the combination of these factors was evaluated.<br><br>METHODS: A total of 220 swab samples from 110 pregnant women, prospectively recruited at the High-Risk Maternal Neonatal Intensive Care Center, were collected between February 2020 and March 2021. This study included 63 patients with cervical insufficiency receiving cerclage and 47 control participants. Endo- and exocervical swabs and fluids were collected simultaneously. Shotgun metagenomic sequencing for the microbiome and the measurement of 34 immune-checkpoint proteins and inflammatory cytokines were performed.<br><br>RESULTS: First, we demonstrated that immune-checkpoint proteins, the key immune-regulatory molecules, could be measured in endocervical and exocervical samples. Secondly, we identified significantly different microenvironments in cervical insufficiency and preterm birth, with precise cervical locations, to provide information about practically useful cervical locations in clinical settings. Finally, the presence of Moraxella osloensis (odds ratio = 14.785; P = 0.037) and chemokine CC motif ligand 2 levels higher than 73 pg/mL (odds ratio = 40.049; P = 0.005) in endocervical samples were associated with preterm birth. Combining M. osloensis and chemokine CC motif ligand 2 yielded excellent performance for predicting preterm birth (area under the receiver operating characteristic curve = 0.846, 95% confidence interval = 0.733-0.925).<br><br>CONCLUSION: Multiple relationships between microbiomes, immune-checkpoint proteins, and inflammatory cytokines in the cervical microenvironment were identified. We focus on these factors to aid in the comprehensive understanding and therapeutic modulation of local microbial and immunologic compositions for the management of cervical insufficiency and preterm birth.},
}
@article {pmid37553697,
year = {2023},
author = {Chen, J and Siliceo, SL and Ni, Y and Nielsen, HB and Xu, A and Panagiotou, G},
title = {Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {178},
pmid = {37553697},
issn = {2049-2618},
support = {H2020-MSCA-ITN-2018//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; E-HKU703/20//European Union (EU) - Hong Kong (HK) Research and Innovation Cooperation Co-funding Mechanism/ ; },
mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Biomarkers ; Diet ; Life Style ; },
abstract = {BACKGROUND: A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the significant inter-individual diversity of the gut microbiota between subjects, lifestyle recommendations are expected to have distinct and highly variable impacts to the microbiome structure.<br><br>RESULTS: Here, through a large-scale meta-analysis including 1448 shotgun metagenomics samples obtained longitudinally from 396 individuals during lifestyle studies, we revealed Bacteroides stercoris, Prevotella copri, and Bacteroides vulgatus as biomarkers of microbiota's resistance to structural changes, and aromatic and non-aromatic amino acid biosynthesis as important regulator of microbiome dynamics. We established criteria for distinguishing between significant compositional changes from normal microbiota fluctuation and classified individuals based on their level of response. We further developed a machine learning model for predicting "responders" and "non-responders" independently of the type of intervention with an area under the curve of up to 0.86 in external validation cohorts of different ethnicities.<br><br>CONCLUSIONS: We propose here that microbiome-based stratification is possible for identifying individuals with highly plastic or highly resistant microbial structures. Identifying subjects that will not respond to generalized lifestyle therapeutic interventions targeting the restructuring of gut microbiota is important to ensure that primary end-points of clinical studies are reached. Video Abstract.},
}
@article {pmid37553373,
year = {2023},
author = {Muzeniek, T and Perera, T and Siriwardana, S and Bas, D and Bayram, F and Öruc, M and Becker-Ziaja, B and Perera, I and Weerasena, J and Handunnetti, S and Schwarz, F and Premawansa, G and Premawansa, S and Yapa, W and Nitsche, A and Kohl, C},
title = {Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12859},
pmid = {37553373},
issn = {2045-2322},
mesh = {Animals ; Humans ; *Chiroptera ; Phylogeny ; Virome ; Sri Lanka ; *Coronavirus/genetics ; },
abstract = {Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.},
}
@article {pmid37157029,
year = {2023},
author = {Yoshiba, S and Nakagawa, H and Kuwata, H and Nabuchi, A and Yaso, A and Shirota, T},
title = {Metagenomic analysis of oral plaques and aortic valve tissues reveals oral bacteria associated with aortic stenosis.},
journal = {Clinical oral investigations},
volume = {27},
number = {8},
pages = {4335-4344},
pmid = {37157029},
issn = {1436-3771},
mesh = {Humans ; Aortic Valve/microbiology ; Bacteria/genetics ; Mouth/microbiology ; *Aortic Valve Stenosis/microbiology ; *Microbiota ; },
abstract = {OBJECTIVES: Bacteria derived from the oral cavity enter the bloodstream and cause the onset of various systemic diseases, including heart valve disease. However, information on the oral bacteria involved in aortic stenosis is limited.<br><br>MATERIALS AND METHODS: We comprehensively analyzed the microbiota in aortic valve tissues collected from aortic stenosis patients using metagenomic sequencing and investigated the relationships between the valve microbiota, the oral microbiota, and oral cavity conditions.<br><br>RESULTS: Metagenomic analysis revealed the presence of 629 bacterial species in five oral plaques and 15 aortic valve clinical specimens. Patients were classified into two groups (A and B) according to their aortic valve microbiota composition using principal coordinate analysis. Examination of the oral conditions of the patients showed no difference in the decayed/missing/filled teeth index. Bacteria in group B tend to be associated with severe disease, and the number of bacteria on the dorsum of the tongue and the positive rate of bleeding during probing were significantly higher in this group than in group A. The pathophysiology of aortic stenosis may be related to the presence of oral bacteria such as Streptococcus oralis and Streptococcus sanguinis following bacteremia.<br><br>CONCLUSIONS: Systemic inflammation in severe periodontitis may be driven by the oral microbiota, supporting the indirect (inflammatory) association between oral bacteria and aortic stenosis.<br><br>CLINICAL RELEVANCE: Appropriate oral hygiene management may contribute to the prevention and treatment of aortic stenosis.},
}
@article {pmid36925044,
year = {2023},
author = {Baldanzi, G and Sayols-Baixeras, S and Theorell-Haglöw, J and Dekkers, KF and Hammar, U and Nguyen, D and Lin, YT and Ahmad, S and Holm, JB and Nielsen, HB and Brunkwall, L and Benedict, C and Cedernaes, J and Koskiniemi, S and Phillipson, M and Lind, L and Sundström, J and Bergström, G and Engström, G and Smith, JG and Orho-Melander, M and Ärnlöv, J and Kennedy, B and Lindberg, E and Fall, T},
title = {OSA Is Associated With the Human Gut Microbiota Composition and Functional Potential in the Population-Based Swedish CardioPulmonary bioImage Study.},
journal = {Chest},
volume = {164},
number = {2},
pages = {503-516},
pmid = {36925044},
issn = {1931-3543},
mesh = {Adult ; Animals ; Humans ; *Sleep Apnea, Obstructive ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Sweden/epidemiology ; Hypoxia ; },
abstract = {BACKGROUND: OSA is a common sleep-breathing disorder linked to increased risk of cardiovascular disease. Intermittent upper airway obstruction and hypoxia, hallmarks of OSA, have been shown in animal models to induce substantial changes to the gut microbiota composition, and subsequent transplantation of fecal matter to other animals induced changes in BP and glucose metabolism.<br><br>RESEARCH QUESTION: Does OSA in adults associate with the composition and functional potential of the human gut microbiota?<br><br>STUDY DESIGN AND METHODS: We used respiratory polygraphy data from up to 3,570 individuals 50 to 64 years of age from the population-based Swedish Cardiopulmonary bioimage Study combined with deep shotgun metagenomics of fecal samples to identify cross-sectional associations between three OSA parameters covering apneas and hypopneas, cumulative sleep time in hypoxia, and number of oxygen desaturation events with gut microbiota composition. Data collection about potential confounders was based on questionnaires, onsite anthropometric measurements, plasma metabolomics, and linkage with the Swedish Prescribed Drug Register.<br><br>RESULTS: We found that all three OSA parameters were associated with lower diversity of species in the gut. Furthermore, in multivariable-adjusted analysis, the OSA-related hypoxia parameters were associated with the relative abundance of 128 gut bacterial species, including higher abundance of Blautia obeum and Collinsella aerofaciens. The latter species was also independently associated with increased systolic BP. Furthermore, the cumulative time in hypoxia during sleep was associated with the abundance of genes involved in nine gut microbiota metabolic pathways, including propionate production from lactate. Finally, we observed two heterogeneous sets of plasma metabolites with opposite association with species positively and negatively associated with hypoxia parameters, respectively.<br><br>INTERPRETATION: OSA-related hypoxia, but not the number of apneas/hypopneas, is associated with specific gut microbiota species and functions. Our findings lay the foundation for future research on the gut microbiota-mediated health effects of OSA.},
}
@article {pmid37553333,
year = {2023},
author = {Hessler, T and Huddy, RJ and Sachdeva, R and Lei, S and Harrison, STL and Diamond, S and Banfield, JF},
title = {Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4768},
pmid = {37553333},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {Metagenomics ; Vitamins ; *Microbiota/genetics ; Metagenome/genetics ; *Comamonadaceae ; Thiamine ; },
abstract = {Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax, supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.},
}
@article {pmid37550758,
year = {2023},
author = {Hao, C and Elias, JE and Lee, PKH and Lam, H},
title = {metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {176},
pmid = {37550758},
issn = {2049-2618},
mesh = {Animals ; Mice ; *Tandem Mass Spectrometry ; Workflow ; Proteomics ; *Microbiota/genetics ; Peptides ; },
abstract = {BACKGROUND: The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on accurate identification of the MS/MS spectra to their corresponding short peptides in the digested samples, followed by protein inference and subsequent taxonomic and functional analysis of the detected proteins. These approaches are dependent on the availability of protein sequence databases derived either from sample-specific metagenomic data or from public repositories. Due to the incompleteness and imperfections of these protein sequence databases, and the preponderance of homologous proteins expressed by different bacterial species in the community, this computational process of peptide identification and protein inference is challenging and error-prone, which hinders the comparison of metaproteomes across multiple samples.<br><br>RESULTS: We developed metaSpectraST, an unsupervised and database-independent metaproteomics workflow, which quantitatively profiles and compares metaproteomics samples by clustering experimentally observed MS/MS spectra based on their spectral similarity. We applied metaSpectraST to fecal samples collected from littermates of two different mother mice right after weaning. Quantitative proteome profiles of the microbial communities of different mice were obtained without any peptide-spectrum identification and used to evaluate the overall similarity between samples and highlight any differentiating markers. Compared to the conventional database-dependent metaproteomics analysis, metaSpectraST is more successful in classifying the samples and detecting the subtle microbiome changes of mouse gut microbiomes post-weaning. metaSpectraST could also be used as a tool to select the suitable biological replicates from samples with wide inter-individual variation.<br><br>CONCLUSIONS: metaSpectraST enables rapid profiling of metaproteomic samples quantitatively, without the need for constructing the protein sequence database or identification of the MS/MS spectra. It maximally preserves information contained in the experimental MS/MS spectra by clustering all of them first and thus is able to better profile the complex microbial communities and highlight their functional changes, as compared with conventional approaches.&#xa0;tag the videobyte in this section as ESM4 Video Abstract.},
}
@article {pmid37550707,
year = {2023},
author = {Zhu, XY and Li, Y and Xue, CX and Lidbury, IDEA and Todd, JD and Lea-Smith, DJ and Tian, J and Zhang, XH and Liu, J},
title = {Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {175},
pmid = {37550707},
issn = {2049-2618},
support = {BB/X005968/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Bacteroidetes/genetics/metabolism ; *Ecosystem ; Polysaccharides/metabolism ; Pectins/metabolism ; },
abstract = {BACKGROUND: Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the proportional importance of complex polysaccharides introduced through deposition from the photic surface waters above. In surface waters, Bacteroidetes are keystone taxa for the cycling of various algal-derived polysaccharides and the flux of carbon through the photic zone. However, their role in the hadal microbial loop is almost unknown.<br><br>RESULTS: Here, culture-dependent and culture-independent methods were used to study the potential of Bacteroidetes to catabolize diverse polysaccharides in Mariana Trench waters. Compared to surface waters, the bathypelagic (1000-4000 m) and hadal (6000-10,500 m) waters harbored distinct Bacteroidetes communities, with Mesoflavibacter being enriched at &#x2265; 4000 m and Bacteroides and Provotella being enriched at 10,400-10,500 m. Moreover, these deep-sea communities possessed distinct gene pools encoding for carbohydrate active enzymes (CAZymes), suggesting different polysaccharide sources are utilised in these two zones. Compared to surface counterparts, deep-sea Bacteroidetes showed significant enrichment of CAZyme genes frequently organized into polysaccharide utilization loci (PULs) targeting algal/plant cell wall polysaccharides (i.e., hemicellulose and pectin), that were previously considered an ecological trait associated with terrestrial Bacteroidetes only. Using a hadal Mesoflavibacter isolate (MTRN7), functional validation of this unique genetic potential was demonstrated. MTRN7 could utilize pectic arabinans, typically associated with land plants and phototrophic algae, as the carbon source under simulated deep-sea conditions. Interestingly, a PUL we demonstrate is likely horizontally acquired from coastal/land Bacteroidetes was activated during growth on arabinan and experimentally shown to encode enzymes that hydrolyze arabinan at depth.<br><br>CONCLUSIONS: Our study implies that hadal Bacteroidetes exploit polysaccharides poorly utilized by surface populations via an expanded CAZyme gene pool. We propose that sinking cell wall debris produced in the photic zone can serve as an important carbon source for hadal heterotrophs and play a role in shaping their communities and metabolism. Video Abstract.},
}
@article {pmid37550406,
year = {2023},
author = {Doane, MP and Reed, MB and McKerral, J and Farias Oliveira Lima, L and Morris, M and Goodman, AZ and Johri, S and Papudeshi, B and Dillon, T and Turnlund, AC and Peterson, M and Mora, M and de la Parra Venegas, R and Pillans, R and Rohner, CA and Pierce, SJ and Legaspi, CG and Araujo, G and Ramirez-Macias, D and Edwards, RA and Dinsdale, EA},
title = {Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12747},
pmid = {37550406},
issn = {2045-2322},
mesh = {Animals ; *Sharks/physiology ; Epidermis ; Epidermal Cells ; *Microbiota/genetics ; Metagenome ; },
abstract = {Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos-Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant 'core'. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.},
}
@article {pmid37545858,
year = {2023},
author = {Yuan, X and Xie, L and Shi, Z and Zhou, M},
title = {Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1200157},
pmid = {37545858},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Pneumonia ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Biomarkers ; Lung ; Sensitivity and Specificity ; Metagenomics ; },
abstract = {BACKGROUND: Pneumoconiosis patients have a high prevalence of pulmonary infections, which can complicate diagnosis and treatment. And there is no comprehensive study of the microbiome of patients with pneumoconiosis. The application of metagenomic next-generation sequencing (mNGS) fills the gap to some extent by analyzing the lung microbiota of pneumoconiosis population while achieving accurate diagnosis.<br><br>METHODS: We retrospectively analyzed 44 patients with suspected pneumoconiosis complicated with pulmonary infection between Jan 2020 and Nov 2022. Bronchoalveolar lavage fluid (BALF) specimens from 44 patients were collected and tested using the mNGS technology.<br><br>RESULTS: Among the lung microbiome of pneumoconiosis patients with complicated pulmonary infection (P group), the most frequently detected bacteria and fungi at the genus level were Streptococcus and Aspergillus, at the species level were Streptococcus pneumoniae and Aspergillus flavus, respectively, and the most frequently detected DNA virus was Human gammaherpesvirus 4. There was no significant difference in &#x3b1; diversity between the P group and the non-pneumoconiosis patients complicated with pulmonary infection group (Non-P group) in pulmonary flora, while P< 0.01 for &#x3b2; diversity analysis, and the differential species between the two groups were Mycobacterium colombiense and Fusobacterium nucleatum. In addition, we monitored a high distribution of Malassezia and Pneumocystis in the P group, while herpes virus was detected in the majority of samples.<br><br>CONCLUSIONS: Overall, we not only revealed a comprehensive lung microbiome profile of pneumoconiosis patients, but also compared the differences between their microbiome and that of non-pneumoconiosis complicated with pulmonary infection patients. This provides a good basis for a better understanding of the relationship between pneumoconiosis and microorganisms, and for the search of potential biomarkers.},
}
@article {pmid37533931,
year = {2023},
author = {Zou, Y and Zeng, S and Chen, M and Li, S and Fu, Q and Zhou, S and Zhou, J},
title = {Gut microbiota in children with split-dose bowel preparations revealed by metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1202007},
pmid = {37533931},
issn = {2235-2988},
mesh = {Humans ; Child ; *Cathartics/adverse effects ; *Gastrointestinal Microbiome ; Metagenomics ; Polyethylene Glycols ; Colonoscopy/adverse effects ; },
abstract = {OBJECTIVE: Split-dose polyethylene glycol (PEG) is routinely used for bowel preparation before colonoscopy. This study aimed to investigate the composition of gut microbiota and its functions in pediatric patients undergoing split-dose PEG bowel preparation for colonoscopy to understand the stability and resilience of gut microbiota.<br><br>MATERIAL AND METHODS: From September to December 2021, 19 pediatric patients were enrolled at Shenzhen Children's Hospital and 76 samples (4 time points) were analyzed using metagenomics. Time points included Time_1 (one day before bowel preparation), Time_2 (one day after colonoscopy), Time_3 (two weeks after bowel preparation), and Time_4 (four weeks after bowel preparation).<br><br>RESULT: Alpha diversity comparison at both the species and gene levels showed a decrease in community richness after colonoscopy, with little statistical significance. However, the Shannon diversity index significantly decreased (P<0.05) and gradually returned to pre-preparation levels at two weeks after bowel preparation. The genus level analysis showed six genera (Eubacterium, Escherichia, Intertinibacter, Veillonella, Ruminococcaceae unclassified, and Coprobacillus) significantly different across the four time periods. Additionally, at the species level, the abundance of Escherichia coli, Bacteroides fragilis, and Veillonella parvula significantly increased at one day after colonoscopy before gradually decreasing at two weeks after bowel preparation. In contrast, the abundance of Intertinibacter bartlettii decreased at one day after colonoscopy but then recovered at two weeks after bowel preparation, reaching the preoperative level at four weeks after bowel preparation. Furthermore, five functional pathways (base excision repair, biosynthesis of ansamycins, biosynthesis of siderophore group nonribosomal peptide, flavonoid biosynthesis, and biosynthesis of type II polyketide products) were significantly different across the four time periods, with recovery at two weeks after bowel preparation and reaching preoperative levels at four weeks after bowel preparation.<br><br>CONCLUSIONS: Gut microbiota at the genus level, species level, and functional pathways are impacted in pediatric patients undergoing split-dose PEG bowel preparation and colonoscopy, with recovery two weeks following bowel preparation. However, the phylum level was not impacted. Modifications in gut microbiota composition and function may be investigated in future studies of bowel preparation. This study highlights the stability and resilience of gut microbiota among pediatric patients during bowel preparation.},
}
@article {pmid37478472,
year = {2023},
author = {Ke, Y and Sun, W and Chen, X and Zhu, Y and Guo, X and Yan, W and Xie, S},
title = {Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {31},
pages = {11430-11441},
doi = {10.1021/acs.est.3c01980},
pmid = {37478472},
issn = {1520-5851},
mesh = {Anti-Bacterial Agents/pharmacology ; Metagenome ; *Drinking Water ; Genes, Bacterial ; *Microbiota ; Biofilms ; },
abstract = {Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.},
}
@article {pmid37462611,
year = {2023},
author = {Hou, R and Zhang, S and Huang, Q and Lin, L and Li, H and Li, J and Liu, S and Sun, C and Xu, X},
title = {Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {31},
pages = {11476-11488},
doi = {10.1021/acs.est.3c03595},
pmid = {37462611},
issn = {1520-5851},
mesh = {Animals ; *Carps ; *Gastrointestinal Microbiome ; Plastics ; Estrone ; *Environmental Pollutants ; },
abstract = {Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.},
}
@article {pmid37301103,
year = {2023},
author = {Dou, L and Liu, C and Chen, X and Yang, Z and Hu, G and Zhang, M and Sun, L and Su, L and Zhao, L and Jin, Y},
title = {Supplemental Clostridium butyricum modulates skeletal muscle development and meat quality by shaping the gut microbiota of lambs.},
journal = {Meat science},
volume = {204},
number = {},
pages = {109235},
doi = {10.1016/j.meatsci.2023.109235},
pmid = {37301103},
issn = {1873-4138},
mesh = {Female ; Sheep ; Animals ; *Clostridium butyricum/physiology ; *Gastrointestinal Microbiome ; Dietary Supplements/analysis ; Meat/analysis ; Muscle Development ; Animal Feed/analysis ; Muscle, Skeletal/metabolism ; },
abstract = {This study evaluated the contributions of Clostridium butyricum on skeletal muscle development, gastrointestinal flora and meat quality of lambs. Eighteen Dorper (♂) × Small Tailed Han sheep (♀) crossed ewe lambs of similar weight (27.43 ± 1.94 kg; age, 88 ± 5 days) were divided into two dietary treatments. The control group was fed the basal diet (C group), and the probiotic group was supplemented with C. butyricum on the basis of the C group (2.5 × 10[8] cfu/g, 5 g/day/lamb; P group) for 90 d. The results showed that dietary C. butyricum elevated growth performance, muscle mass, muscle fiber diameter and cross-sectional area, and decreased the shear force value of meat (P < 0.05). Moreover, C. butyricum supplementation accelerated protein synthesis by regulating the gene expression of IGF-1/Akt/mTOR pathway. We identified 54 differentially expressed proteins that regulated skeletal muscle development through different mechanisms by quantitative proteomics. These proteins were associated with ubiquitin-protease, apoptosis, muscle structure, energy metabolism, heat shock, and oxidative stress. The metagenomics sequencing results showed that Petrimonas at the genus level and Prevotella brevis at the species level in the rumen, while Lachnoclostridium, Alloprevotella and Prevotella at the genus level in the feces, were significantly enriched in the P group. Also, butyric acid and valeric acid levels were elevated in both rumen and feces of the P group. Overall, our results support the idea that C. butyricum could change gastrointestinal flora, and affect skeletal muscle development and meat quality of lambs by modulating gut-muscle axis.},
}
@article {pmid37528457,
year = {2023},
author = {Hoedt, EC and Hueston, CM and Cash, N and Bongers, RS and Keane, JM and van Limpt, K and Ben Amor, K and Knol, J and MacSharry, J and van Sinderen, D},
title = {A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {168},
pmid = {37528457},
issn = {2049-2618},
support = {SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Humans ; Infant ; Animals ; Pregnancy ; Mice ; Female ; *Synbiotics ; *Gastrointestinal Microbiome ; Bifidobacterium ; Anti-Bacterial Agents/pharmacology ; Cesarean Section ; Clindamycin ; Oligosaccharides ; },
abstract = {BACKGROUND: Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these studies are rarely prescribed to infants. Therefore, an early life model was developed in which the murine gastrointestinal microbiota was severely disrupted by clindamycin treatment.<br><br>RESULTS: In this mouse model, we investigated the extent supplementation with a synbiotic mixture of prebiotics, being scGOS/lcFOS with the human milk oligosaccharide 2'-Fucosyllactose (2'-FL), in combination with or without single strain or mix of "infant type" bifidobacteria, can rescue an antibiotic-compromised microbiota. Shotgun metagenomic sequencing showed that the microbiota was severely disrupted by the clindamycin challenge. No recovery was observed 3&#xa0;weeks post-challenge in the scGOS/lcFOS/2'FL group, while the group that received the synbiotic treatment of scGOS/lcFOS/2'-FL with Bifidobacterium breve NRBB01 showed partial recovery. Strikingly in the scGOS/lcFOS/2'-FL group receiving the mixture of bifidobacteria resulted in a recovery of the microbiota disruption. Histological analyses showed that the clindamycin-treated animals at the end of the experiment still suffered from mild oedema and villi/colonic crypt irregularities which was ameliorated by the synbiotic intervention.<br><br>CONCLUSION: Our study demonstrates that supplementation of synbiotic mixture of scGOS/lcFOS/2'-FL in combination with a specific mix of infant-type bifidobacterial strains is able to partially revive an antibiotic-perturbed gastrointestinal microbiota. Video Abstract.},
}
@article {pmid37525141,
year = {2023},
author = {Oliveros, A and Terraube, J and Levengood, AL and Powell, D and Frère, CH},
title = {Influence of scat ageing on the gut microbiome: how old is too old?.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {427},
pmid = {37525141},
issn = {1471-2164},
mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Microbiota ; Animals, Wild ; *Phascolarctidae ; },
abstract = {BACKGROUND: The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).<br><br>RESULTS: We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.<br><br>CONCLUSION: We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.},
}
@article {pmid37392210,
year = {2023},
author = {Coe, GL and Krout, IN and Munro-Ehrlich, M and Beamish, CR and Vorojeikina, D and Colman, DR and Boyd, EJ and Walk, ST and Rand, MD},
title = {Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice.},
journal = {Archives of toxicology},
volume = {97},
number = {9},
pages = {2399-2418},
pmid = {37392210},
issn = {1432-0738},
support = {ES030940/ES/NIEHS NIH HHS/United States ; ES001247/ES/NIEHS NIH HHS/United States ; T32 207026/ES/NIEHS NIH HHS/United States ; ES030940/ES/NIEHS NIH HHS/United States ; ES001247/ES/NIEHS NIH HHS/United States ; T32 207026/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Methylmercury Compounds/toxicity/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Kinetics ; Demethylation ; },
abstract = {The risk of methylmercury (MeHg) toxicity following ingestion of contaminated foodstuffs (e.g., fish) is directly related to the kinetics of MeHg elimination among individuals. Yet, the factors driving the wide range of inter-individual variability in MeHg elimination within a population are poorly understood. Here, we investigated the relationship between MeHg elimination, gut microbiome demethylation activity, and gut microbiome composition using a coordinated human clinical trial and gnotobiotic mouse modeling approach together with metagenomic sequence analysis. We first observed MeHg elimination half-lives (t1/2) ranging from 28 to 90 days across 27 volunteers. Subsequently, we found that ingestion of a prebiotic induced changes in the gut microbiome and mixed effects (increased, decrease, and no effect) on elimination in these same individuals. Nonetheless, elimination rates were found to correlate with MeHg demethylation activity in cultured stool samples. In mice, attempts to remove the microbiome via generation of germ-free (GF) animals or through antibiotic (Abx) treatment both diminished MeHg demethylation to a similar extent. While both conditions substantially slowed elimination, Abx treatment resulted in significantly slower elimination than the GF condition, indicating an additional role for host-derived factors in supporting elimination. Human fecal microbiomes transplanted to GF mice restored elimination rates to that seen in control mice. Metagenomic sequence analysis of human fecal DNA did not identify genes encoding proteins typically involved in demethylation (e.g., merB, organomercury lyase). However, the abundance of several anaerobic taxa, notably Alistipes onderdonkii, were positively correlated with MeHg elimination. Surprisingly, mono-colonization of GF free mice with A. onderdonkii did not restore MeHg elimination to control levels. Collectively, our findings indicate the human gut microbiome uses a non-conventional pathway of demethylation to increase MeHg elimination that relies on yet to be resolved functions encoded by the gut microbes and the hostClinical Trial NCT04060212, prospectively registered 10/1/2019.},
}
@article {pmid37365713,
year = {2023},
author = {Zhu, J and Liu, S and Zhang, H and Zhao, W and Ding, J and Dai, R and Xu, K and He, C and Liu, J and Yang, L and Meng, H},
title = {Dynamic distribution of gut microbiota during Alzheimer's disease progression in a mice model.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {131},
number = {9},
pages = {480-490},
doi = {10.1111/apm.13339},
pmid = {37365713},
issn = {1600-0463},
mesh = {Humans ; Mice ; Animals ; *Alzheimer Disease/pathology ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases ; Mice, Transgenic ; *Microbiota ; Disease Models, Animal ; },
abstract = {Alzheimer's disease (AD) is an irreversible neurodegenerative disease that affects more than 44 million people worldwide. The pathogenic mechanisms of AD still remain unclear. Currently, there are numerous studies investigating the microbiota-gut-brain axis in humans and rodents indicated that gut microbiota played a role in neurodegenerative diseases, including AD. However, the underlying relationship between the progress of AD disease and the dynamic distribution of gut microbiota is not well understood. In the present study, APP[swe] /PS1[ΔE9] transgenic mice of different ages and sex were employed. After the evaluation of the AD mice model, gut metagenomic sequencing was conducted to reveal gut microbiota, moreover, probiotics intervention was treated in the AD mice. The results showed that (1) AD mice had reduced microbiota richness and a changed gut microbiota composition, and AD mice gut microbiota richness was correlated with cognitive performance. We have also found some potential AD-related microbes, for example, in AD-prone mice, the genus Mucispirillum was strongly associated with immune inflammation. (2) Probiotics intervention improved cognitive performance and changed gut microbiota richness and composition of AD mice. We revealed the dynamics distribution of gut microbiota and the effect of probiotics on AD in a mice model, which provides an important reference for the pathogenesis of AD, intestinal microbial markers associated with AD, and AD probiotic intervention.},
}
@article {pmid37269417,
year = {2023},
author = {Jiao, G and Huang, Y and Dai, H and Gou, H and Li, Z and Shi, H and Yang, J and Ni, S},
title = {Responses of rhizosphere microbial community structure and metabolic function to heavy metal coinhibition.},
journal = {Environmental geochemistry and health},
volume = {45},
number = {8},
pages = {6177-6198},
pmid = {37269417},
issn = {1573-2983},
support = {41977289//National Natural Science Foundation of China/ ; 2021YFQ0066//Sichuan Province Science and Technology Support Program/ ; 2020ZF11405//Everest Scientific Research Program/ ; SKLGP2021Z002//State Key Laboratory of Geological Disaster Prevention and Geological Environmental Protection Independent Project/ ; SKLGP2021Z002//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; },
mesh = {Humans ; Cadmium/analysis ; Rhizosphere ; *Metals, Heavy/analysis ; *Microbiota ; Soil/chemistry ; Zea mays/metabolism ; *Soil Pollutants/analysis ; Soil Microbiology ; },
abstract = {Metal mineral mining results in releases of large amounts of heavy metals into the environment, and it is necessary to better understand the response of rhizosphere microbial communities to simultaneous stress from multiple heavy metals (HMs), which directly impacts plant growth and human health. In this study, by adding different concentrations of cadmium (Cd) to a soil with high background concentrations of vanadium (V) and chromium (Cr), the growth of maize during the jointing stage was explored under limiting conditions. High-throughput sequencing was used to explore the response and survival strategies of rhizosphere soil microbial communities to complex HM stress. The results showed that complex HMs inhibited the growth of maize at the jointing stage, and the diversity and abundance of maize rhizosphere soil microorganisms were significantly different at different metal enrichment levels. In addition, according to the different stress levels, the maize rhizosphere attracted many tolerant colonizing bacteria, and cooccurrence network analysis showed that these bacteria interacted very closely. The effects of residual heavy metals on beneficial microorganisms (such as Xanthomonas, Sphingomonas, and lysozyme) were significantly stronger than those of bioavailable metals and soil physical and chemical properties. PICRUSt analysis revealed that the different forms of V and Cd had significantly greater effects on microbial metabolic pathways than all forms of Cr. Cr mainly affected the two major metabolic pathways: microbial cell growth and division and environmental information transmission. In addition, significant differences in rhizosphere microbial metabolism under different concentrations were found, and this can serve as a reference for subsequent metagenomic analysis. This study is helpful for exploring the threshold for the growth of crops in toxic HM soils in mining areas and achieving further biological remediation.},
}
@article {pmid36826808,
year = {2023},
author = {Tan, TC and Chandrasekaran, L and Leung, YY and Purbojati, R and Pettersson, S and Low, AHL},
title = {Gut microbiome profiling in systemic sclerosis: a metagenomic approach.},
journal = {Clinical and experimental rheumatology},
volume = {41},
number = {8},
pages = {1578-1588},
doi = {10.55563/clinexprheumatol/jof7nx},
pmid = {36826808},
issn = {0392-856X},
mesh = {Adult ; Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Feces ; *Scleroderma, Systemic/diagnosis/microbiology ; Bacteria/genetics ; *Scleroderma, Limited ; },
abstract = {OBJECTIVES: The early gastrointestinal (GI) manifestation of systemic sclerosis (SSc) suggests a possible GI microbiota engagement in the pathophysiology and/or progression of SSc. Previous studies have revealed dysbiosis among Caucasian SSc patients. This study extends these findings to Asian SSc patients.<br><br>METHODS: Adult SSc patients, stratified according to 1) on immunosuppressive (On-IS) drugs or 2) no immunosuppressive drugs (No-IS), and age-and-sex-matched healthy controls (HC) were recruited. Metagenomic sequencing of stool DNA was compared between SSc patients and HC, and between SSc (On-IS) and (No-IS) patients. Alpha and beta-diversity, taxonomic and functional profiling were evaluated.<br><br>RESULTS: Twenty-three female SSc patients (12 On-IS; 11 No-IS; 5 diffuse and 18 limited SSc subtype) and 19 female HC, with median age of 54 years and 56 years, respectively, were recruited. Median SSc disease duration was 3.3 years. Alpha diversity was significantly higher in SSc versus HC (p=0.014) and in SSc (No-IS) versus HC (p=0.006). There was no significant difference in beta diversity between SSc and HC (p=0.307). At the phyla level, there were significantly increased abundance of Firmicutes and Actinobacteria in SSc versus HC, and reduced abundance of Bacteroidetes (all p<0.001). At the species level, there were significantly increased abundance of several Lactobacillus, Bifidobacterium, and Coprococcus species in SSc, and increased abundance of Odoribacter, Bacteroides and Prevotella species in HC. KEGG pathway analysis demonstrated distinct differences between SSc versus HC, and between SSc (No-IS) and SSc (On-IS).<br><br>CONCLUSIONS: Using metagenomic sequencing, our study further underlines distinct alterations in microbiota profiling among Asian SSc patients.},
}
@article {pmid37521121,
year = {2023},
author = {Khatiebi, S and Kiprotich, K and Onyando, Z and Wekesa, C and Chi, CN and Mulambalah, C and Okoth, P},
title = {Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution.},
journal = {BioMed research international},
volume = {2023},
number = {},
pages = {3724531},
pmid = {37521121},
issn = {2314-6141},
mesh = {Animals ; Humans ; Lakes ; Ecosystem ; Kenya ; Plastics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; *Microbiota/genetics ; Water ; Pharmaceutical Preparations ; },
abstract = {Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.},
}
@article {pmid37517495,
year = {2023},
author = {Veerasamy, V and Jagannathan, UM and Arakkala, SD and Shafee, WA and Kaliannan, T},
title = {Exploring the bacterial genetic diversity and community structure of crude oil contaminated soils using microbiomics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {116779},
doi = {10.1016/j.envres.2023.116779},
pmid = {37517495},
issn = {1096-0953},
abstract = {The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.},
}
@article {pmid36871189,
year = {2023},
author = {Peterson, BD and Krabbenhoft, DP and McMahon, KD and Ogorek, JM and Tate, MT and Orem, WH and Poulin, BA},
title = {Environmental formation of methylmercury is controlled by synergy of inorganic mercury bioavailability and microbial mercury-methylation capacity.},
journal = {Environmental microbiology},
volume = {25},
number = {8},
pages = {1409-1423},
doi = {10.1111/1462-2920.16364},
pmid = {36871189},
issn = {1462-2920},
support = {CBET-1935173//U.S. National Science Foundation/ ; //U.S. Geological Survey Priority Ecosystems Science Program/ ; //U.S. National Science Foundation - Graduate Research Fellowships Program/ ; },
mesh = {*Methylmercury Compounds ; *Mercury ; Methylation ; Biological Availability ; *Microbiota ; *Water Pollutants, Chemical/analysis ; },
abstract = {Methylmercury (MeHg) production is controlled by the bioavailability of inorganic divalent mercury (Hg(II)i) and Hg-methylation capacity of the microbial community (conferred by the hgcAB gene cluster). However, the relative importance of these factors and their interaction in the environment remain poorly understood. Here, metagenomic sequencing and a full-factorial MeHg formation experiment were conducted across a wetland sulfate gradient with different microbial communities and pore water chemistries. From this experiment, the relative importance of each factor on MeHg formation was isolated. Hg(II)i bioavailability correlated with the dissolved organic matter composition, while the microbial Hg-methylation capacity correlated with the abundance of hgcA genes. MeHg formation responded synergistically to both factors. Notably, hgcA sequences were from diverse taxonomic groups, none of which contained genes for dissimilatory sulfate reduction. This work expands our understanding of the geochemical and microbial constraints on MeHg formation in situ and provides an experimental framework for further mechanistic studies.},
}
@article {pmid37515113,
year = {2023},
author = {Thijssen, M and Khamisipour, G and Maleki, M and Devos, T and Li, G and Van Ranst, M and Matthijnssens, J and Pourkarim, MR},
title = {Characterization of the Human Blood Virome in Iranian Multiple Transfused Patients.},
journal = {Viruses},
volume = {15},
number = {7},
pages = {},
pmid = {37515113},
issn = {1999-4915},
mesh = {Humans ; Iran/epidemiology ; Virome ; *Viruses/genetics ; *Anelloviridae/genetics ; Metagenome ; Metagenomics/methods ; },
abstract = {Blood transfusion safety is an essential element of public health. Current blood screening strategies rely on targeted techniques that could miss unknown or unexpected pathogens. Recent studies have demonstrated the presence of a viral community (virobiota/virome) in the blood of healthy individuals. Here, we characterized the blood virome in patients frequently exposed to blood transfusion by using Illumina metagenomic sequencing. The virome of these patients was compared to viruses present in healthy blood donors. A total number of 155 beta-thalassemia, 149 hemodialysis, and 100 healthy blood donors were pooled with five samples per pool. Members of the Anelloviridae and Flaviviridae family were most frequently observed. Interestingly, samples of healthy blood donors harbored traces of potentially pathogenic viruses, including adeno-, rota-, and Merkel cell polyomavirus. Viruses of the Anelloviridae family were most abundant in the blood of hemodialysis patients and displayed a higher anellovirus richness. Pegiviruses (Flaviviridae) were only observed in patient populations. An overall trend of higher eukaryotic read abundance in both patient groups was observed. This might be associated with increased exposure through blood transfusion. Overall, the findings in this study demonstrated the presence of various viruses in the blood of Iranian multiple-transfused patients and healthy blood donors.},
}
@article {pmid37512841,
year = {2023},
author = {Santiago, BCF and de Souza, ID and Cavalcante, JVF and Morais, DAA and da Silva, MB and Pasquali, MAB and Dalmolin, RJS},
title = {Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512841},
issn = {2076-2607},
support = {312305/2021-4//National Council for Scientific and Technological Development/ ; 302949/2020-8//National Council for Scientific and Technological Development/ ; xxx//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; xxxx//Propesq UFRN/ ; xxx//APC - UFCG/ ; },
abstract = {The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about microbial communities' taxonomic and functional features in different water layer depths. Here, we performed a metagenomic analysis of 76 publicly available samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer-SRF, deep chlorophyll maximum layer-DCM, and mesopelagic zone-MES). The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in most samples, and the MES layer presents the highest proportion of archaea among all samples. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.},
}
@article {pmid37436481,
year = {2023},
author = {Xing, Y and Bian, C and Xue, H and Song, Y and Men, W and Hou, W and Yang, Y and Cai, Q and Xu, L},
title = {The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {17},
pages = {5555-5567},
pmid = {37436481},
issn = {1432-0614},
support = {L201942//019 Liaoning Provincial Department of Education Scientific Research Project/ ; XLYC2002004//Liaoning Revitalization Talents Program/ ; 2020-MS-224//Natural Science Foundation of Liaoning Province/ ; },
mesh = {*Pulsatilla ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota ; Bacteria/genetics ; Soil/chemistry ; *Plants, Medicinal ; },
abstract = {The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.},
}
@article {pmid37417976,
year = {2023},
author = {Santos-Pereira, C and Sousa, J and Costa, &#xc2;MA and Santos, AO and Rito, T and Soares, P and Franco-Duarte, R and Silvério, SC and Rodrigues, LR},
title = {Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {17},
pages = {5379-5401},
pmid = {37417976},
issn = {1432-0614},
support = {UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; POCI-01-0145-FEDER-029773//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BII-BIO/5554/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CPCA/A0/408464/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UMINHO/BID/2021/12//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.11695.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {*Composting ; Metagenomics ; Lignin/metabolism ; Carbohydrates ; *Microbiota ; Bacteria/metabolism ; *Cellulases/metabolism ; },
abstract = {The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.},
}
@article {pmid36093695,
year = {2023},
author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Sonoda, T and Iwasaki, M and Kandaswamy, RS and Senthilkumar, R and Preethy, S and Abraham, SJK},
title = {Benefits of Gut Microbiota Reconstitution by Beta 1,3-1,6 Glucans in Subjects with Autism Spectrum Disorder and Other Neurodegenerative Diseases.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {94},
number = {s1},
pages = {S241-S252},
doi = {10.3233/JAD-220388},
pmid = {36093695},
issn = {1875-8908},
mesh = {Humans ; *Gastrointestinal Microbiome ; alpha-Synuclein ; Glucans ; *Autism Spectrum Disorder/therapy/microbiology ; *Neurodegenerative Diseases/therapy ; },
abstract = {BACKGROUND: Aureobasidium pullulans (black yeast) AFO-202 strain-produced beta glucan, Nichi Glucan, has been shown to improve the behavior and sleep pattern along with an increase in α-synuclein and melatonin in children with autism spectrum disorder (ASD).<br><br>OBJECTIVE: In this randomized pilot clinical study, we have evaluated the gut microbiota of subjects with ASD after consumption of Nichi Glucan.<br><br>METHODS: Eighteen subjects with ASD were randomly allocated: six subjects in the control group (Group 1): conventional treatment comprising remedial behavioral therapies and L-carnosine 500&#x200a;mg per day, and 12 subjects (Group 2) underwent supplementation with Nichi Glucan 0.5&#x200a;g twice daily along with the conventional treatment for 90 days.<br><br>RESULTS: Whole genome metagenome (WGM) sequencing of the stool samples at baseline and after intervention showed that among genera of relevance, the abundance of Enterobacteriaceae was decreased almost to zero in Group 2 after intervention, whereas it increased from 0.36% to 0.85% in Group 1. The abundance of Bacteroides increased in Group 1, whereas it decreased in Group 2. The abundance of Prevotella increased while the abundance of Lactobacillus decreased in both Group 1 and Group 2. Among species, a decrease was seen in Escherichia coli, Akkermansia muciniphila CAG:154, Blautia spp., Coprobacillus sp., and Clostridium bolteae CAG:59, with an increase of Faecalibacterium prausnitzii and Prevotella copri, which are both beneficial.<br><br>CONCLUSION: AFO-202 beta 1,3-1,6 glucan, in addition to balancing the gut microbiome in children with ASD and its role in effective control of curli-producing Enterobacteriaceae that leads to &#x3b1;-synuclein misfolding and accumulation, may have a prophylactic role in Parkinson's and Alzheimer's diseases as well.},
}
@article {pmid37511184,
year = {2023},
author = {Boulangé, CL and Pedersen, HK and Martin, FP and Siegwald, L and Pallejà Caro, A and Eklund, AC and Jia, W and Zhang, H and Berger, B and Sprenger, N and Heine, RG and Cinnamon Study Investigator Group, },
title = {An Extensively Hydrolyzed Formula Supplemented with Two Human Milk Oligosaccharides Modifies the Fecal Microbiome and Metabolome in Infants with Cow's Milk Protein Allergy.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511184},
issn = {1422-0067},
mesh = {Child ; Female ; Animals ; Cattle ; Humans ; Infant ; Child, Preschool ; *Milk Hypersensitivity ; Milk, Human ; Oligosaccharides ; Dietary Supplements ; *Gastrointestinal Microbiome ; Metabolome ; Infant Formula/chemistry ; },
abstract = {Cow's milk protein allergy (CMPA) is a prevalent food allergy among infants and young children. We conducted a randomized, multicenter intervention study involving 194 non-breastfed infants with CMPA until 12 months of age (clinical trial registration: NCT03085134). One exploratory objective was to assess the effects of a whey-based extensively hydrolyzed formula (EHF) supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT) on the fecal microbiome and metabolome in this population. Thus, fecal samples were collected at baseline, 1 and 3 months from enrollment, as well as at 12 months of age. Human milk oligosaccharides (HMO) supplementation led to the enrichment of bifidobacteria in the gut microbiome and delayed the shift of the microbiome composition toward an adult-like pattern. We identified specific HMO-mediated changes in fecal amino acid degradation and bile acid conjugation, particularly in infants commencing the HMO-supplemented formula before the age of three months. Thus, HMO supplementation partially corrected the dysbiosis commonly observed in infants with CMPA. Further investigation is necessary to determine the clinical significance of these findings in terms of a reduced incidence of respiratory infections and other potential health benefits.},
}
@article {pmid37510347,
year = {2023},
author = {Aragão, CF and da Silva, SP and do Nascimento, BLS and da Silva, FS and Nunes Neto, JP and Pinheiro, VCS and Cruz, ACR},
title = {Shotgun Metagenomic Sequencing Reveals Virome Composition of Mosquitoes from a Transition Ecosystem of North-Northeast Brazil.},
journal = {Genes},
volume = {14},
number = {7},
pages = {},
pmid = {37510347},
issn = {2073-4425},
mesh = {Animals ; Humans ; Brazil ; Ecosystem ; Virome ; *Culex ; *Aedes ; *Viruses ; *RNA Viruses ; },
abstract = {A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil.},
}
@article {pmid37508354,
year = {2023},
author = {Machuca-Sepúlveda, J and Miranda, J and Lefin, N and Pedroso, A and Beltrán, JF and Farias, JG},
title = {Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508354},
issn = {2079-7737},
support = {2020/06982-3//Universidad de La Frontera/ ; },
abstract = {Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.},
}
@article {pmid37507809,
year = {2023},
author = {Fredriksen, S and de Warle, S and van Baarlen, P and Boekhorst, J and Wells, JM},
title = {Resistome expansion in disease-associated human gut microbiomes.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {166},
pmid = {37507809},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; },
abstract = {BACKGROUND: The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.<br><br>RESULTS: The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.<br><br>CONCLUSIONS: Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.},
}
@article {pmid37501202,
year = {2023},
author = {Anzà, S and Schneider, D and Daniel, R and Heistermann, M and Sangmaneedet, S and Ostner, J and Schülke, O},
title = {The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {165},
pmid = {37501202},
issn = {2049-2618},
support = {SCHU 1554/6-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Female ; Animals ; Pregnancy ; Humans ; Glucocorticoids ; *Gastrointestinal Microbiome/physiology ; Cross-Sectional Studies ; Primates ; Bacteria/genetics ; *Prenatal Exposure Delayed Effects/microbiology ; },
abstract = {BACKGROUND: During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored.<br><br>RESULTS: In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age.<br><br>CONCLUSIONS: In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.},
}
@article {pmid37496083,
year = {2023},
author = {Liang, X and Zhang, Z and Wang, H and Lu, X and Li, W and Lu, H and Roy, A and Shen, X and Irwin, DM and Shen, Y},
title = {Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {163},
pmid = {37496083},
issn = {2049-2618},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Influenza A Virus, H9N2 Subtype/genetics ; Chickens/microbiology ; *Microbiota ; },
abstract = {BACKGROUND: Antibiotics are widely used for prophylactic therapy and for improving the growth performance of chicken. The problem of bacterial drug resistance caused by antibiotic abuse has previously attracted extensive attention; however, the influence of early-day use of prophylactic antibiotics on the gut microflora and on the disease resistance ability in chicks has not been explored. Here, we comprehensively evaluate the growth performance, gut microbial dynamics, level of antibiotic resistance genes (ARGs) in the gut microbial community, and resistance to H9N2 avian influenza virus (AIV) in chickens following long-term and short-term early-day prophylactic antibiotic treatment.<br><br>RESULTS: Unexpectedly, long-term prophylactic enrofloxacin treatment slowed the growth rate of chickens, whereas short-term antibiotics treatments were found to increase the growth rate, but these changes were not statistically significant. Strikingly, expansions of Escherichia-Shigella populations were observed in early-life prophylactic antibiotics-treated groups of chickens, which is in contrast to the general perception that antibiotics should control their pathogenicity in chicks. The gut microbiota composition of chickens treated long term with antibiotics or received early-day antibiotics treatment tend to be more dramatically disturbed compared to the gut microbiome of chickens treated with antibiotics for a short term at a later date, especially after H9N2 AIV infection.<br><br>CONCLUSIONS: Our data provide evidence that early-day and long-term antibiotic treatments have a more adverse effect on the intestinal microbiome of chickens, compared to short-term late age antibiotic treatment. Furthermore, our metagenomic data reveal that both long-term and short-term antibiotic treatment increase the relative abundance of ARGs. Our findings highlight the adverse effects of prophylactic antibiotic treatment and provide a theoretical basis for the cautious administration of antibiotics in food-producing animal management. Video Abstract.},
}
@article {pmid37494472,
year = {2023},
author = {Thompson, KN and Bonham, KS and Ilott, NE and Britton, GJ and Colmenero, P and Bullers, SJ and McIver, LJ and Ma, S and Nguyen, LH and Filer, A and Brough, I and Pearson, C and Moussa, C and Kumar, V and Lam, LH and Jackson, MA and Pawluk, A and , and Kiriakidis, S and Taylor, PC and Wedderburn, LR and Marsden, B and Young, SP and Littman, DR and Faith, JJ and Pratt, AG and Bowness, P and Raza, K and Powrie, F and Huttenhower, C and , },
title = {Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes.},
journal = {Science translational medicine},
volume = {15},
number = {706},
pages = {eabn4722},
doi = {10.1126/scitranslmed.abn4722},
pmid = {37494472},
issn = {1946-6242},
support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 21226/VAC_/Versus Arthritis/United Kingdom ; 22072/VAC_/Versus Arthritis/United Kingdom ; /DH_/Department of Health/United Kingdom ; 21593/VAC_/Versus Arthritis/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid ; Inflammation ; *Microbiota ; Phenotype ; Metabolic Networks and Pathways ; },
abstract = {Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.},
}
@article {pmid37494371,
year = {2023},
author = {Xie, M and Tsai, CY and McAdams, ZL and Oo, M and Hansen, M and Dougher, M and Sansano, A and Watson, A and LoMauro, K and Antilus-Sainte, R and Ericsson, A and Dartois, V and Gengenbacher, M},
title = {Wild mouse gut microbiota limits initial tuberculosis infection in BALB/c mice.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288290},
pmid = {37494371},
issn = {1932-6203},
support = {U19 AI111143/AI/NIAID NIH HHS/United States ; U19 AI162568/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred BALB C ; *Tuberculosis ; *Latent Tuberculosis/pathology ; Lung/pathology ; Dysbiosis/pathology ; },
abstract = {Mouse models are critical tools in tuberculosis (TB) research. Recent studies have demonstrated that the wild mouse gut microbiota promotes host fitness and improves disease resistance. Here we examine whether the wild mouse gut microbiota alters the immunopathology of TB in BALB/c mice. Conventional BALB/c mice (LabC) and mice born to germ-free BALB/c mothers reconstituted with the wild mouse gut microbiota (WildR) were used in our studies. WildR mice controlled initial TB infection better than LabC mice. The microbial gut communities of LabC mice and WildR mice had similar richness but significantly different composition prior to infection. TB reduced the gut community richness in both cohorts while differences in community composition remained indicating a general TB-induced dysbiosis. The wild mouse gut microbiota did not alter the typical lung histopathology of TB in the BALB/c model that includes unstructured immune cell infiltrates with infected foamy macrophages invading alveolar spaces. Animals of both cohorts mounted robust T cell responses in lungs and spleen with lower absolute counts of CD4 and CD8 T cells in lungs of WildR mice during acute infection, corresponding with observed differences in pathogen load. In summary, LabC mice and WildR mice showed largely overlapping TB immunopathology and pathogen kinetics, with WildR mice controlling early acute infection better than LabC mice.},
}
@article {pmid37493648,
year = {2023},
author = {Breusing, C and Xiao, Y and Russell, SL and Corbett-Detig, RB and Li, S and Sun, J and Chen, C and Lan, Y and Qian, PY and Beinart, RA},
title = {Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028423},
doi = {10.1128/msystems.00284-23},
pmid = {37493648},
issn = {2379-5077},
abstract = {The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with little exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria gastropod symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that occupy contrasting ecological niches. IMPORTANCE Beneficial relationships between animals and microbial organisms (symbionts) are ubiquitous in nature. In the ocean, microbial symbionts are typically acquired from the environment and their composition across geographic locations is often shaped by adaptation to local habitat conditions. However, it is currently unknown how generalizable these patterns are across symbiotic systems that have contrasting ecological characteristics. To address this question, we compared symbiont population structure between deep-sea hydrothermal vent mussels and co-occurring but ecologically distinct snail species. Our analyses show that mussel symbiont populations are less partitioned by geography and do not demonstrate evidence for environmental adaptation. We posit that the mussel's mixotrophic feeding mode may lower its need to affiliate with locally adapted symbiont strains, while microhabitat stability and symbiont genomic mixing likely favors persistence of symbiont strains across geographic locations. Altogether, these findings further our understanding of the mechanisms shaping symbiont population structure in marine environmentally transmitted symbioses.},
}
@article {pmid37491386,
year = {2023},
author = {Zhang, D and Li, X and Wu, Y and Xu, X and Liu, Y and Shi, B and Peng, Y and Dai, D and Sha, Z and Zheng, J},
title = {Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {160},
pmid = {37491386},
issn = {2049-2618},
support = {2022QNLM030004-3 and LSKJ202203100//the Marine S&amp;T Fund of Shandong Province for Qingdao Marine Science and Technology Center/ ; 2022QNLM030004-3 and LSKJ202203100//the Marine S&amp;T Fund of Shandong Province for Qingdao Marine Science and Technology Center/ ; 42249901//NSFC Shiptime Sharing Project/ ; 41876182 and 42025603//the National Natural Science Foundation of China/ ; 41876182 and 42025603//the National Natural Science Foundation of China/ ; XDA22050302//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Manganese/metabolism ; *Ferric Compounds/metabolism ; Geologic Sediments/microbiology ; Bacteria ; Iron/metabolism ; Archaea ; },
abstract = {BACKGROUND: Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.<br><br>RESULTS: Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.<br><br>CONCLUSIONS: This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.},
}
@article {pmid37467988,
year = {2023},
author = {Wu, ZH and Yang, XD and Huang, LY and Li, SL and Xia, FY and Qiu, YZ and Yi, XZ and Jia, P and Liao, B and Liang, JL and Shu, WS and Li, JT},
title = {In situ enrichment of sulphate-reducing microbial communities with different carbon sources stimulating the acid mine drainage sediments.},
journal = {The Science of the total environment},
volume = {898},
number = {},
pages = {165584},
doi = {10.1016/j.scitotenv.2023.165584},
pmid = {37467988},
issn = {1879-1026},
abstract = {The applications of sulphate-reducing microorganisms (SRMs) in acid mine drainage (AMD) treatment systems have received extensive attention due to their ability to reduce sulphate and stabilize metal(loid)s. Despite great phylogenetic diversity of SRMs, only a few have been used in AMD treatment bioreactors. In situ enrichment could be an efficient approach to select new effective SRMs for AMD treatment. Here, we performed in situ enrichment of SRMs in highly stratified AMD sediment cores using different kinds of carbon source mixture. The dsrAB (dissimilatory sulfite reductase) genes affiliated with nine phyla (two archaeal and seven bacterial phyla) and 26 genera were enriched. Remarkably, those genes affiliated with Aciduliprofundum and Vulcanisaeta were enriched in situ in AMD-related environments for the first time, and their relative abundances were negatively correlated with pH. Furthermore, 107 dsrAB-containing metagenome-assembled genomes (MAGs) were recovered from metagenomic datasets, with 14 phyla (two archaeal and 12 bacterial phyla) and 15 genera. The relative abundances of MAGs were positively correlated with total carbon and sulphate contents. Our findings expanded the diversity of SRMs that can be enriched in AMD sediment, and revealed the physiochemical properties that might affect the growth of SRMs, which provided guidance for AMD treatment bioreators.},
}
@article {pmid35928983,
year = {2022},
author = {Hakimjavadi, H and George, SH and Taub, M and Dodds, LV and Sanchez-Covarrubias, AP and Huang, M and Pearson, JM and Slomovitz, BM and Kobetz, EN and Gharaibeh, R and Sowamber, R and Pinto, A and Chamala, S and Schlumbrecht, MP},
title = {The vaginal microbiome is associated with endometrial cancer grade and histology.},
journal = {Cancer research communications},
volume = {2},
number = {6},
pages = {447-455},
pmid = {35928983},
issn = {2767-9764},
support = {P30 CA240139/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Female ; *Endometrial Neoplasms/genetics ; Vagina/microbiology ; Hysterectomy ; *Microbiota/genetics ; *Carcinoma ; },
abstract = {The human microbiome has been strongly correlated with disease pathology and outcomes, yet remains relatively underexplored in patients with malignant endometrial disease. In this study, vaginal microbiome samples were prospectively collected at the time of hysterectomy from 61 racially and ethnically diverse patients from three disease conditions: 1) benign gynecologic disease (controls, n=11), 2) low-grade endometrial carcinoma (n=30), and 3) high-grade endometrial carcinoma (n=20). Extracted DNA underwent shotgun metagenomics sequencing, and microbial α and β diversities were calculated. Hierarchical clustering was used to describe community state types (CST), which were then compared by microbial diversity and grade. Differential abundance was calculated, and machine learning utilized to assess the predictive value of bacterial abundance to distinguish grade and histology. Both α- and β-diversity were associated with patient tumor grade. Four vaginal CST were identified that associated with grade of disease. Different histologies also demonstrated variation in CST within tumor grades. Using supervised clustering algorithms, critical microbiome markers at the species level were used to build models that predicted benign vs carcinoma, high-grade carcinoma versus benign, and high-grade versus low-grade carcinoma with high accuracy. These results confirm that the vaginal microbiome segregates not just benign disease from endometrial cancer, but is predictive of histology and grade. Further characterization of these findings in large, prospective studies is needed to elucidate their potential clinical applications.},
}
@article {pmid37464937,
year = {2023},
author = {Chen, HY and Li, CQ and Chen, SY and Xiao, H},
title = {Metagenomic analysis reveals hidden links between gut microbes and habitat adaptation among cave and surface dwelling Sinocyclocheilus species.},
journal = {Zoological research},
volume = {44},
number = {4},
pages = {793-807},
doi = {10.24272/j.issn.2095-8137.2022.195},
pmid = {37464937},
issn = {2095-8137},
mesh = {Animals ; Phylogeny ; Caves ; *Gastrointestinal Microbiome ; *Cyprinidae/genetics ; Ecosystem ; },
abstract = {Intestinal microbes are closely related to vital host functions such as digestion and nutrient absorption, which play important roles in enhancing host adaptability. As a natural "laboratory", caves provide an outstanding model for understanding the significance of gut microbes and feeding habits in the habitat adaptability of hosts. However, research on the relationship between gut microbes, feeding habits, and the adaptability of troglobites remains insufficient. In this study, we compared the characteristics of the intestinal microbes of Sinocyclocheilus cavefish and surface fish and further established the relationship between intestinal and habitat microbes. Furthermore, we conducted environmental DNA (eDNA) (metabarcoding) analysis of environmental samples to clarify the composition of potential food resources in the habitats of the Sinocyclocheilus cavefish and surface fish. Results showed that the structure of the Sinocyclocheilus gut microbes was more related to ecological type (habitat type) than phylogenetic relationships. While horizontal transfer of habitat microbes was a source of gut microbes, hosts also showed strong selection for inherent microbes as dominant microorganisms. Differences in the composition and structure of gut microbes, especially dominant microbes, may enhance the adaptability of the two Sinocyclocheilus fish types from the perspectives of food intake, nutrient utilization, and harmful substance metabolism, suggesting that food resources, predation patterns, intestinal flora, digestive and absorptive capacity, and feeding habits and preferences are linked to habitat adaptability. These results should facilitate our understanding of the significance of fish gut microbes to habitat adaptation and provide a new perspective for studying the adaptive mechanisms of cavefish.},
}
@article {pmid37432727,
year = {2023},
author = {Wang, J and Shi, K and Jing, Z and Ge, Y},
title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {29},
pages = {10640-10651},
doi = {10.1021/acs.est.3c02181},
pmid = {37432727},
issn = {1520-5851},
mesh = {*Cobamides ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.},
}
@article {pmid37413798,
year = {2023},
author = {Wu, T and Zhong, L and Ding, J and Pang, JW and Sun, HJ and Ding, MQ and Ren, NQ and Yang, SS},
title = {Microplastics perturb nitrogen removal, microbial community and metabolism mechanism in biofilm system.},
journal = {Journal of hazardous materials},
volume = {458},
number = {},
pages = {131971},
doi = {10.1016/j.jhazmat.2023.131971},
pmid = {37413798},
issn = {1873-3336},
mesh = {*Denitrification ; Wastewater ; Microplastics ; Plastics ; Nitrogen/metabolism ; Bioreactors ; *Microbiota ; Biofilms ; Polystyrenes ; },
abstract = {Microplastics (MPs) are a significant component of global pollution and cause widespread concern, particularly in wastewater treatment plants. While understanding the impact of MPs on nutrient removal and potential metabolism in biofilm systems is limited. This work investigated the impact of polystyrene (PS) and polyethylene terephthalate (PET) on the performance of biofilm systems. The results revealed that at concentrations of 100 and 1000 μg/L, both PS and PET had almost no effect on the removal of ammonia nitrogen, phosphorus, and chemical oxygen demand, but reduced the removal of total nitrogen by 7.40-16.6%. PS and PET caused cell and membrane damage, as evidenced by increases in reactive oxygen species and lactate dehydrogenase to 136-355% and 144-207% of the control group. Besides, metagenomic analysis demonstrated both PS and PET changed the microbial structure and caused functional differences. Some important genes in nitrite oxidation (e.g. nxrA), denitrification (e.g. narB, nirABD, norB, and nosZ), and electron production process (e.g. mqo, sdh, and mdh) were restrained, meanwhile, species contribution to nitrogen-conversion genes was altered, therefore disturbing nitrogen-conversion metabolism. This work contributes to evaluating the potential risks of biofilm systems exposed to PS and PET, maintaining high nitrogen removal and system stability.},
}
@article {pmid37406526,
year = {2023},
author = {Meng, J and Li, W and Diao, C and Li, Z and Zhao, J and Haider, G and Zhang, H and Xu, J and Hu, M and Shan, S and Chen, H},
title = {Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability.},
journal = {Journal of hazardous materials},
volume = {458},
number = {},
pages = {131973},
doi = {10.1016/j.jhazmat.2023.131973},
pmid = {37406526},
issn = {1873-3336},
mesh = {Microplastics ; Soil ; Plastics ; *Metals, Heavy/analysis ; Bacteria ; *Microbiota ; Hydrogen-Ion Concentration ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl2-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.},
}
@article {pmid37464386,
year = {2023},
author = {McGregor, BA and Razmjou, E and Hooshyar, H and Seeger, DR and Golovko, SA and Golovko, MY and Singer, SM and Hur, J and Solaymani-Mohammadi, S},
title = {A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {239},
pmid = {37464386},
issn = {1756-3305},
support = {P20 GM113123/GM/NIGMS NIH HHS/United States ; NIH/NIGMSP20GM113123/NH/NIH HHS/United States ; },
mesh = {Humans ; *Giardia lamblia ; *Giardiasis/parasitology ; Phylogeny ; Genotype ; *Microbiota ; Feces/parasitology ; Multilocus Sequence Typing ; },
abstract = {BACKGROUND: The mechanisms underlying the clinical outcome disparity during human infection with Giardia duodenalis are still unclear. In recent years, evidence has pointed to the roles of host factors as well as parasite's genetic heterogeneity as major contributing factors in the development of symptomatic human giardiasis. However, it remains contested as to how only a small fraction of individuals infected with G. duodenalis develop clinical gastrointestinal manifestations, whereas the majority of infected individuals remain asymptomatic. Here, we demonstrate that diversity in the fecal microbiome correlates with the clinical outcome of human giardiasis.<br><br>METHODS: The genetic heterogeneity of G. duodenalis clinical isolates from human subjects with asymptomatic and symptomatic giardiasis was determined using a multilocus analysis approach. We also assessed the genetic proximity of G. duodenalis isolates by constructing phylogenetic trees using the maximum likelihood. Total genomic DNA (gDNA) from fecal specimens was utilized to construct DNA libraries, followed by performing paired-end sequencing using the HiSeq X platform. The Kraken2-generated, filtered FASTQ files were assigned to microbial metabolic pathways and functions using HUMAnN 3.04 and the UniRef90 diamond annotated full reference database (version 201901b). Results from HUMAnN for each sample were evaluated for differences among the biological groups using the Kruskal-Wallis non-parametric test with a post hoc Dunn test.<br><br>RESULTS: We found that a total of 8/11 (72.73%) human subjects were infected with assemblage A (sub-assemblage AII) of G. duodenalis, whereas 3/11 (27.27%) human subjects in the current study were infected with assemblage B of the parasite. We also found that the parasite's genetic diversity was not associated with the clinical outcome of the infection. Further phylogenetic analysis based on the tpi and gdh loci indicated that those clinical isolates belonging to assemblage A of G. duodenalis subjects clustered compactly together in a monophyletic clade despite being isolated from human subjects with asymptomatic and symptomatic human giardiasis. Using a metagenomic shotgun sequencing approach, we observed that infected individuals with asymptomatic and symptomatic giardiasis represented distinctive microbial diversity profiles, and that both were distinguishable from the profiles of healthy volunteers.<br><br>CONCLUSIONS: These findings identify a potential association between host microbiome disparity with the development of clinical disease during human giardiasis, and may provide insights into the mechanisms by which the parasite induces pathological changes in the gut. These observations may also lead to the development of novel selective therapeutic targets for preventing human enteric microbial infections.},
}
@article {pmid37211644,
year = {2023},
author = {Urvois, T and Perrier, C and Roques, A and Sauné, L and Courtin, C and Kajimura, H and Hulcr, J and Cognato, AI and Auger-Rozenberg, MA and Kerdelhué, C},
title = {The worldwide invasion history of a pest ambrosia beetle inferred using population genomics.},
journal = {Molecular ecology},
volume = {32},
number = {15},
pages = {4381-4400},
doi = {10.1111/mec.16993},
pmid = {37211644},
issn = {1365-294X},
mesh = {Animals ; *Coleoptera/genetics ; *Weevils ; Ambrosia/genetics ; Metagenomics ; Europe ; Introduced Species ; },
abstract = {Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas and did not include Europe. Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus' invasion history on a global level and identify the origins of the invasion in Europe. We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic data set for any ambrosia beetle to date. The results were largely consistent between markers. Two differentiated genetic clusters were invasive, albeit in different regions of the world. The markers were inconsistent only for a few specimens found exclusively in Japan. Mainland USA could have acted as a source for further expansion to Canada and Argentina through stepping stone expansion and bridgehead events. We showed that Europe was only colonized by Cluster II through a complex invasion history including several arrivals from multiple origins in the native area, and possibly including bridgehead from the United States. Our results also suggested that Spain was colonized directly from Italy through intracontinental dispersion. It is unclear whether the mutually exclusive allopatric distribution of the two clusters is due to neutral effects or due to different ecological requirements.},
}
@article {pmid37442576,
year = {2023},
author = {Grandchamp, A and Kühl, L and Lebherz, M and Brüggemann, K and Parsch, J and Bornberg-Bauer, E},
title = {Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster.},
journal = {Genome research},
volume = {33},
number = {6},
pages = {872-890},
doi = {10.1101/gr.277482.122},
pmid = {37442576},
issn = {1549-5469},
mesh = {Animals ; *Drosophila melanogaster/genetics ; Open Reading Frames ; *Metagenomics ; DNA Transposable Elements/genetics ; Biological Evolution ; Evolution, Molecular ; },
abstract = {Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.},
}
@article {pmid37401151,
year = {2023},
author = {Daga-Quisbert, J and Rajarao, GK and Ugarte, F and van Maris, AJA and Quillaguamán, J},
title = {Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {8},
pages = {},
doi = {10.1093/femsec/fiad073},
pmid = {37401151},
issn = {1574-6941},
mesh = {Humans ; *Lakes/microbiology ; Bolivia ; Altitude ; *Microbiota/genetics ; Sodium Chloride ; Water ; },
abstract = {Lake Pastos Grandes in Bolivia is mainly composed of salt flats, which are sporadically and only partially submerged during the wet season. In the present study, the chemical composition of water samples of the lake and some influent rivers was determined. We found that it is likely that the lake was influenced by the dilution of metals from ancient evaporites. We performed the first metagenomic studies of this lake. Analyses of shotgun metagenomics revealed that the relative abundances of Burkholderiales and Pseudomonadales were noteworthy in the water samples, whereas the archaea belonging to the Halobacteriales and Cyanobacteria from subsection III had high abundances in the salt flat. The eukaryotes Crustacea and Diatomea exhibited the highest abundances in the water samples. We investigated further the potential effect of human activities on the nitrogen cycle mobilization in the lake and the propagation of antimicrobial resistance genes. This is the first report about the cycle in the lake. Additionally, rifamycin resistance genes and genes related to efflux pumps, which are not considered a hazard when identified in metagenomes, had the uppermost relative abundances in all sampling points. We found that Lake Pastos Grandes hitherto does not show an appreciable influence by anthropogenic actions.},
}
@article {pmid37355217,
year = {2023},
author = {Wanvimonsuk, S and Somboonwiwat, K},
title = {Peroxiredoxin-4 supplementation modulates the immune response, shapes the intestinal microbiome, and enhances AHPND resistance in Penaeus vannamei.},
journal = {Fish &amp; shellfish immunology},
volume = {139},
number = {},
pages = {108915},
doi = {10.1016/j.fsi.2023.108915},
pmid = {37355217},
issn = {1095-9947},
mesh = {Animals ; Immunity, Innate/genetics ; *Penaeidae ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Dietary Supplements ; Peroxiredoxins ; *Vibrio parahaemolyticus/physiology ; },
abstract = {Peroxiredoxin-4 from Penaeus vannamei (LvPrx4) is considered a damage-associated molecular pattern (DAMP) that can activate the expression of immune-related genes through the Toll pathway. We previously demonstrated that the recombinant LvPrx4 (rLvPrx4) can enhance shrimp resistance against Vibrio parahaemolyticus, causing acute hepatopancreatic necrosis disease (VPAHPND), which causes great production losses in shrimp farming. Herein, we showed that the rLvPrx4 had a thermal tolerance of around 60 °C and that the ionic strength had no noticeable effect on its activity. We discovered that feeding a diet containing rLvPrx4 to shrimp for three weeks increased the expression of the immune-related genes LvPEN4 and LvVago5. Furthermore, pre-treatment with rLvPrx4 feeding could significantly prolong shrimp survival following the VPAHPND challenge. The shrimp intestinal microbiome was then characterized using PCR amplification of the 16S rRNA gene and Illumina sequencing. Three weeks of rLvPrx4 supplementation altered the bacterial community structure (beta diversity) and revealed the induction of differentially abundant families, including Cryomorphaceae, Flavobacteriaceae, Pirellulaceae, Rhodobacteraceae, and Verrucomicrobiaceae, in the rLvPrx4 group. Metagenomic predictions indicated that some amino acid metabolism pathways, such as arginine and proline metabolism, and genetic information processing were significantly elevated in the rLvPrx4 group compared to the control group. This study is the first to describe the potential use of rLvPrx4 supplementation to enhance shrimp resistance to VPAHPND and alter the composition of a beneficial bacterial community in shrimp, making rLvPrx4 a promising feed supplement as an alternative to antibiotics for controlling VPAHPND infection in shrimp aquaculture.},
}
@article {pmid37341942,
year = {2023},
author = {Li, X and Zhang, M and Dang, C and Wu, Z and Xia, Y},
title = {In situ Nanopore sequencing reveals metabolic characteristics of the Qilian glacier meltwater microbiome.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {35},
pages = {84805-84813},
pmid = {37341942},
issn = {1614-7499},
support = {42277103//National Natural Science Foundation of China/ ; 42177357//National Natural Science Foundation of China/ ; },
mesh = {Ice Cover ; *Nanopore Sequencing ; China ; Lakes ; *Microbiota ; },
abstract = {Nanopore metagenomic sequencing enables rapid annotating microbiological ecosystems, and the previous glacier-related sequencing applications (e.g., targeted ice sheets, ice lake, and cryoconite holes) inspire us to explore high-altitude glacier meltwater at Qilian Mountain, China (3000 to 4000 m above sea level, MASL). Our findings suggest that (1) despite only several hundred meters apart, the microbial communities and functionalities are quite different among vertical alpine distributions; (2) the high-altitude Qilian meltwater microbiome serve several main metabolic functions, including sulfur oxidation, selenite decomposing, photosynthesis, energy production, enzymic, and UV tolerant activities. Meanwhile, our Nanopore metagenomic results indicate that the microbial classifications and functionalities (e.g., chaperones, cold-shock, specific tRNA species, oxidative stress, and resistance to toxic compounds) of Qilian meltwater are highly consistent with the other glacial microbiome, emphasizing that only certain microbial species can survive in the cold environment and the molecular adaptions and lifestyles remain stable all over the world. Besides, we have shown Nanopore metagenomic sequencing can provide reliable prokaryotic classifications within or among studies, which therefore can encourage more applications in the field given faster turnaround time. However, we recommend accumulating at least 400 ng nucleic acids (after extraction) and maximizing Nanopore library preparation efficiency before on-site sequencing to obtain better resolutions.},
}
@article {pmid35914737,
year = {2023},
author = {Liu, Y and Lau, HC and Cheng, WY and Yu, J},
title = {Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {21},
number = {1},
pages = {84-96},
doi = {10.1016/j.gpb.2022.07.002},
pmid = {35914737},
issn = {2210-3244},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/diagnosis/etiology/therapy ; *Microbiota ; Biomarkers ; Carcinogenesis ; },
abstract = {Colorectal cancer (CRC) is one of the most frequently diagnosed cancers and the leading cause of cancer-associated deaths. Epidemiological studies have shown that both genetic and environmental risk factors contribute to the development of CRC. Several metagenomic studies of CRC have identified gut dysbiosis as a fundamental risk factor in the evolution of colorectal malignancy. Although enormous efforts and substantial progresses have been made in understanding the relationship between human gut microbiome and CRC, the precise mechanisms involved remain elusive. Recent data have shown a direct causative role of the gut microbiome in DNA damage, inflammation, and drug resistance in CRC, suggesting that modulation of gut microbiome could act as a powerful tool in CRC prevention and therapy. Here, we provide an overview of the relationship between gut microbiome and CRC, and explore relevant mechanisms of colorectal tumorigenesis. We next highlight the potential of bacterial species as clinical biomarkers, as well as their roles in therapeutic response. Factors limiting the clinical translation of gut microbiome and strategies for resolving current challenges are further discussed.},
}
@article {pmid37459167,
year = {2023},
author = {Cisneros-Martínez, AM and Eguiarte, LE and Souza, V},
title = {Metagenomic comparisons reveal a highly diverse and unique viral community in a seasonally fluctuating hypersaline microbial mat.},
journal = {Microbial genomics},
volume = {9},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001063},
pmid = {37459167},
issn = {2057-5858},
support = {BB/P024378/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Metagenomics ; Seasons ; *Microbiota ; *Virome ; },
abstract = {In spring 2016, a shallow hypersaline pond (50×25 m) was found in the Cuatro Cienegas Basin (CCB). This pond, known as Archaean Domes (AD) because of its elastic microbial mats that form dome-shaped structures due to the production of reducing gases reminiscent of the Archaean eon, such as methane and hydrogen sulfide, harbour a highly diverse microbial community, rich in halophilic and methanogenic archaea. AD is a seasonally fluctuating hypersaline site, with salinity ranging from low hypersaline (5.3%) during the wet season to high hypersaline (saturation) during the dry season. To characterize the viral community and to test whether it resembles those of other hypersaline sites (whose diversity is conditioned by salinity), or if it is similar to other CCB sites (with which it shares a common geological history), we generated 12 metagenomes from different seasons and depths over a 4 year period and compared them to 35 metagenomes from varied environments. Haloarchaeaviruses were detected, but were never dominant (average of 15.37 % of the total viral species), and the viral community structure and diversity were not affected by environmental fluctuations. In fact, unlike other viral communities at hypersaline sites, AD remained more diverse than other environments regardless of season. β-Diversity analyses show that AD is closely related to other CCB sites, although it has a unique viral community that forms a cluster of its own. The similarity of two surface samples to the 30 and 50 cm depth samples, as well as the observed increase in diversity at greater depths, supports the hypothesis that the diversity of CCB has evolved as a result of a long time environmental stability of a deep aquifer that functions as a 'seed bank' of great microbial diversity that is transported to the surface by sporadic groundwater upwelling events.},
}
@article {pmid37455607,
year = {2023},
author = {Hutchins, L and Mc Cartney, A and Graham, N and Gillespie, R and Guzman, A},
title = {Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13822},
pmid = {37455607},
issn = {1755-0998},
support = {//Berkeley Food Institute Faculty Seed Grant/ ; //National Science Foundation Innovations at the Nexus of Food, Energy, and Water Systems/ ; },
abstract = {Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.},
}
@article {pmid37349537,
year = {2023},
author = {Lin, L and Yi, X and Liu, H and Meng, R and Li, S and Liu, X and Yang, J and Xu, Y and Li, C and Wang, Y and Xiao, N and Li, H and Liu, Z and Xiang, Z and Shu, W and Guan, WJ and Zheng, XY and Sun, J and Wang, Z},
title = {The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans.},
journal = {Nature medicine},
volume = {29},
number = {7},
pages = {1750-1759},
pmid = {37349537},
issn = {1546-170X},
mesh = {Humans ; Respiratory System ; *Pulmonary Disease, Chronic Obstructive/etiology/microbiology ; Environmental Exposure/adverse effects ; *Microbiota ; Sputum/microbiology ; },
abstract = {Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.},
}
@article {pmid37270585,
year = {2023},
author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q},
title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.},
journal = {The ISME journal},
volume = {17},
number = {8},
pages = {1278-1289},
pmid = {37270585},
issn = {1751-7370},
mesh = {Antimony/analysis/chemistry ; Soil/chemistry ; Phosphates/analysis ; Phosphorus/analysis ; Phylogeny ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Bacteria/genetics ; *Microbiota ; China ; Soil Microbiology ; },
abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.},
}
@article {pmid37452041,
year = {2023},
author = {Tarracchini, C and Alessandri, G and Fontana, F and Rizzo, SM and Lugli, GA and Bianchi, MG and Mancabelli, L and Longhi, G and Argentini, C and Vergna, LM and Anzalone, R and Viappiani, A and Turroni, F and Taurino, G and Chiu, M and Arboleya, S and Gueimonde, M and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M},
title = {Genetic strategies for sex-biased persistence of gut microbes across human life.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4220},
pmid = {37452041},
issn = {2041-1723},
support = {SFI/12/RC/2273-P1//Science Foundation Ireland (SFI)/ ; },
mesh = {Male ; Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Bifidobacterium/genetics/metabolism ; *Microbiota ; Bacteria/genetics ; },
abstract = {Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.},
}
@article {pmid37450589,
year = {2023},
author = {Shi, B and Zhang, X and Song, Z and Dai, Z and Luo, K and Chen, B and Zhou, Z and Cui, Y and Feng, B and Zhu, Z and Zheng, J and Zhang, H and He, X},
title = {Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart.},
journal = {Science advances},
volume = {9},
number = {28},
pages = {eadg7417},
pmid = {37450589},
issn = {2375-2548},
mesh = {Animals ; Mice ; *Kynurenine/metabolism ; *Gastrointestinal Microbiome ; Heart ; Fibroblasts/metabolism ; Metabolomics ; },
abstract = {Pressure-overloaded left ventricular remodeling in young population is progressive and readily degenerate into heart failure. The aims of this study were to identify a plasma metabolite that predicts and is mechanistically linked to the disease. Untargeted metabolomics determined elevated plasma kynurenine (Kyn) in both the patient cohorts and the mice model, which was correlated with remodeling parameters. In vitro and in vivo evidence, combined with single-nucleus RNA sequencing (snRNA-seq), demonstrated that Kyn affected both cardiomyocytes and cardiac fibroblasts by activating aryl hydrocarbon receptors (AHR) to up-regulate hypertrophy- and fibrosis-related genes. Shotgun metagenomics and fecal microbiota transplantation revealed the existence of the altered gut microbiota-Kyn relationship. Supplementation of selected microbes reconstructed the gut microbiota, reduced plasma Kyn, and alleviated ventricular remodeling. Our data collectively discovered a gut microbiota-derived metabolite to activate AHR and its gene targets in remodeling young heart, a process that could be prevented by specific gut microbiota modulation.},
}
@article {pmid37382555,
year = {2023},
author = {Yi, S and Zhang, C and Yin, P and Yu, L and Tian, F and Chen, W and Zhai, Q},
title = {Compositional and functional features of the intestinal lactobacilli associated with different long-term diet types.},
journal = {Food &amp; function},
volume = {14},
number = {14},
pages = {6570-6581},
doi = {10.1039/d3fo02182c},
pmid = {37382555},
issn = {2042-650X},
mesh = {Humans ; Lactobacillus/genetics/metabolism ; Diet ; *Gastrointestinal Microbiome ; *Probiotics ; },
abstract = {It is well known that diet is one of the most important factors in shaping the host's intestinal microbiota. Lactobacillus, a common group of probiotic bacteria, is widely distributed in the host gut, and studies have linked changes in lactobacilli in the gut to differences in dietary habits. Different dietary habits may affect not only the structural composition but also the function of lactobacilli in the intestine. Therefore, we dissected 283 metagenomes from samples collected from individuals with different dietary habits, investigating the presence of different species of lactobacilli. We demonstrated that the highest abundance of lactobacilli was found in stool samples from omnivorous populations and that Ligilactobacillus ruminis (L. ruminis) and Lactiplantibacillus plantarum (L. plantarum) were more prevalent in these samples than in vegetarian and vegan samples. In addition, we determined that different dietary structures affected the functional potential of lactobacilli by reconstructing the metagenome-assembled genomes (MAGs) of L. ruminis (highest abundance) in the samples. L. ruminis strains associated with a vegetarian diet had a higher "replication, recombination and repair" functional potential and may also have a greater capacity for glutathione (GSH) synthesis and metabolism. The results of our analysis provide evidence for the possibility of a specific selection of lactobacillus strains for people with different dietary habits.},
}
@article {pmid37178322,
year = {2023},
author = {Pandey, U and Tambat, S and Aich, P},
title = {Postnatal 14D is the Key Window for Mice Intestinal Development- An Insight from Age-Dependent Antibiotic-Mediated Gut Microbial Dysbiosis Study.},
journal = {Advanced biology},
volume = {7},
number = {7},
pages = {e2300089},
doi = {10.1002/adbi.202300089},
pmid = {37178322},
issn = {2701-0198},
mesh = {Mice ; Animals ; *Intestines/microbiology ; Intestinal Mucosa/metabolism ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Dysbiosis/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; },
abstract = {The postnatal period is one of the critical windows for the structure-function development of the gastrointestinal tract and associated mucosal immunity. Along with other constituent members, recent studies suggest the contribution of gut microbiota in maintaining host health, immunity, and development. Although the gut microbiota's role in maintaining barrier integrity is known, its function in early life development still needs to be better understood. To understand the details of gut microbiota's effects on intestinal integrity, epithelium development, and immune profile, the route of antibiotic-mediated perturbation is taken. Mice on days 7(P7D), 14(P14D), 21(P21D) and 28(P28D) are sacrificed and 16S rRNA metagenomic analysis is performed. The barrier integrity, tight junction proteins (TJPs) expression, intestinal epithelial cell (IEC) markers, and inflammatory cytokines are analyzed. Results reveal a postnatal age-related impact of gut microbiota perturbation, with a gradual increase in the relative abundance of Proteobacteria and a reduction in Bacteroidetes and Firmicutes. Significant barrier integrity disruption, reduced TJPs and IECs marker expression, and increased systemic inflammation at P14D of AVNM-treated mice are found. Moreover, the microbiota transplantation shows recolonization of Verrucomicrobia, proving a causal role in barrier functions. The investigation reveals P14D as a critical period for neonatal intestinal development, regulated by specific microbiota composition.},
}
@article {pmid36637649,
year = {2023},
author = {Wani, AK and Akhtar, N and Naqash, N and Rahayu, F and Djajadi, D and Chopra, C and Singh, R and Mulla, SI and Sher, F and Américo-Pinheiro, JHP},
title = {Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {34},
pages = {81450-81473},
pmid = {36637649},
issn = {1614-7499},
mesh = {Humans ; Microplastics ; Plastics/metabolism ; Metagenomics ; Ecosystem ; *Microbiota ; *Environmental Pollutants/analysis ; *Water Pollutants, Chemical/analysis ; },
abstract = {Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation.},
}
@article {pmid37118004,
year = {2021},
author = {Zhang, X and Zhong, H and Li, Y and Shi, Z and Ren, H and Zhang, Z and Zhou, X and Tang, S and Han, X and Lin, Y and Yang, F and Wang, D and Fang, C and Fu, Z and Wang, L and Zhu, S and Hou, Y and Xu, X and Yang, H and Wang, J and Kristiansen, K and Li, J and Ji, L},
title = {Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities.},
journal = {Nature aging},
volume = {1},
number = {1},
pages = {87-100},
pmid = {37118004},
issn = {2662-8465},
mesh = {Humans ; Female ; Adult ; Male ; *Gastrointestinal Microbiome/genetics ; Feces ; *Microbiota ; Ethnicity ; Metagenomics ; },
abstract = {Lifelong sex- and age-related trajectories of the human gut microbiota remain largely unexplored. Using metagenomics, we derived the gut microbial composition of 2,338 adults (26-76 years) from a Han Chinese population-based cohort where metabolic health, hormone levels and aspects of their lifestyles were also recorded. In this cohort, and in three independent cohorts distributed across China, Israel and the Netherlands, we observed sex differences in the gut microbial composition and a shared age-related decrease in sex-dependent differences in gut microbiota. Compared to men, the gut microbiota of premenopausal women exhibited higher microbial diversity and higher abundances of multiple species known to have beneficial effects on host metabolism. We also found consistent sex-independent, age-related gut microbial characteristics across all populations, with the presence of members of the oral microbiota being the strongest indicator of older chronological age. Our findings highlight the existence of sex- and age-related trajectories in the human gut microbiota that are shared between populations of different ethnicities and emphasize the pivotal links between sex hormones, gut microbiota and host metabolism.},
}
@article {pmid37450112,
year = {2023},
author = {Ji, X and Ni, S and Tian, G and Zhang, L and Wang, W},
title = {Detection of Microorganisms in Body Fluid Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2695},
number = {},
pages = {73-88},
pmid = {37450112},
issn = {1940-6029},
mesh = {RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Body Fluids ; },
abstract = {Next-generation sequencing (NGS) has been widely applied to the identification of microbiome in body fluids. The methodology of 16S rRNA amplicon sequencing is simple, fast, and cost-effective. It overcomes the problem that some microorganisms cannot be isolated or cultured. Low abundant bacteria can also be amplified and sequenced, but the resolution of classification can hardly reach species or sub-species level; moreover, this methodology is mainly used to identify bacterial populations, and other microorganisms like viruses or fungi cannot be sequenced. On the other hand, the microbiome profiling obtained by shotgun metagenomic sequencing is more comprehensive with better resolution, and more accurate classification can be expected due to higher coverage of genomic sequences from microorganisms. By combining the capture-based method with metagenomic sequencing, we can further enrich and detect low abundant microorganisms and identify the viral integration sites in host gDNA at once.},
}
@article {pmid37448812,
year = {2023},
author = {Chafra, F and Borim Correa, F and Oni, F and Konu Karakayalı, &#xd6; and Stadler, PF and Nunes da Rocha, U},
title = {StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins.},
journal = {Bioinformatics advances},
volume = {3},
number = {1},
pages = {vbad069},
pmid = {37448812},
issn = {2635-0041},
abstract = {MOTIVATION: Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis.<br><br>RESULTS: StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence-absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways.<br><br>StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}
@article {pmid37448101,
year = {2023},
author = {Bao, S and Wang, H and Li, W and Wu, H and Lu, C and Yong, L and Zhang, Q and Lu, X and Zhao, M and Lu, J and Liu, J and Ikechukwu, CK and Xu, J and Ni, P and Xiong, Y and Zhang, W and Zhou, C},
title = {Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2234653},
doi = {10.1080/19490976.2023.2234653},
pmid = {37448101},
issn = {1949-0984},
mesh = {Humans ; Child ; *Rotavirus/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; China/epidemiology ; Diarrhea/epidemiology ; *Rotavirus Infections ; Feces ; },
abstract = {Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae. Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales. The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.},
}
@article {pmid37446198,
year = {2023},
author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J},
title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37446198},
issn = {1422-0067},
support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; },
mesh = {Metagenomics ; Bacteria/genetics/metabolism ; *Rhodophyta/genetics ; Metagenome ; *Seaweed ; Polysaccharides/metabolism ; },
abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.},
}
@article {pmid37446076,
year = {2023},
author = {Xu, J and Molin, G and Davidson, S and Roth, B and Sjöberg, K and Håkansson, &#xc5;},
title = {CRP in Outpatients with Inflammatory Bowel Disease Is Linked to the Blood Microbiota.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37446076},
issn = {1422-0067},
support = {Dnr 143587//Direkt&#xf6;r Albert P&#xe5;hlssons Stiftelse f&#xf6;r V&#xe4;lg&#xf6;renhet/ ; },
mesh = {Humans ; C-Reactive Protein ; Outpatients ; *Inflammatory Bowel Diseases/microbiology ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; *Microbiota ; },
abstract = {The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The present study aimed to map the blood microbiota of outpatients with Crohn's disease (CD) or with ulcerative colitis (UC) by 16S metagenomics. A diverse microbiota was observed in the blood samples. Regardless of the type of disease, the alpha diversity of the microbiota was positively associated with C-reactive protein (CRP). The blood microbiota had a surprisingly high proportion of Proteobacteria in comparison with human oral and colonic microbiotas. There was no clear difference in the overall pattern of the microbiota between CD and UC. A non-template control (NTC) was included in the whole process to control for the potential contamination from the environment and reagents. Certain bacterial taxa were concomitantly detected in both blood samples and NTC. However, Acinetobacter, Lactobacillus, Thermicanus and Paracoccus were found in blood from both CD and UC patients but not in NTC, indicating the existence of a specific blood-borne microbiota in the patients. Achromobacter dominated in all blood samples, but a minor amount was also found in NTC. Micrococcaceae was significantly enriched in CD, but it was also detected in high abundance in NTC. Whether the composition of the blood microbiota could be a marker of a particular phenotype in inflammatory bowel disease (IBD) or whether the blood microbiota could be used for diagnostic or therapeutic purposes deserves further attention.},
}
@article {pmid37443184,
year = {2023},
author = {Tataru, C and Peras, M and Rutherford, E and Dunlap, K and Yin, X and Chrisman, BS and DeSantis, TZ and Wall, DP and Iwai, S and David, MM},
title = {Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {11353},
pmid = {37443184},
issn = {2045-2322},
support = {NIDA R44DA04395402//NBLational Institutes of Health/ ; },
mesh = {Child ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; RNA, Ribosomal, 16S/genetics ; *Autistic Disorder ; *Microbiota/genetics ; },
abstract = {While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial processes, and is especially useful in understanding complex conditions such as Autism. Challenges with integrating heterogeneous data produced by multiple profiling methods can be overcome using Latent Dirichlet Allocation (LDA), a promising natural language processing technique that identifies topics in heterogeneous documents. In this study, we apply LDA to multi-omic microbial data (16S rRNA amplicon, shotgun metagenomic, shotgun metatranscriptomic, and untargeted metabolomic profiling) from the stool of 81 children with and without Autism. We identify topics, or microbial processes, that summarize complex phenomena occurring within gut microbial communities. We then subset stool samples by topic distribution, and identify metabolites, specifically neurotransmitter precursors and fatty acid derivatives, that differ significantly between children with and without Autism. We identify clusters of topics, deemed "cross-omic topics", which we hypothesize are representative of generalizable microbial processes observable regardless of profiling method. Interpreting topics, we find each represents a particular diet, and we heuristically label each cross-omic topic as: healthy/general function, age-associated function, transcriptional regulation, and opportunistic pathogenesis.},
}
@article {pmid37439894,
year = {2023},
author = {Torres Manno, MA and Gizzi, FO and Martín, M and Espariz, M and Magni, C and Blancato, VS},
title = {Metagenomic approach to infer rumen microbiome derived traits of cattle.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {39},
number = {9},
pages = {250},
pmid = {37439894},
issn = {1573-0972},
support = {PICT2019-1771//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT2015-2361//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT2014-3482//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PIP 11220150100855//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; },
mesh = {Female ; Cattle ; Animals ; *Rumen ; *Microbiota/genetics ; Metagenome ; Bacteria ; Glycoside Hydrolases/genetics/metabolism ; Methane/metabolism ; Animal Feed ; Diet ; },
abstract = {Ruminants enable the conversion of indigestible plant material into animal consumables, including dairy products, meat, and valuable fibers. Microbiome research is gaining popularity in livestock species because it aids in the knowledge of illnesses and efficiency processes in animals. In this study, we use WGS metagenomic data to thoroughly characterize the ruminal ecosystem of cows to infer positive and negative livestock traits determined by the microbiome. The rumen of cows from Argentina were described by combining different gene biomarkers, pathways composition and taxonomic information. Taxonomic characterization indicated that the two major phyla were Bacteroidetes and Firmicutes; in third place, Proteobacteria was highly represented followed by Actinobacteria; Prevotella, and Bacteroides were the most abundant genera. Functional profiling of carbohydrate-active enzymes indicated that members of the Glycoside Hydrolase (GH) class accounted for 52.2 to 55.6% of the total CAZymes detected, among them the most abundant were the oligosaccharide degrading enzymes. The diversity of GH families found suggested efficient hydrolysis of complex biomass. Genes of multidrug, macrolides, polymyxins, beta-lactams, rifamycins, tetracyclines, and bacitracin resistance were found below 0.12% of relative abundance. Furthermore, the clustering analysis of genera and genes that correlated to methane emissions or feed efficiency, suggested that the cows analysed could be regarded as low methane emitters and clustered with high feed efficiency reference animals. Finally, the combination of bioinformatic analyses used in this study can be applied to assess cattle traits difficult to measure and guide enhanced nutrition and breeding methods.},
}
@article {pmid37439777,
year = {2023},
author = {Holman, DB and Gzyl, KE and Kommadath, A},
title = {The gut microbiome and resistome of conventionally vs. pasture-raised pigs.},
journal = {Microbial genomics},
volume = {9},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001061},
pmid = {37439777},
issn = {2057-5858},
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; },
abstract = {Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.},
}
@article {pmid37358243,
year = {2023},
author = {He, Y and Liang, J and Liu, Y and Zhou, X and Peng, C and Long, C and Huang, P and Feng, J and Zhang, Z},
title = {Combined supplementation with Lactobacillus sp. and Bifidobacterium thermacidophilum isolated from Tibetan pigs improves growth performance, immunity, and microbiota composition in weaned piglets.},
journal = {Journal of animal science},
volume = {101},
number = {},
pages = {},
pmid = {37358243},
issn = {1525-3163},
support = {U2002206//National Natural Science Foundation of China/ ; CARS-35//Youth Innovation Promotion Association/ ; KFZDSW-219//Key Research Program of the Chinese Academy of Sciences/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 202001BB050001//Major Science and Technology Project in Yunnan Province of China/ ; },
mesh = {Animals ; Swine ; *Lactobacillus ; Prospective Studies ; Tibet ; Dietary Supplements ; *Microbiota ; Bifidobacterium ; Weaning ; },
abstract = {Probiotics, such as Lactobacillus and Bifidobacterium, promote growth in piglets by modulating gut microbiota composition and improving the host immune system. A strain of Lactobacillus sp. and Bifidobacterium thermacidophilum were previously isolated from fresh feces of Tibetan pigs. The effects of these isolated strains on growth performance, intestinal morphology, immunity, microbiota composition, and their metabolites were evaluated in weaned piglets. Thirty crossbred piglets were selected and fed either a basal diet (CON), a basal diet supplemented with aureomycin (ANT), or a basal diet supplemented with Lactobacillus sp. and B. thermacidophilum (LB) for 28 d. The piglets in the ANT and LB groups had significantly higher body weight gain than those in the CON group (P < 0.05). Piglets in the ANT and LB groups had regularly arranged villi and microvilli in the small intestine. Furthermore, they had improved immune function, as indicated by decreased serum concentrations of inflammatory cytokines (P < 0.05), improved components of immune cells in the blood, mesenteric lymph nodes, and spleen. Additionally, metagenomic sequencing indicated a significant shift in cecal bacterial composition and alterations in microbiota functional profiles following Lactobacillus sp. and B. thermacidophilum supplementation. Metabolomic results revealed that the metabolites were also altered, and Kyoto Encyclopedia of Genes and Genomes analysis revealed that several significantly altered metabolites were enriched in glycerophospholipid and cholesterol metabolism (P < 0.05). Furthermore, correlation analysis showed that several bacterial members were closely related to the alterations in metabolites, including Bacteroides sp., which were negatively correlated with triglyceride (16:0/18:0/20:4[5Z,8Z,11Z,14Z]), the metabolite that owned the highest variable importance of projection scores. Collectively, our findings suggest that combined supplementation with Lactobacillus sp. and B. thermacidophilum significantly improved the growth performance, immunity, and microbiota composition in weaned piglets, making them prospective alternatives to antibiotics in swine production.},
}
@article {pmid37343363,
year = {2023},
author = {Kang, X and Ng, SK and Liu, C and Lin, Y and Zhou, Y and Kwong, TNY and Ni, Y and Lam, TYT and Wu, WKK and Wei, H and Sung, JJY and Yu, J and Wong, SH},
title = {Altered gut microbiota of obesity subjects promotes colorectal carcinogenesis in mice.},
journal = {EBioMedicine},
volume = {93},
number = {},
pages = {104670},
pmid = {37343363},
issn = {2352-3964},
mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Colonic Neoplasms ; Carcinogenesis ; Obesity/complications ; Azoxymethane/toxicity ; *Colorectal Neoplasms/genetics ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {BACKGROUND: Obesity is a risk factor for colorectal cancer (CRC). The role of gut microbiota in mediating the cancer-promoting effect of obesity is unknown.<br><br>METHODS: Azoxymethane (AOM)-treated, Apc[Min/+] and germ-free mice were gavaged with feces from obese individuals and control subjects respectively. The colonic tumor load and number were recorded at the endpoint in two carcinogenic models. The gut microbiota composition and colonic transcriptome were assessed by metagenomic sequencing and RNA sequencing, respectively. The anticancer effects of bacteria depleted in fecal samples of obese individuals were validated.<br><br>FINDINGS: Conventional AOM-treated and Apc[Min/+] mice receiving feces from obese individuals showed significantly increased colon tumor formation compared with those receiving feces from control subjects. AOM-treated mice receiving feces from obese individuals showed impaired intestinal barrier function and significant upregulation of pro-inflammatory cytokines and activation of oncogenic Wnt signaling pathway. Consistently, transferring feces from obese individuals to germ-free mice led to increased colonic cell proliferation, intestinal barrier function impairment, and induction of oncogenic and proinflammatory gene expression. Moreover, germ-free mice transplanted with feces from obese human donors had increased abundance of potential pathobiont Alistipes finegoldii, and reduced abundance of commensals Bacteroides vulgatus and Akkermansia muciniphila compared with those receiving feces from human donors with normal body mass index (BMI). Validation experiments showed that B.&#xa0;vulgatus and A.&#xa0;muciniphila demonstrated anti-proliferative effects in CRC, while A.&#xa0;finegoldii promoted CRC tumor growth.<br><br>INTERPRETATION: Our results supported the role of obesity-associated microbiota in colorectal carcinogenesis and identified putative bacterial candidates that may mediate its mechanisms. Microbiota modulation in obese individuals may provide new approaches to prevent or treat obesity-related cancers including CRC.<br><br>FUNDING: This work was funded by National Key Research and Development Program of China (2020YFA0509200/2020YFA0509203), National Natural Science Foundation of China (81922082), RGC Theme-based Research Scheme Hong Kong (T21-705/20-N), RGC Research Impact Fund Hong Kong (R4632-21F), RGC-CRF Hong Kong (C4039-19GF and C7065-18GF), RGC-GRF Hong Kong (14110819, 14111621), and NTU Start-Up Grant (021337-00001).},
}
@article {pmid37339626,
year = {2023},
author = {Frioux, C and Ansorge, R and Özkurt, E and Ghassemi Nedjad, C and Fritscher, J and Quince, C and Waszak, SM and Hildebrand, F},
title = {Enterosignatures define common bacterial guilds in the human gut microbiome.},
journal = {Cell host &amp; microbe},
volume = {31},
number = {7},
pages = {1111-1125.e6},
doi = {10.1016/j.chom.2023.05.024},
pmid = {37339626},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Metagenome ; Firmicutes ; Bacteroides/genetics ; Feces/microbiology ; },
abstract = {The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.},
}
@article {pmid37315663,
year = {2023},
author = {Xiao, J and Tsim, KWK and Hajisamae, S and Wang, WX},
title = {Chromosome-level genome and population genomics provide novel insights into adaptive divergence in allopatric Eleutheronema tetradactylum.},
journal = {International journal of biological macromolecules},
volume = {244},
number = {},
pages = {125299},
doi = {10.1016/j.ijbiomac.2023.125299},
pmid = {37315663},
issn = {1879-0003},
mesh = {Animals ; *Metagenomics ; *Genome/genetics ; Fishes ; Base Sequence ; Chromosomes ; },
abstract = {Understanding the adaptive ecological divergence provides important information for revealing biodiversity generation and maintenance. Adaptive ecology divergence in populations occurs in various environments and locations, but its genetic underpinnings remain elusive. We generated a chromosome-level genome of Eleutheronema tetradactylum (~582 Mb) and re-sequenced 50 allopatric E. tetradactylum in two independent environmental axes in China and Thailand Coastal waters as well as 11 cultured relatives. A low level of whole genome-wide diversity explained their decreased adaptive potential in the wild environment. Demographic analysis showed evidence of historically high abundance followed by a continuous distinct decline, plus signs of recent inbreeding and accumulation of deleterious mutations. Extensive signals of selective sweeps with signs of local adaptation to environmental differentiation between China and Thailand at genes related to thermal and salinity adaptation were discovered, which might be the driving factors of the geographical divergence of E. tetradactylum. Many genes and pathways subjected to strong selection under artificial breeding were associated with fatty acids and immunity (ELOVL6L, MAPK, p53/NF-kB), likely contributing to the eventual adaptation of artificial selective breeding. Our comprehensive study provided crucial genetic information for E. tetradactylum, with implications for the further conservation efforts of this threatened and ecologically valuable fish.},
}
@article {pmid37306708,
year = {2023},
author = {Amin, AB and Zhang, L and Zhang, J and Mao, S},
title = {Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {15},
pages = {4887-4902},
pmid = {37306708},
issn = {1432-0614},
support = {2021YFF1000703-01//National key Research and Development program of China/ ; },
mesh = {Female ; Cattle ; Animals ; *Milk Proteins/metabolism ; Lactation ; Rumen/microbiology ; Metagenomics ; Lysine/metabolism ; Diet/veterinary ; *Microbiota ; Carbohydrates ; Nitrogen/metabolism ; Fermentation ; Animal Feed/analysis ; },
abstract = {Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed at investigating the difference in the composition and functions of rumen microbiota as well as fermentation metabolites in Holstein cows with high and low milk protein concentrations. In this study, 20 lactating Holstein cows on the same diet were divided into two groups (10 cows each), high degree of milk protein group (HD), and low degree of milk protein (LD) concentrations based on previous milk composition history. Rumen content samples were obtained to explore the rumen fermentation parameters and rumen microbial composition. Shotgun metagenomics sequencing was employed to investigate the rumen microbial composition and sequences were assembled via the metagenomics binning technique. Metagenomics revealed that 6 Archaea genera, 5 Bacteria genera, 7 Eukaryota genera, and 7 virus genera differed significantly between the HD and LD group. The analysis of metagenome-assembled genomes (MAGs) showed that 2 genera (g__Eubacterium_H and g__Dialister) were significantly enriched (P < 0.05, linear discriminant analysis (LDA) > 2) in the HD group. However, the LD group recorded an increased abundance (P < 0.05, LDA > 2) of 8 genera (g__CAG-603, g__UBA2922, g__Ga6A1, g__RUG13091, g__Bradyrhizobium, g__Sediminibacterium, g__UBA6382, and g__Succinivibrio) when compared to the HD group. Furthermore, investigation of the KEGG genes revealed an upregulation in a higher number of genes associated with nitrogen metabolism and lysine biosynthesis pathways in the HD group as compared to the LD group. Therefore, the high milk protein concentration in the HD group could be explained by an increased ammonia synthesis by ruminal microbes which were converted to microbial amino acids and microbial protein (MCP) in presence of an increased energy source made possible by higher activities of carbohydrate-active enzymes (CAZymes). This MCP gets absorbed in the small intestine as amino acids and might be utilized for the synthesis of milk protein. KEY POINTS: • Rumen microbiota and their functions differed between cows with high milk protein % and those with low milk protein %. • The rumen microbiome of cows with high milk protein recorded a higher number of enriched genes linked to the nitrogen metabolism pathway and lysine biosynthesis pathway. • The activities of carbohydrate-active enzymes were found to be higher in the rumen of cows with high milk protein %.},
}
@article {pmid37290262,
year = {2023},
author = {Mokhtari, P and Jambal, P and Metos, JM and Shankar, K and Anandh Babu, PV},
title = {Microbial taxonomic and functional shifts in adolescents with type 1 diabetes are associated with clinical and dietary factors.},
journal = {EBioMedicine},
volume = {93},
number = {},
pages = {104641},
pmid = {37290262},
issn = {2352-3964},
support = {R01 AT010247/AT/NCCIH NIH HHS/United States ; },
mesh = {Humans ; Adolescent ; *Diabetes Mellitus, Type 1 ; Feces/microbiology ; *Microbiota ; Bacteria ; Vitamins/metabolism ; Amino Acids/metabolism ; },
abstract = {BACKGROUND: Evidence indicates a link between the pathogenesis of type 1 diabetes (T1D) and the gut microbiome. However, the regulation of microbial metabolic pathways and the associations of bacterial species with dietary factors in T1D are largely unknown. We investigated whether microbial metagenomic signatures in adolescents with T1D are associated with clinical/dietary factors.<br><br>METHODS: Adolescents with T1D (case) and healthy adolescents (control) were recruited, and microbiome profiling in participants' stool samples was performed using shotgun metagenomic sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan 4 and HUMAnN) was used to assign taxonomy and functional annotations. Clinical (HbA1c) and dietary information (3-day food record) were collected for conducting association analysis using Spearman's correlation.<br><br>FINDINGS: Adolescents with T1D exhibited modest changes in taxonomic composition of gut microbiome. Nineteen microbial metabolic pathways were altered in T1D, including downregulation of biosynthesis of vitamins (B2/flavin, B7/biotin and B9/folate), enzyme cofactors (NAD[+] and s-adenosyl methionine) and amino acids (aspartate, asparagine and lysine) with an upregulation in the fermentation pathways. Furthermore, bacterial species associated with dietary and clinical factors differed between healthy adolescents and adolescents with T1D. Supervised models modeling identified taxa predictive of T1D status, and the top features included Coprococcus and Streptococcus.<br><br>INTERPRETATION: Our study provides new insight into the alteration of microbial and metabolic signatures in adolescents with T1D, suggesting that microbial biosynthesis of vitamins, enzyme cofactors and amino acids may be potentially altered in T1D.<br><br>FUNDING: Research grants from NIH/NCCIH: R01AT010247 and USDA/NIFA: 2019-67017-29253; and Larry &amp; Gail Miller Family Foundation Assistantship.},
}
@article {pmid37279013,
year = {2023},
author = {Medina-Chávez, NO and Viladomat-Jasso, M and Zarza, E and Islas-Robles, A and Valdivia-Anistro, J and Thalasso-Siret, F and Eguiarte, LE and Olmedo-Álvarez, G and Souza, V and De la Torre-Zavala, S},
title = {A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico.},
journal = {Astrobiology},
volume = {23},
number = {7},
pages = {796-811},
doi = {10.1089/ast.2021.0047},
pmid = {37279013},
issn = {1557-8070},
mesh = {*Archaea/genetics ; Mexico ; Phylogeny ; Bacteria/genetics ; *Microbiota ; Water ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.},
}
@article {pmid36801350,
year = {2023},
author = {Sammouri, J and Wong, MC and Lynn, EJ and El Alam, MB and Lo, DK and Lin, D and Harris, TH and Karpinets, TV and Court, K and Napravnik, TC and Wu, X and Zhang, J and Klopp, AH and Ajami, NJ and Colbert, LE},
title = {Serial Genotyping of the Human Papillomavirus in Cervical Cancer: An Insight Into Virome Dynamics During Chemoradiation Therapy.},
journal = {International journal of radiation oncology, biology, physics},
volume = {116},
number = {5},
pages = {1043-1054},
doi = {10.1016/j.ijrobp.2023.02.018},
pmid = {36801350},
issn = {1879-355X},
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/pathology ; Human Papillomavirus Viruses ; *Papillomavirus Infections/complications ; Prospective Studies ; Genotype ; Virome ; Papillomaviridae/genetics ; DNA, Viral/analysis ; },
abstract = {PURPOSE: Human papillomavirus (HPV) is the primary driver of cervical cancer. Although studies in other malignancies correlated peripheral blood DNA clearance with favorable outcomes, research on the prognostic value of HPV clearance in gynecologic cancers using intratumoral HPV is scarce. We aimed to quantify the intratumoral HPV virome in patients undergoing chemoradiation therapy (CRT) and associate this with clinical characteristics and outcomes.<br><br>METHODS AND MATERIALS: This prospective study enrolled 79 patients with stage IB-IVB cervical cancer undergoing definitive CRT. Cervical tumor swabs collected at baseline and week 5 (end of intensity modulated radiation therapy) were sent for shotgun metagenome sequencing and processed via VirMAP, a viral genome sequencing and identification tool for all known HPV types. The data were categorized into HPV groups (16, 18, high risk [HR], and low risk [LR]). We used independent t tests and Wilcoxon signed-rank to compare continuous variables and &#x3c7;[2] and Fisher exact tests to compare categorical variables. Kaplan-Meier survival modeling was performed with log-rank testing. HPV genotyping was verified using quantitative polymerase chain reaction to validate VirMAP results using receiver operating characteristic curve and Cohen's kappa.<br><br>RESULTS: At baseline, 42%, 12%, 25%, and 16% of patients were positive for HPV 16, HPV 18, HPV HR, and HPV LR, respectively, and 8% were HPV negative. HPV type was associated with insurance status and CRT response. Patients with HPV 16+ and other HPV HR+ tumors were significantly more likely to have a complete response to CRT versus patients with HPV 18 and HPV LR/HPV-negative tumors. Overall HPV viral loads predominantly decreased throughout CRT, except for HPV LR viral load.<br><br>CONCLUSIONS: Rarer, less well-studied HPV types in cervical tumors are clinically significant. HPV 18 and HPV LR/negative tumors are associated with poor CRT response. This feasibility study provides a framework for a larger study of intratumoral HPV profiling to predict outcomes in patients with cervical cancer.},
}
@article {pmid37445967,
year = {2023},
author = {He, K and Xiong, J and Yang, W and Zhao, L and Wang, T and Qian, W and Hu, S and Wang, Q and Aleem, MT and Miao, W and Yan, W},
title = {Metagenome of Gut Microbiota Provides a Novel Insight into the Pathogenicity of Balantioides coli in Weaned Piglets.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37445967},
issn = {1422-0067},
support = {31772733//National Natural Science Foundation of China/ ; },
abstract = {Balantioides coli plays an important role in the diarrhea of weaned piglets, but its pathogenic potential and interaction with gut microbes remain unclear. To investigate the impact of B. coli colonization on the gut bacterial structure and function of weaned piglets, a metagenomic analysis based on shotgun sequencing was performed on fresh fecal samples collected from ten B. coli-colonized piglets and eight B. coli-free ones in this study. The results showed that decreasing diversity and shifted composition and function of the bacterial community were detected in the weaned piglets infected by B. coli. In contrast to the B. coli-negative group, the relative abundances of some members of the Firmicutes phylum including Clostridium, Ruminococcus species, and Intestinimonas butyriciproducens, which produce short-chain fatty acids, were significantly reduced in the B. coli-positive group. Notably, some species of the Prevotella genus (such as Prevotella sp. CAG:604 and Prevotella stercorea) were significantly increased in abundance in the B. coli-positive piglets. A functional analysis of the gut microbiota demonstrated that the differential gene sets for the metabolism of carbohydrates and amino acids were abundant in both groups, and the more enriched pathways in B. coli-infected piglets were associated with the sugar-specific phosphotransferase system (PTS) and the two-component regulatory system, as well as lipopolysaccharide (LPS) biosynthesis. Furthermore, several species of Prevotella were significantly positively correlated to the synthesis of lipid A, leading to the exporting of endotoxins and, thereby, inducing inflammation in the intestines of weaned piglets. Taken together, these findings revealed that colonization by B. coli was distinctly associated with the dysbiosis of gut bacterial structure and function in weaned piglets. Lower relative abundances of Clostridiaceae and Ruminococcaceae and higher abundances of Prevotella species were biomarkers of B. coli infection in weaned piglets.},
}
@article {pmid37442461,
year = {2023},
author = {Yang, J and He, J and Jia, L and Gu, H},
title = {Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {165486},
doi = {10.1016/j.scitotenv.2023.165486},
pmid = {37442461},
issn = {1879-1026},
abstract = {As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.},
}
@article {pmid37438876,
year = {2023},
author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I},
title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2226921},
pmid = {37438876},
issn = {1949-0984},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; },
abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.},
}
@article {pmid37438797,
year = {2023},
author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS},
title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.},
journal = {Genome medicine},
volume = {15},
number = {1},
pages = {49},
pmid = {37438797},
issn = {1756-994X},
support = {K23DK125838/DK/NIDDK NIH HHS/United States ; K01DK120742/BC/NCI NIH HHS/United States ; },
mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<br><br>METHODS: We profiled 127 hospitalized patients with COVID-19 (n&#x2009;=&#x2009;79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<br><br>RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.<br><br>CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.},
}
@article {pmid37438354,
year = {2023},
author = {Lacunza, E and Fink, V and Salas, ME and Canzoneri, R and Naipauer, J and Williams, S and Coso, O and Sued, O and Cahn, P and Mesri, EA and Abba, MC},
title = {Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {48},
pmid = {37438354},
issn = {2055-5008},
support = {CA221208//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; CA221208//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Male ; Humans ; Female ; *HIV Infections/complications ; Homosexuality, Male ; *Sexual and Gender Minorities ; *Microbiota ; Metabolic Networks and Pathways ; },
abstract = {Evidence indicates that the microbiome plays a significant role in HIV immunopathogenesis and associated complications. This study aimed to characterize the oral and anal microbiome of Men who have Sex with Men (MSM) and Transgender Women (TGW), with and without HIV. One hundred and thirty oral and anal DNA-derived samples were obtained from 78 participants and subjected to shotgun metagenomics sequencing for further microbiome analysis. Significant differences in the microbiome composition were found among subjects associated with HIV infection, gender, sex behavior, CD4+ T-cell counts, antiretroviral therapy (ART), and the presence of HPV-associated precancerous anal lesions. Results confirm the occurrence of oncogenic viromes in this high HIV-risk population. The oral microbiome in HIV-associated cases exhibited an enrichment of bacteria associated with periodontal disease pathogenesis. Conversely, anal bacteria showed a significant decrease in HIV-infected subjects (Coprococcus comes, Finegoldia magna, Blautia obeum, Catenibacterium mitsuokai). TGW showed enrichment in species related to sexual transmission, which concurs that most recruited TGW are or have been sex workers. Prevotella bivia and Fusobacterium gonidiaformans were positively associated with anal precancerous lesions among HIV-infected subjects. The enrichment of Holdemanella biformis and C. comes was associated with detectable viral load and ART-untreated patients. Metabolic pathways were distinctly affected by predominant factors linked to sexual behavior or HIV pathogenesis. Gene family analysis identified bacterial gene signatures as potential prognostic and predictive biomarkers for HIV/AIDS-associated malignancies. Conclusions: Identified microbial features at accessible sites are potential biomarkers for predicting precancerous anal lesions and therapeutic targets for HIV immunopathogenesis.},
}
@article {pmid37434868,
year = {2023},
author = {Martinez-Hernandez, JE and Berrios, P and Santibáñez, R and Cuesta Astroz, Y and Sanchez, C and Martin, AJM and Trombert, AN},
title = {First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15235},
pmid = {37434868},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Falconiformes ; Acclimatization ; Chile ; Clostridium perfringens ; },
abstract = {BACKGROUND: The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome.<br><br>METHODS: This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways.<br><br>RESULTS: Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.},
}
@article {pmid37434780,
year = {2023},
author = {Xie, G and Hu, Q and Cao, X and Wu, W and Dai, P and Guo, W and Wang, O and Wei, L and Ren, R and Li, Y},
title = {Clinical identification and microbiota analysis of Chlamydia psittaci- and Chlamydia abortus- pneumonia by metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1157540},
pmid = {37434780},
issn = {2235-2988},
mesh = {Humans ; *Chlamydophila psittaci/genetics ; *Chlamydial Pneumonia/diagnosis ; *Coinfection ; *Chlamydia/genetics ; *Microbiota ; *Pneumonia/diagnosis ; *Chlamydia Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; },
abstract = {INTRODUCTION: Recently, the incidence of chlamydial pneumonia caused by rare pathogens such as C. psittaci or C. abortus has shown a significant upward trend. The non-specific clinical manifestations and the limitations of traditional pathogen identification methods determine that chlamydial pneumonia is likely to be poorly diagnosed or even misdiagnosed, and may further result in delayed treatment or unnecessary antibiotic use. mNGS's non-preference and high sensitivity give us the opportunity to obtain more sensitive detection results than traditional methods for rare pathogens such as C. psittaci or C. abortus.<br><br>METHODS: In the present study, we investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of pneumonia patients with different chlamydial infection patterns using mNGS.<br><br>RESULTS: More co-infecting pathogens were found to be detectable in clinical samples from patients infected with C. psittaci compared to C. abortus, suggesting that patients infected with C. psittaci may have a higher risk of mixed infection, which in turn leads to more severe clinical symptoms and a longer disease course cycle. Further, we also used mNGS data to analyze for the first time the characteristic differences in the lower respiratory tract microbiota of patients with and without chlamydial pneumonia, the impact of the pattern of Chlamydia infection on the lower respiratory tract microbiota, and the clinical relevance of these characteristics. Significantly different profiles of lower respiratory tract microbiota and microecological diversity were found among different clinical subgroups, and in particular, mixed infections with C. psittaci and C. abortus resulted in lower lung microbiota diversity, suggesting that chlamydial infections shape the unique lung microbiota pathology, while mixed infections with different Chlamydia may have important effects on the composition and diversity of the lung microbiota.<br><br>DISCUSSION: The present study provides possible evidences supporting the close correlation between chlamydial infection, altered microbial diversity in patients' lungs and clinical parameters associated with infection or inflammation in patients, which also provides a new research direction to better understand the pathogenic mechanisms of pulmonary infections caused by Chlamydia.},
}
@article {pmid37433843,
year = {2023},
author = {Hintikka, JE and Ahtiainen, JP and Permi, P and Jalkanen, S and Lehtonen, M and Pekkala, S},
title = {Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {11228},
pmid = {37433843},
issn = {2045-2322},
mesh = {Adult ; Humans ; Female ; *Overweight/therapy ; *Gastrointestinal Microbiome ; Multiomics ; Exercise ; Obesity/therapy ; Lecithins ; },
abstract = {Physical activity is essential in weight management, improves overall health, and mitigates obesity-related risk markers. Besides inducing changes in systemic metabolism, habitual exercise may improve gut's microbial diversity and increase the abundance of beneficial taxa in a correlated fashion. Since there is a lack of integrative omics studies on exercise and overweight populations, we studied the metabolomes and gut microbiota associated with programmed exercise in obese individuals. We measured the serum and fecal metabolites of 17 adult women with overweight during a 6-week endurance exercise program. Further, we integrated the exercise-responsive metabolites with variations in the gut microbiome and cardiorespiratory parameters. We found clear correlation with several serum and fecal metabolites, and metabolic pathways, during the exercise period in comparison to the control period, indicating increased lipid oxidation and oxidative stress. Especially, exercise caused co-occurring increase in levels of serum lyso-phosphatidylcholine moieties and fecal glycerophosphocholine. This signature was associated with several microbial metagenome pathways and the abundance of Akkermansia. The study demonstrates that, in the absence of body composition changes, aerobic exercise can induce metabolic shifts that provide substrates for beneficial gut microbiota in overweight individuals.},
}
@article {pmid36634616,
year = {2023},
author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Jang, JY and Choi, J and Lee, HN},
title = {Anti-PD-L1 Antibody and/or 17β-Estradiol Treatment Induces Changes in the Gut Microbiome in MC38 Colon Tumor Model.},
journal = {Cancer research and treatment},
volume = {55},
number = {3},
pages = {894-909},
doi = {10.4143/crt.2022.1427},
pmid = {36634616},
issn = {2005-9256},
support = {2019R1A2C2085149//National Research Foundation of Korea/ ; },
mesh = {Male ; Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Cell Line, Tumor ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; *Colonic Neoplasms/drug therapy ; Estradiol/pharmacology ; Estrogens/pharmacology ; },
abstract = {PURPOSE: 17β-Estradiol (E2) supplementation suppresses MC38 tumor growth by downregulating the expression of programmed death-ligand 1 (PD-L1). This study aims to figure out the gut microbiota that respond to anti-PD-L1 and/or estrogen treatment in MC38 colon cancer model.<br><br>MATERIALS AND METHODS: A syngeneic colon tumor model was developed by injection of MC38 cells into C57BL/6 background male and female mice. Three days before MC38 cells injection, E2 was supplemented to male mice daily for 1 week. Male and female mice with MC38 tumors (50-100 mm3) were injected with anti-PD-L1 antibody. Fresh feces were collected 26 days after injection of MC38 cells and 16S rRNA metagenomics sequencing of DNA extracted from feces was used to assess gut microbial composition.<br><br>RESULTS: At the taxonomic family level, Muribaculaceae was enriched only in the MC38 male control group. In male mice, linear discriminant analysis effect size analysis at the species level revealed that the four microorganisms were commonly regulated in single and combination treatment with anti-PD-L1 and/or E2; a decrease in PAC001068_g_uc and PAC001070_s (family Muribaculaceae) and increase in PAC001716_s and PAC001785_s (family Ruminococcaceae). Interestingly, in the anti-PD-L1 plus E2 group, a decrease in opportunistic pathogens (Enterobacteriaceae group) and an increase in commensal bacteria (Lactobacillus murinus group and Parabacteroides goldsteinii) were observed. Furthermore, the abundance of Parabacteroides goldsteinii was increased in both males and females in the anti-PD-L1 group.<br><br>CONCLUSION: Our results suggest that gut microbial changes induced by the pretreatment of estrogen before anti-PD-L1 might contribute to treatment of MC38 colon cancer.},
}
@article {pmid37432374,
year = {2023},
author = {Silvano, A and Meriggi, N and Renzi, S and Seravalli, V and Torcia, MG and Cavalieri, D and Di Tommaso, M},
title = {Vaginal Microbiome in Pregnant Women with and without Short Cervix.},
journal = {Nutrients},
volume = {15},
number = {9},
pages = {},
pmid = {37432374},
issn = {2072-6643},
support = {B15F21003630007//Ente Cassa di Risparmio di Firenze/ ; },
mesh = {Pregnancy ; Humans ; Female ; *Cervix Uteri ; Pregnant Women ; Vagina ; *Microbiota ; Metagenome ; },
abstract = {Cervical shortening is a recognised risk factor for pre-term birth. The vaginal microbiome plays an essential role in pregnancy and in maternal and foetal outcomes. We studied the vaginal microbiome in 68 women with singleton gestation and a cervical length ≤25 mm and in 29 pregnant women with a cervix >25 mm in the second or early third trimester. Illumina protocol 16S Metagenomic Sequencing Library Preparation was used to detail amplified 16SrRNA gene. Statistical analyses were performed in R environment. Firmicutes was the phylum most represented in all pregnant women. The mean relative abundance of Proteobacteria and Actinobacteriota was higher in women with a short cervix. Bacterial abundance was higher in women with a normal length cervix compared to the group of women with a short cervix. Nonetheless, a significant enrichment in bacterial taxa poorly represented in vaginal microbiome was observed in the group of women with a short cervix. Staphylococcus and Pseudomonas, taxa usually found in aerobic vaginitis, were more common in women with a short cervix compared with the control group, while Lactobacillus iners and Bifidobacterium were associated with a normal cervical length. Lactobacillus jensenii and Gardenerella vaginalis were associated with a short cervix.},
}
@article {pmid37432207,
year = {2023},
author = {Chen, BY and Li, YL and Lin, WZ and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Zhang, J and Liu, Y and Zhu, H and Zhang, WC and Zhang, ZY and Duan, SZ},
title = {Integrated Omic Analysis of Human Plasma Metabolites and Microbiota in a Hypertension Cohort.},
journal = {Nutrients},
volume = {15},
number = {9},
pages = {},
pmid = {37432207},
issn = {2072-6643},
support = {81725003, 81991503, 81991500, 81921002//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; *Hypertension ; },
abstract = {Hypertension is closely related to metabolic dysregulation, which is associated with microbial dysbiosis and altered host-microbiota interactions. However, plasma metabolite profiles and their relationships to oral/gut microbiota in hypertension have not been evaluated in depth. Plasma, saliva, subgingival plaques, and feces were collected from 52 hypertensive participants and 24 healthy controls in a cross-sectional cohort. Untargeted metabolomic profiling of plasma was performed using high-performance liquid chromatography-mass spectrometry. Microbial profiling of oral and gut samples was determined via 16S rRNA and metagenomic sequencing. Correlations between metabolites and clinic parameters/microbiota were identified using Spearman's correlation analysis. Metabolomic evaluation showed distinct clusters of metabolites in plasma between hypertensive participants and control participants. Hypertensive participants had six significantly increased and thirty-seven significantly decreased plasma metabolites compared to controls. The plasma metabolic similarity significantly correlated with the community similarity of microbiota. Both oral and gut microbial community composition had significant correlations with metabolites such as Sphingosine 1-phosphate, a molecule involved in the regulation of blood pressure. Plasma metabolites had a larger number of significant correlations with bacterial genera than fungal genera. The shared oral/gut bacterial genera had more correlations with metabolites than unique genera but shared fungal genera and metabolites did not show clear clusters. The hypertension group had fewer correlations between plasma metabolites and bacteria/fungi than controls at species level. The integrative analysis of plasma metabolome and oral/gut microbiome identified unreported alterations of plasma metabolites in hypertension and revealed correlations between altered metabolites and oral/gut microbiota. These observations suggested metabolites and microbiota may become valuable targets for therapeutic and preventive interventions of hypertension.},
}
@article {pmid37431863,
year = {2023},
author = {Han, B and Lv, X and Liu, G and Li, S and Fan, J and Chen, L and Huang, Z and Lin, G and Xu, X and Huang, Z and Zhan, L and Lv, X},
title = {Gut microbiota-related bile acid metabolism-FXR/TGR5 axis impacts the response to anti-α4β7-integrin therapy in humanized mice with colitis.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2232143},
pmid = {37431863},
issn = {1949-0984},
mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Caco-2 Cells ; *Colitis/chemically induced/drug therapy ; *Inflammatory Bowel Diseases ; Bile Acids and Salts ; Integrins ; },
abstract = {The gut microbiota and bile acid metabolism are key determinants of the response of inflammatory bowel disease to biologic therapy. However, the molecular mechanisms underlying the interactions between the response to anti-α4β7-integrin therapy and the gut microbiota and bile acid metabolism remain unknown. In this research, we investigated the role of gut microbiota-related bile acid metabolism on the response to anti-α4β7-integrin therapy in a humanized immune system mouse model with colitis induced by 2,4,6-trinitrobenzene sulfonic acid. We found that anti-α4β7-integrin significantly mitigated intestinal inflammation, pathological symptoms, and gut barrier disruption in remission-achieving colitis mice. Whole-genome shotgun metagenomic sequencing demonstrated that employing baseline microbiome profiles to predict remission and the treatment response was a promising strategy. Antibiotic-mediated gut microbiota depletion and fecal microbiome transplantation revealed that the baseline gut microbiota contained common microbes with anti-inflammatory effects and reduced mucosal barrier damage, improving the treatment response. Targeted metabolomics analysis illustrated that bile acids associated with microbial diversity were involved in colitis remission. Furthermore, the activation effects of the microbiome and bile acids on FXR and TGR5 were evaluated in colitis mice and Caco-2 cells. The findings revealed that the production of gastrointestinal bile acids, particularly CDCA and LCA, further directly promoted the stimulation of FXR and TGR5, significantly improving gut barrier function and suppressing the inflammatory process. Taken together, gut microbiota-related bile acid metabolism-FXR/TGR5 axis may be a potential mechanism for impacting the response to anti-α4β7-integrin in experimental colitis. Thus, our research provides novel insights into the treatment response in inflammatory bowel disease.},
}
@article {pmid37428148,
year = {2023},
author = {Serghiou, IR and Baker, D and Evans, R and Dalby, MJ and Kiu, R and Trampari, E and Phillips, S and Watt, R and Atkinson, T and Murphy, B and Hall, LJ and Webber, MA},
title = {An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs.},
journal = {Microbial genomics},
volume = {9},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001058},
pmid = {37428148},
issn = {2057-5858},
support = {BB/T508974/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T014644/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adult ; Humans ; DNA, Bacterial/genetics ; *Metagenomics/methods ; Molecular Weight ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA ; },
abstract = {The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.},
}
@article {pmid37419993,
year = {2023},
author = {Bei, Q and Reitz, T and Schnabel, B and Eisenhauer, N and Schädler, M and Buscot, F and Heintz-Buschart, A},
title = {Extreme summers impact cropland and grassland soil microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37419993},
issn = {1751-7370},
abstract = {The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.},
}
@article {pmid37379127,
year = {2023},
author = {Deek, RA and Li, H},
title = {Inference of microbial covariation networks using copula models with mixture margins.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {7},
pages = {},
pmid = {37379127},
issn = {1367-4811},
support = {GM123056/NH/NIH HHS/United States ; },
mesh = {Likelihood Functions ; RNA, Ribosomal, 16S/genetics ; *Microbial Consortia ; Computer Simulation ; *Metagenome ; },
abstract = {MOTIVATION: Quantification of microbial covariations from 16S rRNA and metagenomic sequencing data is difficult due to their sparse nature. In this article, we propose using copula models with mixed zero-beta margins for the estimation of taxon-taxon covariations using data of normalized microbial relative abundances. Copulas allow for separate modeling of the dependence structure from the margins, marginal covariate adjustment, and uncertainty measurement.<br><br>RESULTS: Our method shows that a two-stage maximum-likelihood approach provides accurate estimation of model parameters. A corresponding two-stage likelihood ratio test for the dependence parameter is derived and is used for constructing covariation networks. Simulation studies show that the test is valid, robust, and more powerful than tests based upon Pearson's and rank correlations. Furthermore, we demonstrate that our method can be used to build biologically meaningful microbial networks based on a dataset from the American Gut Project.<br><br>R package for implementation is available at https://github.com/rebeccadeek/CoMiCoN.},
}
@article {pmid37074327,
year = {2023},
author = {Elnaggar, JH and Lammons, JW and Taylor, CM and Toh, E and Ardizzone, CM and Dong, A and Aaron, KJ and Luo, M and Tamhane, A and Lefkowitz, EJ and Quayle, AJ and Nelson, DE and Muzny, CA},
title = {Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study.},
journal = {Sexually transmitted diseases},
volume = {50},
number = {8},
pages = {523-530},
doi = {10.1097/OLQ.0000000000001821},
pmid = {37074327},
issn = {1537-4521},
support = {R01 AI118860/AI/NIAID NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; K23 AI106957/AI/NIAID NIH HHS/United States ; R01 AI146065/AI/NIAID NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; },
mesh = {Female ; Humans ; *Vaginosis, Bacterial/diagnosis ; Pilot Projects ; Vagina/microbiology ; Gardnerella vaginalis/genetics ; *Microbiota ; Bacteria/genetics ; Lactobacillus/genetics ; },
abstract = {BACKGROUND: Despite more than 60 years of research, the etiology of bacterial vaginosis (BV) remains controversial. In this pilot study, we used shotgun metagenomic sequencing to characterize vaginal microbial community changes before the development of incident BV (iBV).<br><br>METHODS: A cohort of African American women with a baseline healthy vaginal microbiome (no Amsel criteria, Nugent score 0-3 with no Gardnerella vaginalis morphotypes) were followed for 90 days with daily self-collected vaginal specimens for iBV (&#x2265;2 consecutive days of a Nugent score of 7-10). Shotgun metagenomic sequencing was performed on select vaginal specimens from 4 women, every other day for 12 days before iBV diagnosis. Sequencing data were analyzed through Kraken2 and bioBakery 3 workflows, and specimens were classified into community state types. Quantitative polymerase chain reaction was performed to compare the correlation of read counts with bacterial abundance.<br><br>RESULTS: Common BV-associated bacteria such as G. vaginalis , Prevotella bivia , and Fannyhessea vaginae were increasingly identified in the participants before iBV. Linear modeling indicated significant increases in G. vaginalis and F . vaginae relative abundance before iBV, whereas the relative abundance of Lactobacillus species declined over time. The Lactobacillus species decline correlated with the presence of Lactobacillus phages. We observed enrichment in bacterial adhesion factor genes on days before iBV. There were also significant correlations between bacterial read counts and abundances measured by quantitative polymerase chain reaction.<br><br>CONCLUSIONS: This pilot study characterizes vaginal community dynamics before iBV and identifies key bacterial taxa and mechanisms potentially involved in the pathogenesis of iBV.},
}
@article {pmid36509943,
year = {2023},
author = {Li, W and Ma, ZS},
title = {The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1428-1437},
pmid = {36509943},
issn = {1432-184X},
mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19 ; *Chiroptera ; *Microbiota/genetics ; Bacteria/genetics ; Respiratory System ; },
abstract = {The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.},
}
@article {pmid36239777,
year = {2023},
author = {Tian, C and Lv, Y and Yang, Z and Zhang, R and Zhu, Z and Ma, H and Li, J and Zhang, Y},
title = {Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {933-946},
pmid = {36239777},
issn = {1432-184X},
support = {41676177//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; 41676175//National Natural Science Foundation of China/ ; 41676188//National Natural Science Foundation of China/ ; SL2020MS022//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; },
mesh = {*Soil/chemistry ; Svalbard ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Ice Cover/microbiology ; Soil Microbiology ; },
abstract = {Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.},
}
@article {pmid37406521,
year = {2023},
author = {Zeng, J and Pan, Y and Hu, R and Liu, F and Gu, H and Ding, J and Liu, S and Liu, S and Yang, X and Peng, Y and Tian, Y and He, Q and Wu, Y and Yan, Q and Shu, L and He, Z and Wang, C},
title = {The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity.},
journal = {Journal of hazardous materials},
volume = {458},
number = {},
pages = {131974},
doi = {10.1016/j.jhazmat.2023.131974},
pmid = {37406521},
issn = {1873-3336},
abstract = {Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.},
}
@article {pmid37402745,
year = {2023},
author = {Amit, G and Bashan, A},
title = {Top-down identification of keystone taxa in the microbiome.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3951},
pmid = {37402745},
issn = {2041-1723},
mesh = {Humans ; Cross-Sectional Studies ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Microbial Interactions ; },
abstract = {Keystone taxa in ecological communities are native taxa that play an especially important role in the stability of their ecosystem. However, we still lack an effective framework for identifying these taxa from the available high-throughput sequencing without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. In addition, while most microbial interaction models assume pair-wise relationships, it is yet unclear whether pair-wise interactions dominate the system, or whether higher-order interactions are relevant. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the taxa. Our method does not assume a priori knowledge of pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real high-throughput sequencing of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module - multiple candidate keystone species with correlated occurrence. The keystone analysis of single-time-point cross-sectional data is also later verified by the evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.},
}
@article {pmid37350694,
year = {2023},
author = {Li, JM and Ou, JH and Verpoort, F and Surmpalli, RY and Huang, WY and Kao, CM},
title = {Toxicity evaluation of a heavy-metal-polluted river: Pollution identification and bacterial community assessment.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {95},
number = {7},
pages = {e10904},
doi = {10.1002/wer.10904},
pmid = {37350694},
issn = {1554-7531},
support = {//Taiwan National Science and Technology Council/ ; },
mesh = {Humans ; Wastewater ; Geologic Sediments ; *Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/toxicity/analysis ; Proteobacteria ; Risk Assessment ; *Microbiota ; China ; },
abstract = {The Salt River is an important urban river in Kaohsiung, Taiwan. In this study, the source identification and risk and toxicity assessment of the heavy-metal-contaminated sediments in the Salt River were investigated. The geo-accumulation index (Igeo), enrichment factor (EF), sediment quality guidelines (SQGs), potential ecological risk index (RI), pollution load index (PLI), and toxic units (TU) were applied to determine effects of heavy metals on microbial diversities and ecosystems. Results from the ecological and environmental risk assessment show that high concentrations of Zn, Cr, and Ni were detected in the midstream area and the sum of toxic units (ΣTUs) in the midstream (7.2-32.0) is higher than in the downstream (14.0-19.7) and upstream (9.2-17.1). It could be because of the continuous inputs of heavy-metal-contained wastewaters from adjacent industrial parks. Results also inferred that the detected heavy metals in the upstream residential and commercial areas were possibly caused by nearby vehicle emissions, non-point source pollution, and domestic wastewater discharges. Results of metagenomic assays show that the sediments contained significant microbial diversities. Metal-tolerant bacterial phyla (Proteobacteria: 24.4%-46.4%, Bacteroidetes: 1.3%-14.8%, and Actinobacteria: 2.3%-11.1%) and pathogenic bacterial phyla (Chlamydiae: 0.5%-37.6% and Chloroflexi: 5.8%-7.2%) with relatively high abundance were detected. Metal-tolerant bacteria would adsorb metals and cause the increased metal concentrations in sediments. Results indicate that the bacterial composition in sediment environments was affected by anthropogenic pollution and human activities and the heavy-metal-polluted ecosystem caused the variations in bacterial communities. PRACTITIONER POINTS: Microbial community in sediments is highly affected by heavy metal pollution. Wastewaters and vehicle traffic contribute to river sediments pollution by heavy metals. Proteobacteria, Bacteroidota, and Actinobacteria are dominant heavy-metal-tolerant bacterial phyla in sediments. Toxicity assessment is required to study risk levels of heavy-metal contained sediments.},
}
@article {pmid37260265,
year = {2023},
author = {Hosszu-Fellous, K and Zanella, MC and Kaiser, L and Neofytos, D},
title = {The present and future of blood virome in allogeneic hematopoietic cell transplant recipients.},
journal = {Current opinion in infectious diseases},
volume = {36},
number = {4},
pages = {243-249},
doi = {10.1097/QCO.0000000000000928},
pmid = {37260265},
issn = {1473-6527},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Transplant Recipients ; Virome ; Immunosuppression Therapy ; },
abstract = {PURPOSE OF REVIEW: Allogeneic hematopoietic cell transplantation (allogeneic HCT) is a highly effective therapy for a broad range of hematological diseases and its use is increasing worldwide. Despite advances in antiviral prophylaxis and treatment, viral infections are still one of the leading causes of post-HCT morbidity and mortality. In this patient population, metagenomic next-generation sequencing (mNGS) revealed a much larger diversity of viruses than previously suspected via the targeted screening approach. In the context of profound immunosuppression, these viral infections may cause transient viremia or protracted replication and potentially be associated with yet unrecognized or unspecific clinical manifestations. On the contrary, by constantly interacting with the immune system, viral infections may have a significant impact on posttransplant outcomes. Here, we review the latest advances in research assessing the role of the blood virome in the development of post-HCT complications.<br><br>RECENT FINDINGS: Research efforts are under way to uncover the potential role of several previously undetected viruses in the development of allogeneic HCT complications and their impact on transplant outcomes.<br><br>SUMMARY: The identification of viral actors impacting post-HCT morbidity and survival is key to optimize monitoring and infection prevention/treatment strategies.},
}
@article {pmid37202853,
year = {2023},
author = {Velsko, IM and Gallois, S and Stahl, R and Henry, AG and Warinner, C},
title = {High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.},
journal = {Molecular ecology},
volume = {32},
number = {14},
pages = {3872-3891},
doi = {10.1111/mec.16988},
pmid = {37202853},
issn = {1365-294X},
mesh = {Humans ; *Dental Plaque ; *Microbiota/genetics ; Mouth ; Diet ; North America ; },
abstract = {Industrialization-including urbanization, participation in the global food chain and consumption of heavily processed foods-is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.},
}
@article {pmid37348505,
year = {2023},
author = {Carter, MM and Olm, MR and Merrill, BD and Dahan, D and Tripathi, S and Spencer, SP and Yu, FB and Jain, S and Neff, N and Jha, AR and Sonnenburg, ED and Sonnenburg, JL},
title = {Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.},
journal = {Cell},
volume = {186},
number = {14},
pages = {3111-3124.e13},
pmid = {37348505},
issn = {1097-4172},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome ; Eukaryota ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.},
}
@article {pmid37327948,
year = {2023},
author = {Naz, S and Ali, Z and Minhas, A and Fatima, A and Waseem, S},
title = {Generation of dysbiotic microbiota in cutaneous leishmaniasis and enhancement of skin inflammation.},
journal = {Microbial pathogenesis},
volume = {181},
number = {},
pages = {106202},
doi = {10.1016/j.micpath.2023.106202},
pmid = {37327948},
issn = {1096-1208},
mesh = {Humans ; *Leishmaniasis, Cutaneous ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Proteobacteria/genetics ; Inflammation/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cutaneous Leishmaniasis (CL) affects millions of people globally and has a significant impact on morbidity and mortality. Innate immune mediators are likely to influence the clinical phenotype of CL through primary responses that restrict or facilitate parasite spread. The aim of this preliminary study was to bring to attention the significance of microbiota in the development of CL and emphasized the necessity of including the role of microbiota in CL while promoting a One Health approach for managing diseases. To achieve this, we used 16S amplicon metagenome sequencing and QIIME2 pipeline to analyze the microbiome composition of CL-infected patients compared to non-infected, healthy subjects. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota, and Actinobacteria. CL-infected individuals, Proteobacteria were the most prevalent (27.63 ± 9.79), with the relative abundance (10.73 ± 5.33) of Proteobacteria in control. Bacilli class was found to be the most prevalent in healthy controls (30.71 ± 8.44) while (20.57 ± 9.51) in CL-infected individuals. The class Alphaproteobacteria was found to be more in CL-infected individuals (5.47 ± 2.07) as compared to healthy controls (1.85 ± 0.39). The CL-infected individuals had a significantly lower relative abundance of the Clostridia class (p < 0.0001). An altered serum microbiome of CL infection and higher microbial abundance in the serum of healthy individuals was observed.},
}
@article {pmid37257591,
year = {2023},
author = {Guo, Y and Li, D and Gao, Y and Gao, J and Zhang, S and Bao, F},
title = {The knock-on effects of different wastewater feeding modes: Change in microbial communities versus resistance genes in pilot-scale aerobic sludge granulation reactors.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164500},
doi = {10.1016/j.scitotenv.2023.164500},
pmid = {37257591},
issn = {1879-1026},
mesh = {*Wastewater ; Sewage/microbiology ; Waste Disposal, Fluid ; Bioreactors/microbiology ; Bacteria/genetics ; *Microbiota ; Anti-Bacterial Agents ; },
abstract = {To explore the effects of wastewater feeding modes on the formation of aerobic granular sludge (AGS) and the complex relationships between resistance genes and bacteria, two pilot-scale sequencing batch reactors (SBRs) were established. The SBR with influent wastewater introduced uniformly through pipes at bottom was designated as BSBR, and the SBR with inlet wastewater flowing directly from top was TSBR. BSBR formed dense AGS due to uniform wastewater feeding at bottom, while TSBR failed to cultivate AGS. Metagenomic sequencing illustrated that rapid growth of AGS in BSBR was accompanied with increase of antibiotic resistance genes (ARGs) abundance, but ARGs diminished when the size of AGS was stable. The ARGs continued to elevate in TSBR, and abundance of metal resistance genes (MRGs) was always higher than that in BSBR. Two reactors had markedly different bacterial community, microbes in BSBR owned stronger activity, conferred greater potential to proliferate. AdeF in two systems had the most complex gene-bacteria relationships which would undergo HGT within bacterial genus. The different feeding modes of wastewater directly led to the changing size of sludge, which caused knock-on effects of variations in the abundance of microbial communities and resistance genes. This study provided promising suggestions for the rapid cultivation of AGS and control of resistance genes at pilot-scale.},
}
@article {pmid37249085,
year = {2023},
author = {Ting, HSL and Chen, Z and Chan, JYK},
title = {Systematic review on oral microbial dysbiosis and its clinical associations with head and neck squamous cell carcinoma.},
journal = {Head &amp; neck},
volume = {45},
number = {8},
pages = {2120-2135},
doi = {10.1002/hed.27422},
pmid = {37249085},
issn = {1097-0347},
mesh = {Humans ; Squamous Cell Carcinoma of Head and Neck ; Dysbiosis/diagnosis/microbiology ; Bacteria ; *Microbiota/genetics ; *Head and Neck Neoplasms/diagnosis ; },
abstract = {OBJECTIVES: The relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome has been drawn in various studies. Microbial diversities, microbiome profiles, metagenomic analysis, and host-pathogen interactions were collected from these studies to highlight similarities and account for inconsistencies. We also evaluate the possible clinical applications of the microbiome regarding screening and diagnosis of HNSCC.<br><br>METHODS: Systematic analysis of studies regarding HNSCC and the microbiome was done according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines. Articles were retrieved from four databases (PubMed, ScienceDirect, CUHK Full-Text Journals, and Cochrane database) and were screened using predefined criteria.<br><br>RESULTS: Twenty studies were chosen after screening for full-text review. &#x3b1;-diversity comparison was inconsistent whereas &#x3b2;-diversity between HNSCC and normal samples showed distinct clustering. Microbial dysbiosis characterized by change in the relative abundances of several bacterial species were also seen in HNSCC patients. At a phylum level, inconsistencies were seen between studies using HNSCC tumor tissue samples and saliva samples. At a genus level, Fusobacterium, Peptostreptococcus, Alloprevotella, Capnocytophaga, Catonella, and Prevotella were differentially enriched in HNSCC while Streptococcus, Actinomyces Veillonella, and Rothia were differentially depleted. Co-occurrence network analysis revealed a positive correlation of HNSCC with periodontal pathogens and a negative correlation with commensal bacteria. Metagenomic analysis of microbiota revealed a differential enrichment of pro-inflammatory genomic pathways which was consistent across various studies. Microbial dysbiosis was applied in clinical use as a tool for HNSCC screening. Random-forest analysis was adopted to differentiate between tumor and normal tissue, at 95.7% and 70.0% accuracies respectively in two studies. Microbial dysbiosis index was also used to predict prognosis.<br><br>CONCLUSIONS: Oral microbial dysbiosis could be a promising tool for HNSCC screening and diagnosis. However, more research should be conducted pertaining to clinical applications to improve diagnostic accuracy and explore other clinical uses.},
}
@article {pmid37247730,
year = {2023},
author = {Liu, Y and Yan, Y and Fu, L and Li, X},
title = {Metagenomic insights into the response of rhizosphere microbial to precipitation changes in the alpine grasslands of northern Tibet.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164212},
doi = {10.1016/j.scitotenv.2023.164212},
pmid = {37247730},
issn = {1879-1026},
mesh = {Tibet ; *Ecosystem ; Grassland ; Rhizosphere ; *Microbiota ; Soil Microbiology ; Soil/chemistry ; Water ; },
abstract = {Water changes caused by precipitation may affect the elemental cycle of ecosystems by influencing soil microorganisms. In this study, precipitation control experiment was conducted in semi-arid alpine grasslands in northern Tibet, and plots were set up and divided into increased water (IW) and decreased water (DW) plots. Moreover, the link between functional genes and soil environmental factors, and the responses of the microbial community functions to precipitation-induced water variations were studied using metagenomic sequencing. To clarify the roles of various proteins and metabolites in the semi-arid alpine grasslands of northern Tibet, functional annotations of clusters of orthologous groups of proteins, Kyoto Encyclopedia of Genes and Genomes, and carbohydrate-active enzyme of the sequencing data were conducted. The results showed that the absolute abundance of microbial functional genes in IW was significantly higher than that in the control check (CK, natural precipitation) and DW. However, the absolute abundance did not significantly differ between CK and DW. There was no significant difference among the four plant species (Stipa purpurea, Carex moocroftii, Othropis microphylla, and Artemisia capillaris) considered in this study. These results indicated that microbial functions were mainly affected by water and do not depend on the species, and that the effect of IW was greater than that of DW. Further, we found that soil C, N, K, and other nutrients play vital roles in microbial growth, microbial functional genes were not affected by pH; however, soil C, N, and K nutrients and functional genes were negative correlated. Overall, this study enhances our understanding of the responses of microorganisms to precipitation and can be used as a valuable reference for understanding the drought resistance of soil microorganisms in semi-arid and alpine regions.},
}
@article {pmid37137684,
year = {2023},
author = {Ben-Yacov, O and Godneva, A and Rein, M and Shilo, S and Lotan-Pompan, M and Weinberger, A and Segal, E},
title = {Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes.},
journal = {Gut},
volume = {72},
number = {8},
pages = {1486-1496},
doi = {10.1136/gutjnl-2022-329201},
pmid = {37137684},
issn = {1468-3288},
mesh = {Adult ; Humans ; *Prediabetic State ; *Gastrointestinal Microbiome ; Blood Glucose Self-Monitoring ; Blood Glucose/metabolism ; Diet ; *Diet, Mediterranean ; *Cardiovascular Diseases ; },
abstract = {OBJECTIVE: To explore the interplay between dietary modifications, microbiome composition and host metabolic responses in a dietary intervention setting of a personalised postprandial-targeting (PPT) diet versus a Mediterranean (MED) diet in pre-diabetes.<br><br>DESIGN: In a 6-month dietary intervention, adults with pre-diabetes were randomly assigned to follow an MED or PPT diet (based on a machine-learning algorithm for predicting postprandial glucose responses). Data collected at baseline and 6 months from 200 participants who completed the intervention included: dietary data from self-recorded logging using a smartphone application, gut microbiome data from shotgun metagenomics sequencing of faecal samples, and clinical data from continuous glucose monitoring, blood biomarkers and anthropometrics.<br><br>RESULTS: PPT diet induced more prominent changes to the gut microbiome composition, compared with MED diet, consistent with overall greater dietary modifications observed. Particularly, microbiome alpha-diversity increased significantly in PPT (p=0.007) but not in MED arm (p=0.18). Post hoc analysis of changes in multiple dietary features, including food-categories, nutrients and PPT-adherence score across the cohort, demonstrated significant associations between specific dietary changes and species-level changes in microbiome composition. Furthermore, using causal mediation analysis we detect nine microbial species that partially mediate the association between specific dietary changes and clinical outcomes, including three species (from Bacteroidales, Lachnospiraceae, Oscillospirales orders) that mediate the association between PPT-adherence score and clinical outcomes of hemoglobin A1c (HbA1c), high-density lipoprotein cholesterol (HDL-C) and triglycerides. Finally, using machine-learning models trained on dietary changes and baseline clinical data, we predict personalised metabolic responses to dietary modifications and assess features importance for clinical improvement in cardiometabolic markers of blood lipids, glycaemic control and body weight.<br><br>CONCLUSIONS: Our findings support the role of gut microbiome in modulating the effects of dietary modifications on cardiometabolic outcomes, and advance the concept of precision nutrition strategies for reducing comorbidities in pre-diabetes.<br><br>TRIAL REGISTRATION NUMBER: NCT03222791.},
}
@article {pmid37401755,
year = {2023},
author = {Ronkainen, A and Khan, I and Krzyżewska-Dudek, E and Hiippala, K and Freitag, TL and Satokari, R},
title = {In vitro adhesion, pilus expression, and in vivo amelioration of antibiotic-induced microbiota disturbance by Bifidobacterium spp. strains from fecal donors.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2229944},
pmid = {37401755},
issn = {1949-0984},
mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; Bifidobacterium ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Clostridioides difficile ; Mice, Inbred C57BL ; Feces/microbiology ; Fecal Microbiota Transplantation ; *Microbiota ; *Clostridium Infections/microbiology ; },
abstract = {Fecal microbiota transplantation (FMT) is used routinely to treat recurrent Clostridioides difficile infection (rCDI) and investigated as a treatment for numerous conditions associated with gut microbiota alterations. Metagenomic analyses have indicated that recipient colonization by donor bacteria may be associated with favorable clinical outcomes. Bifidobacteria are abundant gut commensals associated with health. We have previously demonstrated that Bifidobacterium strains transferred in FMT can colonize recipients in long term, at least for a year, and recovered such strains by cultivation. This study addressed in vitro adhesion and pilus gene expression of long-term colonizing Bifidobacterium strains from FMT donors as well as in vivo colonization and capability to ameliorate antibiotic-induced microbiota disturbance. RNA-Seq differential gene expression analysis showed that the strongly adherent B. longum strains DY_pv11 and DX_pv23 expressed tight adherence and sortase-dependent pilus genes, respectively. Two B. longum strains, adherent DX_pv23 and poorly adhering DX_pv18, were selected to address in vivo colonization and efficacy to restore antibiotic-disturbed microbiota in C57BL/6 murine model. DX_pv23 colonized mice transiently with a rate comparable to that of the B. animalis BB-12 used as a reference. Although long-term colonization was not observed with any of the three strains, 16S rRNA gene profiling revealed that oral administration of DX_pv23 enhanced the recovery of antibiotic-disturbed microbiota to the original configuration significantly better than the other strains. The findings suggest that selected strains from FMT donors, such as DX_pv23 in this study, may have therapeutic potential by in vitro expression of colonization factors and boosting endogenous gut microbiota.},
}
@article {pmid37400907,
year = {2023},
author = {Casto-Rebollo, C and Argente, MJ and García, ML and Pena, RN and Blasco, A and Ibáñez-Escriche, N},
title = {Selection for environmental variance shifted the gut microbiome composition driving animal resilience.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {147},
pmid = {37400907},
issn = {2049-2618},
mesh = {Animals ; Rabbits ; *Gastrointestinal Microbiome/genetics ; Feces ; *Microbiota ; Phenotype ; Metagenome ; },
abstract = {BACKGROUND: Understanding how the host's microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance (V E), the within-individual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced V E could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the V E of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low (n = 36) and high (n = 34) V E of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations.<br><br>RESULTS: We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the V E rabbit populations of over than 80%. Compared to the high V E population, the low V E (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, Ruminococcus bromii, Bacteroidetes togonis, and Eggerthella sp. and greater abundances of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, Limosilactobacillus fermentum, and Sutterella, among others. Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience.<br><br>CONCLUSIONS: This is the first study to show that selection for V E of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the V E rabbit populations. Video Abstract.},
}
@article {pmid37345674,
year = {2023},
author = {Feng, K and Zhang, H and Chen, C and Ho, CT and Kang, M and Zhu, S and Xu, J and Deng, X and Huang, Q and Cao, Y},
title = {Heptamethoxyflavone Alleviates Metabolic Syndrome in High-Fat Diet-Fed Mice by Regulating the Composition, Function, and Metabolism of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {71},
number = {26},
pages = {10050-10064},
doi = {10.1021/acs.jafc.3c01881},
pmid = {37345674},
issn = {1520-5118},
mesh = {Mice ; Animals ; *Metabolic Syndrome/drug therapy/genetics ; *Gastrointestinal Microbiome ; Diet, High-Fat/adverse effects ; Lipid Metabolism ; Fatty Acids, Volatile/pharmacology ; Bile Acids and Salts/pharmacology ; Mice, Inbred C57BL ; },
abstract = {3,5,6,7,8,3',4'-Heptamethoxyflavone (HMF) could prevent obesity and hyperlipidemia, but its effects on gut microbiota and fecal metabolites remain unclear. Here, the effect of HMF on metabolic syndrome (MS) was evaluated in high-fat diet (HFD)-fed mice, and its underlying mechanisms were revealed by integrative metagenomic and metabolomic analyses. We demonstrated that HMF could effectively ameliorate HFD-induced MS by alleviating body-weight gain, fat accumulation, hepatic steatosis, and lipid and glucose abnormalities. HMF significantly altered the gut microbiota composition in HFD-fed mice with enrichment of short-chain fatty acid (SCFA)- and bile acid-producing beneficial bacteria and inhibition of harmful bacteria. Also, HMF improved microbial functions by up-regulating bile acid metabolism and down-regulating fatty acid metabolism and inflammatory response-related pathways. Consistent with the gut microbial changes, HMF altered the fecal metabolite profile of HFD-fed mice, mainly characterized by increasing SCFA and several bile acid levels as well as lowering several lysophospholipids and fatty acid levels. Correlation analysis indicated that three key species Faecalibaculum rodentium, Collinsella aerofaciens, and Lactobacillus fermentum and the increase in microbial metabolites, i.e., SCFAs and secondary bile acids, might play a positive role in alleviating MS. Our results suggested that HMF alleviated HFD-induced MS possibly by modulating the composition, function, and metabolism of gut microbiota.},
}
@article {pmid37125649,
year = {2023},
author = {Zheng, J and Ge, Q and Yan, Y and Zhang, X and Huang, L and Yin, Y},
title = {dbCAN3: automated carbohydrate-active enzyme and substrate annotation.},
journal = {Nucleic acids research},
volume = {51},
number = {W1},
pages = {W115-W121},
pmid = {37125649},
issn = {1362-4962},
support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R21 AI171952/AI/NIAID NIH HHS/United States ; },
mesh = {*Carbohydrates ; Carbohydrate Metabolism/genetics ; Polysaccharides ; Databases, Factual ; *Microbiota ; },
abstract = {Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.},
}
@article {pmid37398670,
year = {2023},
author = {Park, EJ and Yadav, H and Singh, TP},
title = {Editorial: Microbiota in skin inflammatory diseases.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1235314},
pmid = {37398670},
issn = {1664-3224},
mesh = {Humans ; Skin ; *Skin Diseases ; *Microbiota ; },
}
@article {pmid37392645,
year = {2023},
author = {Sułowicz, S and Borymski, S and Dulski, M and Nowak, A and Bondarczuk, K and Markowicz, A},
title = {Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO35-45 nm and captan@SiO220-30 nm treated orchard soil.},
journal = {Journal of hazardous materials},
volume = {458},
number = {},
pages = {131948},
doi = {10.1016/j.jhazmat.2023.131948},
pmid = {37392645},
issn = {1873-3336},
abstract = {Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.},
}
@article {pmid37391847,
year = {2023},
author = {Lv, J and Wang, J and Yu, Y and Zhao, M and Yang, W and Liu, J and Zhao, Y and Yang, Y and Wang, G and Guo, L and Zhao, H},
title = {Alterations of gut microbiota are associated with blood pressure: a cross-sectional clinical trial in Northwestern China.},
journal = {Journal of translational medicine},
volume = {21},
number = {1},
pages = {429},
pmid = {37391847},
issn = {1479-5876},
support = {2022qn07//Xi'an Municipal Health Commission of China/ ; 2023ms11//Xi'an Municipal Health Commission of China/ ; 2020ms14//Xi'an Municipal Health Commission of China/ ; 81702067//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; Male ; Blood Pressure ; China ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Hypertension ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The human gut microbiota (GM) is involved in the pathogenesis of hypertension (HTN), and could be affected by various factors, including sex and geography. However, available data directly linking GM to HTN based on sex differences are limited.<br><br>METHODS: This study investigated the GM characteristics in HTN subjects in Northwestern China, and evaluate the associations of GM with blood pressure levels based on sex differences. A total of 87 HTN subjects and 45 controls were recruited with demographic and clinical characteristics documented. Fecal samples were collected for 16S rRNA gene sequencing and metagenomic sequencing.<br><br>RESULTS: GM diversity was observed higher in females compared to males, and principal coordinate analysis showed an obvious segregation of females and males. Four predominant phyla of fecal GM included Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. LEfSe analysis indicated that phylum unidentified_Bacteria was enriched in HTN females, while Leuconostocaceae, Weissella and Weissella_cibaria were enriched in control females (P&#x2009;<&#x2009;0.05). Functionally, ROC analysis revealed that Cellular Processes (0.796, 95% CI 0.620&#x2009;~&#x2009;0.916), Human Diseases (0.773, 95% CI 0.595&#x2009;~&#x2009;0.900), Signal transduction (0.806, 95% CI 0.631&#x2009;~&#x2009;0.922) and Two-component system (0.806, 95% CI 0.631&#x2009;~&#x2009;0.922) could differentiate HTN females as effective functional classifiers, which were also positively correlated with systolic blood pressure levels.<br><br>CONCLUSIONS: This work provides evidence of fecal GM characteristics in HTN females and males in a northwestern Chinese population, further supporting the notion that GM dysbiosis may participate in the pathogenesis of HTN, and the role of sex differences should be considered. Trial registration&#xa0;Chinese Clinical Trial Registry, ChiCTR1800019191. Registered 30 October 2018 - Retrospectively registered, http://www.chictr.org.cn/ .},
}
@article {pmid37391160,
year = {2023},
author = {Hsiao, TH and Chen, PH and Wang, PH and Brandon-Mong, GJ and Li, CW and Horinouchi, M and Hayashi, T and Ismail, W and Meng, M and Chen, YL and Chiang, YR},
title = {Harnessing microbial phylum-specific molecular markers for assessment of environmental estrogen degradation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {165152},
doi = {10.1016/j.scitotenv.2023.165152},
pmid = {37391160},
issn = {1879-1026},
abstract = {Steroidal estrogens are ubiquitous contaminants that have garnered attention worldwide due to their endocrine-disrupting and carcinogenic activities at sub-nanomolar concentrations. Microbial degradation is one of the main mechanisms through which estrogens can be removed from the environment. Numerous bacteria have been isolated and identified as estrogen degraders; however, little is known about their contribution to environmental estrogen removal. Here, our global metagenomic analysis indicated that estrogen degradation genes are widely distributed among bacteria, especially among aquatic actinobacterial and proteobacterial species. Thus, by using the Rhodococcus sp. strain B50 as the model organism, we identified three actinobacteria-specific estrogen degradation genes, namely aedGHJ, by performing gene disruption experiments and metabolite profile analysis. Among these genes, the product of aedJ was discovered to mediate the conjugation of coenzyme A with a unique actinobacterial C17 estrogenic metabolite, 5-oxo-4-norestrogenic acid. However, proteobacteria were found to exclusively adopt an α-oxoacid ferredoxin oxidoreductase (i.e., the product of edcC) to degrade a proteobacterial C18 estrogenic metabolite, namely 3-oxo-4,5-seco-estrogenic acid. We employed actinobacterial aedJ and proteobacterial edcC as specific biomarkers for quantitative polymerase chain reaction (qPCR) to elucidate the potential of microbes for estrogen biodegradation in contaminated ecosystems. The results indicated that aedJ was more abundant than edcC in most environmental samples. Our results greatly expand the understanding of environmental estrogen degradation. Moreover, our study suggests that qPCR-based functional assays are a simple, cost-effective, and rapid approach for holistically evaluating estrogen biodegradation in the environment.},
}
@article {pmid37330070,
year = {2023},
author = {Liang, J and Chang, J and Zhang, R and Fang, W and Chen, L and Ma, W and Zhang, Y and Yang, W and Li, Y and Zhang, P and Zhang, G},
title = {Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression.},
journal = {Chemosphere},
volume = {336},
number = {},
pages = {139242},
doi = {10.1016/j.chemosphere.2023.139242},
pmid = {37330070},
issn = {1879-1298},
mesh = {Cattle ; Animals ; Male ; *Zea mays ; Rumen/microbiology ; Fermentation ; *Microbiota/genetics ; Bacteria/genetics ; Gene Expression ; Digestion ; },
abstract = {Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.},
}
@article {pmid37285993,
year = {2023},
author = {Wu, F and Ding, X and Zhang, Y and Gu, JD and Liu, X and Guo, Q and Li, J and Feng, H},
title = {Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China.},
journal = {The Science of the total environment},
volume = {893},
number = {},
pages = {164616},
doi = {10.1016/j.scitotenv.2023.164616},
pmid = {37285993},
issn = {1879-1026},
mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/physiology ; Bacteria/metabolism ; Sulfur/metabolism ; },
abstract = {Metagenomics and metaproteomics analyses were used to determine the microbial diversity and taxon composition, as well as the biochemical potentials of the microbiome on the sandstone of Beishiku Temple located in Northwest China. Taxonomic annotation of the metagenomic dataset revealed the predominant taxa of the stone microbiome on this cave temple with characteristics of resistance to harsh environmental conditions. Meanwhile, there were also taxa in the microbiome that showed sensitivity to environmental factors. The taxa distribution and the metabolic functional distribution patterns by the metagenome and metaproteome, respectively, showed clear differences. The high abundance of energy metabolism represented in the metaproteome suggested that there were active geomicrobiological cycles of elements within the microbiome. The taxa responsible for reactions in the nitrogen cycle from both metagenome and metaproteome supported a metabolically active nitrogen cycle, and the high activity of Comammox bacteria indicated the strong metabolic activity of ammonia oxidation to nitrate in the outdoor site. The SOX-related taxa involved in the sulfur cycle showed higher activity outdoors than indoors, and on the outdoor ground than at the outdoor cliff, as detected through metaproteomic analysis. The development of petrochemical industry in the vicinity resulting in the deposition of sulfur/oxidized sulfur via atmosphere may stimulate the physiological activity of SOX. Our findings provide metagenomic and metaproteomic evidence for microbially driven geobiochemical cycles that result in the biodeterioration of stone monuments.},
}
@article {pmid37269991,
year = {2023},
author = {Peng, K and Liu, YX and Sun, X and Wang, Q and Du, P and Zhang, Y and Wang, M and Wang, Z and Li, R},
title = {Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome.},
journal = {The Science of the total environment},
volume = {893},
number = {},
pages = {164585},
doi = {10.1016/j.scitotenv.2023.164585},
pmid = {37269991},
issn = {1879-1026},
mesh = {Animals ; Female ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Chickens/genetics ; *Microbiota ; Drug Resistance, Multiple, Bacterial ; Plasmids ; },
abstract = {The emergence and prevalence of animal-derived antibiotic resistance genes (ARGs) pose a great threat to public health globally. Long-read metagenomic sequencing is increasingly being used to decipher the fate of environmental ARGs. However, the investigations of the distribution, co-occurrence patterns, and host information of animal-derived environmental ARGs with long-read metagenomic sequencing have received little attention. To cover the gap, we employed a novel QitanTech nanopore long-read metagenomic sequencing method to perform a comprehensive and systematic investigation of the microbial communities and antibiotic resistance profiles, as well as to analyze the host information and genetic structures of ARGs in the feces of laying hens. Our results showed that highly abundant and diverse ARGs were detected in the feces of different ages of laying hens, indicating that feeding animal feces was an important reservoir for the enrichment and maintenance of ARGs. The distribution pattern of chromosomal ARGs was more strongly associated with fecal microbial communities than plasmid-mediated ARGs. Further long-read host tracking analysis revealed that ARGs from Proteobacteria are commonly located on plasmids, whereas in Firmicutes, they are usually carried by chromosomes. Co-occurrence analysis displayed that co-selection phenomena of different ARGs were common occurrences and highly active insertion sequences (ISs) could result in the serious prevalence of many ARGs. Notably, small high-copy plasmids played a significant role in the dissemination of several ARGs, such as floR and tet(L), which could disturb the compositions of fecal ARGs. Overall, our findings significantly expand our knowledge of the comprehensive landscape of feeding animal feces resistome, which is important for the prevention and management of multi-drug resistant bacteria in laying hens.},
}
@article {pmid37183784,
year = {2023},
author = {Ma, L and Lyu, W and Song, Y and Chen, K and Lv, L and Yang, H and Wang, W and Xiao, Y},
title = {Anti-Inflammatory Effect of Clostridium butyricum-Derived Extracellular Vesicles in Ulcerative Colitis: Impact on Host microRNAs Expressions and Gut Microbiome Profiles.},
journal = {Molecular nutrition &amp; food research},
volume = {67},
number = {13},
pages = {e2200884},
doi = {10.1002/mnfr.202200884},
pmid = {37183784},
issn = {1613-4133},
mesh = {Mice ; Animals ; *Colitis, Ulcerative/chemically induced/drug therapy ; *Clostridium butyricum/genetics ; *Gastrointestinal Microbiome ; *Colitis/drug therapy ; *Inflammatory Bowel Diseases ; Inflammation/drug therapy ; Colon ; *MicroRNAs/genetics ; Anti-Inflammatory Agents ; Dextran Sulfate/toxicity ; Disease Models, Animal ; *Extracellular Vesicles ; },
abstract = {SCORE: Probiotics extracellular vesicles (EVs) have shown potential as EV-based nanomaterials therapy for the treatment of inflammatory bowel disease (IBD). Although probiotic Clostridium butyricum has been reported to be protective in various models of intestinal inflammation, the therapeutic effects of C. butyricum-derived extracellular vesicles (CbEVs) in IBD remain to be demonstrated.<br><br>METHODS AND RESULTS: In this study, multi-omics sequencing is combined with an in vitro model of lipopolysaccharide-induced RAW264.7 cells and an in vivo mouse model of dextran sodium sulfate-induced colitis to explore the regulatory impact and mechanism of CbEVs in ulcerative colitis. Through small RNA sequencing, the study finds that microRNA is involved in the alleviation of colonic inflammation under CbEVs treatment. Mechanistically, CbEVs restore miR-199a-3p expression, interacting with map3k4, and thereby suppress proinflammatory MAPK and NF-&#x3ba;B signaling. Additionally, metagenomic sequencing demonstrate that CbEVs alleviate bacterial dysbiosis in colitis mice and significantly reduces the abundance of the bacterial pathogens Escherichia coli and Shigella flexneri. Furthermore, CbEVs regulate the microbial tryptophan metabolites, which further improve intestinal barrier integrity and inhibit the inflammatory response in colitis mice.<br><br>CONCLUSION: C. butyricum-derived extracellular vesicles can be a novel agent for the treatment of colitis and miR-199a-3p can be a potential target for IBD treatment.},
}
@article {pmid36130883,
year = {2023},
author = {Kato-Kogoe, N and Kamiya, K and Sakaguchi, S and Omori, M and Komori, E and Kudo, A and Nakamura, S and Nakano, T and Ueno, T and Tamaki, J and Hoshiga, M},
title = {Salivary Microbiota Associated with Peripheral Microvascular Endothelial Dysfunction.},
journal = {Journal of atherosclerosis and thrombosis},
volume = {30},
number = {7},
pages = {820-833},
doi = {10.5551/jat.63681},
pmid = {36130883},
issn = {1880-3873},
mesh = {Humans ; Aged ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Hyperemia ; *Atherosclerosis ; },
abstract = {AIMS: Oral health is associated with atherosclerotic cardiovascular disease (ACVD). We previously identified the salivary microbiota characteristics of patients with ACVD. However, whether salivary microbiota is characteristic under impaired vascular endothelial function before ACVD onset remains unclear. Therefore, we aimed to evaluate the characteristics of salivary microbiota associated with peripheral microvascular endothelial dysfunction.<br><br>METHODS: We collected saliva samples from 172 community-dwelling elderly individuals without a history of ACVD and performed 16S rRNA metagenomic analysis. We assessed the peripheral microvascular endothelial function using reactive hyperemia index (RHI) and compared the salivary microbiota in the groups with normal (RHI &#x2265; 2.10), borderline, and abnormal (RHI &#xff1c;1.67) peripheral endothelial function. Furthermore, we applied machine learning techniques to evaluate whether salivary microbiota could discriminate between individuals with normal and abnormal endothelial function.<br><br>RESULTS: The number of operational taxonomic units (OTUs) was higher in the abnormal group than in the normal group (p=0.037), and differences were found in the overall salivary microbiota structure (unweighted UniFrac distances, p=0.038). The linear discriminant analysis (LDA) effect size (LEfSe) algorithm revealed several significantly differentially abundant bacterial genera between the two groups. An Extra Trees classifier model was built to discriminate between groups with normal and abnormal vascular endothelial function based on the microbial composition at the genus level (AUC=0.810).<br><br>CONCLUSIONS: The salivary microbiota in individuals with endothelial dysfunction was distinct from that in individuals with normal endothelial function, indicating that the salivary microbiota may be related to endothelial function.},
}
@article {pmid37387148,
year = {2023},
author = {Wang, Q and Nute, M and Treangen, TJ},
title = {Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {39 Suppl 1},
pages = {i47-i56},
pmid = {37387148},
issn = {1367-4811},
support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R21 NS106640/NS/NINDS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenome ; Bacteria/genetics ; *Crohn Disease ; },
abstract = {MOTIVATION: Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.<br><br>RESULTS: We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.<br><br>Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.},
}
@article {pmid37381590,
year = {2023},
author = {Han, Z and Cheng, S and Dai, D and Kou, Y and Zhang, X and Li, F and Yin, X and Ji, J and Zhang, Z and Wang, X and Zhu, N and Zhang, Q and Tan, Y and Guo, X and Shen, L and Peng, Z},
title = {The gut microbiome affects response of treatments in HER2-negative advanced gastric cancer.},
journal = {Clinical and translational medicine},
volume = {13},
number = {7},
pages = {e1312},
pmid = {37381590},
issn = {2001-1326},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; B7-H1 Antigen/genetics ; *Stomach Neoplasms/drug therapy/genetics ; Immune Checkpoint Inhibitors ; Reproducibility of Results ; *Adenocarcinoma ; Lactobacillus ; },
abstract = {BACKGROUND: Common treatments for metastatic/unresectable HER2-negative gastric cancer include chemotherapy, immune checkpoint inhibitor monotherapy and chemotherapy plus immune checkpoint inhibitor. However, significant drug resistance exists regardless of the treatment regimen.<br><br>METHODS: Patients with metastatic/unresectable HER2-negative gastric/gastroesophageal junction adenocarcinoma were enrolled. All patients were divided into three groups according to the treatment regimen and were further divided into responders and non-responders according to efficacy evaluation. Metagenomics sequencing were performed to analyze gut microbiome signature of patients receiving different treatments at baseline and throughout treatment.<br><br>RESULTS: One hundred seventeen patients with HER2-negative advanced gastric or gastroesophageal junction adenocarcinoma receiving chemotherapy alone, anti PD-1/PD-L1 immunotherapy alone or combined regimen were included in this study. Microbiome signatures related to clinical response are distinct among the three treatment groups. Among which, 14, 8 and 13 species were significantly different between responders and non-responders in immunotherapy, immunotherapy plus chemotherapy and chemotherapy group, respectively. Patients with higher relative abundance of Lactobacillus possessed higher microbiome diversity and significantly better response to anti-PD-1/PD-L1 immunotherapy and had a trend to achieve better progression-free survival. Another cohort of 101 patients has been used as an external validation set to confirm the stability and reliability of these findings.<br><br>CONCLUSIONS: Gut microbiome affects response of treatments in HER2-negative advanced gastric cancer in a treatment-specific way, immunotherapy plus chemotherapy did not equal to a simple superposition of immunotherapy and chemotherapy. Lactobacillus is expected to become a novel choice as an adjuvant agent in promoting the efficacy of immunotherapy in gastric cancer.},
}
@article {pmid37336455,
year = {2023},
author = {Xiao, C and Wan, K and Hu, J and Deng, X and Liu, X and Zhou, F and Yu, J and Chi, R},
title = {Performance changes in the anammox process under the stress of rare-earth element Ce(III) and the evolution of microbial community and functional genes.},
journal = {Bioresource technology},
volume = {384},
number = {},
pages = {129349},
doi = {10.1016/j.biortech.2023.129349},
pmid = {37336455},
issn = {1873-2976},
mesh = {*Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; *Microbiota ; Wastewater ; Bacteria/genetics/metabolism ; Anaerobiosis ; Nitrogen/metabolism ; Bioreactors/microbiology ; Sewage/microbiology ; Denitrification ; },
abstract = {The high Ce(III) content in ionic rare-earth tailings wastewater has hindered the application of anammox process in this field. Here, the effect of Ce(III) on the performance of anammox processes was investigated, and the evolution of microbial communities and functional genes was explored using metagenomic sequencing. The results showed that the reactor nitrogen removal rate decreased when the Ce(III) concentration reached 25 mg/L, although ammonia nitrogen removal (92.31%) and nitrogen removal efficiency (81.33%) remained at a high level; however, both showed a significant decreasing trend. The relative abundance of anammox bacteria increased continuously from P1-P5, reaching 48.81%, whereas the relative abundance of Candidatus jettenia reached 33.71% at P5, which surpassed that of Candidatus brocadia as the most abundant anammox bacteria, and further analysis of functional genes and metabolic pathways revealed that Candidatus brocadia was richer in biochemical metabolic genes, whereas Candidatus jettenia had richer efflux genes.},
}
@article {pmid37327214,
year = {2023},
author = {Potgieter, MG and Nel, AJM and Fortuin, S and Garnett, S and Wendoh, JM and Tabb, DL and Mulder, NJ and Blackburn, JM},
title = {MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.},
journal = {PLoS computational biology},
volume = {19},
number = {6},
pages = {e1011163},
pmid = {37327214},
issn = {1553-7358},
mesh = {Humans ; *Tandem Mass Spectrometry ; RNA, Ribosomal, 16S/genetics ; Databases, Protein ; Peptides/genetics/analysis ; *Microbiota/genetics ; Bacteria/genetics ; Proteome/genetics ; },
abstract = {BACKGROUND: Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines.<br><br>RESULTS: We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database-but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation.<br><br>CONCLUSIONS: By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.},
}
@article {pmid37278524,
year = {2023},
author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B},
title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0075722},
pmid = {37278524},
issn = {2379-5077},
support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; T32 HL007427/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Microbial Interactions ; Models, Theoretical ; Models, Biological ; Bacteria ; },
abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities. IMPORTANCE Although mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.},
}
@article {pmid37273228,
year = {2023},
author = {Liu, F and Li, R and Zhong, Y and Liu, X and Deng, W and Huang, X and Price, M and Li, J},
title = {Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0025223},
pmid = {37273228},
issn = {2379-5077},
support = {KLSFGAGP2020.006//National Forestry and Grassland Administration (NFGA)/ ; },
mesh = {Animals ; *Ursidae/genetics ; RNA, Ribosomal, 16S/genetics ; Chromatography, Liquid ; Tandem Mass Spectrometry ; *Microbiota ; *Carnivora/genetics ; Metabolome ; Diet ; Bacteria/genetics ; Cellulose/metabolism ; },
abstract = {We conducted UPLC-MS-based metabolomics, 16S rRNA, and metagenome sequencing on the fecal samples of 44 captive giant pandas (Ailuropoda melanoleuca) from four age groups (i.e., Cub, Young, Adult, and Old) to comprehensively understand age-related changes in the metabolism and gut microbiota of giant pandas. We characterized the metabolite profiles of giant pandas based on 1,376 identified metabolites, with 152 significantly differential metabolites (SDMs) found across the age groups. We found that the metabolites and the composition/function of the gut microbiota changed in response to the transition from a milk-dominant diet in panda cubs to a bamboo-specific diet in young and adult pandas. Lipid metabolites such as choline and hippuric acid were enriched in the Cub group, and many plant secondary metabolites were significantly higher in the Young and Adult groups, while oxidative stress and inflammatory related metabolites were only found in the Old group. However, there was a decrease in the α-diversity of gut microbiota in adult and old pandas, who exclusively consume bamboo. The abundance of bacteria related to the digestion of cellulose-rich food, such as Firmicutes, Streptococcus, and Clostridium, significantly increased from the Cub to the Adult group, while the abundance of beneficial bacteria such as Faecalibacterium, Sarcina, and Blautia significantly decreased. Notably, several potential pathogenic bacteria had relatively high abundances, especially in the Young group. Metagenomic analysis identified 277 CAZyme genes including cellulose degrading genes, and seven of the CAZymes had abundances that significantly differed between age groups. We also identified 237 antibiotic resistance genes (ARGs) whose number and diversity increased with age. We also found a significant positive correlation between the abundance of bile acids and gut bacteria, especially Lactobacillus and Bifidobacterium. Our results from metabolome, 16S rRNA, and metagenome data highlight the important role of the gut microbiota-bile acid axis in the regulation of age-related metabolism and provide new insights into the lipid metabolism of giant pandas. IMPORTANCE The giant panda is a member of the order Carnivora but is entirely herbivorous. The giant panda's specialized diet and related metabolic mechanisms have not been fully understood. It is therefore crucial to investigate the dynamic changes in metabolites as giant pandas grow and physiologically adapt to their herbivorous diet. This study conducted UPLC-MS-based metabolomics 16S rRNA, and metagenome sequencing on the fecal samples of captive giant pandas from four age groups. We found that metabolites and the composition/function of gut microbiota changed in response to the transition from a milk-dominant diet in cubs to a bamboo-specific diet in young and adult pandas. The metabolome, 16S rRNA, and metagenome results highlight that the gut microbiota-bile acid axis has an important role in the regulation of age-related metabolism, and our study provides new insights into the lipid metabolism of giant pandas.},
}
@article {pmid37249588,
year = {2023},
author = {Li, W and Zhao, J and Tian, H and Shen, Y and Wang, Y and Shao, M and Xiong, T and Yao, Y and Zhang, L and Chen, X and Xiao, H and Xiong, Y and Yang, S and Tan, C and Xu, H},
title = {Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {14},
pages = {4635-4646},
pmid = {37249588},
issn = {1432-0614},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Proteobacteria ; Birds/genetics/microbiology ; Cellulose ; },
abstract = {Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.},
}
@article {pmid37227475,
year = {2023},
author = {Bou Orm, E and Sauvagère, S and Rocher, J and Benezet, JC and Bayle, S and Siatka, C and Bergeret, A and Malhautier, L},
title = {Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {14},
pages = {4665-4681},
pmid = {37227475},
issn = {1432-0614},
mesh = {*Cannabis/genetics/metabolism ; DNA/metabolism ; Bacteria/genetics ; *Microbiota ; Soil ; },
abstract = {The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.},
}
@article {pmid37204286,
year = {2023},
author = {Shankar, A and Das, DJ and Nayar, S and Thomas, S},
title = {Deciphering the effect of maternal postpartum antibiotic prophylaxis on the infant gut microbiome: a whole metagenomic analysis.},
journal = {Future microbiology},
volume = {18},
number = {},
pages = {427-441},
doi = {10.2217/fmb-2022-0200},
pmid = {37204286},
issn = {1746-0921},
support = {AC1-250/2018/SPHCL//Department of Health and Family Welfare, Government of Kerala, India/ ; },
mesh = {Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; Antibiotic Prophylaxis ; Mothers ; Milk, Human ; Postpartum Period ; Feces ; },
abstract = {Aim: To analyze the impact of postpartum antibiotic (Ab) prophylaxis on the infant gut microbiome. Materials &amp; methods: Whole metagenomic analysis was performed on breast milk and infant fecal samples collected from mother-infant pairs who belonged to two groups: an Ab group comprising mothers who had received a single course of Abs in the immediate postpartum period and a non-Ab group comprising mothers who had not received Abs. Results: The characteristic presence of Citrobacter werkmanii, an emerging multidrug-resistant uropathogen, and a higher relative abundance of genes encoding resistance to specific Abs were noted in samples from the Ab group compared with those from the non-Ab group. Conclusion: Policies regarding prophylactic Ab prescription across government and private health sectors in the postpartum period need to be strengthened.},
}
@article {pmid37193854,
year = {2023},
author = {Atsawawaranunt, K and Ewart, KM and Major, RE and Johnson, RN and Santure, AW and Whibley, A},
title = {Tracing the introduction of the invasive common myna using population genomics.},
journal = {Heredity},
volume = {131},
number = {1},
pages = {56-67},
pmid = {37193854},
issn = {1365-2540},
mesh = {Humans ; Animals ; *Metagenomics ; India ; *Starlings ; Genomics ; Australia ; Introduced Species ; },
abstract = {The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.},
}
@article {pmid37142190,
year = {2023},
author = {Moore, RL and Feehily, C and Killeen, SL and Yelverton, CA and Geraghty, AA and Walsh, CJ and O'Neill, IJ and Nielsan, IB and Lawton, EM and Sanchez-Gallardo, R and Nori, SRC and Shanahan, F and Murphy, EF and Van Sinderen, D and Cotter, PD and McAuliffe, FM},
title = {Ability of Bifidobacterium breve 702258 to transfer from mother to infant: the MicrobeMom randomized controlled trial.},
journal = {American journal of obstetrics &amp; gynecology MFM},
volume = {5},
number = {7},
pages = {100994},
doi = {10.1016/j.ajogmf.2023.100994},
pmid = {37142190},
issn = {2589-9333},
mesh = {Infant, Newborn ; Humans ; Infant ; Female ; Pregnancy ; Adult ; *Bifidobacterium breve ; Mothers ; *Probiotics ; Gestational Age ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: The composition of the infant microbiome can have a variety of short- and long-term implications for health. It is unclear if maternal probiotic supplementation in pregnancy can affect the infant gut microbiome.<br><br>OBJECTIVE: This study aimed to investigate if maternal supplementation of a formulation of Bifidobacterium breve 702258 from early pregnancy until 3 months postpartum could transfer to the infant gut.<br><br>STUDY DESIGN: This was a double-blinded, placebo-controlled, randomized controlled trial of B breve 702258 (minimum 1&#x202f;&#xd7;&#x202f;10[9] colony-forming units) or placebo taken orally from 16 weeks' gestation until 3 months postpartum in healthy pregnant women. The primary outcome was presence of the supplemented strain in infant stool up to 3 months of life, detected by at least 2 of 3 methods: strain-specific polymerase chain reaction, shotgun metagenomic sequencing, or genome sequencing of cultured B breve. A total of 120 individual infants' stool samples were required for 80% power to detect a difference in strain transfer between groups. Rates of detection were compared using the Fisher exact test.<br><br>RESULTS: A total of 160 pregnant women with average age of 33.6 (3.9) years and mean body mass index of 24.3 (22.5-26.5) kg/m[2], of whom 43% were nulliparous (n=58), were recruited from September 2016 to July 2019. Neonatal stool samples were obtained from 135 infants (65 in intervention and 70 in control group). The presence of the supplemented strain was detected through at least 2 methods (polymerase chain reaction and culture) in 2 infants in the intervention group (n=2/65; 3.1%) and none in the control group (n=0; 0%; P=.230).<br><br>CONCLUSION: Direct mother-to-infant strain transfer of B breve 702258 occurred, albeit infrequently. This study highlights the potential for maternal supplementation to introduce microbial strains into the infant microbiome.},
}
@article {pmid36847620,
year = {2023},
author = {Gu, BH and Choi, JP and Park, T and Kim, AS and Jung, HY and Choi, DY and Lee, SJ and Chang, YS and Kim, M and Park, HK},
title = {Adult asthma with symptomatic eosinophilic inflammation is accompanied by alteration in gut microbiome.},
journal = {Allergy},
volume = {78},
number = {7},
pages = {1909-1921},
doi = {10.1111/all.15691},
pmid = {36847620},
issn = {1398-9995},
support = {NRF-2022R1C1C1003256//Korea Government/ ; NRF-2020R1C1C1011678//Korea Government/ ; },
mesh = {Humans ; Adult ; *Gastrointestinal Microbiome ; *Asthma/genetics ; *Pulmonary Eosinophilia ; Inflammation/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Accumulating evidence suggests that the gut microbiome is associated with asthma. However, altered gut microbiome in adult asthma is not yet well established. We aimed to investigate the gut microbiome profiles of adult asthmatic patients with symptomatic eosinophilic inflammation.<br><br>METHODS: The 16&#x2009;s rRNA gene metagenomic analysis of feces in the symptomatic eosinophilic asthma group (EA, n&#xa0;=&#xa0;28) was compared with the healthy control (HC, n&#xa0;=&#xa0;18) and the chronic cough control (CC, n&#xa0;=&#xa0;13). A correlation analysis between individual taxa and clinical markers was performed within the EA group. Changes in the gut microbiome were examined in patients with significant symptom improvement in the EA group.<br><br>RESULTS: The relative abundances of Lachnospiraceae and Oscillospiraceae significantly decreased and Bacteroidetes increased in the EA group. Within EA group, Lachnospiraceae was negatively correlated with indicators of type 2 inflammation and lung function decline. Enterobacteriaceae and Prevotella was positively associated with type 2 inflammation and lung function decline, respectively. The abundance of predicted genes associated with amino acid metabolism and secondary bile acid biosynthesis was diminished in the EA group. These functional gene family alterations could be related to gut permeability, and the serum lipopolysaccharide concentration was actually high in the EA group. EA patients with symptom improvement after 1&#xa0;month did not show a significant change in the gut microbiome.<br><br>CONCLUSIONS: Symptomatic eosinophilic adult asthma patients showed altered the gut microbiome composition. Specifically, a decrease in commensal clostridia was observed, and a decrease in Lachnospiraceae was correlated with blood eosinophilia and lung function decline.},
}
@article {pmid36198381,
year = {2023},
author = {Chen, F and Li, S and Guo, R and Song, F and Zhang, Y and Wang, X and Huo, X and Lv, Q and Ullah, H and Wang, G and Ma, Y and Yan, Q and Ma, X},
title = {Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment.},
journal = {Journal of advanced research},
volume = {49},
number = {},
pages = {103-114},
doi = {10.1016/j.jare.2022.09.012},
pmid = {36198381},
issn = {2090-1224},
mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; *Viruses ; *Adenoma/diagnosis ; Risk Assessment ; Biomarkers ; *Colorectal Neoplasms/diagnosis/microbiology ; },
abstract = {INTRODUCTION: Viruses have been reported as inducers of tumorigenesis. Little studies have explored the impact of the gut virome on the progression of colorectal cancer. However, there is still a problem with the repeatability of viral signatures across multiple cohorts.<br><br>OBJECTIVES: The present study aimed to reveal the repeatable gut vial signatures of colorectal cancer and adenoma patients and decipher the potential of viral markers in disease risk assessment for diagnosis.<br><br>METHODS: 1,282 available fecal metagenomes from 9 published studies for colorectal cancer and adenoma were collected. A gut viral catalog was constructed via a reference-independent approach. Viral signatures were identified by cross-cohort meta-analysis and used to build predictive models based on machine learning algorithms. New fecal samples were collected to validate the generalization of predictive models.<br><br>RESULTS: The gut viral composition of colorectal cancer patients was drastically altered compared with healthy, as evidenced by changes in some Siphoviridae and Myoviridae viruses and enrichment of Microviridae, whereas the virome variation in adenoma patients was relatively low. Cross-cohort meta-analysis identified 405 differential viruses for colorectal cancer, including several phages of Porphyromonas, Fusobacterium, and Hungatella that were enriched in patients and some control-enriched Ruminococcaceae phages. In 9 discovery cohorts, the optimal risk assessment model obtained an average cross-cohort area under the curve of 0.830 for discriminating colorectal cancer patients from controls. This model also showed consistently high accuracy in 2 independent validation cohorts (optimal area under the curve, 0.906). Gut virome analysis of adenoma patients identified 88 differential viruses and achieved an optimal area under the curve of 0.772 for discriminating patients from controls.<br><br>CONCLUSION: Our findings demonstrate the gut virome characteristics in colorectal cancer and adenoma and highlight gut virus-bacterial synergy in the progression of colorectal cancer. The gut viral signatures may be new targets for colorectal cancer treatment. In addition, high repeatability and predictive power of the prediction models suggest the potential of gut viral biomarkers in non-invasive diagnostic tests of colorectal cancer and adenoma.},
}
@article {pmid37380422,
year = {2023},
author = {Fan, YF and Li, ZP and Yu, XJ and Li, Z and Zhou, HJ and Zhang, YL and Gan, XT and Hua, D and Lu, X and Kan, B},
title = {[Study of the urban-impact on microbial communities and their virulence factors and antibiotic resistance genomes in the Nandu River, Haikou].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {44},
number = {6},
pages = {974-981},
doi = {10.3760/cma.j.cn112338-20221229-01090},
pmid = {37380422},
issn = {0254-6450},
support = {2020YFE0205700, 2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; 2018ZX10714002//National Science and Technology Major Project of China/ ; },
mesh = {Humans ; *Rivers ; Virulence Factors/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; },
abstract = {Objective: To explore the changes in bacterial community structure, antibiotic resistance genome, and pathogen virulence genome in river water before and after the river flowing through Haikou City and their transmission and dispersal patterns and to reveal anthropogenic disturbance's effects on microorganisms and resistance genes in the aquatic environment. Methods: The Nandu River was divided into three study areas: the front, middle and rear sections from the upstream before it flowed through Haikou City to the estuary. Three sampling sites were selected in each area, and six copies of the sample were collected in parallel at each site and mixed for 3 L per sample. Microbial community structure, antibiotic resistance, virulence factors, and mobile genetic elements were analyzed through bioinformatic data obtained by metagenomic sequencing and full-length sequencing of 16S rRNA genes. Variations in the distribution of bacterial communities between samples and correlation of transmission patterns were analyzed by principal co-ordinates analysis, procrustes analysis, and Mantel test. Results: As the river flowed through Haikou City, microbes' alpha diversity gradually decreased. Among them, Proteobacteria dominates in the bacterial community in the front, middle, and rear sections, and the relative abundance of Proteobacteria in the middle and rear sections was higher than that in the front segment. The diversity and abundance of antibiotic resistance genes, virulence factors, and mobile genetic elements were all at low levels in the front section and all increased significantly after flow through Haikou City. At the same time, horizontal transmission mediated by mobile genetic elements played a more significant role in the spread of antibiotic-resistance genes and virulence factors. Conclusions: Urbanization significantly impacts river bacteria and the resistance genes, virulence factors, and mobile genetic elements they carry. The Nandu River in Haikou flows through the city, receiving antibiotic-resistant and pathogen-associated bacteria excreted by the population. In contrast, antibiotic-resistant genes and virulence factors are enriched in bacteria, which indicates a threat to environmental health and public health. Comparison of river microbiomes and antibiotic resistance genomes before and after flow through cities is a valuable early warning indicator for monitoring the spread of antibiotic resistance.},
}
@article {pmid37379385,
year = {2023},
author = {Wang, J and Qu, YN and Evans, PN and Guo, Q and Zhou, F and Nie, M and Jin, Q and Zhang, Y and Zhai, X and Zhou, M and Yu, Z and Fu, QL and Xie, YG and Hedlund, BP and Li, WJ and Hua, ZS and Wang, Z and Wang, Y},
title = {Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.},
journal = {Science advances},
volume = {9},
number = {26},
pages = {eadg6004},
pmid = {37379385},
issn = {2375-2548},
mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Hot Springs ; Methane/metabolism ; Temperature ; Phylogeny ; },
abstract = {Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on [13]C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.},
}
@article {pmid37375584,
year = {2023},
author = {Fernandes, A and Oliveira, A and Carvalho, AL and Soares, R and Barata, P},
title = {Faecalibacterium prausnitzii in Differentiated Thyroid Cancer Patients Treated with Radioiodine.},
journal = {Nutrients},
volume = {15},
number = {12},
pages = {},
pmid = {37375584},
issn = {2072-6643},
support = {UID/BIM/04293/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
mesh = {Humans ; Faecalibacterium prausnitzii ; Iodine Radioisotopes/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Fatty Acids, Volatile ; *Thyroid Neoplasms/radiotherapy ; },
abstract = {BACKGROUND: Faecalibacterium prausnitzii, one of the most important bacteria of the human gut microbiota, produces butyrate (a short-chain fatty acid). Short-chain fatty acids are known to influence thyroid physiology and thyroid cancer's response to treatment. We aimed to analyze the relative abundance of Faecalibacterium prausnitzii on the gut microbiota of differentiated thyroid cancer patients compared to controls and its variation after radioiodine therapy (RAIT).<br><br>METHODS: Fecal samples were collected from 37 patients diagnosed with differentiated thyroid cancer before and after radioiodine therapy and from 10 volunteers. The abundance of F. prausnitzii was determined using shotgun metagenomics.<br><br>RESULTS: Our study found that the relative abundance of F. prausnitzii is significantly reduced in thyroid cancer patients compared to volunteers. We also found that there was a mixed response to RAIT, with an increase in the relative and absolute abundances of this bacterium in most patients.<br><br>CONCLUSIONS: Our study confirms that thyroid cancer patients present a dysbiotic gut microbiota, with a reduction in F. prausnitzii's relative abundance. In our study, radioiodine did not negatively affect F. prausnitzii, quite the opposite, suggesting that this bacterium might play a role in resolving radiation aggression issues.},
}
@article {pmid37371491,
year = {2023},
author = {Stupak, A and Kwaśniewski, W},
title = {Evaluating Current Molecular Techniques and Evidence in Assessing Microbiome in Placenta-Related Health and Disorders in Pregnancy.},
journal = {Biomolecules},
volume = {13},
number = {6},
pages = {},
pmid = {37371491},
issn = {2218-273X},
mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Placenta ; *Microbiota ; *Gastrointestinal Microbiome ; Pregnancy Trimester, First ; *Pre-Eclampsia ; },
abstract = {The microbiome is of great interest due to its potential influence on the occurrence and treatment of some human illnesses. It may be regarded as disruptions to the delicate equilibrium that humans ordinarily maintain with their microorganisms or the microbiota in their environment. The focus of this review is on the methodologies and current understanding of the functional microbiome in pregnancy outcomes. We present how novel techniques bring new insights to the contemporary field of maternal-fetal medicine with a critical analysis. The maternal microbiome in late pregnancy has been extensively studied, although data on maternal microbial changes during the first trimester are rare. Research has demonstrated that, in healthy pregnancies, the origin of the placental microbiota is oral (gut) rather than vaginal. Implantation, placental development, and maternal adaptation to pregnancy are complex processes in which fetal and maternal cells interact. Microbiome dysbiosis or microbial metabolites are rising as potential moderators of antenatal illnesses related to the placenta, such as fetal growth restriction, preeclampsia, and others, including gestational diabetes and preterm deliveries. However, because of the presence of antimicrobial components, it is likely that the bacteria identified in placental tissue are (fragments of) bacteria that have been destroyed by the placenta's immune cells. Using genomic techniques (metagenomics, metatranscriptomics, and metaproteomics), it may be possible to predict some properties of a microorganism's genome and the biochemical (epigenetic DNA modification) and physical components of the placenta as its environment. Despite the results described in this review, this subject needs further research on some major and crucial aspects. The phases of an in utero translocation of the maternal gut microbiota to the fetus should be explored. With a predictive knowledge of the impacts of the disturbance on microbial communities that influence human health and the environment, genomics may hold the answer to the development of novel therapies for the health of pregnant women.},
}
@article {pmid37272792,
year = {2023},
author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R},
title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {6},
pages = {e0050023},
pmid = {37272792},
issn = {1098-5336},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Bacteria/metabolism ; *Microbiota ; Carbon/metabolism ; Tennessee ; },
abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.},
}
@article {pmid37249060,
year = {2023},
author = {Wolf, M and Schallert, K and Knipper, L and Sickmann, A and Sczyrba, A and Benndorf, D and Heyer, R},
title = {Advances in the clinical use of metaproteomics.},
journal = {Expert review of proteomics},
volume = {20},
number = {4-6},
pages = {71-86},
doi = {10.1080/14789450.2023.2215440},
pmid = {37249060},
issn = {1744-8387},
mesh = {Humans ; *Proteomics/methods ; *Microbiota/genetics ; Bacterial Proteins/metabolism ; Computational Biology/methods ; Obesity ; },
abstract = {INTRODUCTION: Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context.<br><br>AREAS COVERED: This review summarizes the recent progress from a technical side and an application-related point of view.<br><br>EXPERT OPINION: Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.},
}
@article {pmid37191511,
year = {2023},
author = {Zhang, JW and Wang, R and Liang, X and Han, P and Zheng, YL and Li, XF and Gao, DZ and Liu, M and Hou, LJ and Dong, HP},
title = {Novel Gene Clusters for Natural Product Synthesis Are Abundant in the Mangrove Swamp Microbiome.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {6},
pages = {e0010223},
pmid = {37191511},
issn = {1098-5336},
support = {41971125//MOST | National Natural Science Foundation of China (NSFC)/ ; 41971125//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Biological Products ; Wetlands ; Phylogeny ; *Microbiota ; Multigene Family ; },
abstract = {Natural microbial communities produce a diverse array of secondary metabolites with ecologically and biotechnologically relevant activities. Some of them have been used clinically as drugs, and their production pathways have been identified in a few culturable microorganisms. However, since the vast majority of microorganisms in nature have not been cultured, identifying the synthetic pathways of these metabolites and tracking their hosts remain a challenge. The microbial biosynthetic potential of mangrove swamps remains largely unknown. Here, we examined the diversity and novelty of biosynthetic gene clusters in dominant microbial populations in mangrove wetlands by mining 809 newly reconstructed draft genomes and probing the activities and products of these clusters by using metatranscriptomic and metabolomic techniques. A total of 3,740 biosynthetic gene clusters were identified from these genomes, including 1,065 polyketide and nonribosomal peptide gene clusters, 86% of which showed no similarity to known clusters in the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Of these gene clusters, 59% were harbored by new species or lineages of Desulfobacterota-related phyla and Chloroflexota, whose members are highly abundant in mangrove wetlands and for which few synthetic natural products have been reported. Metatranscriptomics revealed that most of the identified gene clusters were active in field and microcosm samples. Untargeted metabolomics was also used to identify metabolites from the sediment enrichments, and 98% of the mass spectra generated were unrecognizable, further supporting the novelty of these biosynthetic gene clusters. Our study taps into a corner of the microbial metabolite reservoir in mangrove swamps, providing clues for the discovery of new compounds with valuable activities. IMPORTANCE At present, the majority of known clinical drugs originated from cultivated species of a few bacterial lineages. It is vital for the development of new pharmaceuticals to explore the biosynthetic potential of naturally uncultivable microorganisms using new techniques. Based on the large numbers of genomes reconstructed from mangrove wetlands, we identified abundant and diverse biosynthetic gene clusters in previously unsuspected phylogenetic groups. These gene clusters exhibited a variety of organizational architectures, especially for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS), implying the presence of new compounds with valuable activities in the mangrove swamp microbiome.},
}
@article {pmid37169166,
year = {2023},
author = {Chen, MM and Wang, P and Xie, XH and Nie, Z and Xu, SX and Zhang, N and Wang, W and Yao, L and Liu, Z},
title = {Young Adults with Major Depression Show Altered Microbiome.},
journal = {Neuroscience},
volume = {522},
number = {},
pages = {23-32},
doi = {10.1016/j.neuroscience.2023.05.002},
pmid = {37169166},
issn = {1873-7544},
mesh = {Humans ; Young Adult ; *Depressive Disorder, Major ; Depression ; Pilot Projects ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {There is growing basic and clinical evidence that major depressive disorder (MDD) is associated with gut microbiome alterations, but clinical studies have tended not to adjust for confounding factors. And few studies on the gut microbiome focused on young adults with MDD. Here we performed a pilot study to compare the gut microbiome of young adults with MDD with healthy controls. Shotgun metagenomic sequencing was performed on stool samples obtained from 40 young adults with MDD and 42 healthy controls. After controlling for confounding factors including sex, age, BMI, alcohol or cigarette consumption, bowel movement quality, exercise or defecation frequency, we compared microbiome diversity between groups, identified differentially abundant taxa, and further compared functional differences through gut-brain and gut-metabolic module analysis. There were no significant differences in overall gut microbiome structure and function in young adults with MDD compared with controls. Abundance of Sutterellaceae and species belonging to Clostridium, Eubacterium, and Ruminococcus were significantly different between groups. The cysteine degradation I pathway was increased in MDD. After controlling for most confounding factors, this pilot study provides new evidence on the specific, often subtle gut dysbiosis affecting young adults with depression.},
}
@article {pmid37155936,
year = {2023},
author = {Peng, Y and Jin, M and Li, Z and Li, H and Zhang, L and Yu, S and Zhang, Z and Fan, R and Liu, J and Xu, Q and Wilson, K and Xiao, Y},
title = {Population Genomics Provide Insights into the Evolution and Adaptation of the Asia Corn Borer.},
journal = {Molecular biology and evolution},
volume = {40},
number = {5},
pages = {},
pmid = {37155936},
issn = {1537-1719},
support = {2022ZD04021//Sci-Tech Innovation 2030 Agenda/ ; //Chinese Academy of Agricultural Sciences/ ; //Science, Technology and Innovation Commission of Shenzhen Municipality/ ; },
mesh = {Animals ; *Zea mays/genetics ; Metagenomics ; Biodiversity ; Temperature ; *Moths/genetics ; Asia ; },
abstract = {Understanding the genetic basis of pest adaptive evolution and the risk of adaptation in response to climate change is essential for the development of sustainable agricultural practices. However, the genetic basis of climatic adaptation for the Asian corn borer (ACB), Ostrinia furnacalis, the main pest of corn in Asia and Oceania, is poorly understood. Here, we revealed the genomic loci underlying the climatic adaptation and evolution in ACB by integrating population genomic and environmental factors. We assembled a 471-Mb chromosome-scale reference genome of ACB and resequenced 423 individuals covering 27 representative geographic areas. We inferred that the ACB effective population size changes tracked with the global temperature and followed by a recent decline. Based on an integrated analysis of whole-genome selection scans and genome-wide genotype-environment association studies, we revealed the genetic basis of ACB adaption to diverse climates. For diapause traits, we identified a major effect association locus containing a circadian clock gene (period) by analyzing a diapause-segregating population. Moreover, our predictions indicated that the northern populations were more ecologically resilient to climate change than the southern populations. Together, our results revealed the genomic basis for ACB environmental adaptation and provided potential candidate genes for future evolutionary studies and genetic adaptation to climate change, intending to maintain the efficacy and sustainability of novel control techniques.},
}
@article {pmid36751730,
year = {2023},
author = {Nørgaard, JC and Jørgensen, M and Moestrup, KS and Ilett, EE and Zucco, AG and Marandi, RZ and Julian, MN and Paredes, R and Lundgren, JD and Sengeløv, H and MacPherson, C},
title = {Impact of Antibiotic Treatment on the Gut Microbiome and its Resistome in Hematopoietic Stem Cell Transplant Recipients.},
journal = {The Journal of infectious diseases},
volume = {228},
number = {1},
pages = {28-36},
doi = {10.1093/infdis/jiad033},
pmid = {36751730},
issn = {1537-6613},
support = {DNRF126//Danish National Research Foundation/ ; R167-A108665-17-S2//Danish Cancer Society/ ; R218-2016-1482//Lundbeck Foundation/ ; NNF15OC0014158//Novo Nordisk Foundation/ ; //Svend Anderson Foundation/ ; RD16/0025/0041//RED de SIDA/ ; //ISCIII/ ; //European Regional Development Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/adverse effects ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Hematopoietic Stem Cell Transplantation/adverse effects ; },
abstract = {Antibiotic-resistant bacterial infections are increasingly an issue in allogenic hematopoietic stem cell transplant patients. How antibiotic treatment impacts antibiotic resistance in the human gut microbiome remains poorly understood in vivo. Here, a total of 577 fecal samples from 233 heavily antibiotic-treated transplant patients were examined using high-resolution prescription data and shotgun metagenomics. The 13 most frequently used antibiotics were significantly associated with 154 (40% of tested associations) microbiome features. Use of broad-spectrum β-lactam antibiotics was most markedly associated with microbial disruption and increase in resistome features. The enterococcal vanA gene was positively associated with 8 of the 13 antibiotics, and in particular piperacillin/tazobactam and vancomycin. Here, we highlight the need for a high-resolution approach in understanding the development of antibiotic resistance in the gut microbiome. Our findings can be used to inform antibiotic stewardship and combat the increasing threat of antibiotic resistance.},
}
@article {pmid37369825,
year = {2023},
author = {Österdahl, MF and Whiston, R and Sudre, CH and Asnicar, F and Cheetham, NJ and Blanco Miguez, A and Bowyer, V and Antonelli, M and Snell, O and Dos Santos Canas, L and Hu, C and Wolf, J and Menni, C and Malim, M and Hart, D and Spector, T and Berry, S and Segata, N and Doores, K and Ourselin, S and Duncan, EL and Steves, CJ},
title = {Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {10407},
pmid = {37369825},
issn = {2045-2322},
support = {215010/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 203148/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; MC_PC_20059/MRC_/Medical Research Council/United Kingdom ; MR/T005351/1/MRC_/Medical Research Council/United Kingdom ; MR/T005351/1/MRC_/Medical Research Council/United Kingdom ; MR/T005351/1/MRC_/Medical Research Council/United Kingdom ; MR/T005351/1/MRC_/Medical Research Council/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; },
mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; *Pneumonia ; Hospitalization ; },
abstract = {Whilst most individuals with SARS-CoV-2 infection have relatively mild disease, managed in the community, it was noted early in the pandemic that individuals with cardiovascular risk factors were more likely to experience severe acute disease, requiring hospitalisation. As the pandemic has progressed, increasing concern has also developed over long symptom duration in many individuals after SARS-CoV-2 infection, including among the majority who are managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. Here, we examine post-illness metabolomic profiles, using nuclear magnetic resonance (Nightingale Health Oyj), and gut-microbiome profiles, using shotgun metagenomic sequencing (Illumina Inc), in 2561 community-dwelling participants with SARS-CoV-2. Illness duration ranged from asymptomatic (n = 307) to Post-COVID Syndrome (n = 180), and included participants with prolonged non-COVID-19 illnesses (n = 287). We also assess a pre-established metabolomic biomarker score, previously associated with hospitalisation for both acute pneumonia and severe acute COVID-19 illness, for its association with illness duration. We found an atherogenic-dyslipidaemic metabolic profile, including biomarkers such as fatty acids and cholesterol, was associated with longer duration of illness, both in individuals with and without SARS-CoV-2 infection. Greater values of a pre-existing metabolomic biomarker score also associated with longer duration of illness, regardless of SARS-CoV-2 infection. We found no association between illness duration and gut microbiome profiles in convalescence. This highlights the potential role of cardiometabolic dysfunction in relation to the experience of long duration symptoms after symptoms of acute infection, both COVID-19 as well as other illnesses.},
}
@article {pmid37365664,
year = {2023},
author = {Zhao, L and Lin, LZ and Zeng, Y and Teng, WK and Chen, MY and Brand, JJ and Zheng, LL and Gan, NQ and Gong, YH and Li, XY and Lv, J and Chen, T and Han, BP and Song, LR and Shu, WS},
title = {The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {142},
pmid = {37365664},
issn = {2049-2618},
mesh = {*Microcystis/genetics/metabolism ; Ecosystem ; *Organophosphonates/metabolism ; *Cyanobacteria/genetics ; Phytoplankton ; Lakes/microbiology ; Phosphorus/metabolism ; },
abstract = {BACKGROUND: Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples.<br><br>RESULTS: Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus.<br><br>CONCLUSIONS: The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.},
}
@article {pmid37361045,
year = {2023},
author = {Wang, D and Ren, H},
title = {Microbial community in buckwheat rhizosphere with different nitrogen application rates.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15514},
pmid = {37361045},
issn = {2167-8359},
mesh = {Rhizosphere ; *Fagopyrum/metabolism ; Nitrogen/analysis ; Fertilizers/analysis ; *Neurodegenerative Diseases ; Soil Microbiology ; *Microbiota/genetics ; },
abstract = {Microorganism plays a pivotal role in regulating sustainable development of agriculture. The excessive application of nitrogen fertilizer is considered to affect the microbial structure in many agricultural systems. The present study aimed to assess the impacts of nitrogen application rate on microbial diversity, community and functionality in rhizosphere of Tartary buckwheat in short-time. The nitrogen fertilizer was applied at rates of 90 kg (N90), 120 kg (N120) and 150 kg (N150) urea per hectare, respectively. The soil properties were measured chemical analysis and displayed no difference among treatments. Metagenome analysis results showed that the microbial diversity was not affected, but the microbial community and functionality were affected by the nitrogen application rate. According to the Linear discriminant analysis effect size (LEfSe) analysis, 15 taxa were significantly enriched in the N120 and N150 groups, no taxon was enriched in the N90 group. Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation results revealed that the genes related to butanoate and beta alanine metabolism were significantly enriched in the N90 group, the genes related to thiamine metabolism, lipopolysaccharide biosynthesis and biofilm formation were significantly enriched in the N120 group, and the genes related to neurodegenerative disease was significantly enriched in the N150 group. In conclusion, short-time nitrogen fertilizer application shifted the microbial community structure and functionality.},
}
@article {pmid37102874,
year = {2023},
author = {Colbert, JF and Kirsch, JM and Erzen, CL and Langouët-Astrié, CJ and Thompson, GE and McMurtry, SA and Kofonow, JM and Robertson, CE and Kovacs, EJ and Sullivan, RC and Hippensteel, JA and Sawant, NV and De Nisco, NJ and McCollister, BD and Schwartz, RS and Horswill, AR and Frank, DN and Duerkop, BA and Schmidt, EP},
title = {Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity.},
journal = {mBio},
volume = {14},
number = {3},
pages = {e0005223},
pmid = {37102874},
issn = {2150-7511},
support = {I01 BX002711/BX/BLRD VA/United States ; },
mesh = {Humans ; Animals ; Mice ; Aged ; *Gastrointestinal Microbiome/physiology ; Virulence ; Bacteria/genetics ; Aging ; *Sepsis/microbiology ; },
abstract = {Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition but also an overabundance of genomic virulence factors that have functional consequence on host immune evasion. IMPORTANCE Older adults suffer more frequent and worse outcomes from sepsis, a critical illness secondary to infection. The reasons underlying this unique susceptibility are incompletely understood. Prior work in this area has focused on how the immune response changes with age. The current study, however, focuses instead on alterations in the community of bacteria that humans live with within their gut (i.e., the gut microbiome). The central concept of this paper is that the bacteria in our gut evolve along with the host and "age," making them more efficient at causing sepsis.},
}
@article {pmid37357866,
year = {2023},
author = {Wang, YH and Luan, YX and Luo, JY and Men, Y and Engel, MS and Damgaard, J and Khila, A and Chen, PP and Figueiredo Moreira, FF and Rafael, JA and Xie, Q},
title = {300 Million years of coral treaders (Insecta: Heteroptera: Hermatobatidae) back to the ocean in the phylogenetic context of Arthropoda.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2001},
pages = {20230855},
doi = {10.1098/rspb.2023.0855},
pmid = {37357866},
issn = {1471-2954},
mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Ecosystem ; *Arthropods ; *Heteroptera ; Coral Reefs ; Insecta ; },
abstract = {Among hundreds of insect families, Hermatobatidae (commonly known as coral treaders) is one of the most unique. They are small, wingless predaceous bugs in the suborder Heteroptera. Adults are almost black in colour, measuring about 5 mm in body length and 3 mm in width. Thirteen species are known from tropical coral reefs or rocky shores, but their origin and evolutionary adaptation to their unusual marine habitat were unexplored. We report here the genome and metagenome of Hermatobates lingyangjiaoensis, hitherto known only from its type locality in the South China Sea. We further reconstructed the evolutionary history and origin of these marine bugs in the broader context of Arthropoda. The dated phylogeny indicates that Hexapoda diverged from their marine sister groups approximately 498 Ma and that Hermatobatidae originated 192 Ma, indicating that they returned to an oceanic life some 300 Myr after their ancestors became terrestrial. Their origin is consistent with the recovery of tropical reef ecosystems after the end-Triassic mass extinction, which might have provided new and open niches for them to occupy and thrive. Our analyses also revealed that both the genome changes and the symbiotic bacteria might have contributed to adaptations necessary for life in the sea.},
}
@article {pmid37355726,
year = {2023},
author = {Elie, C and Perret, M and Hage, H and Sentausa, E and Hesketh, A and Louis, K and Fritah-Lafont, A and Leissner, P and Vachon, C and Rostaing, H and Reynier, F and Gervasi, G and Saliou, A},
title = {Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {10279},
pmid = {37355726},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA ; *Microbiota/genetics ; },
abstract = {The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.},
}
@article {pmid35965269,
year = {2023},
author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA},
title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {392-407},
pmid = {35965269},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; Metagenome ; Coral Reefs ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Seawater/microbiology ; },
abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.},
}
@article {pmid35864173,
year = {2023},
author = {Tian, C and Pang, J and Bu, C and Wu, S and Bai, H and Li, Y and Guo, Q and Siddique, KHM},
title = {The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {497-508},
pmid = {35864173},
issn = {1432-184X},
support = {2016YFE0203400//National Key Research and Development Program of China/ ; 2017YFC0504703//National Key Research and Development Program of China/ ; 41971131//National Natural Scientific Foundation of China/ ; },
mesh = {Ecosystem ; *Lichens ; Carbon ; Nitrates ; Soil/chemistry ; *Bryophyta ; Nitrogen Fixation ; *Microbiota ; Soil Microbiology ; Nitrogen/chemistry ; },
abstract = {Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.},
}
@article {pmid35705745,
year = {2023},
author = {Song, L and Wang, Y and Zhang, R and Yang, S},
title = {Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {311-324},
pmid = {35705745},
issn = {1432-184X},
support = {52000016//National Natural Science Foundation of China/ ; 51578642//National Natural Science Foundation of China/ ; },
mesh = {*Solid Waste/analysis ; Nitrogen/analysis ; Carbon ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; Sulfur ; Waste Disposal Facilities ; },
abstract = {Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.},
}
@article {pmid35657425,
year = {2023},
author = {Meena, M and Yadav, G and Sonigra, P and Nagda, A and Mehta, T and Swapnil, P and Harish, and Marwal, A and Kumar, S},
title = {Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {49-74},
pmid = {35657425},
issn = {1432-184X},
mesh = {*Ecosystem ; Climate Change ; Soil/chemistry ; Forests ; *Microbiota ; Nitrogen/analysis ; Soil Microbiology ; Carbon ; },
abstract = {Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.},
}
@article {pmid35618944,
year = {2023},
author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC},
title = {Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {575-588},
pmid = {35618944},
issn = {1432-184X},
mesh = {Animals ; *Brachyura ; *Gastrointestinal Microbiome ; Fatty Acids, Unsaturated/metabolism ; Diet ; Lipid Metabolism ; },
abstract = {Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.},
}
@article {pmid37355675,
year = {2023},
author = {Wang, Y and Guo, A and Zou, Y and Mu, W and Zhang, S and Shi, Z and Liu, Z and Cai, X and Zhu, XQ and Wang, S},
title = {Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {43},
pmid = {37355675},
issn = {2055-5008},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; *Colitis/metabolism ; *Helminths ; },
abstract = {Tissue-dwelling helminths affect billions of people around the world. They are potent manipulators of the host immune system, prominently by promoting regulatory T cells (Tregs) and are generally associated with a modified host gut microbiome. However, the role of the gut microbiota in the immunomodulatory processes for these non-intestinal parasites is still unclear. In the present study, we used an extra-intestinal cestode helminth model-larval Echinococcus multilocularis to explore the tripartite partnership (host-helminth-bacteria) in the context of regulating colonic Tregs in Balb/c mice. We showed that larval E. multilocularis infection in the peritoneal cavity attenuated colitis in Balb/c mice and induced a significant expansion of colonic Foxp3[+] Treg populations. Fecal microbiota depletion and transplantation experiments showed that the gut microbiota contributed to increasing Tregs after the helminth infection. Shotgun metagenomic and metabolic analyses revealed that the gut microbiome structure after infection was significantly shifted with a remarkable increase of Lactobacillus reuteri and that the microbial metabolic capability was reprogrammed to produce more Treg cell regulator-short-chain fatty acids in feces. Furthermore, we also prove that the L. reuteri strain elevated in infected mice was sufficient to promote the colonic Treg frequency and its growth was potentially associated with T cell-dependent immunity in larval E. multilocularis infection. Collectively, these findings indicate that the extraintestinal helminth drives expansions of host colonic Tregs through the gut microbes. This study suggests that the gut microbiome serves as a critical component of anti-inflammation effects even for a therapy based on an extraintestinal helminth.},
}
@article {pmid37355612,
year = {2023},
author = {Lin, X and Qiao, B and Chang, R and Li, Y and Zheng, W and He, Z and Tian, Y},
title = {Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {139},
pmid = {37355612},
issn = {2049-2618},
support = {No. 91951207//National Natural Science Foundation of China/ ; No. 91951207//National Natural Science Foundation of China/ ; No. 91951207//National Natural Science Foundation of China/ ; No. 91951207//National Natural Science Foundation of China/ ; No. 91951207//National Natural Science Foundation of China/ ; No. 91951207//National Natural Science Foundation of China/ ; },
mesh = {*Nitrates/metabolism ; Benzo(a)pyrene/metabolism ; Bacteria ; *Microbiota/genetics ; Sulfur/metabolism ; Oxidation-Reduction ; },
abstract = {BACKGROUND: Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characterization and manipulation of such taxa is a major challenge due to the complexity of microbial communities and rapid turnover in both time and space. Here, microcosms were set up with benzo[a]-pyrene (BaP) and/or nitrate based on C-rich, S-rich, and N-limited mangrove sediments as reductive experimental models to trigger and track the turnover of keystone taxa to address this challenge.<br><br>RESULTS: Based on microbial co-occurrence network analysis, two keystone taxa, Sulfurovum and Sulfurimonas, were found to exhibit significant role transitions in different microcosms, where these two taxa played nonkeystone roles with neutral relationships in in situ mangrove sediments. However, Sulfurimonas transitioned to be keystone taxa in nitrate-replenished microcosms and formed a keystone guild with Thioalkalispira. Sulfurovum stood out in BaP-added microcosms and mutualized in a densely polycyclic aromatic hydrocarbon (PAH)-degrader-centric keystone guild with Novosphingobium and Robiginitalea, where 63.25% of added BaP was removed. Under the occurrence of nitrate and BaP, they simultaneously played roles as keystone taxa in their respective guilds but exhibited significant competition. Comparative genomics and metagenome-assembled genome (MAG) analysis was then performed to reveal the metabolic potential of those keystone taxa and to empirically deduce their functional role in keystone guilds. Sulfurimonas possesses a better sense system and motility, indicative of its aggressive role in nitrate acquisition and conversion; Sulfurovum exhibited a better ability for oxidation resistance and transporting nutrients and electrons. High-efficiency thermal asymmetric interlaced polymerase reaction (hiTAIL-PCR) and enhanced green fluorescent protein (eGFP)-labeling approaches were employed to capture and label the BaP key degrader to further experimentally verify the roles of keystone taxa Sulfurovum in the keystone guilds. Observations of the enhancement in reactive oxygen species (ROS) removal, cell growth, and degradation efficiency by co-culture of isolated keystone taxa strains experimentally demonstrated that Sulfurovum contributes to the BaP degradative microbiome against BaP toxicity.<br><br>CONCLUSIONS: Our findings suggest that the combined use of co-occurrence network analysis, comparative genomics, and co-culture of captured keystone taxa (3C-strategy) in microbial communities whose structure is strongly shaped by changing environmental factors can characterize keystone taxa roles in keystone guilds and may provide targets for manipulation to improve the function of the microbiome. Video Abstract.},
}
@article {pmid37349979,
year = {2023},
author = {Fan, G and Cao, F and Kuang, T and Yi, H and Zhao, C and Wang, L and Peng, J and Zhuang, Z and Xu, T and Luo, Y and Xie, Y and Li, H and Zhang, K and Zeng, Y and Zhang, X and Peng, S and Qiu, X and Zhou, D and Liang, H and Yang, B and Kang, J and Liu, Y and Zhang, Y},
title = {Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2226925},
doi = {10.1080/19490976.2023.2226925},
pmid = {37349979},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies ; Virome ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Bacteriophages/genetics ; Bacteria/genetics ; },
abstract = {Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we characterized the gut virome alterations in T2D and its complications diabetic nephropathy (DN) by metagenomic sequencing of fecal viral-like particles. Compared with controls, T2D subjects, especially those with DN, had significantly lower viral richness and diversity. 81 viral species were identified to be significantly altered in T2D subjects, including a decrease in some phages (e.g. Flavobacterium phage and Cellulophaga phaga). DN subjects were depleted of 12 viral species, including Bacteroides phage, Anoxybacillus virus and Brevibacillus phage, and enriched in 2 phages (Shigella phage and Xylella phage). Multiple viral functions, particularly those of phage lysing host bacteria, were markedly reduced in T2D and DN. Strong viral-bacterial interactions in healthy controls were disrupted in both T2D and DN. Moreover, the combined use of gut viral and bacterial markers achieved a powerful diagnostic performance for T2D and DN, with AUC of 99.03% and 98.19%, respectively. Our results suggest that T2D and its complication DN are characterized by a significant decrease in gut viral diversity, changes in specific virus species, loss of multiple viral functions, and disruption of viral-bacterial correlations. The combined gut viral and bacterial markers have diagnostic potential for T2D and DN.},
}
@article {pmid37349686,
year = {2023},
author = {Li, H and Fu, J and Erlong, N and Li, R and Xu, C and Hao, L and Chen, J and Chai, W},
title = {Characterization of periprosthetic environment microbiome in patients after total joint arthroplasty and its potential correlation with inflammation.},
journal = {BMC infectious diseases},
volume = {23},
number = {1},
pages = {423},
pmid = {37349686},
issn = {1471-2334},
support = {No.82102585//Youth Project of National Natural Science Foundation of China/ ; No.2020YFC2004900//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Prosthesis-Related Infections/microbiology ; Prospective Studies ; Arthroplasty/adverse effects ; Inflammation/complications ; *Arthritis, Infectious/etiology ; *Microbiota ; Staphylococcus ; Retrospective Studies ; *Arthroplasty, Replacement, Hip/adverse effects ; Sensitivity and Specificity ; },
abstract = {AIMS: Periprosthetic joint infection (PJI) is one of the most serious complications after total joint arthroplasty (TJA) but the characterization of the periprosthetic environment microbiome after TJA remains unknown. Here, we performed a prospective study based on metagenomic next-generation sequencing to explore the periprosthetic microbiota in patients with suspected PJI.<br><br>METHODS: We recruited 28 patients with culture-positive PJI, 14 patients with culture-negative PJI, and 35 patients without PJI, which was followed by joint aspiration, untargeted metagenomic next-generation sequencing (mNGS), and bioinformatics analysis. Our results showed that the periprosthetic environment microbiome was significantly different between the PJI group and the non-PJI group. Then, we built a "typing system" for the periprosthetic microbiota based on the RandomForest Model. After that, the 'typing system' was verified externally.<br><br>RESULTS: We found the periprosthetic microbiota can be classified into four types generally: "Staphylococcus type," "Pseudomonas type," "Escherichia type," and "Cutibacterium&#xa0;type." Importantly, these four types of microbiotas had different clinical signatures, and the patients with the former two microbiota types showed obvious inflammatory responses compared to the latter ones. Based on the 2014 Musculoskeletal Infection Society (MSIS) criteria, clinical PJI was more likely to be confirmed when the former two types were encountered. In addition, the Staphylococcus spp. with compositional changes were correlated with C-reactive protein levels, the erythrocyte sedimentation rate, and the synovial fluid white blood cell count and granulocyte percentage.<br><br>CONCLUSIONS: Our study shed light on the characterization of the periprosthetic environment microbiome in patients after TJA. Based on the RandomForest model, we established a basic "typing system" for the microbiota in the periprosthetic environment. This work can provide a reference for future studies about the characterization of periprosthetic microbiota in periprosthetic joint infection patients.},
}
@article {pmid37346030,
year = {2023},
author = {Yu, H and Wang, Q and Tang, J and Dong, L and Dai, G and Zhang, T and Zhang, G and Xie, K and Wang, H and Zhao, Z},
title = {Comprehensive analysis of gut microbiome and host transcriptome in chickens after Eimeria tenella infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1191939},
pmid = {37346030},
issn = {2235-2988},
mesh = {Animals ; *Eimeria tenella/genetics ; Chickens/genetics ; *Gastrointestinal Microbiome/genetics ; Transcriptome ; *Poultry Diseases/genetics ; },
abstract = {BACKGROUND: Coccidiosis is an intestinal parasitic disease caused by Eimeria protozoa, which endangers the health and growth of animals, and causes huge economic losses to the poultry industry worldwide every year. Studies have shown that poultry gut microbiota plays an important role in preventing the colonization of pathogens and maintaining the health of the host. Coccidia infection also affects host gene expression. However, the underlying potential relationship between gut microbiome and host transcriptome during E. tenella infection in chickens remain unclear.<br><br>METHODS: In this study, metagenomic and transcriptome sequencing were applied to identify microbiota and genes in cecal contents and cecal tissues of infected (JS) and control (JC) chickens on day 4.5 postinfection (pi), respectively.<br><br>RESULTS: First, microbial sequencing results of cecal contents showed that the abundance of Lactobacillus, Roseburia sp. and Faecalibacterium sp decreased significantly after E. tenella infection (P < 0.05), while the abundance of Alistipes and Prevotella pectinovora increased significantly (P < 0.05). Second, transcriptome sequencing results showed that a total of 434 differentially expressed mRNAs were identified, including 196 up-regulated and 238 down-regulated genes. These differentially expressed genes related to inflammation and immunity, such as GAMA, FABP1, F2RL1 and RSAD2, may play an important role in the process of host resistance to coccidia infection. Functional studies showed that the enriched pathways of differentially expressed genes included the TGF-beta signaling pathway and the ErbB signaling pathways. Finally, the integrated analysis of gut microbiome and host transcriptome suggested that Prevotella pectinovora associated with FABP1, Butyricicoccus porcorum and Colidextribacter sp. associated with RSAD2 were involved in the immune response upon E. tenella infection.<br><br>CONCLUSION: In conclusion, this study provides valuable information on the microbiota and key immune genes after chicken E. tenella infection, with the aim of providing reference for the impact of coccidia infection on cecal microbiome and host.},
}
@article {pmid37345233,
year = {2023},
author = {Shtossel, O and Isakov, H and Turjeman, S and Koren, O and Louzoun, Y},
title = {Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2224474},
pmid = {37345233},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Artificial Intelligence ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Machine Learning ; },
abstract = {The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine-learning-based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing or shotgun metagenomics. However, several properties of microbial sequence-based studies hinder machine learning (ML), including non-uniform representation, a small number of samples compared with the dimension of each sample, and sparsity of the data, with the majority of taxa present in a small subset of samples. We show here using a graph representation that the cladogram structure is as informative as the taxa frequency. We then suggest a novel method to combine information from different taxa and improve data representation for ML using microbial taxonomy. iMic (image microbiome) translates the microbiome to images through an iterative ordering scheme, and applies convolutional neural networks to the resulting image. We show that iMic has a higher precision in static microbiome gene sequence-based ML than state-of-the-art methods. iMic also facilitates the interpretation of the classifiers through an explainable artificial intelligence (AI) algorithm to iMic to detect taxa relevant to each condition. iMic is then extended to dynamic microbiome samples by translating them to movies.},
}
@article {pmid37342148,
year = {2023},
author = {Gugliucci, W and Cirillo, V and Maggio, A and Romano, I and Ventorino, V and Pepe, O},
title = {Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1180061},
pmid = {37342148},
issn = {1664-462X},
abstract = {Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.},
}
@article {pmid37340081,
year = {2023},
author = {Yang, C and Xu, J and Xu, X and Xu, W and Tong, B and Wang, S and Ji, R and Tan, Y and Zhu, Y},
title = {Characteristics of gut microbiota in patients with metabolic associated fatty liver disease.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {9988},
pmid = {37340081},
issn = {2045-2322},
support = {No. B2022201//Medical Science and Technology Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Hepatocellular ; RNA, Ribosomal, 16S/genetics ; *Liver Neoplasms ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; Bacteroidetes ; Clostridiaceae ; },
abstract = {Metabolic associated fatty liver disease (MAFLD) is rising in incidence and is an increasingly common cause of cirrhosis and hepatocellular carcinoma (HCC). Alterations in the gut microbiota have been shown to correlate with the development and progression of MAFLD. However, little is known regarding differences in the gut microbiomes of MAFLD patients and healthy cohorts, and subgroups at the abnormal activity of hepatic enzymes in China. In this study, we enrolled 81 MAFLD patients and 25 healthy volunteers. The fecal microbiota was assessed using 16S rRNA gene sequencing and metagenomic sequencing. The results suggested that Ruminococcus obeum and Alistipes were most enriched in healthy individuals when compared with MAFLD patients. Microbe-set Enrichment Analysis (MSEA) results showed Dorea, Lactobacillus and Megasphaera are enriched in MAFLD group. We also found that Alistipes has negatively related to serum glucose (GLU), gamma-glutamyl transferase (GGT), and alanine aminotransferase (ALT). Moreover, the abundance of Dorea was found to be significantly overrepresented in the MAFLD patients and the degree of enrichment increased with the increasing abnormal liver enzyme. An increase in Dorea, combined with decreases in Alistipes appears to be characteristic of MAFLD patients. Further study of microbiota may provide a novel insight into the pathogenesis of MAFLD as well as a novel treatment strategy.},
}
@article {pmid37285974,
year = {2023},
author = {Ya, H and Zhang, T and Xing, Y and Lv, M and Wang, X and Jiang, B},
title = {Co-existence of polyethylene microplastics and tetracycline on soil microbial community and ARGs.},
journal = {Chemosphere},
volume = {335},
number = {},
pages = {139082},
doi = {10.1016/j.chemosphere.2023.139082},
pmid = {37285974},
issn = {1879-1298},
mesh = {Humans ; *Microplastics ; Plastics ; Polyethylene ; Soil/chemistry ; Genes, Bacterial ; Soil Microbiology ; Anti-Bacterial Agents ; Tetracycline/pharmacology ; *Microbiota ; Aminoglycosides ; },
abstract = {Microplastics are plastic particles with particle size less than 5 mm in the environment. As an emerging organic pollutant, the presence of microplastics in the soil environment has been widely noticed. Also, due to the overuse of antibiotics, a large amount of antibiotics that cannot be fully absorbed by humans and livestock enter the soil environment in the form of urine or manure, making the soils suffer from serious antibiotic contamination problems. To address the environmental problems of microplastics and antibiotic contamination in soils, this study was conducted to investigate the effects of PE microplastics on antibiotic degradation, microbial community characteristics and ARGs in tetracycline-contaminated soils. The results showed that the addition of PE microplastics inhibited the degradation of tetracycline, and significantly increased the organic carbon content and decreased the neutral phosphatase activity. The addition of PE microplastics significantly reduced the alpha diversity of soil microbial community. Compared to the single tetracycline contamination. In addition, combined contamination with PE microplastics and tetracycline significantly affected bacterial genera such as Aeromicrobium, Rhodococcus, Mycobacterium and Intrasporangium. Metagenome sequencing studies revealed that the addition of PE microplastics inhibited the dissipation of ARGs in tetracycline-contaminated soils. There were strong positive correlations between Multidrug, Aminoglycoside and Clycopeptide resistance genes and Chloroflexi and Proteobacteria in tetracycline contaminated soils, and there was a strong positive correlation between Aminoglycoside resistance genes and Actinobacteria in combined contamination of PE microplastics and tetracycline. This study will provide some data support for the current environmental risk assessment of the coexistence of multiple contaminants in soil.},
}
@article {pmid37115265,
year = {2023},
author = {Houttu, N and Benchraka, C and Lotankar, M and Muhli, E and Niinikoski, H and Lahti, L and Laitinen, K},
title = {Gut microbiota composition and function in pregnancy as determinants of prediabetes at two-year postpartum.},
journal = {Acta diabetologica},
volume = {60},
number = {8},
pages = {1045-1054},
pmid = {37115265},
issn = {1432-5233},
support = {258606//Academy of Finland/ ; 295741//Academy of Finland/ ; },
mesh = {Pregnancy ; Humans ; Female ; *Prediabetic State ; *Gastrointestinal Microbiome ; *Diabetes, Gestational ; Blood Glucose ; Postpartum Period ; },
abstract = {AIMS: Deep metagenomics offers an advanced tool for examining the relationship between gut microbiota composition and function and the onset of disease; in this case, does the composition and function of gut microbiota during pregnancy differ in women who develop prediabetes and those who do not at two-year postpartum, and whether the gut microbiota composition associates with glycemic traits.<br><br>METHODS: In total, 439 women were recruited in early pregnancy. Gut microbiota was assessed by metagenomics analysis in early (13.9&#x2009;&#xb1;&#x2009;2.0 gestational weeks) and late pregnancy (35.1&#x2009;&#xb1;&#x2009;1.0 gestational weeks). Prediabetes was determined using American Diabetes Association criteria as fasting plasma glucose 5.6-6.9&#xa0;mmol/l analyzed by an enzymatic hexokinase method. Of the women, 39 (22.1%) developed prediabetes by two-year postpartum.<br><br>RESULTS: The relative abundances of Escherichia unclassified (FDR&#x2009;<&#x2009;0.05), Clostridiales bacterium 1_7_ 47FAA (FDR&#x2009;<&#x2009;0.25) and Parabacteroides (FDR&#x2009;<&#x2009;0.25) were higher, and those of Ruminococcaceae bacterium D16 (FDR&#x2009;<&#x2009;0.25), Anaerotruncus unclassified (FDR&#x2009;<&#x2009;0.25) and Ruminococcaceae noname (FDR&#x2009;<&#x2009;0.25) were lower in early pregnancy in those women who later developed prediabetes. In late pregnancy, Porphyromonas was higher and Ruminococcus sp 5_1_39BFAA was lower in prediabetes (FDR&#x2009;<&#x2009;0.25). Furthermore, fasting glucose concentrations associated inversely with Anaerotruncus unclassified in early pregnancy and directly with Ruminococcus sp 5_1_39BFAA in late pregnancy (FDR&#x2009;<&#x2009;0.25). &#x3b1;-Diversity or &#x3b2;-diversity did not differ significantly between the groups. Predictions of community function during pregnancy were not associated with prediabetes.<br><br>CONCLUSIONS: Our study shows that some bacterial species during pregnancy contributed to the onset of prediabetes within two-year postpartum. These were attributable primarily to a lower abundance of short-chain fatty acids-producing bacteria.},
}
@article {pmid37339968,
year = {2023},
author = {Narat, V and Salmona, M and Kampo, M and Heyer, T and Rachik, AS and Mercier-Delarue, S and Ranger, N and Rupp, S and Ambata, P and Njouom, R and Simon, F and Le Goff, J and Giles-Vernick, T},
title = {Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3674},
pmid = {37339968},
issn = {2041-1723},
support = {ANR-14-CE31-0004-001//Agence Nationale de la Recherche (French National Research Agency)/ ; No number//National Endowment for the Humanities (NEH)/ ; },
mesh = {Animals ; Humans ; Eukaryota ; *One Health ; Virome ; *Hominidae ; Gorilla gorilla ; },
abstract = {Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.},
}
@article {pmid37069233,
year = {2023},
author = {Xia, R and Sun, M and Balcázar, JL and Yu, P and Hu, F and Alvarez, PJJ},
title = {Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes.},
journal = {The ISME journal},
volume = {17},
number = {7},
pages = {1004-1014},
pmid = {37069233},
issn = {1751-7370},
support = {42077106, 42277115, 42177113, 42277418//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277418//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Benzo(a)pyrene/toxicity ; *Oligochaeta ; Virome ; *Bacteriophages/genetics ; Prophages/genetics ; },
abstract = {The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg[-1]) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg[-1]) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.},
}
@article {pmid37339742,
year = {2023},
author = {Arora, J and Buček, A and Hellemans, S and Beránková, T and Arias, JR and Fisher, BL and Clitheroe, C and Brune, A and Kinjo, Y and Šobotník, J and Bourguignon, T},
title = {Evidence of cospeciation between termites and their gut bacteria on a geological time scale.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2001},
pages = {20230619},
pmid = {37339742},
issn = {1471-2954},
mesh = {Animals ; *Isoptera ; Phylogeny ; Symbiosis ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Mammals ; },
abstract = {Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.},
}
@article {pmid37338635,
year = {2023},
author = {Salam, LB and Obayori, OS and Ilori, MO and Amund, OO},
title = {Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {39},
number = {9},
pages = {228},
pmid = {37338635},
issn = {1573-0972},
mesh = {Soil/chemistry ; *Soil Pollutants/analysis ; *Metals, Heavy/toxicity/analysis ; Chromium/toxicity/analysis ; Cadmium/analysis ; *Microbiota ; Environmental Monitoring ; China ; },
abstract = {The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.},
}
@article {pmid37333852,
year = {2023},
author = {Xu, Y and Xu, J and Liu, T and Liu, P and Chen, XG},
title = {Metagenomic analysis reveals the virome profiles of Aedes albopictus in Guangzhou, China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1133120},
pmid = {37333852},
issn = {2235-2988},
mesh = {Animals ; *Aedes ; Metagenomics ; Phylogeny ; Virome/genetics ; Mosquito Vectors ; *Viruses/genetics ; },
abstract = {INTRODUCTION: Aedes albopictus is an aggressive invasive mosquito species widely distributed around the world, and it is also a known vector of arboviruses. Virus metagenomics and RNA interference (RNAi) are important in studying the biology and antiviral defense of Ae. albopictus. However, the virome and potential transmission of plant viruses by Ae. albopictus remain understudied.<br><br>METHODS: Mosquito samples of Ae. albopictus were collected from Guangzhou, China, and small RNA sequencing was performed. Raw data were filtered, and virus-associated contigs were generated using VirusDetect. The small RNA profiles were analyzed, and maximum-likelihood phylogenetic trees were constructed.<br><br>RESULTS: The small RNA sequencing of pooled Ae. albopictus revealed the presence of five known viruses, including Wenzhou sobemo-like virus 4, mosquito nodavirus, Aedes flavivirus, Hubei chryso-like virus 1, and Tobacco rattle virus RNA1. Additionally, 21 new viruses that had not been previously reported were identified. The mapping of reads and contig assembly provided insights into the viral diversity and genomic characteristics of these viruses. Field survey confirmed the detection of the identified viruses in Ae. albopictus collected from Guangzhou.<br><br>DISCUSSION: The comprehensive analysis of the virus metagenomics of Ae. albopictus in this study sheds light on the diversity and prevalence of viruses in mosquito populations. The presence of known and novel viruses highlights the need for continued surveillance and investigation into their potential impact on public health. The findings also emphasize the importance of understanding the virome and potential transmission of plant viruses by Ae. albopictus.<br><br>CONCLUSION: This study provides valuable insights into the virome of Ae. albopictus and its potential role as a vector for both known and novel viruses. Further research is needed to expand the sample size, explore additional viruses, and investigate the implications for public health.},
}
@article {pmid37330554,
year = {2023},
author = {Zhang, L and Rahman, J and Chung, M and Lashua, L and Gordon, A and Balmaseda, A and Kuan, G and Bonneau, R and Ghedin, E},
title = {CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {136},
pmid = {37330554},
issn = {2049-2618},
support = {U01 AI088654/AI/NIAID NIH HHS/United States ; U01 AI111598/AI/NIAID NIH HHS/United States ; HHSN272201400031C/NH/NIH HHS/United States ; },
mesh = {Humans ; Clustered Regularly Interspaced Short Palindromic Repeats ; *Influenza, Human/prevention &amp; control ; Bacteria ; Metagenome/genetics ; *Microbiota/genetics ; *Micrococcaceae/genetics ; },
abstract = {BACKGROUND: Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether metagenomic-type analyses of the microbiome provide the resolution necessary to track transmission of airway bacteria. Microbiome studies have shown that the microbial community across various body sites tends to be more similar between individuals who cohabit in the same household than between individuals from different households. We tested whether there was increased sharing of bacteria from the airways within households with influenza infections as compared to control households with no influenza.<br><br>RESULTS: We obtained 221 respiratory samples that were collected from 54 individuals at 4 to 5 time points across 10 households, with and without influenza infection, in Managua, Nicaragua. From these samples, we generated metagenomic (whole genome shotgun sequencing) datasets to profile microbial taxonomy. Overall, specific bacteria and phages were differentially abundant between influenza positive households and control (no influenza infection) households, with bacteria like Rothia, and phages like Staphylococcus P68virus that were significantly enriched in the influenza-positive households. We identified CRISPR spacers detected in the metagenomic sequence reads and used these to track bacteria transmission within and across households. We observed a clear sharing of bacterial commensals and pathobionts, such as Rothia, Neisseria, and Prevotella, within and between households. However, due to the relatively small number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.<br><br>CONCLUSION: We observed that airway microbial composition differences across households were associated with what appeared to be different susceptibility to influenza infection. We also demonstrate that CRISPR spacers from the whole microbial community can be used as markers to study bacterial transmission between individuals. Although additional evidence is needed to study transmission of specific bacterial strains, we observed sharing of respiratory commensals and pathobionts within and across households. Video Abstract.},
}
@article {pmid37245312,
year = {2023},
author = {Gong, X and Ge, Z and Ma, Z and Li, Y and Huang, D and Zhang, J},
title = {Effect of different size microplastic particles on the construction of algal-bacterial biofilms and microbial communities.},
journal = {Journal of environmental management},
volume = {343},
number = {},
pages = {118246},
doi = {10.1016/j.jenvman.2023.118246},
pmid = {37245312},
issn = {1095-8630},
mesh = {*Microplastics/metabolism/pharmacology ; Plastics ; Sewage ; Bacteria/metabolism ; Biofilms ; *Microbiota ; },
abstract = {Algal-bacterial symbiotic system is a biological purification system that combines sewage treatment with resource utilization and has the dual effects of carbon sequestration and pollution reduction. In this study, an immobilized algal-bacterial biofilm system was constructed for the treatment of natural sewage. Effects of exposure to microplastics (MPs) with different particle diameters (0.065 μm, 0.5 μm and 5 μm) were determined in terms of algal biomass recovery efficiency, the composition of extracellular polymeric substances (EPS) and morphologic characteristics. The impacts of MPs on the bacterial diversity and community structure of biofilms were also examined. The metagenomic analysis of key microorganisms and related metabolism pathways involved in system was further investigated. Results showed that following exposure to 5 μm MP, a maximum algal recovery efficiency of 80% was achieved, with a minimum PSII primary light energy conversion efficiency (Fv/Fm ratio) of 0.513. Furthermore, 5 μm MP caused the highest level of damage to the algal-bacterial biofilm, enhancing the secretion of protein-rich EPS. The biofilm morphology became rough and loose following exposure to 0.5 μm and 5 μm MP. Community diversity and richness were significantly high in biofilms exposed to 5 μm MP. Proteobacteria (15.3-24.1%), Firmicutes (5.0-7.8%) and Actinobacteria (4.2-4.9%) were dominant in all groups, with exposure to 5 μm MP resulting in the highest relative abundance for these species. The addition of MPs promoted the related metabolic functions while inhibited the degradation of harmful substances by algal-bacterial biofilms. The findings have environmental significance for the practical application of algal-bacterial biofilms for sewage treatment, providing novel insights into the potential effects of MPs on immobilized algal-bacterial biofilm systems.},
}
@article {pmid37328529,
year = {2023},
author = {Guan, Y and Zhang, Y and Zhu, Y and Wang, Y},
title = {CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {9754},
pmid = {37328529},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid/genetics/metabolism ; Computational Biology ; *Microbiota ; *Inflammatory Bowel Diseases/genetics ; Chemokine CXCL10/genetics ; },
abstract = {This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA's gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate gene CXCL10 was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, and CXCL10 was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella, Ruminococcus, and Ruminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the gene CXCL10 shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.},
}
@article {pmid37325707,
year = {2023},
author = {Wang, Y and Zhang, R and Pu, Y and Wang, D and Wang, Y and Wu, X and Pan, Y and Luo, C and Zhao, G and Quan, Z and Zheng, Y},
title = {Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project.},
journal = {Phenomics (Cham, Switzerland)},
volume = {3},
number = {3},
pages = {300-308},
pmid = {37325707},
issn = {2730-5848},
abstract = {UNLABELLED: The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results. This protocol provides detailed operation methods of human microbial sample collection, DNA extraction, and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity, oral cavity, and skin, as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult participants. This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-023-00097-y.},
}
@article {pmid37212075,
year = {2023},
author = {Brown, EL and Essigmann, HT and Hoffman, KL and Alexander, AS and Newmark, M and Jiang, ZD and Suescun, J and Schiess, MC and Hanis, CL and DuPont, HL},
title = {IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes.},
journal = {Journal of Parkinson's disease},
volume = {13},
number = {4},
pages = {501-513},
doi = {10.3233/JPD-230066},
pmid = {37212075},
issn = {1877-718X},
mesh = {Humans ; *Parkinson Disease/complications ; Tremor/etiology ; *Gastrointestinal Microbiome/physiology ; Disease Progression ; Immunoglobulin A ; },
abstract = {BACKGROUND: Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity.<br><br>OBJECTIVE: Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes.<br><br>METHODS: Flow cytometry was used to separate IgA-coated and -uncoated bacteria from stool samples obtained from AR and TD patients followed by amplification and sequencing of the V4 region of the 16&#x200a;S rDNA gene on the MiSeq platform (Illumina).<br><br>RESULTS: IgA-Biome analyses identified significant alpha and beta diversity differences between the Parkinson's disease phenotypes and the Firmicutes/Bacteroides ratio was significantly higher in those with TD compared to those with AR. In addition, discriminant taxa analyses identified a more pro-inflammatory bacterial profile in the IgA+ fraction of those with the AR clinical subclass compared to IgA-Biome analyses of those with the TD subclass and with the taxa identified in the unsorted control samples.<br><br>CONCLUSION: IgA-Biome analyses underscores the importance of the host immune response in shaping the gut microbiome potentially affecting disease progression and presentation. In the present study, IgA-Biome analyses identified a unique proinflammatory microbial signature in the IgA+ fraction of those with AR that would have otherwise been undetected using conventional microbiome analysis approaches.},
}
@article {pmid37209654,
year = {2023},
author = {Xiong, X and Xu, J and Yan, X and Wu, S and Ma, J and Wang, Z and He, Q and Gong, J and Rao, Y},
title = {Gut microbiome and serum metabolome analyses identify biomarkers associated with sexual maturity in quails.},
journal = {Poultry science},
volume = {102},
number = {7},
pages = {102762},
pmid = {37209654},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome ; Chickens ; Metabolome ; Metagenome ; Bacteria ; Biomarkers ; },
abstract = {Increasing evidence indicates that the gut microbiome plays an important role in host aging and sexual maturity. However, the gut microbial taxa associated with sexual maturity in quails are unknown. This study used shotgun metagenomic sequencing to identify bacterial taxa associated with sexual maturity in d 20 and d 70 quails. We found that 17 bacterial species and 67 metagenome-assembled genomes (e.g., Bacteroides spp. and Enterococcus spp.) significantly differed between the d 20 and d 70 groups, including 5 bacterial species (e.g., Enterococcus faecalis) enriched in the d 20 group and 12 bacterial species (e.g., Christensenella massiliensis, Clostridium sp. CAG:217, and Bacteroides neonati) which had high abundances in the d 70 group. The bacterial species enriched in d 20 or d 70 were key biomarkers distinguishing sexual maturity and significantly correlated with the shifts in the functional capacities of the gut microbiome. Untargeted serum metabolome analysis revealed that 5 metabolites (e.g., nicotinamide riboside) were enriched in the d 20 group, and 6 metabolites (e.g., D-ribose, stevioside, and barbituric acid) were enriched in the d 70 group. Furthermore, metabolites with high abundances in the d 20 group were significantly enriched for the KEGG pathways of arginine biosynthesis, nicotinate and nicotinamide metabolism, and lysine degradation. However, glutathione metabolism and valine, leucine and isoleucine biosynthesis were enriched in high-abundance metabolites from the d 70 group. These results provide important insights into the effects of gut microbiome and host metabolism on quail sexual maturity.},
}
@article {pmid37323848,
year = {2023},
author = {Soundararajan, S and Selvakumar, J and Maria Joseph, ZM and Gopinath, Y and Saravanan, V and Santhanam, R},
title = {Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1153769},
pmid = {37323848},
issn = {2297-1769},
abstract = {INTRODUCTION: This study aimed to assess the effects of supplementing chicken feed with Moringa oleifera leaf powder, a phytobiotic, on the gastrointestinal microbiota. The objective was to examine the microbial changes induced by the supplementation.<br><br>METHODS: A total of 40, one-day-old chickens were fed their basal diet for 42 days and then divided into two groups: SG1 (basal diet) and SG2 (basal diet + 10 g/kg Moringa oleifera leaf powder). Metagenomics analysis was conducted to analyze operational taxonomic units (OTUs), species annotation, and biodiversity. Additionally, 16S rRNA sequencing was performed for molecular characterization of isolated gut bacteria, identified as Enterococcus faecium. The isolated bacteria were tested for essential metabolites, demonstrating antibacterial, antioxidant, and anticancer activities.<br><br>RESULTS AND DISCUSSION: The analysis revealed variations in the microbial composition between the control group (SG1) and the M. oleifera-treated group (SG2). SG2 showed a 47% increase in Bacteroides and a 30% decrease in Firmicutes, Proteobacteria, Actinobacteria, and Tenericutes compared to SG1. TM7 bacteria were observed exclusively in the M. oleifera-treated group. These findings suggest that Moringa oleifera leaf powder acts as a modulator that enhances chicken gut microbiota, promoting the colonization of beneficial bacteria. PICRUSt analysis supported these findings, showing increased carbohydrate and lipid metabolism in the M.oleifera-treated gut microbiota.<br><br>CONCLUSION: This study indicates that supplementing chicken feed with Moringa oleifera leaf powder as a phytobiotic enhances the gut microbiota in chicken models, potentially improving overall health. The observed changes in bacterial composition, increased presence of Bacteroides, and exclusive presence of TM7 bacteria suggest a positive modulation of microbial balance. The essential metabolites from isolated Enterococcus faecium bacteria further support the potential benefits of Moringa oleifera supplementation.},
}
@article {pmid37322412,
year = {2023},
author = {Yang, R and Li, X and Ying, Z and Zhao, Z and Wang, Y and Wang, Q and Shen, B and Peng, W},
title = {Prematurely delivering mothers show reductions of lachnospiraceae in their gut microbiomes.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {169},
pmid = {37322412},
issn = {1471-2180},
mesh = {Infant, Newborn ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mothers ; *Premature Birth ; *Microbiota ; Bacteria/genetics ; Clostridiales ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Preterm birth is the leading cause of perinatal morbidity and mortality. Despite evidence shows that imbalances in the maternal microbiome associates to the risk of preterm birth, the mechanisms underlying the association between a perturbed microbiota and preterm birth remain poorly understood.<br><br>METHOD: Applying shotgun metagenomic analysis on 80 gut microbiotas of 43 mothers, we analyzed the taxonomic composition and metabolic function in gut microbial communities between preterm and term mothers.<br><br>RESULTS: Gut microbiome of mothers delivering prematurely showed decreased alpha diversity and underwent significant reorganization, especially during pregnancy. SFCA-producing microbiomes, particularly species of Lachnospiraceae, Ruminococcaceae, and Eubacteriaceae, were significantly depleted in preterm mothers. Lachnospiraceae and its species were the main bacteria contributing to species' differences and metabolic pathways.<br><br>CONCLUSION: Gut microbiome of mothers delivering prematurely has altered and demonstrates the reduction of Lachnospiraceae.},
}
@article {pmid37322285,
year = {2023},
author = {López, JL and Fourie, A and Poppeliers, SWM and Pappas, N and Sánchez-Gil, JJ and de Jonge, R and Dutilh, BE},
title = {Growth rate is a dominant factor predicting the rhizosphere effect.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37322285},
issn = {1751-7370},
abstract = {The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.},
}
@article {pmid37321733,
year = {2023},
author = {Yao, T and Deemer, DG and Chen, MH and Reuhs, BL and Hamaker, BR and Lindemann, SR},
title = {Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota.},
journal = {Carbohydrate polymers},
volume = {316},
number = {},
pages = {121039},
doi = {10.1016/j.carbpol.2023.121039},
pmid = {37321733},
issn = {1879-1344},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Scattering, Small Angle ; X-Ray Diffraction ; *Microbiota ; Feces/microbiology ; Dietary Fiber ; Fermentation ; },
abstract = {Dietary fibers are known to modulate microbiome composition, but it is unclear to what extent minor fiber structural differences impact community assembly, microbial division of labor, and organismal metabolic responses. To test the hypothesis that fine linkage variations afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fecal fermentation with four fecal inocula and measured responses using an integrated multi-omics approach. Two sorghum arabinoxylans (SAXs) were fermented, with one (RSAX) having slightly more complex branch linkages than the other (WSAX). Although there were minor glycoysl linkage differences, consortia on RSAX retained much higher species diversity (42 members) than on WSAX (18-23 members) with distinct species-level genomes and metabolic outcomes (e.g., higher short chain fatty acid production from RSAX and more lactic acid produced from WSAX). The major SAX-selected members were from genera of Bacteroides and Bifidobacterium and family Lachnospiraceae. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials among key members; however, CAZyme genes enriched in different consortia displayed various catabolic domain fusions with diverse accessory motifs that differ among the two SAX types. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia.},
}
@article {pmid37279755,
year = {2023},
author = {Münch, PC and Eberl, C and Woelfel, S and Ring, D and Fritz, A and Herp, S and Lade, I and Geffers, R and Franzosa, EA and Huttenhower, C and McHardy, AC and Stecher, B},
title = {Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects.},
journal = {Cell host &amp; microbe},
volume = {31},
number = {6},
pages = {1007-1020.e4},
doi = {10.1016/j.chom.2023.05.013},
pmid = {37279755},
issn = {1934-6069},
mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Germ-Free Life ; },
abstract = {Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is still poorly understood. We investigated strain-specific responses and evolution during repeated AB perturbations by three clinically relevant ABs, using gnotobiotic mice colonized with a synthetic bacterial community (oligo-mouse-microbiota). Over 80 days, we observed resilience effects at the strain and community levels, and we found that they were correlated with modulations of the estimated growth rate and levels of prophage induction as determined from metagenomics data. Moreover, we tracked mutational changes in the bacterial populations, and this uncovered clonal expansion and contraction of haplotypes and selection of putative AB resistance-conferring SNPs. We functionally verified these mutations via reisolation of clones with increased minimum inhibitory concentration (MIC) of ciprofloxacin and tetracycline from evolved communities. This demonstrates that host-associated microbial communities employ various mechanisms to respond to selective pressures that maintain community stability.},
}
@article {pmid37276653,
year = {2023},
author = {Huang, S and Zhang, B and Zhao, Z and Yang, C and Zhang, B and Cui, F and Lens, PNL and Shi, W},
title = {Metagenomic analysis reveals the responses of microbial communities and nitrogen metabolic pathways to polystyrene micro(nano)plastics in activated sludge systems.},
journal = {Water research},
volume = {241},
number = {},
pages = {120161},
doi = {10.1016/j.watres.2023.120161},
pmid = {37276653},
issn = {1879-2448},
mesh = {*Sewage/chemistry ; Plastics ; Polystyrenes ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; *Microbiota ; Microplastics ; Metabolic Networks and Pathways ; },
abstract = {Microplastics (MPs) and nanoplastics (NPs) are prevalent in sewage and pose a potential threat to nitrogen biotransformation in wastewater treatment systems. However, investigations on how MPs and NPs affect the microbial nitrogen conversion and metabolism of the activated sludge are still scanty. Herein, the responses of microbiomes and functional genes to polystyrene MPs and NPs in activated sludge systems were investigated by metagenomic analysis. Results indicated that 1 mg/L MPs and NPs had marginal impacts on the nitrogen removal performance of the activated sludge systems, whereas high concentrations of MPs and NPs (20 and 100 mg/L) decreased the total nitrogen removal efficiency (13.4%-30.6%) by suppressing the nitrogen transformation processes. Excessive reactive oxygen species induced by MPs and NPs caused cytotoxicity, as evidenced by impaired cytomembranes and decreased bioactivity. Metagenomic analysis revealed that MPs and NPs diminished the abundance of denitrifiers (e.g. Mesorhizobium, Rhodobacter and Thauera), and concurrently reduced the abundance of functional genes (e.g. napA, napB and nirS) encoding for key enzymes involved in the nitrogen transformations, as well as the genes (e.g. mdh) related to the electron donor production, thereby declining the nitrogen removal efficiency. Network analysis further clarified the attenuate association between denitrifiers and denitrification-related genes in the plastic-exposed systems, elucidating that MPs and NPs restrained the nitrogen removal by inhibiting the contributions of microorganisms to nitrogen transformation processes. This study provides vital insights into the responses of the microbial community structure and nitrogen conversion processes to micro(nano)plastics disturbance in activated sludge systems.},
}
@article {pmid37208257,
year = {2023},
author = {Wang, Q and Wu, S and Ye, X and Tan, S and Huang, F and Su, G and Kijlstra, A and Yang, P},
title = {Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.},
journal = {Journal of autoimmunity},
volume = {137},
number = {},
pages = {103055},
doi = {10.1016/j.jaut.2023.103055},
pmid = {37208257},
issn = {1095-9157},
mesh = {Humans ; *Uveomeningoencephalitic Syndrome ; Leukocytes, Mononuclear ; *Gastrointestinal Microbiome ; *Uveitis/etiology ; *Behcet Syndrome ; },
abstract = {BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities.<br><br>METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP)161-180 was investigated using a similarity search in the NCBI protein BLAST program (BLASTP). Enzyme-linked Immunosorbent Assay (ELISA) was performed to evaluate the cross-reactive responses of experimental autoimmune uveitis (EAU)-derived lymphocytes and BU patients-derived peripheral blood mononuclear cells (PBMCs) against homologous peptides. The area under the curve (AUC) analysis was used to test the sensitivity and specificity of gut microbial biomarkers.<br><br>RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP161-180. In vitro experiments showed that lymphocytes from EAU or PBMCs from BU patients reacted to this peptide antigen as shown by the production of IFN-&#x3b3; and IL-17. Addition of the SteTDR peptide to the classical IRBP immunization protocol exacerbated EAU severity. Gut microbial marker profiles consisted of 24 species and 32 species respectively differentiated BU and VKH from each other as well as from the other four immune-mediated diseases and healthy controls. Protein annotation identified 148 and 119 specific microbial proteins associated with BU and VKH, respectively. For metabolic function analysis, 108 and 178 metabolic pathways were shown to be associated with BU and VKH, respectively.<br><br>CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.},
}
@article {pmid37201335,
year = {2023},
author = {Laragione, T and Harris, C and Azizgolshani, N and Beeton, C and Bongers, G and Gulko, PS},
title = {Magnesium increases numbers of Foxp3+ Treg cells and reduces arthritis severity and joint damage in an IL-10-dependent manner mediated by the intestinal microbiome.},
journal = {EBioMedicine},
volume = {92},
number = {},
pages = {104603},
pmid = {37201335},
issn = {2352-3964},
mesh = {Mice ; Animals ; T-Lymphocytes, Regulatory ; Magnesium/metabolism/pharmacology ; Interleukin-10/genetics/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; *Arthritis, Rheumatoid/metabolism ; Mice, Knockout ; Th17 Cells ; Forkhead Transcription Factors/genetics/metabolism ; },
abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a common autoimmune disease with emerging environmental and microbiome risk factors. The western diet is typically deficient in magnesium (Mg), and there is some evidence suggesting that Mg may have anti-inflammatory properties. But the actual role of Mg supplementation in arthritis or in T cell subsets has not been explored.<br><br>METHODS: We investigated the role of a high Mg diet in two different mouse models of RA induced with the KRN serum, and collagen-induced arthritis. We also characterized the phenotypes of splenocytes, gene expression, and an extensive intestinal microbiome analyses including fecal material transplantation (FMT).<br><br>FINDINGS: The high Mg diet group was significantly protected with reduced arthritis severity and joint damage, and reduced expression of IL-1&#x3b2;, IL-6, and TNF&#x3b1;. The high Mg group also had increased numbers of Foxp3+ Treg cells and IL-10-producing T cells. The high Mg protective effect disappeared in IL-10 knockout mice. FMT from the high Mg diet mice recreated the phenotypes seen in the diet-treated mice, with reduced arthritis severity, increased Foxp3+ Treg, and increased IL-10-producing T cells. Intestinal microbiome analyses using 16S rDNA sequencing revealed diet-specific changes, including reduced levels of RA-associated Prevotella in the high Mg group, while increasing levels of Bacteroides and other bacteria associated with increased production of short-chain fatty acids. Metagenomic analyses implicated additional pathways including L-tryptophan biosynthesis and arginine deiminase.<br><br>INTERPRETATION: We describe a new role for Mg in suppressing arthritis, in expanding Foxp3+ T reg cells and in the production of IL-10, and show that these effects are mediated by the intestinal microbiome. Our discoveries suggest a novel strategy for modifying the intestinal microbiome to treat RA and other autoimmune and inflammatory diseases.<br><br>FUNDING: None.},
}
@article {pmid37199622,
year = {2023},
author = {Kristensen, M and de Koff, EM and Chu, ML and Groendijk, S and Tramper-Stranders, GA and de Winter-de Groot, KM and Janssens, HM and Tiddens, HA and van Westreenen, M and Sanders, EAM and Arets, BHGM and van der Ent, CK and Prevaes, SMPJ and Bogaert, D},
title = {16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0405722},
pmid = {37199622},
issn = {2165-0497},
mesh = {Infant ; Humans ; Child ; Infant, Newborn ; *Cystic Fibrosis/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory System/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; },
abstract = {16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.},
}
@article {pmid37191543,
year = {2023},
author = {Rizzo, SM and Alessandri, G and Lugli, GA and Fontana, F and Tarracchini, C and Mancabelli, L and Viappiani, A and Bianchi, MG and Bussolati, O and van Sinderen, D and Ventura, M and Turroni, F},
title = {Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0066523},
pmid = {37191543},
issn = {2165-0497},
mesh = {Infant ; Humans ; Infant, Newborn ; Female ; Pregnancy ; Milk, Human/metabolism/microbiology ; Bifidobacterium/genetics/metabolism ; Insulin/metabolism ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/microbiology ; },
abstract = {Multiple millennia of human evolution have shaped the chemical composition of breast milk toward an optimal human body fluid for nutrition and protection and for shaping the early gut microbiota of newborns. This biological fluid is composed of water, lipids, simple and complex carbohydrates, proteins, immunoglobulins, and hormones. Potential interactions between hormones present in mother's milk and the microbial community of the newborn are a very fascinating yet unexplored topic. In this context, insulin, in addition to being one of the most prevalent hormones in breast milk, is also involved in a metabolic disease that affects many pregnant women, i.e., gestational diabetes mellitus (GDM). Analysis of 3,620 publicly available metagenomic data sets revealed that the bifidobacterial community varies in relation to the different concentrations of this hormone in breast milk of healthy and diabetic mothers. Starting from this assumption, in this study, we explored possible molecular interactions between this hormone and bifidobacterial strains that represent bifidobacterial species commonly occurring in the infant gut using 'omics' approaches. Our findings revealed that insulin modulates the bifidobacterial community by apparently improving the persistence of the Bifidobacterium bifidum taxon in the infant gut environment compared to other typical infant-associated bifidobacterial species. IMPORTANCE Breast milk is a key factor in modulating the infant's intestinal microbiota composition. Even though the interaction between human milk sugars and bifidobacteria has been extensively studied, there are other bioactive compounds in human milk that may influence the gut microbiota, such as hormones. In this article, the molecular interaction of the human milk hormone insulin and the bifidobacterial communities colonizing the human gut in the early stages of life has been explored. This molecular cross talk was assessed using an in vitro gut microbiota model and then analyzed by various omics approaches, allowing the identification of genes associated with bacterial cell adaptation/colonization in the human intestine. Our findings provide insights into the manner by which assembly of the early gut microbiota may be regulated by host factors such as hormones carried by human milk.},
}
@article {pmid37187112,
year = {2023},
author = {Bargheet, A and Klingenberg, C and Esaiassen, E and Hjerde, E and Cavanagh, JP and Bengtsson-Palme, J and Pettersen, VK},
title = {Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.},
journal = {EBioMedicine},
volume = {92},
number = {},
pages = {104613},
pmid = {37187112},
issn = {2352-3964},
mesh = {Infant ; Infant, Newborn ; Humans ; Gestational Age ; *Microbiota ; Gastrointestinal Tract/microbiology ; Infant, Extremely Premature ; Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Probiotics/therapeutic use ; },
abstract = {BACKGROUND: Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent.<br><br>METHODS: We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n&#xa0;=&#xa0;29), antibiotic-exposed very preterm (n&#xa0;=&#xa0;25), antibiotic-unexposed very preterm (n&#xa0;=&#xa0;8), and antibiotic-unexposed full-term (n&#xa0;=&#xa0;10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis.<br><br>FINDINGS: The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes.<br><br>INTERPRETATION: Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk.<br><br>FUNDING: Odd-Berg Group, Northern Norway Regional Health Authority.},
}
@article {pmid37178644,
year = {2023},
author = {Wang, M and Qin, Y and Liu, Y and Yang, H and Wang, J and Ru, S and Cui, P},
title = {Short-term exposure to enrofloxacin causes hepatic metabolism disorder associated with intestinal flora dysbiosis in adult marine medaka (Oryzias melastigma).},
journal = {Marine pollution bulletin},
volume = {192},
number = {},
pages = {114966},
doi = {10.1016/j.marpolbul.2023.114966},
pmid = {37178644},
issn = {1879-3363},
mesh = {Animals ; *Oryzias/physiology ; Enrofloxacin ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced/veterinary ; Metabolomics ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Enrofloxacin (ENR) is a widely used fluoroquinolone antibiotic that is frequently detected in the environment. Our study assessed the impact of short-term ENR exposure on the intestinal and liver health of marine medaka (Oryzias melastigma) using gut metagenomic shotgun sequencing and liver metabolomics. We found that ENR exposure resulted in imbalances of Vibrio and Flavobacteria and enrichments of multiple antibiotic resistance genes. Additionally, we found a potential link between the host's response to ENR exposure and the intestinal microbiota disorder. Liver metabolites, including phosphatidylcholine, lysophosphatidylcholine, taurocholic acid, and cholic acid, in addition to several metabolic pathways in the liver that are closely linked to the imbalance of intestinal flora were severely maladjusted. These findings suggest that ENR exposure has the potential to negatively affect the gut-liver axis as the primary toxicological mechanism. Our findings provide evidence regarding the negative physiological impacts of antibiotics on marine fish.},
}
@article {pmid37166318,
year = {2023},
author = {Chen, Q and Zhang, X and Shi, W and Du, X and Ma, L and Wang, W and Tao, S and Xiao, Y},
title = {Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0002323},
pmid = {37166318},
issn = {2165-0497},
mesh = {Pregnancy ; Swine ; Animals ; Male ; Female ; Longitudinal Studies ; *Virome ; Lactation ; Feces/microbiology ; Bacteria/genetics ; *Enterovirus Infections ; },
abstract = {To date, studies on the swine gut microbiome have focused almost exclusively on bacteria. Despite recent advances in the understanding of the swine gut bacteriome at different growth stages, a comprehensive longitudinal study of the lifetime dynamics of the swine gut virome is lacking. Here, we used metagenomic sequencing combined with bioinformatic analysis techniques to characterize the gut viromes of parental-generation and offspring pigs at different biological classification levels. We collected 54 fecal samples from 36 parental-generation pigs (18 breeding boars [Duroc] and 18 pregnant/lactating sows [Landrace]) and 108 fecal samples from 18 offspring pigs during the lactation (day 3), nursery (days 26, 35, and 49), growing (day 120), and finishing (day 180) stages. Alpha diversity, including community richness (richness index) and diversity (Shannon index), showed an overall increasing trend in offspring pigs. Distinct shifts (beta diversity) in the microbiome structure along different growth stages were observed. The linear discriminant analysis effect size (LEfSe) algorithm revealed 53 viral genus that are stage specific. Host prediction results showed that enteric viruses are probably correlated with carbohydrate decomposition. We identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from enteric viruses, most of which are glycoside hydrolase genes and participate in the biolysis of complex polysaccharides. IMPORTANCE This study shows that distinct stage-associated swine gut viromes may be determined by age and/or gut physiology at different growth stages, and enteric viruses probably manipulate carbohydrate decomposition by abundant glycoside hydrolases. These findings fill a gap in the longitudinal pattern of the swine gut virome and lay the foundation for research on the function of swine enteric viruses.},
}
@article {pmid37140369,
year = {2023},
author = {Castañeda, S and Muñoz, M and Hotez, PJ and Bottazzi, ME and Paniz-Mondolfi, AE and Jones, KM and Mejia, R and Poveda, C and Ramírez, JD},
title = {Microbiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0019923},
pmid = {37140369},
issn = {2165-0497},
mesh = {Mice ; Animals ; Disease Models, Animal ; Mice, Inbred C57BL ; *Chagas Disease/parasitology ; *Trypanosoma cruzi ; *Microbiota ; },
abstract = {Alterations caused by Trypanosoma cruzi in the composition of gut microbiome may play a vital role in the host-parasite interactions that shapes physiology and immune responses against infection. Thus, a better understanding of this parasite-host-microbiome interaction may yield relevant information in the comprehension of the pathophysiology of the disease and the development of new prophylactic and therapeutic alternatives. Therefore, we implemented a murine model with two mice strains (BALB/c and C57BL/6) to evaluate the impact of Trypanosoma cruzi (Tulahuen strain) infection on the gut microbiome utilizing cytokine profiling and shotgun metagenomics. Higher parasite burdens were observed in cardiac and intestinal tissues, including changes in anti-inflammatory (interleukin-4 [IL-4] and IL-10) and proinflammatory (gamma interferon, tumor necrosis factor alpha, and IL-6) cytokines. Bacterial species such as Bacteroides thetaiotaomicron, Faecalibaculum rodentium, and Lactobacillus johnsonii showed a decrease in relative abundance, while Akkermansia muciniphila and Staphylococcus xylosus increased. Likewise, as infection progressed, there was a decrease in gene abundances related to metabolic processes such as lipid synthesis (including short-chain fatty acids) and amino acid synthesis (including branched-chain amino acids). High-quality metagenomic assembled genomes of L. johnsonii and A. muciniphila among other species were reconstructed, confirming, functional changes associated with metabolic pathways that are directly affected by the loss of abundance of specific bacterial taxa. IMPORTANCE Chagas disease (CD) is caused by the protozoan Trypanosoma cruzi, presenting acute and chronic phases where cardiomyopathy, megaesophagus, and/or megacolon stand out. During the course of its life cycle, the parasite has an important gastrointestinal tract transit that leads to severe forms of CD. The intestinal microbiome plays an essential role in the immunological, physiological, and metabolic homeostasis of the host. Therefore, parasite-host-intestinal microbiome interactions may provide information on certain biological and pathophysiological aspects related to CD. The present study proposes a comprehensive evaluation of the potential effects of this interaction based on metagenomic and immunological data from two mice models with different genetic, immunological, and microbiome backgrounds. Our findings suggest that there are alterations in the immune and microbiome profiles that affect several metabolic pathways that can potentially promote the infection's establishment, progression, and persistence. In addition, this information may prove essential in the research of new prophylactic and therapeutic alternatives for CD.},
}
@article {pmid37102867,
year = {2023},
author = {Zhang, W and Fan, X and Shi, H and Li, J and Zhang, M and Zhao, J and Su, X},
title = {Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0056323},
pmid = {37102867},
issn = {2165-0497},
mesh = {RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; *Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is always considered only at the genus level; however, it has not been verified on a wide range of microbes yet. To fully explore the ability and potential of the 16S rRNA gene in microbial profiling, here, we propose Qscore, a comprehensive method to evaluate the performance of amplicons by integrating the amplification rate, multitier taxonomic annotation, sequence type, and length. Our in silico assessment by a "global view" of 35,889 microbe species across multiple reference databases summarizes the optimal sequencing strategy for 16S short reads. On the other hand, since microbes are unevenly distributed according to their habitats, we also provide the recommended configuration for 16 typical ecosystems based on the Qscores of 157,390 microbiomes in the Microbiome Search Engine (MSE). Detailed data simulation further proves that the 16S amplicons produced with Qscore-suggested parameters exhibit high precision in microbiome profiling, which is close to that of shotgun metagenomes under CAMI metrics. Therefore, by reconsidering the precision of 16S-based microbiome profiling, our work not only enables the high-quality reusability of massive sequence legacy that has already been produced but is also significant for guiding microbiome studies in the future. We have implemented the Qscore as an online service at http://qscore.single-cell.cn to parse the recommended sequencing strategy for specific habitats or expected microbial structures. IMPORTANCE 16S rRNA has long been used as a biomarker to identify distinct microbes from complex communities. However, due to the influence of the amplification region, sequencing type, sequence processing, and reference database, the accuracy of 16S rRNA has not been fully verified on a global range. More importantly, the microbial composition of different habitats varies greatly, and it is necessary to adopt different strategies according to the corresponding target microbes to achieve optimal analytical performance. Here, we developed Qscore, which evaluates the comprehensive performance of 16S amplicons from multiple perspectives, thus providing the best sequencing strategies for common ecological environments by using big data.},
}
@article {pmid37067438,
year = {2023},
author = {Pu, J and Yang, J and Lu, S and Jin, D and Luo, X and Xiong, Y and Bai, X and Zhu, W and Huang, Y and Wu, S and Niu, L and Liu, L and Xu, J},
title = {Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0349522},
pmid = {37067438},
issn = {2165-0497},
mesh = {Animals ; Humans ; Ecosystem ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Lagomorpha/genetics/microbiology ; },
abstract = {Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.},
}
@article {pmid37067419,
year = {2023},
author = {Bhattacharyya, C and Barman, D and Tripathi, D and Dutta, S and Bhattacharya, C and Alam, M and Choudhury, P and Devi, U and Mahanta, J and Rasaily, R and Basu, A and Paine, SK},
title = {Influence of Maternal Breast Milk and Vaginal Microbiome on Neonatal Gut Microbiome: a Longitudinal Study during the First Year.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0496722},
pmid = {37067419},
issn = {2165-0497},
mesh = {Infant ; Infant, Newborn ; Adult ; Humans ; Pregnancy ; Female ; Cesarean Section ; *Gastrointestinal Microbiome ; Milk, Human ; Longitudinal Studies ; *Microbiota ; },
abstract = {It is believed that establishment of the gut microbiome starts very early in life and is crucial for growth, immunity, and long-term metabolic health. In this longitudinal study, we recruited 25 mothers in their third trimester, of whom 15 had vaginal delivery while 10 had an unplanned cesarean section (C-section). The mother-neonate pairs were followed for 1 year, and we generated 16S metagenomic data to study the neonatal gut microbiome along with mother's breast milk and vaginal microbiomes through 12 months after delivery, at 1, 3, 6, and 12 months. We inferred (i) mode of delivery is an important factor influencing both composition and entropy of the neonatal gut microbiome, and the genus Streptococcus plays an important role in the temporal differentiation. (ii) Microbial diversity monotonically increases with age, irrespective of the mode of delivery, and it is significantly altered once exclusive breastfeeding is stopped. (iii) We found little evidence in favor of the microflora of mother's breast milk and a vaginal swab being directly reflected in the offspring's gut microbiome; however, some distinction could be made in the gut microbiome of neonates whose mothers were classified as community state type III (CSTIII) and CSTIV, based on their vaginal microbiomes. (iv) A lot of the mature gut microbiome is possibly acquired from the environment, as the genera Prevotella and Faecalibacterium, two of the most abundant flora in the neonatal gut microbiome, are introduced after initiation of solidified food. The distinction between the gut microbiome of babies born by vaginal delivery and babies born by C-section becomes blurred after introduction of solid food, although the diversity in the gut microbiota drastically increases in both cases. IMPORTANCE Gut microbiome architecture seems to have a potential impact on host metabolism, health, and nutrition. Early life gut microbiome development is considered a crucial phenomenon for neonatal health as well as adulthood metabolic complications. In this longitudinal study, we examined the association of neonatal gut microbiome entropy and its temporal variation. The study revealed that adult-like gut microbiome architecture starts taking shape after initiation of solidified food. Further, we also observed that the difference of microbial diversity was reduced between vaginally delivered and C-section babies compared to exclusive breastfeeding tenure. We found evidence in favor of the inheritance of the microflora of mother's posterior vaginal wall to the offspring's gut microbiome.},
}
@article {pmid37052495,
year = {2023},
author = {Morgan, SJ and Chaston, JM},
title = {Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0458522},
pmid = {37052495},
issn = {2165-0497},
support = {R15 GM140388/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Drosophila melanogaster/genetics/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Bacteria/genetics ; Phenotype ; },
abstract = {In this work, we use Drosophila melanogaster as a model to identify bacterial genes necessary for bacteria to colonize their hosts independent of the bulk flow of diet. Early work on this model system established that dietary replenishment drives the composition of the D. melanogaster gut microbiota, and subsequent research has shown that some bacterial strains can stably colonize, or persist within, the fly independent of dietary replenishment. Here, we reveal transposon insertions in specific bacterial genes that influence the bacterial colonization persistence phenotype by using a gene association approach. We initially established that different bacterial strains persist at various levels, independent of dietary replenishment. We then repeated the analysis with an expanded panel of bacterial strains and performed a metagenome-wide association (MGWA) study to identify distinct bacterial genes that are significantly correlated with the level of colonization by persistent bacterial strains. Based on the MGWA study, we tested if 44 bacterial transposon insertion mutants from 6 gene categories affect bacterial persistence within the flies. We identified that transposon insertions in four flagellar genes, one urea carboxylase gene, one phosphatidylinositol gene, one bacterial secretion gene, and one antimicrobial peptide (AMP) resistance gene each significantly influenced the colonization of D. melanogaster by an Acetobacter fabarum strain. Follow-up experiments revealed that each flagellar mutant was nonmotile, even though the wild-type strain was motile. Taken together, these results reveal that transposon insertions in specific bacterial genes, including motility genes, are necessary for at least one member of the fly microbiota to persistently colonize the fly. IMPORTANCE Despite the growing body of research on the microbiota, the mechanisms by which the microbiota colonizes a host can still be further elucidated. This study identifies bacterial genes that are associated with the colonization persistence phenotype of the microbiota in Drosophila melanogaster, which reveals specific bacterial factors that influence the establishment of the microbiota within its host. The identification of specific genes that affect persistence can help inform how the microbiota colonizes a host. Furthermore, a deeper understanding of the genetic mechanisms of the establishment of the microbiota could aid in the further development of the Drosophila microbiota as a model for microbiome research.},
}
@article {pmid37042774,
year = {2023},
author = {Ley, Y and Cheng, XY and Ying, ZY and Zhou, NY and Xu, Y},
title = {Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0442422},
pmid = {37042774},
issn = {2165-0497},
mesh = {*Lignin/metabolism ; *Microbial Consortia ; Biodegradation, Environmental ; Bacteria/metabolism ; Alkalies ; Carbon/metabolism ; },
abstract = {Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.},
}
@article {pmid37042768,
year = {2023},
author = {Zhang, P and Zhang, Y and Cao, L and Li, J and Wu, C and Tian, M and Zhang, Z and Zhang, C and Zhang, W and Li, Y},
title = {A Diverse Virome Is Identified in Parasitic Flatworms of Domestic Animals in Xinjiang, China.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0070223},
pmid = {37042768},
issn = {2165-0497},
mesh = {Adult ; Animals ; Dogs ; Humans ; Animals, Domestic ; Phylogeny ; Virome ; *Viruses/genetics ; *RNA Viruses ; Metagenome ; *Platyhelminths ; },
abstract = {Parasitic flatworms infect diverse vertebrates and are major threats to animal and even human health; however, little is known about the virome of these lower life forms. Using viral metagenomic sequencing, we characterized the virome of the parasitic flatworms collected from major domestic animals, including Dicrocoelium lanceatum and Taenia hydatigena, Echinococcus granulosus sensu stricto and Echinococcus multilocularis. Seven and three different viruses were discovered from D. lanceatum and T. hydatigena, respectively, and no viral sequences were found in adult tapeworms and protoscoleces of E. granulosus sensu stricto and E. multilocularis. Two out of the five parasitic flatworm species carry viruses, showing a host specificity of these viruses. These viruses belong to the Parvoviridae, Circoviridae, unclassified circular, Rep-encoding single-stranded (CRESS) DNA virus, Rhabdoviridae, Endornaviridae, and unclassified RNA viruses. The presence of multiple highly divergent RNA viruses, especially those that cluster with viruses found in marine animals, implies a deep evolutionary history of parasite-associated viruses. In addition, we found viruses with high identity to common pathogens in dogs, including canine circovirus and canine parvovirus 2. The presence of these viruses in the parasites implies that they may infect parasitic flatworms but does not completely exclude the possibility of contamination from host intestinal contents. Furthermore, we demonstrated that certain viruses, such as CRESS DNA virus may integrate into the genome of their host. Our results expand the knowledge of viral diversity in parasites of important domestic animals, highlighting the need for further investigations of their prevalence among other parasites of key animals. IMPORTANCE Characterizing the virome of parasites is important for unveiling the viral diversity, evolution, and ecology and will help to understand the "Russian doll" pattern among viruses, parasites, and host animals. Our data indicate that diverse viruses are present in specific parasitic flatworms, including viruses that may have an ancient evolutionary history and viruses currently circulating in parasite-infected host animals. These data also raise the question of whether parasitic flatworms acquire and/or carry some viruses that may have transmission potential to animals. In addition, through the study of virus-parasite-host interactions, including the influence of viral infection on the life cycle of the parasite, as well as its fitness and pathogenicity to the host, we could find new strategies to prevent and control parasitic diseases.},
}
@article {pmid37040073,
year = {2023},
author = {Wurm, P and Stampfer, L and Greimel, T and Leitner, E and Zechner, EL and Bauchinger, S and Hauer, AC and Gorkiewicz, G and Högenauer, C and Hoffmann, KM},
title = {Gut Microbiota Dysbiosis in Suspected Food Protein Induced Proctocolitis-A Prospective Comparative Cohort Trial.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {77},
number = {1},
pages = {31-38},
doi = {10.1097/MPG.0000000000003789},
pmid = {37040073},
issn = {1536-4801},
mesh = {Infant ; Humans ; *Gastrointestinal Microbiome ; *Proctocolitis ; Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Bifidobacterium ; Feces/microbiology ; },
abstract = {OBJECTIVES: In infants with suspected food protein induced proctocolitis (sFPIP) only a minority of patients are finally diagnosed with the disease following diagnostic dietary intervention (DDI). There is a need for a pathophysiological explanation for the cause of hematochezia in the majority of sFPIP infants.<br><br>METHODS: We prospectively recruited infants with sFPIP and healthy controls. Fecal samples were collected at inclusion, week 4 (end of DDI in sFPIP), and week 8. For 16S rRNA sequencing (515F/806R) we used Illumina MiSeq sequencing system. Amplicon sequence variants were generated using Qiime2 and DADA2. Qiime diversity alpha and beta group comparisons and linear discriminant analysis effect size analysis was performed. For shotgun metagenomic analysis on species level we used KneadData and MetaPhlAn2.<br><br>RESULTS: Fourteen sFPIP infants were compared to 55 healthy infants. At inclusion overall microbial composition of sFPIP infants differed significantly from controls (weighted UniFrac; Pairwise PERMANOVA, P = 0.002, pseudo- F = 5.008). On genus level healthy infant microbiota was significantly enriched with Bifidobacterium (B) compared to sFPIP patients (linear discriminant analysis [LDA] = 5.5, P < 0.001, 31.3% vs 12.1%). sFPIP stool was significantly enriched by Clostridium sensu stricto 1 over controls (LDA = 5.3, P = 0.003, 3.5% vs 18.3%). DDI caused a significant and sustained increase of Bifidobacterium (LDA = 5.4, P = 0.048, 27.9%) in sFPIP infants. Species level analysis revealed significant reduction of abundance of B longum in sFPIP patients, which after DDI was reversed by B. species other than B longum .<br><br>CONCLUSIONS: We revealed a gut microbiota dysbiosis phenomenon in sFPIP infants. DDI induces a microbiota composition comparable to that of healthy infants. In most sFPIP infants hematochezia might be triggered by a gut microbiota dysbiosis phenomenon.},
}
@article {pmid37039637,
year = {2023},
author = {Gemler, BT and Mukherjee, C and Howland, C and Fullerton, PA and Spurbeck, RR and Catlin, LA and Smith, A and Minard-Smith, AT and Bartling, C},
title = {UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0416022},
pmid = {37039637},
issn = {2165-0497},
mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; },
abstract = {Applied metagenomics is a powerful emerging capability enabling the untargeted detection of pathogens, and its application in clinical diagnostics promises to alleviate the limitations of current targeted assays. While metagenomics offers a hypothesis-free approach to identify any pathogen, including unculturable and potentially novel pathogens, its application in clinical diagnostics has so far been limited by workflow-specific requirements, computational constraints, and lengthy expert review requirements. To address these challenges, we developed UltraSEQ, a first-of-its-kind accurate and scalable metagenomic bioinformatic tool for potential clinical diagnostics and biosurveillance utility. Here, we present the results of the evaluation of our novel UltraSEQ pipeline using an in silico-synthesized metagenome, mock microbial community data sets, and publicly available clinical data sets from samples of different infection types, including both short-read and long-read sequencing data. Our results show that UltraSEQ successfully detected all expected species across the tree of life in the in silico sample and detected all 10 bacterial and fungal species in the mock microbial community data set. For clinical data sets, even without requiring data set-specific configuration setting changes, background sample subtraction, or prior sample information, UltraSEQ achieved an overall accuracy of 91%. Furthermore, as an initial demonstration with a limited patient sample set, we show UltraSEQ's ability to provide antibiotic resistance and virulence factor genotypes that are consistent with phenotypic results. Taken together, the above-described results demonstrate that the UltraSEQ platform offers a transformative approach for microbial and metagenomic sample characterization, employing a biologically informed detection logic, deep metadata, and a flexible system architecture for the classification and characterization of taxonomic origin, gene function, and user-defined functions, including disease-causing infections. IMPORTANCE Traditional clinical microbiology-based diagnostic tests rely on targeted methods that can detect only one to a few preselected organisms or slow, culture-based methods. Although widely used today, these methods have several limitations, resulting in rates of cases of an unknown etiology of infection of >50% for several disease types. Massive developments in sequencing technologies have made it possible to apply metagenomic methods to clinical diagnostics, but current offerings are limited to a specific disease type or sequencer workflow and/or require laboratory-specific controls. The limitations associated with current clinical metagenomic offerings result from the fact that the backend bioinformatic pipelines are optimized for the specific parameters described above, resulting in an excess of unmaintained, redundant, and niche tools that lack standardization and explainable outputs. In this paper, we demonstrate that UltraSEQ uses a novel, information-based approach that enables accurate, evidence-based predictions for diagnosis as well as the functional characterization of a sample.},
}
@article {pmid37023405,
year = {2023},
author = {Cavattoni, M and Comin, M},
title = {ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {30},
number = {6},
pages = {633-647},
doi = {10.1089/cmb.2022.0208},
pmid = {37023405},
issn = {1557-8666},
mesh = {*Algorithms ; Sequence Analysis, DNA ; Metagenome ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; },
abstract = {Current technologies allow the sequencing of microbial communities directly from the environment without prior culturing. One of the major problems when analyzing a microbial sample is to taxonomically annotate its reads to identify the species it contains. Most methods that are currently available focus on the classification of reads using a set of reference genomes and their k-mers. While in terms of precision these methods have reached percentages of correctness close to perfection, in terms of sensitivity (the actual number of classified reads), the performance is often poor. One reason is that the reads in a sample can be very different from the corresponding reference genomes; for example, viral genomes are usually highly mutated. To address this issue, in this article, we propose ClassGraph, a new taxonomic classification method that makes use of the read overlap graph and applies a label propagation algorithm to refine the results of existing tools. We evaluated its performance on simulated and real datasets with several taxonomic classification tools, and the results showed an improved sensitivity and F-measure, while maintaining high precision. ClassGraph is capable of improving the classification accuracy, especially in difficult cases such as virus and real datasets, where traditional tools can classify <40% of reads.},
}
@article {pmid36995244,
year = {2023},
author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S},
title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0466722},
pmid = {36995244},
issn = {2165-0497},
mesh = {Animals ; Mice ; Humans ; *Streptococcus thermophilus/genetics ; Conjugation, Genetic ; Gastrointestinal Tract ; Gene Transfer, Horizontal ; *Microbiota ; },
abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.},
}
@article {pmid37316519,
year = {2023},
author = {Jin, X and Yu, FB and Yan, J and Weakley, AM and Dubinkina, V and Meng, X and Pollard, KS},
title = {Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3510},
pmid = {37316519},
issn = {2041-1723},
mesh = {Humans ; Mucins ; Hydrogels ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Excipients ; },
abstract = {Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.},
}
@article {pmid37314057,
year = {2023},
author = {Van Etten, J and Stephens, TG and Bhattacharya, D},
title = {A k-mer-based approach for phylogenetic classification of taxa in environmental genomic data.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syad037},
pmid = {37314057},
issn = {1076-836X},
abstract = {In the age of genome sequencing, whole genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here we compare the results of one alignment-free approach (which utilizes the D 2 statistic) to traditional multi-gene maximum likelihood trees in three algal groups that have high quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there is significant missing data, that includes marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.},
}
@article {pmid37313947,
year = {2023},
author = {El Mouzan, MI and Assiri, AA and Al Sarkhy, AA and Alasmi, MM},
title = {Gut virome profile in healthy Saudi children.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {29},
number = {3},
pages = {171-176},
doi = {10.4103/sjg.sjg_444_22},
pmid = {37313947},
issn = {1998-4049},
mesh = {Male ; Humans ; Child ; Adolescent ; Female ; *Virome ; Phylogeny ; Saudi Arabia/epidemiology ; *DNA, Viral ; Feces ; },
abstract = {BACKGROUND: The role of viruses is well known in health and disease. The aim of this report was to describe the profile of viruses in the gut of healthy Saudi children.<br><br>METHODS: In 20 randomly selected school age children from Riyadh, stool samples were collected in cryovials and stored at -80&#xb0; C. At the time of analysis, the samples were sent by express mail in a temperature-controlled container to the laboratory in the USA, Viral DNA was isolated and shotgun metagenomic sequencing was performed. The abundance of each organism was expressed as an average relative percentage across the viral phylogenetic tree from phyla to species.<br><br>RESULTS: The median age of the children was 11.3 (range 6.8-15.4) years, and 35% were males. Caudovirales were the most abundant bacteriophage order (77%) and Siphoviridae, Myoviridae, and Podoviridae families predominated, accounting for 41%, 25%, and 11%, respectively. Among the viral bacteriophage species, the most abundant were the Enterobacteria phages.<br><br>CONCLUSION: The profile and abundance of the gut virome in healthy Saudi children reveal important differences from the literature. Further studies from different populations with larger sample sizes are needed to understand the role of gut viruses in the pathogenesis of disease in general and in the response to fecal microbiota therapy in particular.},
}
@article {pmid37311764,
year = {2023},
author = {Ruff, SE and Humez, P and de Angelis, IH and Diao, M and Nightingale, M and Cho, S and Connors, L and Kuloyo, OO and Seltzer, A and Bowman, S and Wankel, SD and McClain, CN and Mayer, B and Strous, M},
title = {Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3194},
pmid = {37311764},
issn = {2041-1723},
mesh = {Oxygen ; Oxygen Isotopes ; *Groundwater ; Hydrogen ; *Microbiota ; },
abstract = {Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 10[7] mL[-1]) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L[-1] [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.},
}
@article {pmid37308527,
year = {2023},
author = {Kozhakhmetov, S and Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Mureyev, S and Kozhakhmetova, S and Morenko, M and Shnaider, K and Duisbayeva, A and Kushugulova, A},
title = {Compositional and functional variability of the gut microbiome in children with infantile colic.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {9530},
pmid = {37308527},
issn = {2045-2322},
mesh = {Infant, Newborn ; Infant ; Humans ; Child ; *Gastrointestinal Microbiome ; *Colic ; *Microbiota ; Amino Acids ; Anxiety ; Bacteroides ; },
abstract = {The inconsolable crying of a child for no apparent reason at an early age is a source of excitement and anxiety for parents. Previous studies have reported that crying may be caused by discomfort associated with the occupation of the intestines of the newborn by microbiota and its vital activity. We conducted a prospective observational study in which 62 newborns and their mothers were recruited. The study comprised two groups, each consisting of 15 infants with colic and 21 controls. Colic and control groups were vaginally born and exclusively breastfed. Fecal samples from children were collected over time from day 1 to 12 months. Full metagenomic sequencing of fecal samples from children and their mothers was carried out. It was determined that the trajectory of the development of the intestinal microbiome of children with colic was different from the group without colic. In the colic group, a depleted relative abundance of Bifidobacterium and enrichment of Bacteroides Clostridiales was found, while the microbial biodiversity in this group was enriched. Metabolic pathway profiling showed that the non-colic group was enriched by amino acid biosynthetic pathways, while the feces microbiome of the colic group was enriched by glycolysis metabolic pathways that correlated with the Bacteroides taxon. This study shows that infantile colic has a definite relationship with the microbiome structure of infants.},
}
@article {pmid37254732,
year = {2023},
author = {Chittimalli, K and Jahan, J and Sakamuri, A and McAdams, ZL and Ericsson, AC and Jarajapu, YPR},
title = {Restoration of the gut barrier integrity and restructuring of the gut microbiome in aging by angiotensin-(1-7).},
journal = {Clinical science (London, England : 1979)},
volume = {137},
number = {11},
pages = {913-930},
doi = {10.1042/CS20220904},
pmid = {37254732},
issn = {1470-8736},
mesh = {Mice ; Male ; Animals ; *Gastrointestinal Microbiome ; Angiotensin-Converting Enzyme 2 ; Dysbiosis ; Claudin-1 ; Occludin ; Angiotensin I/pharmacology/metabolism ; Peptidyl-Dipeptidase A/metabolism ; Peptide Fragments/pharmacology/metabolism ; Aging ; Angiotensin II/metabolism ; },
abstract = {Compromised barrier function of colon epithelium with aging is largely due to gut microbial dysbiosis. Recent studies implicate an important role for angiotensin converting enzymes, ACE and ACE2, angiotensins, and the receptors, AT1 receptor (AT1R) and Mas receptor (MasR), in the regulation of colon functions. The present study tested the hypothesis that leaky gut in aging is associated with an imbalance in ACE2/ACE and that the treatment with angiotenisn-(1-7) (Ang-(1-7)) will restore gut barrier integrity and microbiome. Studies were carried out in Young (3-4 months) and old (20-24 months) male mice. Ang-(1-7) was administered by using osmotic pumps. Outcome measures included expressions of ACE, ACE2, AT1R, and MasR, intestinal permeability by using FITC-dextran, and immunohistochemistry of claudin 1 and occludin, and intestinal stem cells (ISCs). ACE2 protein and activity were decreased in Old group while that of ACE were unchanged. Increased intestinal permeability and plasma levels of zonulin-1 in the Old group were normalized by Ang-(1-7). Epithelial disintegrity, reduced number of goblet cells and ISCs in the old group were restored by Ang-(1-7). Expression of claudin 1 and occludin in the aging colon was increased by Ang-(1-7). Infiltration of CD11b+ or F4/80+ inflammatory cells in the old colons were decreased by Ang-(1-7). Gut microbial dysbiosis in aging was evident by decreased richness and altered beta diversity that were reversed by Ang-(1-7) with increased abundance of Lactobacillus or Lachnospiraceae. The present study shows that Ang-(1-7) restores gut barrier integrity and reduces inflammation in the aging colon by restoring the layer of ISCs and by restructuring the gut microbiome.},
}
@article {pmid37204034,
year = {2023},
author = {Liu, M and Liu, H and Li, F and Shen, Y and Zhang, L and Wang, G and Wang, H and Qu, C and Chen, G and Zhao, X and Liu, L and Zhou, J},
title = {Metagenomic surveillance in Jinan, China, reveals serum microbiome and biochemistry features in fever of unknown origin (FUO) patients.},
journal = {Letters in applied microbiology},
volume = {76},
number = {6},
pages = {},
doi = {10.1093/lambio/ovad060},
pmid = {37204034},
issn = {1472-765X},
mesh = {Humans ; *Fever of Unknown Origin/diagnosis ; Metagenomics/methods ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; },
abstract = {Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria was found, belonging to Enterobacteriaceae, Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), and Comamonadaceae (4.25%). The major virus families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae, and Herpesviridae, showing up in 34.96%, 47.37%, 30.89%, 5.69%, 3.25%, and 1.63% of patients, respectively. Using the Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in the high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold > 10, P = 0.021); tetra-PGDM (fold = 5.29, P = 0.037); and 20-HETE (fold > 10, P = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.},
}
@article {pmid37196884,
year = {2023},
author = {Lehman, PC and Cady, N and Ghimire, S and Shahi, SK and Shrode, RL and Lehmler, HJ and Mangalam, AK},
title = {Low-dose glyphosate exposure alters gut microbiota composition and modulates gut homeostasis.},
journal = {Environmental toxicology and pharmacology},
volume = {100},
number = {},
pages = {104149},
doi = {10.1016/j.etap.2023.104149},
pmid = {37196884},
issn = {1872-7077},
support = {I01 CX002212/CX/CSRD VA/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; R01 AI137075/AI/NIAID NIH HHS/United States ; T90 DE023520/DE/NIDCR NIH HHS/United States ; },
mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Herbicides/toxicity ; Homeostasis ; },
abstract = {The widespread use of glyphosate, a broad-spectrum herbicide, has resulted in significant human exposure, and recent studies have challenged the notion that glyphosate is safe for humans. Although the link between disease states and glyphosate exposure is increasingly appreciated, the mechanistic links between glyphosate and its toxic effects on human health are poorly understood. Recent studies have suggested that glyphosate may cause toxicity through modulation of the gut microbiome, but evidence for glyphosate-induced gut dysbiosis and its effect on host physiology at doses approximating the U.S. Acceptable Daily Intake (ADI = 1.75 mg/kg body weight) is limited. Here, utilizing shotgun metagenomic sequencing of fecal samples from C57BL/6 J mice, we show that glyphosate exposure at doses approximating the U.S. ADI significantly impacts gut microbiota composition. These gut microbial alterations were associated with effects on gut homeostasis characterized by increased proinflammatory CD4[+]IL17A[+] T cells and Lipocalin-2, a known marker of intestinal inflammation.},
}
@article {pmid37306587,
year = {2023},
author = {Cheng, H and Zhang, Y and Guo, Z and He, X and Liu, R and Zhu, XY and Li, J and Liu, J and Zhang, XH},
title = {Microbial Dimethylsulfoniopropionate Cycling in Deep Sediment of the Mariana Trench.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0025123},
doi = {10.1128/aem.00251-23},
pmid = {37306587},
issn = {1098-5336},
abstract = {Dimethylsulfoniopropionate (DMSP) and related organic sulfur compounds play key roles in global sulfur cycling. Bacteria have been found to be important DMSP producers in seawater and surface sediments of the aphotic Mariana Trench (MT). However, detailed bacterial DMSP cycling in the Mariana Trench subseafloor remains largely unknown. Here, the bacterial DMSP-cycling potential in a Mariana Trench sediment core (7.5 m in length) obtained at a 10,816-m water depth was investigated using culture-dependent and -independent methods. The DMSP content fluctuated along the sediment depth and reached the highest concentration at 15 to 18 cm below the seafloor (cmbsf). dsyB was the dominant known DMSP synthetic gene, existing in 0.36 to 1.19% of the bacteria, and was identified in the metagenome-assembled genomes (MAGs) of previously unknown bacterial DMSP synthetic groups such as Acidimicrobiia, Phycisphaerae, and Hydrogenedentia. dddP, dmdA, and dddX were the major DMSP catabolic genes. The DMSP catabolic activities of DddP and DddX retrieved from Anaerolineales MAGs were confirmed by heterologous expression, indicating that such anaerobic bacteria might participate in DMSP catabolism. Moreover, genes involved in methanethiol (MeSH) production from methylmercaptopropionate (MMPA) and dimethyl sulfide (DMS), MeSH oxidation, and DMS production were highly abundant, suggesting active conversions between different organic sulfur compounds. Finally, most culturable DMSP synthetic and catabolic isolates possessed no known DMSP synthetic and catabolic genes, and actinomycetes could be important groups involved in both DMSP synthesis and catabolism in Mariana Trench sediment. This study extends the current understanding of DMSP cycling in Mariana Trench sediment and highlights the need to uncover novel DMSP metabolic genes/pathways in extreme environments. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is an abundant organosulfur molecule in the ocean and is the precursor for the climate-active volatile gas dimethyl sulfide. Previous studies focused mainly on bacterial DMSP cycling in seawater, coastal sediment, and surface trench sediment samples, but DMSP metabolism in the Mariana Trench (MT) subseafloor sediments remains unknown. Here, we describe the DMSP content and metabolic bacterial groups in the subseafloor of the MT sediment. We found that the tendency for vertical variation of the DMSP content in the MT was distinct from that of the continent shelf sediment. Although dsyB and dddP were the dominant DMSP synthetic and catabolic genes in the MT sediment, respectively, both metagenomic and culture methods revealed multiple previously unknown DMSP metabolic bacterial groups, especially anaerobic bacteria and actinomycetes. The active conversion of DMSP, DMS, and methanethiol may also occur in the MT sediments. These results provide novel insights for understanding DMSP cycling in the MT.},
}
@article {pmid37306468,
year = {2023},
author = {Shen, Y and Qu, W and Yu, F and Zhang, D and Zou, Q and Han, D and Xie, M and Chen, X and Yuan, L and Lou, B and Xie, G and Wang, R and Yang, X and Chen, W and Wang, Q and Teng, Y and Dong, Y and Huang, L and Bao, J and Liu, C and Wu, W and Shen, E and Fan, L and Timko, MP and Zheng, S and Chen, Y},
title = {Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2223340},
doi = {10.1080/19490976.2023.2223340},
pmid = {37306468},
issn = {1949-0984},
mesh = {Humans ; Anti-Bacterial Agents ; Vancomycin ; Leukocytes, Mononuclear ; *COVID-19 ; *Gastrointestinal Microbiome ; Respiratory System ; Patient Acuity ; },
abstract = {The antibiotic resistome is the collection of all antibiotic resistance genes (ARGs) present in an individual. Whether an individual's susceptibility to infection and the eventual severity of coronavirus disease 2019 (COVID-19) is influenced by their respiratory tract antibiotic resistome is unknown. Additionally, whether a relationship exists between the respiratory tract and gut ARGs composition has not been fully explored. We recruited 66 patients with COVID-19 at three disease stages (admission, progression, and recovery) and conducted a metagenome sequencing analysis of 143 sputum and 97 fecal samples obtained from them. Respiratory tract, gut metagenomes, and peripheral blood mononuclear cell (PBMC) transcriptomes are analyzed to compare the gut and respiratory tract ARGs of intensive care unit (ICU) and non-ICU (nICU) patients and determine relationships between ARGs and immune response. Among the respiratory tract ARGs, we found that Aminoglycoside, Multidrug, and Vancomycin are increased in ICU patients compared with nICU patients. In the gut, we found that Multidrug, Vancomycin, and Fosmidomycin were increased in ICU patients. We discovered that the relative abundances of Multidrug were significantly correlated with clinical indices, and there was a significantly positive correlation between ARGs and microbiota in the respiratory tract and gut. We found that immune-related pathways in PBMC were enhanced, and they were correlated with Multidrug, Vancomycin, and Tetracycline ARGs. Based on the ARG types, we built a respiratory tract-gut ARG combined random-forest classifier to distinguish ICU COVID-19 patients from nICU patients with an AUC of 0.969. Cumulatively, our findings provide some of the first insights into the dynamic alterations of respiratory tract and gut antibiotic resistome in the progression of COVID-19 and disease severity. They also provide a better understanding of how this disease affects different cohorts of patients. As such, these findings should contribute to better diagnosis and treatment scenarios.},
}
@article {pmid37306408,
year = {2023},
author = {Tang, W and Zheng, H and Xu, S and Li, P and Zhan, L and Luo, X and Dai, Z and Wang, Q and Yu, G},
title = {MMINP: A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2223349},
doi = {10.1080/19490976.2023.2223349},
pmid = {37306408},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Least-Squares Analysis ; Algorithms ; Computational Biology ; Metabolome ; },
abstract = {The gut metabolome acts as an intermediary between the gut microbiota and host, and has tremendous diagnostic and therapeutic potential. Several studies have utilized bioinformatic tools to predict metabolites based on the different aspects of the gut microbiome. Although these tools have contributed to a better understanding of the relationship between the gut microbiota and various diseases, most of them have focused on the impact of microbial genes on the metabolites and the relationship between microbial genes. In contrast, relatively little is known regarding the effect of metabolites on the microbial genes or the relationship between these metabolites. In this study, we constructed a computational framework of Microbe-Metabolite INteractions-based metabolic profiles Predictor (MMINP), based on the Two-Way Orthogonal Partial Least Squares (O2-PLS) algorithm to predict the metabolic profiles associated with gut microbiota. We demonstrated the predictive value of MMINP relative to that of similar methods. Additionally, we identified the features that would profoundly impact the prediction performance of data-driven methods (O2-PLS, MMINP, MelonnPan, and ENVIM), including the training sample size, host disease state, and the upstream data processing methods of the different technical platforms. We suggest that when using data-driven methods, similar host disease states and preprocessing methods, and a sufficient number of training samples are necessary to achieve accurate prediction.},
}
@article {pmid37178843,
year = {2023},
author = {Liu, B and Yu, D and Ge, C and Luo, X and Du, L and Zhang, X and Hui, C},
title = {Combined effects of microplastics and chlortetracycline on the intestinal barrier, gut microbiota, and antibiotic resistome of Muscovy ducks (Cairina moschata).},
journal = {The Science of the total environment},
volume = {887},
number = {},
pages = {164050},
doi = {10.1016/j.scitotenv.2023.164050},
pmid = {37178843},
issn = {1879-1026},
mesh = {Animals ; Microplastics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Plastics ; Ducks ; Polystyrenes ; *Chlortetracycline/pharmacology ; Intestines ; *Microbiota ; },
abstract = {Antibiotics and microplastics (MPs) have become critical concerns worldwide because of their increasing amount and ecological risks to ecosystems. However, how MPs exposure affects the bioaccumulation and risks of antibiotics in waterfowls remains poorly understood. In this study, Muscovy ducks were exposed to single and combined contamination with polystyrene MPs and chlortetracycline (CTC) for 56 days, and the effects of MPs on CTC bioaccumulation and their risks in duck intestines were investigated. MPs exposure reduced the bioaccumulation of CTC in the intestine and liver of ducks and increased their fecal CTC excretion. MPs exposure caused severe oxidative stress, inflammatory response, and intestinal barrier damages. Microbiome analysis showed that MPs exposure induced microbiota dysbiosis by increasing the abundance of Streptococcus and Helicobacter, the increase of which may exacerbate intestinal damages. Co-exposure to MPs and CTC alleviated the intestinal damage by regulating the gut microbiome. Metagenomic sequencing revealed that the combined exposure to MPs and CTC increased the abundance of Prevotella, Faecalibacterium, and Megamonas and incidence of total antibiotic resistance genes (ARGs), especially tetracycline ARGs subtypes in the gut microbiota. The results obtained herein provide new insights into the potential risks of polystyrene MPs and antibiotics in waterfowls living in aquatic environments.},
}
@article {pmid37092330,
year = {2023},
author = {Castillo, DF and Denson, LA and Haslam, DB and Hommel, KA and Ollberding, NJ and Sahay, R and Santucci, NR},
title = {The microbiome in adolescents with irritable bowel syndrome and changes with percutaneous electrical nerve field stimulation.},
journal = {Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society},
volume = {35},
number = {7},
pages = {e14573},
doi = {10.1111/nmo.14573},
pmid = {37092330},
issn = {1365-2982},
mesh = {Humans ; Female ; Adolescent ; Child ; *Irritable Bowel Syndrome/diagnosis ; *Microbiota ; Abdominal Pain/complications ; Catastrophization ; Carbohydrates ; },
abstract = {BACKGROUND: Irritable bowel syndrome (IBS), a disorder of the gut-brain axis, is affected by the microbiome. Microbial studies in pediatric IBS, especially for centrally mediated treatments, are lacking. We compared the microbiome between pediatric IBS patients and healthy controls (HC), in relation to symptom severity, and with percutaneous electrical nerve field stimulation (PENFS), a non-invasive treatment targeting central pain pathways.<br><br>METHODS: We collected a stool sample, questionnaires and a 1-2&#x2009;week stool and pain diary from 11 to 18&#x2009;years patients with IBS. A patient subset completed 4&#x2009;weeks of PENFS and repeated data collection immediately after and/or 3&#x2009;months after treatment. Stool samples were collected from HC. Samples underwent metagenomic sequencing to evaluate diversity, composition, and abundance of species and MetaCyc pathways.<br><br>KEY RESULTS: We included 27 cases (15.4&#x2009;&#xb1;&#x2009;2.5&#x2009;year) and 34 HC (14.2&#x2009;&#xb1;&#x2009;2.9&#x2009;year). Twelve species including Firmicutes spp., and carbohydrate degradation/long-chain fatty acid (LCFA) synthesis pathways, were increased in IBS but not statistically significantly associated with symptom severity. Seventeen participants (female) who completed PENFS showed improvements in pain (p&#x2009;=&#x2009;0.012), disability (p&#x2009;=&#x2009;0.007), and catastrophizing (p&#x2009;=&#x2009;0.003). Carbohydrate degradation and LCFA synthesis pathways decreased post-treatment and at follow-up (FDR p-value <0.1).<br><br>CONCLUSIONS AND INFERENCES: Firmicutes, including Clostridiaceae spp., and LCFA synthesis pathways were increased in IBS patients suggesting pain-potentiating effects. PENFS led to marked improvements in abdominal pain, functioning, and catastrophizing, while Clostridial species and LCFA microbial pathways decreased with treatment, suggesting these as potential targets for IBS centrally mediated treatments.},
}
@article {pmid37039269,
year = {2023},
author = {Riveros Escalona, MA and Poloni, JF and Krause, MJ and Dorn, M},
title = {Meta-analyses of host metagenomes from colorectal cancer patients reveal strong relationship between colorectal cancer-associated species.},
journal = {Molecular omics},
volume = {19},
number = {5},
pages = {429-444},
doi = {10.1039/d3mo00021d},
pmid = {37039269},
issn = {2515-4184},
mesh = {Humans ; Metagenome ; *Colorectal Neoplasms ; *Gastrointestinal Microbiome ; Cell Transformation, Neoplastic ; Carcinogenesis ; },
abstract = {Colorectal cancer (CRC) is one of the most common types of cancer, with many studies associating its development with changes in the gut microbiota. Recent developments in sequencing technologies and subsequent meta-analyses of gut metagenome provided a better understanding of species related to CRC tumorigenesis. Still, the importance of high-importance taxonomic singletons (i.e. species highly associated with a given condition but observed only in the minority of datasets) and the species interactions and co-occurrence across cohorts need further exploration. It has been shown that the gut metagenome presents a high functional redundancy, meaning that species interactions could mitigate the absence of any given species. In a CRC framework, this implies that species co-occurrence could play a role in tumorigenesis, even if CRC-associated species show low abundance. We propose to evaluate the prevalence of microbial species in tumor by initially analyzing each dataset individually and subsequently intersecting the results for differentially abundant species between CRC and healthy samples. We then identify metabolic pathways from these species based on KEGG orthologs, highlighting metabolic pathways associated with CRC. Our results indicate seven species with high prevalence across all projects and with high association to CRC, including the genus Bacteroides, Enterocloster and Prevotella. Finally, we show that CRC is also characterized by the co-occurrence of species that do not present significant differential abundance, but have been described in the literature as potential CRC biomarkers. These results indicate that between-species interactions could also play a role in CRC tumorigenesis.},
}
@article {pmid37305949,
year = {2023},
author = {Nandi, D and Parida, S and Sharma, D},
title = {The gut microbiota in breast cancer development and treatment: The good, the bad, and the useful!.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2221452},
doi = {10.1080/19490976.2023.2221452},
pmid = {37305949},
issn = {1949-0984},
mesh = {Female ; Humans ; *Breast Neoplasms/therapy ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Cognition ; },
abstract = {Regardless of the global progress in early diagnosis and novel therapeutic regimens, breast carcinoma poses a devastating threat, and the advances are somewhat marred by high mortality rates. Breast cancer risk prediction models based on the known risk factors are extremely useful, but a large number of breast cancers develop in women with no/low known risk. The gut microbiome exerts a profound impact on the host health and physiology and has emerged as a pivotal frontier in breast cancer pathogenesis. Progress in metagenomic analysis has enabled the identification of specific changes in the host microbial signature. In this review, we discuss the microbial and metabolomic changes associated with breast cancer initiation and metastatic progression. We summarize the bidirectional impact of various breast cancer-related therapies on gut microbiota and vice-versa. Finally, we discuss the strategies to modulate the gut microbiota toward a more favorable state that confers anticancer effects.},
}
@article {pmid37301875,
year = {2023},
author = {Li, L and Wang, T and Ning, Z and Zhang, X and Butcher, J and Serrana, JM and Simopoulos, CMA and Mayne, J and Stintzi, A and Mack, DR and Liu, YY and Figeys, D},
title = {Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3428},
pmid = {37301875},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Proteome ; Proteomics ; Xenobiotics ; Feces ; *Microbiota ; },
abstract = {Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.},
}
@article {pmid37257294,
year = {2023},
author = {Chen, J and Ke, Y and Zhu, Y and Chen, X and Xie, S},
title = {Deciphering of sulfonamide biodegradation mechanism in wetland sediments: from microbial community and individual populations to pathway and functional genes.},
journal = {Water research},
volume = {240},
number = {},
pages = {120132},
doi = {10.1016/j.watres.2023.120132},
pmid = {37257294},
issn = {1879-2448},
mesh = {Humans ; Biodegradation, Environmental ; *Wetlands ; Anti-Bacterial Agents/metabolism ; Sulfonamides ; Sulfanilamide ; Sulfadiazine ; *Microbiota ; },
abstract = {Figuring out the comprehensive metabolic mechanism of sulfonamide antibiotics (SA) is critical to improve and optimize SA removal in the bioremediation process, but relevant studies are still lacking. Here, an approach integrating metagenomic analysis, degraders' isolation, reverse transcriptional quantification and targeted metabolite determination was used to decipher microbial interactions and functional genes' characteristics in SA-degrading microbial consortia enriched from wetland sediments. The SA-degrading consortia could rapidly catalyze ipso-hydroxylation and subsequent reactions of SA to achieve the complete mineralization of sulfadiazine and partial mineralization of the other two typical SA (sulfamethoxazole and sulfamethazine). Paenarthrobacter, Achromobacter, Pseudomonas and Methylobacterium were identified as the primary participants for the initial transformation of SA. Among them, Methylobacterium could metabolize the heterocyclic intermediate of sulfadiazine (2-aminopyrimidine), and the owning of sadABC genes (SA degradation genes) made Paenarthrobacter have relatively higher SA-degrading activity. Besides, the coexistence of sadABC genes and sul1 gene (SA resistance gene) gave Paenarthrobacter a dual resistance mechanism to SA. The results of reverse transcription quantification further demonstrated that the activity of sadA gene was related to the biodegradation of SA. Additionally, sadABC genes were relatively conserved in a few Microbacteriaceae and Micrococcaceae SA-degraders, but the multiple recombination events caused by densely nested transposase encoding genes resulted in the differential sequence of sadAB genes in Paenarthrobacter genome. These new findings provide valuable information for the selection and construction of engineered microbiomes.},
}
@article {pmid37298483,
year = {2023},
author = {Park, S and Zhang, T and Kang, S},
title = {Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {11},
pages = {},
pmid = {37298483},
issn = {1422-0067},
mesh = {Adult ; Humans ; Metagenome ; *Diabetes Mellitus, Type 2/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Bacteria/genetics ; },
abstract = {T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.},
}
@article {pmid37298198,
year = {2023},
author = {Zubeldia-Varela, E and Barker-Tejeda, TC and Mera-Berriatua, L and Bazire, R and Cabrera-Freitag, P and Ubeda, C and Barber, D and Francino, MP and Rojo, D and Ibáñez-Sandín, MD and Pérez-Gordo, M},
title = {Further Insights into the Gut Microbiota of Cow's Milk Allergic Infants: Analysis of Microbial Functionality and Its Correlation with Three Fecal Biomarkers.},
journal = {International journal of molecular sciences},
volume = {24},
number = {11},
pages = {},
pmid = {37298198},
issn = {1422-0067},
mesh = {Female ; Animals ; Cattle ; Milk/chemistry ; *Gastrointestinal Microbiome ; Lactoferrin/metabolism ; *Milk Hypersensitivity/diagnosis ; Feces/chemistry ; Biomarkers/analysis ; },
abstract = {Cow's milk allergy (CMA) is one of the most prevalent food allergies in children. Several studies have demonstrated that gut microbiota influences the acquisition of oral tolerance to food antigens at initial stages of life. Changes in the gut microbiota composition and/or functionality (i.e., dysbiosis) have been linked to inadequate immune system regulation and the emergence of pathologies. Moreover, omic sciences have become an essential tool for the analysis of the gut microbiota. On the other hand, the use of fecal biomarkers for the diagnosis of CMA has recently been reviewed, with fecal calprotectin, α-1 antitrypsin, and lactoferrin being the most relevant. This study aimed at evaluating functional changes in the gut microbiota in the feces of cow's milk allergic infants (AI) compared to control infants (CI) by metagenomic shotgun sequencing and at correlating these findings with the levels of fecal biomarkers (α-1 antitrypsin, lactoferrin, and calprotectin) by an integrative approach. We have observed differences between AI and CI groups in terms of fecal protein levels and metagenomic analysis. Our findings suggest that AI have altered glycerophospholipid metabolism as well as higher levels of lactoferrin and calprotectin that could be explained by their allergic status.},
}
@article {pmid37295406,
year = {2023},
author = {Nguyen, CL and Markey, KA and Miltiadous, O and Dai, A and Waters, N and Sadeghi, K and Fei, T and Shouval, R and Taylor, BP and Liao, C and Slingerland, JB and Slingerland, AE and Clurman, AG and Maloy, MA and Bohannon, L and Giardina, PA and Brereton, DG and Armijo, GK and Fontana, E and Gradissimo, A and Gyurkocza, B and Sung, AD and Chao, NJ and Devlin, SM and Taur, Y and Giralt, SA and Perales, MA and Xavier, JB and Pamer, EG and Peled, JU and Gomes, ALC and van den Brink, MRM},
title = {High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients.},
journal = {Cell},
volume = {186},
number = {12},
pages = {2705-2718.e17},
doi = {10.1016/j.cell.2023.05.007},
pmid = {37295406},
issn = {1097-4172},
mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenome ; *Hematopoietic Stem Cell Transplantation ; Anti-Bacterial Agents ; *Neoplasms/drug therapy ; },
abstract = {Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic exposures. We integrated drug-microbiome associations to predict clinical outcomes in two validation cohorts on the basis of drug exposures alone, suggesting that this approach can generate biologically and clinically relevant insights into how pharmacological exposures can perturb or preserve microbiota composition. The application of a computational method called PARADIGM to a large dataset of cancer patients' longitudinal fecal specimens and detailed daily medication records reveals associations between drug exposures and the intestinal microbiota that recapitulate in vitro findings and are also predictive of clinical outcomes.},
}
@article {pmid37292198,
year = {2023},
author = {Han, X and He, X and Zhan, X and Yao, L and Sun, Z and Gao, X and Wang, S and Wang, Z},
title = {Disturbed microbiota-metabolites-immune interaction network is associated with olfactory dysfunction in patients with chronic rhinosinusitis.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1159112},
pmid = {37292198},
issn = {1664-3224},
mesh = {Humans ; *Rhinitis/diagnosis ; *Olfaction Disorders/diagnosis/etiology ; Smell ; *Sinusitis/diagnosis ; Chronic Disease ; Inflammation/complications ; *Microbiota ; },
abstract = {PURPOSE: Olfactory dysfunction (OD) is a debilitating symptom frequently reported by patients with chronic rhinosinusitis (CRS) and it is associated with a dysregulated sinonasal inflammation. However, little information is available about the effect of the inflammation-related nasal microbiota and related metabolites on the olfactory function in these patients. Therefore, the current study aimed to investigate the nasal microbiota-metabolites-immune interactions and their role in the pathogenesis of OD in CRS patients.<br><br>METHODS: 23 and 19 CRS patients with and without OD, respectively, were enrolled in the present study. The "Sniffin' Sticks" was used to measure the olfactory function, while the metagenomic shotgun sequencing and the untargeted metabolite profiling were performed to assess the differences in terms of the nasal microbiome and metabolome between the two groups. The levels of nasal mucus inflammatory mediators were investigated by a multiplex flow Cytometric Bead Array (CBA).<br><br>RESULTS: A decreased diversity in the nasal microbiome from the OD group compared to the NOD group was evidenced. The metagenomic analysis revealed a significant enrichment of Acinetobacter johnsonii in the OD group, while Mycoplasma arginini, Aeromonas dhakensis, and Salmonella enterica were significantly less represented (LDA value > 3, p < 0.05). The nasal metabolome profiles were significantly different between the OD and NOD groups (P < 0.05). The purine metabolism was the most significantly enriched metabolic subpathway in OD patients compared with NOD patients (P < 0.001). The expressions of IL-5, IL-8, MIP-1&#x3b1;, MCP-1, and TNF were statistically and significantly increased in the OD group (P < 0.05). All these data, including the dysregulation of the nasal microbiota, differential metabolites, and elevated inflammatory mediators in OD patients demonstrated a clear interaction relationship.<br><br>CONCLUSION: The disturbed nasal microbiota-metabolite-immune interaction networks may be implicated in the pathogenesis of OD in CRS patients and the underlying pathophysiological mechanisms need to be further investigated in future studies.},
}
@article {pmid37290887,
year = {2023},
author = {Yancey, CE and Kiledal, EA and Chaganti, SR and Denef, VJ and Errera, RM and Evans, JT and Hart, LN and Isailovic, D and James, WS and Kharbush, JJ and Kimbrel, JA and Li, W and Mayali, X and Nitschky, H and Polik, CA and Powers, MA and Premathilaka, SH and Rappuhn, NA and Reitz, LA and Rivera, SR and Zwiers, CC and Dick, GJ},
title = {The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome.},
journal = {Harmful algae},
volume = {126},
number = {},
pages = {102440},
doi = {10.1016/j.hal.2023.102440},
pmid = {37290887},
issn = {1878-1470},
mesh = {Humans ; *Microcystis/genetics ; Lakes/microbiology ; *Cyanobacteria/genetics ; *Microbiota ; Genetic Variation ; },
abstract = {Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L[-1]) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.},
}
@article {pmid37290480,
year = {2023},
author = {Gan, J and Chen, J and Ma, RL and Deng, Y and Ding, XS and Zhu, SY and Sun, AJ},
title = {Metagenomics study on taxonomic and functional change of gut microbiota in patients with obesity with PCOS treated with exenatide combination with metformin or metformin alone.},
journal = {Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology},
volume = {39},
number = {1},
pages = {2219342},
doi = {10.1080/09513590.2023.2219342},
pmid = {37290480},
issn = {1473-0766},
mesh = {Female ; Humans ; *Metformin ; *Polycystic Ovary Syndrome/complications/drug therapy/metabolism ; Exenatide/therapeutic use ; *Gastrointestinal Microbiome ; Metagenomics ; Obesity/complications/drug therapy/chemically induced ; },
abstract = {OBJECTIVE: To investigate the effect of exenatide treatment on the composition of intestinal flora and metabolic pathways in patients with obesity with polycystic ovary syndrome.<br><br>METHODS: Patients with obesity with polycystic ovary syndrome (PCOS) were distributed to two groups: one received exenatide combined with metformin (COM group, n&#x2009;=&#x2009;14) and the other used metformin alone (MF group, n&#x2009;=&#x2009;15). Fresh fecal specimens from the participants, including 29 patients with obesity with PCOS and 6 healthy controls, were collected for metagenomic sequencing. The effect of exenatide combination with metformin or metformin alone on the composition and function of intestinal flora in patients with obesity with PCOS were compared by bioinformatics analysis.<br><br>RESULTS: The level of BMI, TT, HbA1c, and HDL-c was significantly improved in both groups. The MF and COM groups were abundant in Firmicutes, Bacteroidetes, Uroviricota, Actinobacteria, and Proteobacteria. Abundance of Bacteroidetes, Proteobacteria, Hungatella, and certain probiotics like Phocaeicola and Anaerobutyricum significantly increased in both groups after treatment. Enriched microbial species in the MF and COM group were different. Clostridium, Fusobacterium, and Oxalobacter were the main bacteria in the post-MF group, while Lactococcus_garvieae, Clostridium_perfringens, and Coprococcus_sp_AF16_5 were the main bacteria in the post-COM group. The post-COM group had more probiotic species including Bifidobacterium, Prevotella, and Anaerobutyricum after treatment.<br><br>CONCLUSION: Both exenatide combined with metformin and metformin monotherapy can improve metabolic and endocrine markers, and the diversity and abundance of gut microbiota in patients with obesity with PCOS. The effects of the combination and monotherapy agents on intestinal flora were consistent to some extent but also unique respectively.},
}
@article {pmid37288545,
year = {2023},
author = {Lu, F and Lei, T and Zhou, J and Liang, H and Cui, P and Zuo, T and Ye, L and Chen, H and Huang, J},
title = {Using gut microbiota as a diagnostic tool for colorectal cancer: machine learning techniques reveal promising results.},
journal = {Journal of medical microbiology},
volume = {72},
number = {6},
pages = {},
doi = {10.1099/jmm.0.001699},
pmid = {37288545},
issn = {1473-5644},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bayes Theorem ; Feces/microbiology ; Escherichia coli/genetics ; Machine Learning ; Prevotella/genetics ; },
abstract = {Introduction. Increasing evidence suggests a correlation between gut microbiota and colorectal cancer (CRC).Hypothesis/Gap Statement. However, few studies have used gut microbiota as a diagnostic biomarker for CRC.Aim. The objective of this study was to explore whether a machine learning (ML) model based on gut microbiota could be used to diagnose CRC and identify key biomarkers in the model.Methodology. We sequenced the 16S rRNA gene from faecal samples of 38 participants, including 17 healthy subjects and 21 CRC patients. Eight supervised ML algorithms were used to diagnose CRC based on faecal microbiota operational taxonomic units (OTUs), and the models were evaluated in terms of identification, calibration and clinical practicality for optimal modelling parameters. Finally, the key gut microbiota was identified using the random forest (RF) algorithm.Results. We found that CRC was associated with the dysregulation of gut microbiota. Through a comprehensive evaluation of supervised ML algorithms, we found that different algorithms had significantly different prediction performance using faecal microbiomes. Different data screening methods played an important role in optimization of the prediction models. We found that naïve Bayes algorithms [NB, accuracy=0.917, area under the curve (AUC)=0.926], RF (accuracy=0.750, AUC=0.926) and logistic regression (LR, accuracy=0.750, AUC=0.889) had high predictive potential for CRC. Furthermore, important features in the model, namely s__metagenome_g__Lachnospiraceae_ND3007_group (AUC=0.814), s__Escherichia_coli_g__Escherichia-Shigella (AUC=0.784) and s__unclassified_g__Prevotella (AUC=0.750), could each be used as diagnostic biomarkers of CRC.Conclusions. Our results suggested an association between gut microbiota dysregulation and CRC, and demonstrated the feasibility of the gut microbiota to diagnose cancer. The bacteria s__metagenome_g__Lachnospiraceae_ND3007_group, s__Escherichia_coli_g__Escherichia-Shigella and s__unclassified_g__Prevotella were key biomarkers for CRC.},
}
@article {pmid37286586,
year = {2023},
author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G},
title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {35},
pmid = {37286586},
issn = {2055-5008},
mesh = {Mice ; Animals ; Bile Acids and Salts ; Ecosystem ; *Cholestasis/complications/pathology ; *Liver Diseases/complications ; Cytokines ; *Gastrointestinal Microbiome ; },
abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.},
}
@article {pmid37283894,
year = {2023},
author = {Adedayo, AA and Fadiji, AE and Babalola, OO},
title = {Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15432},
pmid = {37283894},
issn = {2167-8359},
mesh = {*Solanum lycopersicum/genetics ; Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; Soil/chemistry ; Plants ; },
abstract = {The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.},
}
@article {pmid37280708,
year = {2023},
author = {Rutjens, S and Vereecke, N and Sauer, J and Croubels, S and Devreese, M},
title = {Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur.},
journal = {Veterinary research},
volume = {54},
number = {1},
pages = {45},
pmid = {37280708},
issn = {1297-9716},
mesh = {Swine ; Animals ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Cephalosporins/pharmacology ; Feces/microbiology ; *Anti-Infective Agents/pharmacology ; Escherichia coli/genetics ; },
abstract = {Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg[-1] intramuscular, 3 consecutive days) or cefquinome (2 mg.kg[-1] intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.},
}
@article {pmid37278203,
year = {2023},
author = {Gao, S and Gao, X and Zhu, R and Wu, D and Feng, Z and Jiao, N and Sun, R and Gao, W and He, Q and Liu, Z and Zhu, L},
title = {Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2221428},
pmid = {37278203},
issn = {1949-0984},
mesh = {Humans ; *Crohn Disease/diagnosis/genetics ; Metagenome ; Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; Feces ; Genes, Microbial ; Dysbiosis/diagnosis/genetics ; },
abstract = {Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. We collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. Microbial alterations in CD patients were assessed at multidimensional levels including species, gene, and SNV level, and then diagnostic models were constructed using artificial intelligence algorithm. A total of 227 species, 1047 microbial genes, and 21,877 microbial SNVs were identified that differed between CD and controls. The species, gene, and SNV models achieved an average AUC of 0.97, 0.95, and 0.77, respectively. Notably, the gene model exhibited superior diagnostic capability, achieving an average AUC of 0.89 and 0.91 for internal and external validations, respectively. Moreover, the gene model was specific for CD against other microbiome-related diseases. Furthermore, we found that phosphotransferase system (PTS) contributed substantially to the diagnostic capability of the gene model. The outstanding performance of PTS was mainly explained by genes celB and manY, which demonstrated high predictabilities for CD with metagenomic datasets and was validated in an independent cohort by qRT-PCR analysis. Our global metagenomic analysis unravels the multidimensional alterations of the microbial communities in CD and identifies microbial genes as robust diagnostic biomarkers across geographically and culturally distinct cohorts.},
}
@article {pmid37275543,
year = {2023},
author = {Zheng, K and Dong, Y and Liang, Y and Liu, Y and Zhang, X and Zhang, W and Wang, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M},
title = {Genomic diversity and ecological distribution of marine Pseudoalteromonas phages.},
journal = {Marine life science &amp; technology},
volume = {5},
number = {2},
pages = {271-285},
pmid = {37275543},
issn = {2662-1746},
abstract = {UNLABELLED: Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-022-00160-z.},
}
@article {pmid37272818,
year = {2023},
author = {Wang, H and Ren, L and Liang, Y and Zheng, K and Guo, R and Liu, Y and Wang, Z and Han, Y and Zhang, X and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M},
title = {Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0533522},
doi = {10.1128/spectrum.05335-22},
pmid = {37272818},
issn = {2165-0497},
abstract = {Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.},
}
@article {pmid37272702,
year = {2023},
author = {Lu, J and Wang, H and Wang, C and Zhao, M and Hou, R and Shen, Q and Yang, S and Ji, L and Liu, Y and Wang, X and Liu, S and Shan, T and Zhang, W},
title = {Gut phageome of the giant panda (Ailuropoda melanoleuca) reveals greater diversity than relative species.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016123},
doi = {10.1128/msystems.00161-23},
pmid = {37272702},
issn = {2379-5077},
abstract = {The gut flora is a treasure house of diverse bacteriophages maintaining a harmonious and coexistent relationship with their hosts. The giant panda (Ailuropoda melanoleuca), as a vulnerable endemic species in China, has existed for millions of years and is regarded as a flagship species for biodiversity conservation. And yet, limited studies have analyzed the phage communities in the gut of giant pandas. Using viral metagenomic analysis, the phageomes of giant pandas and other relative species were investigated. Our study explored and compared the composition of phage communities from different animal sources. Giant pandas possessed more diverse and abundant phage communities in the gut compared with other relevant animals. Phylogenetic analyses based on the phage terminase large subunit (TerL) showed that the Caudovirales phages in giant pandas also presented highly genetic diversity. Our study revealed the diversity of phage communities in giant pandas and other relative species, contributing to the health maintenance of giant pandas and laying the groundwork for molecular evolution research of bacteriophages in mammals.IMPORTANCEGut phageome plays an important role in shaping gut microbiomes by direct interactions with bacteria or indirect influences on the host immune system, potentially regulating host health and disease status. The giant panda (Ailuropoda melanoleuca) is a vulnerable and umbrella species for biodiversity conservation. Our work explored and compared the gut phageome of giant pandas and relative species, contributing to the health maintenance of giant pandas.},
}
@article {pmid37166164,
year = {2023},
author = {Sun, H and Lv, B and Zhu, H and Zeng, Z and El-Ashram, S and Li, J and Chao, Y and Wang, J and Wang, Z},
title = {Selenized glucose improves rat semen quality by improving the gut microbiota and serum metabolome.},
journal = {Food &amp; function},
volume = {14},
number = {11},
pages = {5105-5119},
doi = {10.1039/d3fo00692a},
pmid = {37166164},
issn = {2042-650X},
mesh = {Male ; Rats ; Animals ; Semen Analysis ; Semen/metabolism ; *Gastrointestinal Microbiome ; *Selenium/metabolism ; Glucose/metabolism ; Rats, Sprague-Dawley ; Metabolome ; Testosterone ; },
abstract = {Selenium (Se), a well-known antioxidant, is important for male fertility and sperm quality. The gut microbiota is involved in vital activities and cross-talk between reproduction and the gut axis. It is still unclear whether the gut microbiota mediates the impact of selenium on semen quality, and what the underlying mechanisms may be. A selenized glucose (SeGlu) derivative is a novel organic Se compound. After 7 days of acclimation, the Sprague-Dawley (SD) male rats (230 g, 6 weeks) were divided into three drinking groups: deionized water group (CK), SeGlu 0.15 group (0.15 mg Se per L), and SeGlu 0.4 group (0.4 mg Se per L). All animals were euthanized 30 days post-treatment. Serum and intratesticular testosterone and semen parameters were measured. Metagenomic and non-targeted metabolomic approaches were used to study the effects of SeGlu on the gut microbiota and serum metabolites of rats. In both the SeGlu 0.15 Group and the SeGlu 0.4 Group, we found a significant increase in seminiferous epithelium thickness. While the SeGlu 0.4 Group had a tendency to increase with insignificant difference, the SeGlu 0.15 Group significantly improved the sperm viability, survival rate, and seminal plasma fructose. SeGlu had no effect on intratesticular testosterone levels, or abnormal sperm counts. Measured serum testosterone levels using ELISA and LC-MS, which showed a decreasing trend. ELISA did not reveal significant differences, but LC-MS indicated a significant decrease in SeGlu 0.4 group. Meanwhile, the SeGlu 0.15 Group reduced the abundance of harmful bacteria such as Rikenella, Barnesiella, Tenacibaculum, and Aeromonas while increasing the abundance of beneficial microbiota such as Intestinimonas, Christensenella, Coprococcus, and Butyrivibrio. Linear discriminant analysis Effect Size (LEfSe) identified the SeGlu 0.15 group's feature genera as Roseburia, Clostridium, Ruminococcus, and Eubacterium. Serum metabolites showed that the SeGlu 0.15 Group increased 5 beta-androstane-3,17-dione while decreasing estrone and 2-methoxyestradiol (2-MeOE2). In conclusion, the SeGlu 0.15 Group can significantly alter the levels of several sex hormones in serum, improve the quality of rats' sperm, and reduce harmful bacterial colonization. SeGlu 0.15 may be used as an effective dietary supplement.},
}
@article {pmid37271802,
year = {2023},
author = {Rolon, ML and Tan, X and Chung, T and Gonzalez-Escalona, N and Chen, Y and Macarisin, D and LaBorde, LF and Kovac, J},
title = {The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {128},
pmid = {37271802},
issn = {2049-2618},
mesh = {Food Microbiology ; Fruit ; Seasons ; Longitudinal Studies ; Cross-Sectional Studies ; *Listeria monocytogenes/genetics ; *Microbiota/genetics ; Food Contamination/analysis ; },
abstract = {BACKGROUND: Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3).<br><br>METHODS: A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis&#xa0;and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples.<br><br>RESULTS: The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples.<br><br>CONCLUSIONS: This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.},
}
@article {pmid37210808,
year = {2023},
author = {Lamichhane, S and Härkönen, T and Vatanen, T and Hyötyläinen, T and Knip, M and Orešič, M},
title = {Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.},
journal = {Environment international},
volume = {176},
number = {},
pages = {107965},
doi = {10.1016/j.envint.2023.107965},
pmid = {37210808},
issn = {1873-6750},
support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Female ; Humans ; Infant ; Mothers ; *Microbiota ; Maternal Exposure ; Bacteria/genetics ; *Fluorocarbons/toxicity ; *Environmental Pollutants ; *Alkanesulfonic Acids ; },
abstract = {There is growing evidence suggesting that chemical exposure alters gut microbiota composition. However, not much is known about the impact of per- and polyfluoroalkyl substances (PFAS) on the gut microbial community. Here, in a mother-infant study, we set out to identify the gut bacterial species that associate with chemical exposure before (maternal) and after (maternal, infant) birth. Paired serum and stool samples were collected from mother-infant dyads (n = 30) in a longitudinal setting. PFAS were quantified in maternal serum to examine their associations with the microbial compositions (determined by shotgun metagenomic sequencing) in mothers and infants. High maternal exposure to PFAS was consistently associated with increased abundance of Methanobrevibacter smithii in maternal stool. Among individual PFAS compounds, PFOS and PFHpS showed the strongest association with M. smithii. However, maternal total PFAS exposure associated only weakly with the infant microbiome. Our findings suggest that PFAS exposure affects the composition of the adult gut microbiome.},
}
@article {pmid36823282,
year = {2023},
author = {Pérez-Cataluña, A and Randazzo, W and Martínez-Blanch, JF and Codoñer, FM and Sánchez, G},
title = {Sample and library preparation approaches for the analysis of the virome of irrigation water.},
journal = {Journal of the science of food and agriculture},
volume = {103},
number = {9},
pages = {4450-4457},
doi = {10.1002/jsfa.12522},
pmid = {36823282},
issn = {1097-0010},
mesh = {Humans ; Virome ; *Viruses/genetics ; *Bacteriophages/genetics ; Water ; Metagenomics/methods ; },
abstract = {BACKGROUND: The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters.<br><br>RESULTS: Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families.<br><br>CONCLUSION: Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. &#xa9; 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid37267060,
year = {2023},
author = {Du, B and Xiao, X and Wang, H and Li, W and Xia, Z and Yang, P and Huang, SK and Yuan, R and Liu, J and Han, M and Zou, Y and Zhu, J and He, D and Lyu, J and Jin, X and Xu, X and Wang, J and Yang, H and Xiao, L and Liu, X and Kristiansen, K},
title = {Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model.},
journal = {Environmental health perspectives},
volume = {131},
number = {6},
pages = {67004},
pmid = {37267060},
issn = {1552-9924},
mesh = {Humans ; Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Ovalbumin/pharmacology ; Caco-2 Cells ; *Hypersensitivity ; Inflammation ; Bacteria ; },
abstract = {BACKGROUND: Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment-microbiota-immunity triangular relationship and to what extent BaP-induced remodeling of the gut microbiota contributes to intestinal allergic inflammation remain to be established.<br><br>OBJECTIVES: We investigated the impact of BaP on intestinal allergic inflammation and examined the relationship between this effect and gut microbiota dysbiosis. We explored the potential ability of intestinal bacteria to degrade BaP and alleviate cytotoxicity as a detoxification strategy to counteract the effects of BaP exposure.<br><br>METHODS: We combined microbiome shotgun metagenomics with animal histological and intestinal allergic inflammatory responses to assess the effects of BaP (50&#x3bc;g/mouse per day) in a 23-d toxicity test in antigen-induced allergic female mice. In addition, genome annotation, quantitative analysis of BaP, and in vitro cytotoxicity-tests using CaCo-2 cells were conducted to infer the role of intestinal bacteria in BaP detoxification.<br><br>RESULTS: BaP exposure impacted the taxonomic composition and the functional potential of the gut microbiota and aggravated antigen-induced intestinal allergic inflammatory responses. The level of inflammatory cytokines correlated with the abundance of specific bacterial taxa, including Lachnospiraceae bacterium 28-4 and Alistipes inops. We identified 614 bacteria harboring genes implicated in the degradation of BaP, and 4 of these bacterial strains were shown to significantly reduce the cytotoxicity of BaP to CaCo-2 cells in vitro.<br><br>DISCUSSION: Using allergic female mice as a model, we investigated the relationship between BaP, microbiota, and host immune reactions, highlighting the role of gut bacteria in BaP-aggravated allergic reactions. Our findings offer novel insight toward establishing the causal relationship between BaP exposure and the occurrence of allergic disorders. Identifying gut bacteria that degrade BaP may provide new strategies for ameliorating BaP cytotoxicity. https://doi.org/10.1289/EHP11874.},
}
@article {pmid37264481,
year = {2023},
author = {Liu, Y and Daniel, SG and Kim, HE and Koo, H and Korostoff, J and Teles, F and Bittinger, K and Hwang, G},
title = {Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {123},
pmid = {37264481},
issn = {2049-2618},
mesh = {Humans ; Child, Preschool ; *Dental Caries ; Cross-Sectional Studies ; Candida albicans/genetics ; *Microbiota ; Biofilms ; Streptococcus mutans/genetics ; Sugars/metabolism/pharmacology ; },
abstract = {BACKGROUND: Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by the synergistic polymicrobial interaction between the cariogenic bacterium, Streptococcus mutans, and an opportunistic fungal pathogen, Candida albicans. Although cross-sectional studies reveal their important roles in caries development, these exhibit limitations in determining the significance of these microbial interactions in the pathogenesis of the disease. Thus, it remains unclear the mechanism(s) through which the cross-kingdom interaction modulates the composition of the plaque microbiome. Here, we employed a novel ex vivo saliva-derived microcosm biofilm model to assess how exogenous pathogens could impact the structural and functional characteristics of the indigenous native oral microbiota.<br><br>RESULTS: Through shotgun whole metagenome sequencing, we observed that saliva-derived biofilm has decreased richness and diversity but increased sugar-related metabolism relative to the planktonic phase. Addition of S. mutans and/or C. albicans to the native microbiome drove significant changes in its bacterial composition. In addition, the effect of the exogenous pathogens on microbiome diversity and taxonomic abundances varied depending on the sugar type. While the addition of S. mutans induced a broader effect on Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog abundances with glucose/fructose, S. mutans-C. albicans combination under sucrose conditions triggered unique and specific changes in microbiota composition/diversity as well as specific effects on KEGG pathways. Finally, we observed the presence of human epithelial cells within the biofilms via confocal microscopy imaging.<br><br>CONCLUSIONS: Our data revealed that the presence of S. mutans and C. albicans, alone or in combination, as well as the addition of different sugars, induced unique alterations in both the composition and functional attributes of the biofilms. In particular, the combination of S. mutans and C. albicans seemed to drive the development (and perhaps the severity) of a dysbiotic/cariogenic oral microbiome. Our work provides a unique and pragmatic biofilm model for investigating the functional microbiome in health and disease as well as developing strategies to modulate the microbiome. Video Abstract.},
}
@article {pmid37264459,
year = {2023},
author = {Leung, MHY and Tong, X and Shen, Z and Du, S and Bastien, P and Appenzeller, BMR and Betts, RJ and Mezzache, S and Bourokba, N and Cavusoglu, N and Aguilar, L and Misra, N and Clavaud, C and Lee, PKH},
title = {Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {124},
pmid = {37264459},
issn = {2049-2618},
mesh = {*Polycyclic Aromatic Hydrocarbons ; Skin/chemistry ; *Air Pollutants/analysis ; Biodegradation, Environmental ; *Microbiota/genetics ; Environmental Monitoring ; },
abstract = {BACKGROUND: The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.<br><br>RESULTS: The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation.<br><br>CONCLUSIONS: This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin-microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions. Video Abstract.},
}
@article {pmid37264413,
year = {2023},
author = {Lu, DC and Wang, FQ and Amann, RI and Teeling, H and Du, ZJ},
title = {Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {126},
pmid = {37264413},
issn = {2049-2618},
mesh = {*Seaweed/microbiology ; *Ulva/genetics/microbiology ; *Laminaria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Rhodophyta/genetics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species.<br><br>RESULTS: We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~&#x2009;0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera.<br><br>CONCLUSIONS: Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.},
}
@article {pmid37263438,
year = {2023},
author = {Phulpoto, AH and Pirzada, T and Kanhar, NA},
title = {Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {164505},
doi = {10.1016/j.scitotenv.2023.164505},
pmid = {37263438},
issn = {1879-1026},
abstract = {Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at "exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions". The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as "PDB20, 91 %", "PDB14, 81 %", and "PDB16, 87 %" while for the blue B698, "PDB4, 86 %", "PDB20, 89 %", "PDB5, and PDB2, 80%". Moreover, in case of G492, maximum % removal was achieved with "PDB20, 93 %", "PDB5, 90 %", "PDB6, 90 %", "PDB16, 88 %", "PDB2, and PDB4, 89%". Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.},
}
@article {pmid37261715,
year = {2023},
author = {Andrianjakarivony, FH and Bettarel, Y and Desnues, C},
title = {Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {37261715},
issn = {1976-3794},
abstract = {The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.},
}
@article {pmid37261381,
year = {2023},
author = {Shao, Z and Shan, X and Jing, L and Wang, W and Li, W and Ren, Z and Zhang, BN and Huang, Y},
title = {Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes.},
journal = {Translational vision science &amp; technology},
volume = {12},
number = {6},
pages = {1},
doi = {10.1167/tvst.12.6.1},
pmid = {37261381},
issn = {2164-2591},
mesh = {Humans ; Metagenome/genetics ; *Diabetes Mellitus, Type 2/complications/epidemiology/genetics ; *Microbiota/genetics ; Bacteria/genetics ; *Cataract/complications/genetics ; Conjunctiva ; },
abstract = {PURPOSE: Our objective was to investigate differences in the ocular surface bacterial composition in cataract patients with and without type 2 diabetes (T2D).<br><br>METHODS: Twenty-four diabetic patients with cataracts (group D) and 14 sex- and age-matched patients with age-related cataracts (group N) were recruited for this study. All samples underwent DNA extraction, fragmentation, purification, library construction, and metagenomic sequencing.<br><br>RESULTS: The overall conjunctival sac bacterial composition was similar between group D and group N, as determined by alpha diversity and beta diversity. Nevertheless, significant differences were observed in the relative abundance of specific bacteria. At the phylum level, group D had a significantly lower abundance of Chlamydiae, Tenericutes, Chloroflexi, Cyanobacteria, Cossaviricota, Chytridiomycota, Artverviricota, Zoopagomycota, Peploviricota, Deinococcus-Thermus, Preplasmiviricota, and Nucleocytoviricota. At the genus level, group D had a significantly lower abundance of Chlamydia, Mycoplasma, Salmonella, Chryseobacterium, Roseovarius, Desulfococcus, Kangiella, Anaerococcus, and Idiomarina but a significantly higher abundance of Parabacteroides, Phocaeicola, and Sphingomonas. Bacteria such as Aquificae, Parabacteroides, Flavobacterium, Austwickia, Aquifex, Tenacibaculum, and Chryseobacterium in group D and Tenericutes, Chlamydiae, Porphyromonas, Mycoplasma, Chlamydia, Kangiella, Idiomarina, Roseovarius, Aliiroseovarius, and Desulfococcus in group N could be used as conjunctival sac biomarkers, according to the linear discriminant analysis effect size. Gene Ontology functional annotation indicated that bacterial catalytic activity, metabolic processes, locomotion, virion, and reproduction were enriched in group D, while immune system processes were enriched in group N. In addition, the top 30 differentially expressed virulence factors (VFs) were all more enriched in group D.<br><br>CONCLUSIONS: The bacterial composition was similar between the two groups. Several bacterial strains that were reported beneficial in gut were decreased, and pathogenic bacteria were increased in T2D. Furthermore, group D had more active bacterial terms and increased VF expression, suggesting that the susceptibility of diabetic patients to infection is closely related to functional changes in the ocular surface flora. Our conjunctival microbiota atlas provides a reference for investigating ocular complications related to diabetes.<br><br>TRANSLATIONAL RELEVANCE: The altered composition and functional profile of the ocular microbial community in diabetic patients offer evidence for the need to prevent infection during cataract surgery.},
}
@article {pmid37260707,
year = {2023},
author = {Li, X and Yi, Y and Wu, T and Chen, N and Gu, X and Xiang, L and Jiang, Z and Li, J and Jin, H},
title = {Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1170748},
pmid = {37260707},
issn = {2235-2988},
mesh = {Humans ; *Carcinoma, Hepatocellular/diagnosis ; *Liver Neoplasms/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Metabolome ; Biomarkers ; Liver Cirrhosis/diagnosis ; Biomarkers, Tumor ; },
abstract = {Globally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.},
}
@article {pmid37259063,
year = {2023},
author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L},
title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {295},
pmid = {37259063},
issn = {1471-2164},
mesh = {Humans ; Infant ; *Bacteriocins/genetics ; Metagenome ; *Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.<br><br>RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (<&#x2009;2&#xa0;years) compared to adult-like metagenomes (2-107&#xa0;years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.<br><br>CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.},
}
@article {pmid37224782,
year = {2023},
author = {Xu, M and Su, S and Jiang, S and Li, W and Zhang, Z and Zhang, J and Hu, X},
title = {Short-term arecoline exposure affected the systemic health state of mice, in which gut microbes played an important role.},
journal = {Ecotoxicology and environmental safety},
volume = {259},
number = {},
pages = {115055},
doi = {10.1016/j.ecoenv.2023.115055},
pmid = {37224782},
issn = {1090-2414},
mesh = {Animals ; Mice ; *Arecoline/pharmacology/toxicity ; Interleukin-6/metabolism ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Liver ; },
abstract = {Arecoline is a critical bioactive component in areca nuts with toxicity and pharmacological activities. However, its effects on body health remain unclear. Here, we investigated the effects of arecoline on physiologic and biochemical parameters in mouse serum, liver, brain, and intestine. The effect of arecoline on gut microbiota was investigated based on shotgun metagenomic sequencing. The results showed that arecoline promoted lipid metabolism in mice, manifested as significantly reduced serum TC and TG and liver TC levels and a reduction in abdominal fat accumulation. Arecoline intake significantly modulated the neurotransmitters 5-HT and NE levels in the brain. Notably, arecoline intervention significantly increased serum IL-6 and LPS levels, leading to inflammation in the body. High-dose arecoline significantly reduced liver GSH levels and increased MDA levels, which led to oxidative stress in the liver. Arecoline intake promoted the release of intestinal IL-6 and IL-1β, causing intestinal injury. In addition, we observed a significant response of gut microbiota to arecoline intake, reflecting significant changes in diversity and function of the gut microbes. Further mechanistic exploration suggested that arecoline intake can regulate gut microbes and ultimately affect the host's health. This study provided technical help for the pharmacochemical application and toxicity control of arecoline.},
}
@article {pmid37196747,
year = {2023},
author = {Zhang, Z and Yang, H and Wang, B and Chen, C and Zou, X and Cheng, T and Li, J},
title = {Aerobic co-composting of mature compost with cattle manure: Organic matter conversion and microbial community characterization.},
journal = {Bioresource technology},
volume = {382},
number = {},
pages = {129187},
doi = {10.1016/j.biortech.2023.129187},
pmid = {37196747},
issn = {1873-2976},
mesh = {Cattle ; Animals ; Soil ; Manure ; *Composting ; *Microbiota ; Carbohydrates ; },
abstract = {The production of organic fertilizer by aerobic composting of cattle manure is an important way of its resource utilization. This study evaluated the effects of adding mature compost on the decomposition and microbial communities in the aerobic composting of cattle manure. The addition of mature compost shortens the composting cycle and results in a final lignocellulosic degradation rate of 35%. Metagenomic analysis showed that this was due to the proliferation of thermophilic and organic matter-degrading functional microorganisms, which enhanced the activity of carbohydrate-active enzymes. With the addition of mature compost, the microbial community exhibited stronger metabolic functions, especially carbohydrate and amino acid metabolism, which are the driving forces of organic matter degradation. This study deepens the understanding of organic matter conversion and microbial community metabolic functions when mature compost is used for livestock manure composting and provides a promising technology for livestock manure composting.},
}
@article {pmid37191684,
year = {2023},
author = {Lu, J and Sha, H and Chen, J and Yi, X and Xiong, J},
title = {Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {12},
pages = {4093-4107},
pmid = {37191684},
issn = {1432-0614},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota ; Environmental Pollution ; Nitrification ; Sulfates ; },
abstract = {Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.},
}
@article {pmid37188814,
year = {2023},
author = {Johansen, J and Atarashi, K and Arai, Y and Hirose, N and Sørensen, SJ and Vatanen, T and Knip, M and Honda, K and Xavier, RJ and Rasmussen, S and Plichta, DR},
title = {Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan.},
journal = {Nature microbiology},
volume = {8},
number = {6},
pages = {1064-1078},
pmid = {37188814},
issn = {2058-5276},
mesh = {Adult ; Aged, 80 and over ; Humans ; Longevity ; Virome ; Centenarians ; *Viruses/genetics ; *Microbiota ; *Bacteriophages/genetics ; },
abstract = {Distinct gut microbiome ecology may be implicated in the prevention of aging-related diseases as it influences systemic immune function and resistance to infections. Yet, the viral component of the microbiome throughout different stages in life remains unexplored. Here we present a characterization of the centenarian gut virome using previously published metagenomes from 195 individuals from Japan and Sardinia. Compared with gut viromes of younger adults (>18 yr) and older individuals (>60 yr), centenarians had a more diverse virome including previously undescribed viral genera, such as viruses associated with Clostridia. A population shift towards higher lytic activity was also observed. Finally, we investigated phage-encoded auxiliary functions that influence bacterial physiology, which revealed an enrichment of genes supporting key steps in sulfate metabolic pathways. Phage and bacterial members of the centenarian microbiome displayed an increased potential for converting methionine to homocysteine, sulfate to sulfide and taurine to sulfide. A greater metabolic output of microbial hydrogen sulfide in centenarians may in turn support mucosal integrity and resistance to pathobionts.},
}
@article {pmid37169918,
year = {2023},
author = {Sanders, JG and Sprockett, DD and Li, Y and Mjungu, D and Lonsdorf, EV and Ndjango, JN and Georgiev, AV and Hart, JA and Sanz, CM and Morgan, DB and Peeters, M and Hahn, BH and Moeller, AH},
title = {Widespread extinctions of co-diversified primate gut bacterial symbionts from humans.},
journal = {Nature microbiology},
volume = {8},
number = {6},
pages = {1039-1050},
pmid = {37169918},
issn = {2058-5276},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; R01 AI050529/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Humans ; Phylogeny ; Pan troglodytes ; *Gastrointestinal Microbiome ; Primates ; *Hominidae/microbiology ; Bacteria/genetics ; },
abstract = {Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.},
}
@article {pmid37141097,
year = {2023},
author = {Manghi, P and Blanco-Míguez, A and Manara, S and NabiNejad, A and Cumbo, F and Beghini, F and Armanini, F and Golzato, D and Huang, KD and Thomas, AM and Piccinno, G and Punčochář, M and Zolfo, M and Lesker, TR and Bredon, M and Planchais, J and Glodt, J and Valles-Colomer, M and Koren, O and Pasolli, E and Asnicar, F and Strowig, T and Sokol, H and Segata, N},
title = {MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.},
journal = {Cell reports},
volume = {42},
number = {5},
pages = {112464},
doi = {10.1016/j.celrep.2023.112464},
pmid = {37141097},
issn = {2211-1247},
support = {U01 CA230551/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Diet ; Metagenomics/methods ; },
abstract = {Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.},
}
@article {pmid37100126,
year = {2023},
author = {Du, X and Li, X and Cheng, K and Zhao, W and Cai, Z and Chen, G and Zhou, J},
title = {Virome reveals effect of Ulva prolifera green tide on the structural and functional profiles of virus communities in coastal environments.},
journal = {The Science of the total environment},
volume = {883},
number = {},
pages = {163609},
doi = {10.1016/j.scitotenv.2023.163609},
pmid = {37100126},
issn = {1879-1026},
mesh = {Ecosystem ; Virome ; *Ulva ; Bacteria ; Eutrophication ; *Viruses ; China ; },
abstract = {Viruses are widely distributed in marine environments, where they influence the transformation of matter and energy by modulating host metabolism. Driven by eutrophication, green tides are a rising concern in Chinese coastal areas, and are a serious ecological disaster that negatively affects coastal ecosystems and disrupts biogeochemical cycles. Although the composition of bacterial communities in green algae has been investigated, the diversity and roles of viruses in green algal blooms are largely unexplored. Therefore, the diversity, abundance, lifestyle, and metabolic potential of viruses in a natural bloom in Qingdao coastal area were investigated at three different stages (pre-bloom, during-bloom, and post-bloom) by metagenomics analysis. The dsDNA viruses, Siphoviridae, Myoviridae, Podoviridae, and Phycodnaviridae, were found to dominate the viral community. The viral dynamics exhibited distinct temporal patterns across different stages. The composition of the viral community varied during the bloom, especially in populations with low abundance. The lytic cycle was most predominant, and the abundance of lytic viruses increased slightly in the post-bloom stage. The diversity and richness of the viral communities varied distinctly during the green tide, and the post-bloom stage favored viral diversity and richness. The total organic carbon, dissolved oxygen, NO[3-], NO[2-], PO4[3-], chlorophyll-a contents, and temperature variably co-influenced the viral communities. The primary hosts included bacteria, algae, and other microplankton. Network analysis revealed the closer links between the viral communities as the bloom progressed. Functional prediction revealed that the viruses possibly influenced the biodegradation of microbial hydrocarbons and carbon by metabolic augmentation via auxiliary metabolic genes. The composition, structure, metabolic potential, and interaction taxonomy of the viromes differed significantly across the different stages of the green tide. The study demonstrated that the ecological event shaped the viral communities during algal bloom, and the viral communities played a significant role in phycospheric microecology.},
}
@article {pmid37093508,
year = {2023},
author = {Wijdeveld, M and van Olst, N and van der Vossen, EWJ and de Brauw, M and Acherman, YIZ and de Goffau, MC and Gerdes, VEA and Nieuwdorp, M},
title = {Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.},
journal = {Obesity surgery},
volume = {33},
number = {6},
pages = {1635-1645},
pmid = {37093508},
issn = {1708-0428},
mesh = {Humans ; *Gastric Bypass/adverse effects ; *Gastrointestinal Microbiome ; *Obesity, Morbid/surgery ; Quality of Life ; *Microbiota ; },
abstract = {PURPOSE: Roux-en-Y gastric bypasses (RYGB) are frequently accompanied by long-term gastrointestinal (GI) symptoms. Direct mechanistic insight into the causation of these symptoms is lacking, but changes in the intestinal microbiome have been proposed to play a role. With this study, we aimed to investigate whether a microbial predisposition exists before RYGB which is associated with GI symptoms during follow-up and to evaluate which microbial groups are involved.<br><br>MATERIALS AND METHODS: In total, 67 RYGB patients were included. Shotgun metagenomic sequencing was performed on fecal samples obtained just before and 1 year after surgery. To assess GI symptoms, patients filled out Gastrointestinal Quality of Life Index (GIQLI) questionnaires and were divided into groups based on their total GIQLI score and change in score (postsurgery versus baseline). Extremely randomized tree predictor models were used to identify the most distin