@article {pmid34302348, year = {2021}, author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y}, title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, doi = {10.1093/femsec/fiab108}, pmid = {34302348}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Hydrothermal Vents ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides ; }, abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.}, }
@article {pmid33785903, year = {2021}, author = {Liang, G and Bushman, FD}, title = {The human virome: assembly, composition and host interactions.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {8}, pages = {514-527}, pmid = {33785903}, issn = {1740-1534}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; R01 HL113252/HL/NHLBI NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Virome/*genetics ; }, abstract = {The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.}, }
@article {pmid33479378, year = {2021}, author = {Glendinning, L and Genç, B and Wallace, RJ and Watson, M}, title = {Metagenomic analysis of the cow, sheep, reindeer and red deer rumen.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1990}, pmid = {33479378}, issn = {2045-2322}, support = {BB/P013759/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013732/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; TS/J000108/1//Technology Strategy Board/ ; TS/J000116/1//Technology Strategy Board/ ; }, mesh = {Animal Feed ; Animals ; Bacteria/classification/*genetics ; Cattle ; Deer/genetics/microbiology ; Metagenomics ; Microbiota/*genetics ; Reindeer/genetics/microbiology ; Rumen/*microbiology ; Ruminants/classification/*genetics ; Sheep/genetics/microbiology ; }, abstract = {The rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cow (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies.}, }
@article {pmid32985923, year = {2020}, author = {Ghosh, TS and Arnoux, J and O'Toole, PW}, title = {Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1-19}, pmid = {32985923}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Body Mass Index ; Child ; Child, Preschool ; Diabetes Mellitus, Type 2/microbiology ; Diet ; *Disease ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Geography ; *Health ; Humans ; Infant ; Inflammatory Bowel Diseases/microbiology ; Lactobacillus/*classification/genetics/*growth & development/isolation & purification ; Liver Diseases/microbiology ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Sex Factors ; Young Adult ; }, abstract = {Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of defining original niches for lactobacilli - food, environment, the gut - is questionable, and culture-independent analyses of prevalence in different human populations is lacking. Here we analyzed the abundance of lactobacilli in 6,154 subjects from a database of highly curated fecal shotgun metagenomics data spanning 25 nationalities, with ages ranging from infancy to 102 years. Twenty-five species were detected, which we assigned into low, medium, and high prevalence groups. The microbiome of apparently healthy individuals could be categorized into 6 clusters or Lactobacillotypes (LbTypes), with three of the Lbtypes being dominated by L. delbrueckii, L. ruminis, L. casei, and the other three comprising a combination of different species. These Lactobacillus clusters exhibit distinct global abundance patterns. The cluster prevalences also display distinct age-specific trends influenced by geography, with overall lactobacillus prevalence increasing significantly with age in North America and Europe but declining with age in non-Westernized societies. Regression analysis stratified by regional location identified distinct associations of the Lactobacillotypes with age, BMI, and gender. Cirrhosis, fatty-liver, , IBD and T2D were characterized by net gain of lactobacilli, whereas hypertension patients harbored depleted lactobacillus levels. Collectively these data indicate that the species abundance of gut lactobacilli is moderated by geography, diet, and interaction with the whole microbiome, and has strong interactions with diseases associated with a western lifestyle.}, }
@article {pmid32939014, year = {2020}, author = {Yang, J and Moon, HE and Park, HW and McDowell, A and Shin, TS and Jee, YK and Kym, S and Paek, SH and Kim, YK}, title = {Brain tumor diagnostic model and dietary effect based on extracellular vesicle microbiome data in serum.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {9}, pages = {1602-1613}, pmid = {32939014}, issn = {2092-6413}, support = {NRF-2016M3A9B6901516//National Research Foundation of Korea (NRF)/ ; NRF-2020M3A9G80220292//National Research Foundation of Korea (NRF)/ ; 10050154//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; }, mesh = {Aged ; Animals ; Biomarkers, Tumor ; Brain Neoplasms/*diagnosis/*metabolism ; Case-Control Studies ; Computational Biology ; Diet ; Extracellular Vesicles/*metabolism/*microbiology ; Female ; Humans ; Machine Learning ; Male ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Middle Aged ; ROC Curve ; }, abstract = {The human microbiome has been recently associated with human health and disease. Brain tumors (BTs) are a particularly difficult condition to directly link to the microbiome, as microorganisms cannot generally cross the blood-brain barrier (BBB). However, some nanosized extracellular vesicles (EVs) released from microorganisms can cross the BBB and enter the brain. Therefore, we conducted metagenomic analysis of microbial EVs in both serum (152 BT patients and 198 healthy controls (HC)) and brain tissue (5 BT patients and 5 HC) samples based on the V3-V4 regions of 16S rDNA. We then developed diagnostic models through logistic regression and machine learning algorithms using serum EV metagenomic data to assess the ability of various dietary supplements to reduce BT risk in vivo. Models incorporating the stepwise method and the linear discriminant analysis effect size (LEfSe) method yielded 12 and 29 significant genera as potential biomarkers, respectively. Models using the selected biomarkers yielded areas under the curves (AUCs) >0.93, and the model using machine learning resulted in an AUC of 0.99. In addition, Dialister and [Eubacterium] rectale were significantly lower in both blood and tissue samples of BT patients than in those of HCs. In vivo tests showed that BT risk was decreased through the addition of sorghum, brown rice oil, and garlic but conversely increased by the addition of bellflower and pear. In conclusion, serum EV metagenomics shows promise as a rich data source for highly accurate detection of BT risk, and several foods have potential for mitigating BT risk.}, }
@article {pmid32887934, year = {2020}, author = {Choi, DH and Park, J and Choi, JK and Lee, KE and Lee, WH and Yang, J and Lee, JY and Park, YJ and Oh, C and Won, HR and Koo, BS and Chang, JW and Park, YS}, title = {Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia.}, journal = {Experimental & molecular medicine}, volume = {52}, number = {9}, pages = {1564-1573}, pmid = {32887934}, issn = {2092-6413}, support = {2016M3A9B4919639//National Research Foundation of Korea (NRF)/ ; 2017R1A2B4002611//National Research Foundation of Korea (NRF)/ ; 2019M3A9H1032376//National Research Foundation of Korea (NRF)/ ; 2016R1D1A1B04932112//National Research Foundation of Korea (NRF)/ ; }, mesh = {Biomarkers ; Child ; Child, Preschool ; Female ; Humans ; Hyperplasia ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Palatine Tonsil/*microbiology/*pathology/surgery ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Tonsillectomy ; }, abstract = {Oral microbes have the capacity to spread throughout the gastrointestinal system and are strongly associated with multiple diseases. Given that tonsils are located between the oral cavity and the laryngopharynx at the gateway of the alimentary and respiratory tracts, tonsillar tissue may also be affected by microbiota from both the oral cavity (saliva) and the alimentary tract. Here, we analyzed the distribution and association of the microbial communities in the saliva and tonsils of Korean children subjected to tonsillectomy because of tonsil hyperplasia (n = 29). The microbiome profiles of saliva and tonsils were established via 16S rRNA gene sequencing. Based on the alpha diversity indices, the microbial communities of the two groups showed high similarities. According to Spearman's ranking correlation analysis, the distribution of Treponema, the causative bacterium of periodontitis, in saliva and tonsils was found to have a significant positive correlation. Two representative microbes, Prevotella in saliva and Alloprevotella in tonsils, were negatively correlated, while Treponema 2 showed a strong positive correlation between saliva and tonsils. Taken together, strong similarities in the microbial communities of the tonsils and saliva are evident in terms of diversity and composition. The saliva microbiome is expected to significantly affect the tonsil microbiome. Furthermore, we suggest that our study creates an opportunity for tonsillar microbiome research to facilitate the development of novel microbiome-based therapeutic strategies.}, }
@article {pmid34140187, year = {2021}, author = {Cruz-O'Byrne, R and Piraneque-Gambasica, N and Aguirre-Forero, S}, title = {Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia.}, journal = {International journal of food microbiology}, volume = {354}, number = {}, pages = {109282}, doi = {10.1016/j.ijfoodmicro.2021.109282}, pmid = {34140187}, issn = {1879-3460}, mesh = {Bacteria/classification/metabolism ; *Biodiversity ; *Coffea/microbiology ; Colombia ; *Fermentation ; Fungi/classification/metabolism ; *Microbiota/physiology ; *Seeds/metabolism/microbiology ; }, abstract = {Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.}, }
@article {pmid33912174, year = {2021}, author = {Wang, H and Wang, G and Banerjee, N and Liang, Y and Du, X and Boor, PJ and Hoffman, KL and Khan, MF}, title = {Aberrant Gut Microbiome Contributes to Intestinal Oxidative Stress, Barrier Dysfunction, Inflammation and Systemic Autoimmune Responses in MRL/lpr Mice.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {651191}, pmid = {33912174}, issn = {1664-3224}, mesh = {Animals ; Disease Models, Animal ; Dysbiosis/*complications/immunology/microbiology/pathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; Inflammation/immunology/microbiology/pathology ; Intestinal Mucosa/immunology/microbiology/*pathology ; Lupus Erythematosus, Systemic/*immunology/microbiology/pathology ; Mice ; Mice, Inbred MRL lpr ; Oxidative Stress/immunology ; Permeability ; }, abstract = {Microbiome composition and function have been implicated as contributing factors in the pathogenesis of autoimmune diseases (ADs), including systemic lupus erythematosus (SLE), rheumatoid arthritis and autoimmune hepatitis (AIH). Furthermore, dysbiosis of gut microbiome is associated with impaired barrier function and mucosal immune dysregulation. However, mechanisms by which gut microbiome contributes to the ADs and whether antioxidant treatment can restore gut homeostasis and ameliorate the disease outcome are not known. This study was, therefore, focused on examining the involvement of gut microbiome and host responses in the pathogenesis of SLE using unique female mouse models (C57BL/6, MRL+/+ and MRL/lpr) of 6 and 18 weeks with varying degrees of disease progression. Fecal microbiome diversity and composition, gut oxidative stress (OS), barrier function and inflammation, as well as systemic autoimmunity were determined. Interestingly, each mouse strain had distinct bacterial community as revealed by β-diversity. A lower Firmicutes/Bacteroidetes ratio in 6-week-old MRL/lpr mice was observed, evidenced by decrease in Peptostreptococcaceae under Firmicutes phylum along with enrichment of Rikenellaceae under Bacteroidetes phylum. Additionally, we observed increases in colonic OS [4-hydroxynonenal (HNE)-adducts and HNE-specific immune complexes], permeability changes (lower tight junction protein ZO-2; increased fecal albumin and IgA levels) and inflammatory responses (increased phos-NF-κB, IL-6 and IgG levels) in 18-week-old MRL/lpr mice. These changes were associated with markedly elevated AD markers (antinuclear and anti-smooth muscle antibodies) along with hepatic portal inflammation and severe glomerulonephritis. Notably, antioxidant N-acetylcysteine treatment influenced the microbial composition (decreased Rikenellaceae; increased Akkeransiaceae, Erysipelotrichaceae and Muribaculaceae) and attenuated the systemic autoimmunity in MRL/lpr mice. Our data thus show that gut microbiome dysbiosis is associated with increased colonic OS, barrier dysfunction, inflammatory responses and systemic autoimmunity markers. These findings apart from delineating a role for gut microbiome dysbiosis, also support the contribution of gut OS, permeability changes and inflammatory responses in the pathogenesis of ADs.}, }
@article {pmid33880764, year = {2021}, author = {Lin, Y and Wang, G and Yu, J and Sung, JJY}, title = {Artificial intelligence and metagenomics in intestinal diseases.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {841-847}, doi = {10.1111/jgh.15501}, pmid = {33880764}, issn = {1440-1746}, support = {T21-705/20-N//Research Grants Council, University Grants Committee/ ; }, mesh = {*Artificial Intelligence ; Gastrointestinal Diseases/diagnosis/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Gut microbiota has been shown to associate with the development of gastrointestinal diseases. In the last decade, development in whole metagenome sequencing and 16S rRNA sequencing technology has dramatically accelerated the gut microbiome's research and revealed its association with gastrointestinal disorders. Because of high dimensionality and complexity's intrinsic data characteristics, traditional bioinformatical methods could only explain the most significant changes with limited prediction accuracy. In contrast, machine learning is the application of artificial intelligence that provides the computational systems to automatically learn and improve from experience (training cohort) without being explicitly programmed. It is thus capable of unwiring high dimensionality and complicated correlational hitches. With modern computation power, machine learning is widely utilized to analyze microorganisms related to disease onset and other clinical features. It could help explore and identify novel biomarkers or improve the accuracy rate of disease diagnostic. This review summarized the most recent research that utilized machine learning to reveal the role of gut microbiota in intestinal disorders.}, }
@article {pmid33880762, year = {2021}, author = {Zeng, T and Yu, X and Chen, Z}, title = {Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {832-840}, doi = {10.1111/jgh.15503}, pmid = {33880762}, issn = {1440-1746}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 61803360//National Natural Science Foundation of China/ ; 11871456//National Natural Science Foundation of China/ ; XDB38050200//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, mesh = {Artificial Intelligence/*trends ; *Big Data ; Datasets as Topic ; Gastrointestinal Diseases/*etiology/*microbiology ; *Gastrointestinal Microbiome ; Information Storage and Retrieval/*methods ; }, abstract = {For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.}, }
@article {pmid33125759, year = {2021}, author = {Zheng, H and Wei, P and Zhang, G and Xu, W and Li, Y}, title = {The impact of different Saccharomyces cerevisiae strains on microbial composition and quality of Chinese rice wine fermentations.}, journal = {Yeast (Chichester, England)}, volume = {38}, number = {2}, pages = {147-156}, doi = {10.1002/yea.3523}, pmid = {33125759}, issn = {1097-0061}, mesh = {Bioreactors ; *Fermentation ; Lactobacillus brevis/growth & development ; Metagenomics/methods ; *Microbiota/genetics/physiology ; Pantoea/growth & development ; Saccharomyces cerevisiae/*classification/genetics/*metabolism ; Volatile Organic Compounds/analysis ; Wine/*microbiology/*standards ; }, abstract = {Chinese rice wine (CRW) is a popular fermented product in China, with complicated microbial composition and flavour compounds. To reveal the effects of different strains of Saccharomyces cerevisiae (N85 and XZ11) on the microbial composition in the process of brewing, metagenomic sequencing approaches were carried out to explore the dynamic changes of bacteria and fungi. Furthermore, the volatile compounds and organic acids in CRW were identified by headspace solid phase microextraction (HS-SPME)/gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) at the end of the brewing. Our results indicated that different S. cerevisiae strains could influence microbial compositions and especially affected the growth of Lactobacillus brevis and Pantoea ananatis. The changes in the microbial community structure contributed to the remarkable difference in the content of lactic acid, esters, alcohols, and aldehydes. Moreover, functional network analysis provided insights into the biological correlations between microbial species and metabolic pathways, that is, Lactobacillus genus had negative effects on metabolic activities. This study expands the idea of improving the quality of CRW by controlling the microbiome.}, }
@article {pmid33063432, year = {2021}, author = {Paoli, L and Sunagawa, S}, title = {Space, time and microdiversity: towards a resolution revolution in microbiomics.}, journal = {Environmental microbiology reports}, volume = {13}, number = {1}, pages = {31-35}, pmid = {33063432}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Environmental Microbiology ; Gastrointestinal Microbiome ; Humans ; *Metagenomics ; *Microbiota ; Seawater ; }, }
@article {pmid33657385, year = {2021}, author = {Wu, S and Jiang, P and Zhao, XM and Chen, WH}, title = {Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis.}, journal = {Cell metabolism}, volume = {33}, number = {3}, pages = {455-456}, doi = {10.1016/j.cmet.2021.02.012}, pmid = {33657385}, issn = {1932-7420}, mesh = {*Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis ; Metagenomics ; Proton Pump Inhibitors ; }, abstract = {Many of the gut-microbiome-derived signatures for liver cirrhosis, especially the important ones, were likely under the influence of proton pump inhibitors (PPIs). Wu et al. suggest that drug usage is a confounding factor in metagenomics analysis that should be controlled for.}, }
@article {pmid33591640, year = {2021}, author = {Huang, X and She, L and Liu, H and Liu, P and Chen, J and Chen, Y and Zhou, W and Lu, Y and Lin, J}, title = {Study of oral microorganisms contributing to non-carious cervical lesions via bacterial interaction and pH regulation.}, journal = {Journal of cellular and molecular medicine}, volume = {25}, number = {6}, pages = {3103-3112}, pmid = {33591640}, issn = {1582-4934}, support = {2017-1-62//Fujian Provincial Health Commission/ ; 2018QH1108//Fujian Medical University/ ; JAT170080//Young Teachers Education Research/ ; 2020Y0003//Fujian Science and Technology Department/ ; 2018Y9105//Joint Funds for the Innovation of Science and Technology of Fujian Province/ ; }, mesh = {*Bacteria ; Computational Biology/methods ; Disease Susceptibility ; Humans ; *Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; *Microbial Viability ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S ; Stomatognathic Diseases/*etiology ; }, abstract = {There is a lack of evidence about the relationship between microorganisms and non-carious cervical lesions (NCCLs) due to limited technologies. A group of 78 patients was enrolled for microbial 16S rRNA sequencing of dental plaques on normal and defective cervical surfaces. Parallel data from 39 patients were analysed with paired t tests, and Fusobacteriales exhibited significantly less distribution on NCCLs than on normal surfaces. As a result, Fusobacterium nucleatum, the most common oral bacterial strain belonging to the order Fusobacteriales, was selected for further research. From a scanning electron microscopy (SEM) scan, the tooth surface with Fusobacterium nucleatum and Streptococcus mutans culture was more intact than that without Fusobacterium nucleatum. Furthermore, the calcium contents in groups with Fusobacterium nucleatum were significantly higher than that without it. In further mechanistic research, Fusobacterium nucleatum was demonstrated to adhere to and disturb other organisms as well as producing alkaline secretions to neutralize the deleterious acidic environment, protecting the tooth structure. In conclusion, microorganisms and NCCLs were confirmed directly related through adherent bacterial interactions and pH regulation. The research provides a new perspective and experimental evidence for the relation between microorganisms and NCCLs, which guides clinical treatment and preventive dentistry in the future.}, }
@article {pmid34444679, year = {2021}, author = {Juárez-Fernández, M and Román-Sagüillo, S and Porras, D and García-Mediavilla, MV and Linares, P and Ballesteros-Pomar, MD and Urioste-Fondo, A and Álvarez-Cuenllas, B and González-Gallego, J and Sánchez-Campos, S and Jorquera, F and Nistal, E}, title = {Long-Term Effects of Bariatric Surgery on Gut Microbiota Composition and Faecal Metabolome Related to Obesity Remission.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34444679}, issn = {2072-6643}, support = {BFU2017-87960-R//Ministerio de Economía y Competitividad/ ; GRS1888/A/18//Junta de Castilla y León/ ; }, mesh = {*Bariatric Surgery ; DNA/analysis ; Fatty Acids, Volatile/analysis ; Feces/*chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; *Metabolome ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Weight Loss ; }, abstract = {Obesity is one of the main worldwide public health concerns whose clinical management demands new therapeutic approaches. Bariatric surgery is the most efficient treatment when other therapies have previously failed. Due to the role of gut microbiota in obesity development, the knowledge of the link between bariatric surgery and gut microbiota could elucidate new mechanistic approaches. This study aims to evaluate the long-term effects of bariatric surgery in the faecal metagenome and metabolome of patients with severe obesity. Faecal and blood samples were collected before and four years after the intervention from patients with severe obesity. Biochemical, metagenomic and metabolomic analyses were performed and faecal short-chain fatty acids were measured. Bariatric surgery improved the obesity-related status of patients and significantly reshaped gut microbiota composition. Moreover, this procedure was associated with a specific metabolome profile characterized by a reduction in energetic and amino acid metabolism. Acetate, butyrate and propionate showed a significant reduction with bariatric surgery. Finally, correlation analysis suggested the existence of a long-term compositional and functional gut microbiota profile associated with the intervention. In conclusion, bariatric surgery triggered long-lasting effects on gut microbiota composition and faecal metabolome that could be associated with the remission of obesity.}, }
@article {pmid34329005, year = {2021}, author = {Li, J and Jia, C and Lu, Q and Hungate, BA and Dijkstra, P and Wang, S and Wu, C and Chen, S and Li, D and Shim, H}, title = {Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures.}, journal = {Journal of hazardous materials}, volume = {418}, number = {}, pages = {126384}, doi = {10.1016/j.jhazmat.2021.126384}, pmid = {34329005}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Xenobiotics ; }, abstract = {Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.}, }
@article {pmid33941890, year = {2021}, author = {Chen, YJ and Leung, PM and Wood, JL and Bay, SK and Hugenholtz, P and Kessler, AJ and Shelley, G and Waite, DW and Franks, AE and Cook, PLM and Greening, C}, title = {Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2986-3004}, pmid = {33941890}, issn = {1751-7370}, mesh = {Bacteria/genetics ; *Ecosystem ; Geologic Sediments ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.}, }
@article {pmid33911204, year = {2021}, author = {Duan, H and He, P and Shao, L and Lü, F}, title = {Functional genome-centric view of the CO-driven anaerobic microbiome.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2906-2919}, pmid = {33911204}, issn = {1751-7370}, mesh = {Anaerobiosis ; *Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.}, }
@article {pmid34544379, year = {2021}, author = {Zhang, W and Liang, Y and Zheng, K and Gu, C and Liu, Y and Wang, Z and Zhang, X and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Zhang, Y and McMinn, A and Wang, M}, title = {Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {675}, pmid = {34544379}, issn = {1471-2164}, abstract = {BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.<br><br>RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.<br><br>CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.}, }
@article {pmid34537163, year = {2021}, author = {Castillo-Álvarez, F and Pérez-Matute, P and Oteo, JA and Marzo-Sola, ME}, title = {The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis.}, journal = {Neurologia (Barcelona, Spain)}, volume = {36}, number = {7}, pages = {495-503}, doi = {10.1016/j.nrleng.2020.05.006}, pmid = {34537163}, issn = {2173-5808}, mesh = {Animals ; Cross-Sectional Studies ; Feces ; *Gastrointestinal Microbiome ; Humans ; Interferon beta-1b ; *Multiple Sclerosis/drug therapy ; Prevotella ; }, abstract = {INTRODUCTION: The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce.<br><br>METHODS: We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing.<br><br>RESULTS: Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group.<br><br>CONCLUSION: We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship.}, }
@article {pmid34385112, year = {2021}, author = {Puthusseri, RM and Nair, HP and Johny, TK and Bhat, SG}, title = {Insights into the response of mangrove sediment microbiomes to heavy metal pollution: Ecological risk assessment and metagenomics perspectives.}, journal = {Journal of environmental management}, volume = {298}, number = {}, pages = {113492}, doi = {10.1016/j.jenvman.2021.113492}, pmid = {34385112}, issn = {1095-8630}, mesh = {Environmental Monitoring ; Geologic Sediments ; Metagenomics ; *Metals, Heavy/analysis ; *Microbiota/genetics ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; Wetlands ; }, abstract = {Rapid urbanisation and ensuing anthropogenic pollution lead to an escalated occurrence of heavy metals and metal-resistant bacteria in the soil ecosystem. Mangrove ecosystems are particularly vulnerable to heavy metal bioaccumulation and often act as metal sinks of the coastal areas. As a consequence, the microbial population in mangrove sediments develop multifarious metal tolerance mechanisms to combat metal toxicity. In this context, metagenomic investigation of two mangroves, viz. Mangalavanam and Puthuvypin from the heavily populated metropolitan city, Cochin (Central Kerala, India) was undertaken to discern the metal resistance functions and taxonomic diversity of the microbial consortia. Estimation of heavy metal content using Inductively Coupled Plasma Atomic Emission Spectrometer (ICP-MS) identified the abundance of zinc, chromium, nickel copper, lead, arsenic, and cadmium in the mangrove sediments. Ecological risk index values indicated high cadmium contamination of the two estuarine samples. Whole metagenome shotgun sequencing of the Central Kerala mangroves and comparative analysis with mangrove metal resistomes from other geographical regions revealed the prevalence of cobalt-zinc-cadmium resistance and preponderance of Proteobacteria in all the datasets. Cation efflux system protein CusA constituted the majority of the reads at the function level. Comparative analysis of taxonomy identified the dominance of Anaeromyxobacter, Geobacter, Pseudomonas, Candidatus Solibacter, and Pelobacter in the mangrove datasets. Non-metric multidimensional scaling analysis of the metal resistance genes depicted strong geographical clustering of the function and composition of metal resistant bacteria, suggesting a strong innate resilience of microbiome towards anthropogenic perturbations. More robust studies with intensive sampling will enhance our understanding of the occurrence, interactions, and functions of microbial heavy metal resistome in mangrove ecosystems.}, }
@article {pmid34356622, year = {2021}, author = {Torrell, H and Cereto-Massagué, A and Kazakova, P and García, L and Palacios, H and Canela, N}, title = {Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization.}, journal = {Biomolecules}, volume = {11}, number = {7}, pages = {}, pmid = {34356622}, issn = {2218-273X}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples.<br><br>METHODS: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis.<br><br>RESULTS: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile.<br><br>CONCLUSION: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.}, }
@article {pmid33317254, year = {2021}, author = {Lee, NY and Shin, MJ and Youn, GS and Yoon, SJ and Choi, YR and Kim, HS and Gupta, H and Han, SH and Kim, BK and Lee, DY and Park, TS and Sung, H and Kim, BY and Suk, KT}, title = {Lactobacillus attenuates progression of nonalcoholic fatty liver disease by lowering cholesterol and steatosis.}, journal = {Clinical and molecular hepatology}, volume = {27}, number = {1}, pages = {110-124}, pmid = {33317254}, issn = {2287-285X}, mesh = {Animals ; Cholesterol ; Female ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; Liver ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; *Non-alcoholic Fatty Liver Disease ; }, abstract = {BACKGROUND/AIMS: Nonalcoholic fatty liver disease (NAFLD) is closely related to gut-microbiome. There is a paucity of research on which strains of gut microbiota affect the progression of NAFLD. This study explored the NAFLD-associated microbiome in humans and the role of Lactobacillus in the progression of NAFLD in mice.<br><br>METHODS: The gut microbiome was analyzed via next-generation sequencing in healthy people (n=37) and NAFLD patients with elevated liver enzymes (n=57). Six-week-old male C57BL/6J mice were separated into six groups (n=10 per group; normal, Western, and four Western diet + strains [109 colony-forming units/g for 8 weeks; L. acidophilus, L. fermentum, L. paracasei, and L. plantarum]). Liver/body weight ratio, liver pathology, serum analysis, and metagenomics in the mice were examined.<br><br>RESULTS: Compared to healthy subjects (1.6±4.3), NAFLD patients showed an elevated Firmicutes/Bacteroidetes ratio (25.0±29.0) and a reduced composition of Akkermansia and L. murinus (P<0.05). In the animal experiment, L. acidophilus group was associated with a significant reduction in liver/body weight ratio (5.5±0.4) compared to the Western group (6.2±0.6) (P<0.05). L. acidophilus (41.0±8.6), L. fermentum (44.3±12.6), and L. plantarum (39.0±7.6) groups showed decreased cholesterol levels compared to the Western group (85.7±8.6) (P<0.05). In comparison of steatosis, L. acidophilus (1.9±0.6), L. plantarum (2.4±0.7), and L. paracasei (2.0±0.9) groups showed significant improvement of steatosis compared to the Western group (2.6±0.5) (P<0.05).<br><br>CONCLUSION: Ingestion of Lactobacillus, such as L. acidophilus, L. fermentum, and L. plantarum, ameliorates the progression of nonalcoholic steatosis by lowering cholesterol. The use of Lactobacillus can be considered as a useful strategy for the treatment of NAFLD.}, }
@article {pmid34168315, year = {2021}, author = {Nayfach, S and Páez-Espino, D and Call, L and Low, SJ and Sberro, H and Ivanova, NN and Proal, AD and Fischbach, MA and Bhatt, AS and Hugenholtz, P and Kyrpides, NC}, title = {Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.}, journal = {Nature microbiology}, volume = {6}, number = {7}, pages = {960-970}, pmid = {34168315}, issn = {2058-5276}, support = {P30 CA124435/CA/NCI NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/virology ; Bacteria/virology ; Bacteriophages/genetics ; Catalogs as Topic ; DNA Viruses/classification/*genetics ; DNA, Viral/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Viral/*genetics ; Humans ; Metagenomics ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.}, }
@article {pmid34097462, year = {2021}, author = {Breen, P and Winters, AD and Theis, KR and Withey, JH}, title = {The Vibrio cholerae Type Six Secretion System Is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome.}, journal = {Infection and immunity}, volume = {89}, number = {9}, pages = {e0015121}, pmid = {34097462}, issn = {1098-5522}, support = {R01 AI127390/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cholera/*microbiology ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Metagenomics/methods ; RNA, Ribosomal, 16S ; Type VI Secretion Systems/*physiology ; Vibrio cholerae/*physiology ; Zebrafish ; }, abstract = {Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae, an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was important for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, the presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.}, }
@article {pmid34061623, year = {2021}, author = {Breen, P and Winters, AD and Theis, KR and Withey, JH}, title = {Vibrio cholerae Infection Induces Strain-Specific Modulation of the Zebrafish Intestinal Microbiome.}, journal = {Infection and immunity}, volume = {89}, number = {9}, pages = {e0015721}, pmid = {34061623}, issn = {1098-5522}, support = {R01 AI127390/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cholera/*microbiology ; Disease Models, Animal ; *Disease Susceptibility ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Metagenomics/methods ; *Microbial Interactions ; RNA, Ribosomal, 16S ; Vibrio cholerae/*physiology ; Zebrafish ; }, abstract = {Zebrafish (Danio rerio) is an attractive model organism to use for an array of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic and can be significantly altered due to external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae for colonization, and subsequent disease, to occur. Many studies have explored a variety of aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms but few have researched how a V. cholerae infection changes the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was used to examine how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and that specific microbes that are targeted depend on the V. cholerae genotype.}, }
@article {pmid33839314, year = {2021}, author = {Granato, DC and Neves, LX and Trino, LD and Carnielli, CM and Lopes, AFB and Yokoo, S and Pauletti, BA and Domingues, RR and Sá, JO and Persinoti, G and Paixão, DAA and Rivera, C and de Sá Patroni, FM and Tommazetto, G and Santos-Silva, AR and Lopes, MA and de Castro, G and Brandão, TB and Prado-Ribeiro, AC and Squina, FM and Telles, GP and Paes Leme, AF}, title = {Meta-omics analysis indicates the saliva microbiome and its proteins associated with the prognosis of oral cancer patients.}, journal = {Biochimica et biophysica acta. Proteins and proteomics}, volume = {1869}, number = {8}, pages = {140659}, doi = {10.1016/j.bbapap.2021.140659}, pmid = {33839314}, issn = {1878-1454}, mesh = {Adult ; Aged ; Cohort Studies ; Female ; Humans ; Male ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; Mouth Neoplasms/metabolism/microbiology ; Prognosis ; Proteomics/methods ; Saliva/*microbiology ; Squamous Cell Carcinoma of Head and Neck/metabolism/*microbiology ; }, abstract = {Saliva is a biofluid that maintains the health of oral tissues and the homeostasis of oral microbiota. Studies have demonstrated that Oral squamous cell carcinoma (OSCC) patients have different salivary microbiota than healthy individuals. However, the relationship between these microbial differences and clinicopathological outcomes is still far from conclusive. Herein, we investigate the capability of using metagenomic and metaproteomic saliva profiles to distinguish between Control (C), OSCC without active lesion (L0), and OSCC with active lesion (L1) patients. The results show that there are significantly distinct taxonomies and functional changes in L1 patients compared to C and L0 patients, suggesting compositional modulation of the oral microbiome, as the relative abundances of Centipeda, Veillonella, and Gemella suggested by metagenomics are correlated with tumor size, clinical stage, and active lesion. Metagenomics results also demonstrated that poor overall patient survival is associated with a higher relative abundance of Stenophotromonas, Staphylococcus, Centipeda, Selenomonas, Alloscordovia, and Acitenobacter. Finally, compositional and functional differences in the saliva content by metaproteomics analysis can distinguish healthy individuals from OSCC patients. In summary, our study suggests that oral microbiota and their protein abundance have potential diagnosis and prognosis value for oral cancer patients. Further studies are necessary to understand the role of uniquely detected metaproteins in the microbiota of healthy and OSCC patients as well as the crosstalk between saliva host proteins and the oral microbiome present in OSCC.}, }
@article {pmid33782152, year = {2021}, author = {Costantini, C and Nunzi, E and Spolzino, A and Palmieri, M and Renga, G and Zelante, T and Englmaier, L and Coufalikova, K and Spáčil, Z and Borghi, M and Bellet, MM and Acerbi, E and Puccetti, M and Giovagnoli, S and Spaccapelo, R and Talesa, VN and Lomurno, G and Merli, F and Facchini, L and Spadea, A and Melillo, L and Codeluppi, K and Marchesi, F and Marchesini, G and Valente, D and Dragonetti, G and Nadali, G and Pagano, L and Aversa, F and Romani, L}, title = {Pharyngeal Microbial Signatures Are Predictive of the Risk of Fungal Pneumonia in Hematologic Patients.}, journal = {Infection and immunity}, volume = {89}, number = {8}, pages = {e0010521}, pmid = {33782152}, issn = {1098-5522}, mesh = {Animals ; Antifungal Agents/pharmacology/therapeutic use ; Disease Models, Animal ; Hematologic Diseases/*complications ; Hematologic Neoplasms/complications ; Humans ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Mycoses/diagnosis/drug therapy/*etiology ; Pharynx/*microbiology ; Pneumonia/diagnosis/drug therapy/*etiology ; Risk Assessment ; Risk Factors ; }, abstract = {The ability to predict invasive fungal infections (IFI) in patients with hematological malignancies is fundamental for successful therapy. Although gut dysbiosis is known to occur in hematological patients, whether airway dysbiosis also contributes to the risk of IFI has not been investigated. Nasal and oropharyngeal swabs were collected for functional microbiota characterization in 173 patients with hematological malignancies recruited in a multicenter, prospective, observational study and stratified according to the risk of developing IFI. A lower microbial richness and evenness were found in the pharyngeal microbiota of high-risk patients that were associated with a distinct taxonomic and metabolic profile. A murine model of IFI provided biologic plausibility for the finding that loss of protective anaerobes, such as Clostridiales and Bacteroidetes, along with an apparent restricted availability of tryptophan, is causally linked to the risk of IFI in hematologic patients and indicates avenues for antimicrobial stewardship and metabolic reequilibrium in IFI.}, }
@article {pmid32926879, year = {2021}, author = {Vandenborght, LE and Enaud, R and Urien, C and Coron, N and Girodet, PO and Ferreira, S and Berger, P and Delhaes, L}, title = {Type 2-high asthma is associated with a specific indoor mycobiome and microbiome.}, journal = {The Journal of allergy and clinical immunology}, volume = {147}, number = {4}, pages = {1296-1305.e6}, doi = {10.1016/j.jaci.2020.08.035}, pmid = {32926879}, issn = {1097-6825}, mesh = {Adult ; Aged ; Air Pollution, Indoor/*analysis ; Asthma/*microbiology ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Dust/*analysis ; Environmental Monitoring ; Female ; Humans ; Male ; *Microbiota/genetics ; Middle Aged ; Severity of Illness Index ; Sputum/microbiology ; }, abstract = {BACKGROUND: The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters.<br><br>OBJECTIVE: The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA).<br><br>METHODS: A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during "stable" or pulmonary "exacerbation" periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes.<br><br>RESULTS: Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation.<br><br>CONCLUSION: These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.}, }
@article {pmid32804018, year = {2020}, author = {Sánchez-Tapia, M and Miller, AW and Granados-Portillo, O and Tovar, AR and Torres, N}, title = {The development of metabolic endotoxemia is dependent on the type of sweetener and the presence of saturated fat in the diet.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1801301}, pmid = {32804018}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Diet, High-Fat/adverse effects ; Endotoxemia/*etiology/metabolism/microbiology ; Fatty Acids/*adverse effects/metabolism ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Humans ; Male ; Rats ; Rats, Wistar ; Sweetening Agents/*adverse effects/metabolism ; }, abstract = {Fat and sweeteners contribute to obesity. However, it is unknown whether specific bacteria are selectively modified by different caloric and noncaloric sweeteners with or without a high-fat diet (HFD). Here, we combined extensive host phenotyping and shotgun metagenomics of the gut microbiota to investigate this question. We found that the type of sweetener and its combination with an HFD selectively modified the gut microbiota. Sucralose and steviol glycosides led to the lowest α-diversity of the gut microbiota. Sucralose increased the abundance of B. fragilis in particular, resulting in a decrease in the abundance of occludin and an increase in proinflammatory cytokines, glucose intolerance, fatty acid oxidation and ketone bodies. Sucrose+HFD showed the highest metabolic endotoxemia, weight gain, body fat, total short chain fatty acids (SCFAs), serum TNFα concentration and glucose intolerance. Consumption of sucralose or sucrose resulted in enrichment of the bacterial genes involved in the synthesis of LPS and SCFAs. Notably, brown sugar and honey were associated with the absence of metabolic endotoxemia, increases in bacterial gene diversity and anti-inflammatory markers such as IL-10 and sIgA, the maintenance of glucose tolerance and energy expenditure, similar to the control group, despite the consumption of an HFD. These findings indicate that the type of sweetener and an HFD selectively modify the gut microbiota, bacterial gene enrichment of metabolic pathways involved in LPS and SCFA synthesis, and metabolic endotoxemia associated with different metabolic profiles.}, }
@article {pmid34287009, year = {2021}, author = {Aljabr, W and Alruwaili, M and Penrice-Randal, R and Alrezaihi, A and Harrison, AJ and Ryan, Y and Bentley, E and Jones, B and Alhatlani, BY and AlShahrani, D and Mahmood, Z and Rickett, NY and Alosaimi, B and Naeem, A and Alamri, S and Alsran, H and Hamed, ME and Dong, X and Assiri, AM and Alrasheed, AR and Hamza, M and Carroll, MW and Gemmell, M and Darby, A and Donovan-Banfield, I and Stewart, JP and Matthews, DA and Davidson, AD and Hiscox, JA}, title = {Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0021921}, pmid = {34287009}, issn = {2379-5042}, support = {5F40120C00085//HHS | U.S. Food and Drug Administration (FDA)/ ; 019-003//King Fahad Medical City (KFMC)/ ; }, mesh = {Aged ; Animals ; COVID-19/virology ; Coronavirus Infections/*virology ; Female ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Middle East Respiratory Syndrome Coronavirus/*genetics ; SARS-CoV-2/genetics ; }, abstract = {Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.}, }
@article {pmid34282338, year = {2021}, author = {Vogl, T and Klompus, S and Leviatan, S and Kalka, IN and Weinberger, A and Wijmenga, C and Fu, J and Zhernakova, A and Weersma, RK and Segal, E}, title = {Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota.}, journal = {Nature medicine}, volume = {27}, number = {8}, pages = {1442-1450}, pmid = {34282338}, issn = {1546-170X}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Epitopes/*immunology ; Female ; Humans ; Immunoglobulins/*immunology ; Infant ; Infant, Newborn ; Machine Learning ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Peptide Library ; Young Adult ; }, abstract = {Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.}, }
@article {pmid34226711, year = {2021}, author = {Montassier, E and Valdés-Mas, R and Batard, E and Zmora, N and Dori-Bachash, M and Suez, J and Elinav, E}, title = {Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner.}, journal = {Nature microbiology}, volume = {6}, number = {8}, pages = {1043-1054}, pmid = {34226711}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/classification/*drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Cohort Studies ; *Drug Resistance, Bacterial ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Metagenome/drug effects ; Middle Aged ; Probiotics/*administration &amp; dosage ; Young Adult ; }, abstract = {Antimicrobial resistance poses a substantial threat to human health. The gut microbiome is considered a reservoir for potential spread of resistance genes from commensals to pathogens, termed the gut resistome. The impact of probiotics, commonly consumed by many in health or in conjunction with the administration of antibiotics, on the gut resistome is elusive. Reanalysis of gut metagenomes from healthy antibiotics-naïve humans supplemented with an 11-probiotic-strain preparation, allowing direct assessment of the gut resistome in situ along the gastrointestinal (GI) tract, demonstrated that probiotics reduce the number of antibiotic resistance genes exclusively in the gut of colonization-permissive individuals. In mice and in a separate cohort of humans, a course of antibiotics resulted in expansion of the lower GI tract resistome, which was mitigated by autologous faecal microbiome transplantation or during spontaneous recovery. In contrast, probiotics further exacerbated resistome expansion in the GI mucosa by supporting the bloom of strains carrying vancomycin resistance genes but not resistance genes encoded by the probiotic strains. Importantly, the aforementioned effects were not reflected in stool samples, highlighting the importance of direct sampling to analyse the effect of probiotics and antibiotics on the gut resistome. Analysing antibiotic resistance gene content in additional published clinical trials with probiotics further highlighted the importance of person-specific metagenomics-based profiling of the gut resistome using direct sampling. Collectively, these findings suggest opposing person-specific and antibiotic-dependent effects of probiotics on the resistome, whose contribution to the spread of antimicrobial resistance genes along the human GI tract merit further studies.}, }
@article {pmid33846627, year = {2021}, author = {Chang, FY and Siuti, P and Laurent, S and Williams, T and Glassey, E and Sailer, AW and Gordon, DB and Hemmerle, H and Voigt, CA}, title = {Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids.}, journal = {Nature microbiology}, volume = {6}, number = {6}, pages = {792-805}, pmid = {33846627}, issn = {2058-5276}, mesh = {Amines/chemistry/*metabolism ; Diet ; Fatty Acids/chemistry/*metabolism ; Firmicutes/classification/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Neurotransmitter Agents/chemistry/*metabolism ; Receptors, G-Protein-Coupled/genetics/metabolism ; Signal Transduction ; }, abstract = {Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.}, }
@article {pmid33831065, year = {2021}, author = {Crowe, SA and Simister, RL and Spence, JS and Kenward, PA and Van Slyke, AC and Lennox, P and Carr, N}, title = {Microbial community compositions in breast implant biofilms associated with contracted capsules.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249261}, pmid = {33831065}, issn = {1932-6203}, mesh = {*Biofilms ; Breast Implants/*microbiology ; Capsules ; Humans ; Implant Capsular Contracture/*microbiology ; *Microbiota ; }, abstract = {Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation failure due to capsular contracture, and while these infections are generally ascribed to common skin commensals, this remains largely unsubstantiated through robust cultivation independent analyses. To determine capsule biofilm microbial community compositions, we employed amplicon sequencing of the 16S rRNA gene using DNA extracted from breast implant capsule samples. These cultivation independent analyses revealed that capsule associated biofilms are more diverse than canonical single-species infections, but have relatively low diversity (~ <100 species) compared to many host-associated microbial communities. In addition to taxa commonly associated with capsular contracture, the biofilms analyzed comprised a number of taxa that escaped detection in cultivation-dependent work. We have also isolated several key taxa identified through the culture-independent analyses. Together our analyses reveal that capsule biofilms are more diverse than cultivation studies suggest and can be heterogeneous within an individual capsule, between breasts of the same patient, across similar implant types, and over a range in severity of contracture. The complex nature of these communities requires further study across a broader suite of patients in addition to higher resolution analyses including metagenomics to better assess the fundamental role of microorganisms in capsular contracture.}, }
@article {pmid33798253, year = {2021}, author = {Cho, JC}, title = {Human microbiome privacy risks associated with summary statistics.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249528}, pmid = {33798253}, issn = {1932-6203}, mesh = {*Computer Simulation ; Humans ; *Metagenomics ; *Microbiota ; *Privacy ; }, abstract = {Recognizing that microbial community composition within the human microbiome is associated with the physiological state of the host has sparked a large number of human microbiome association studies (HMAS). With the increasing size of publicly available HMAS data, the privacy risk is also increasing because HMAS metadata could contain sensitive private information. I demonstrate that a simple test statistic based on the taxonomic profiles of an individual's microbiome along with summary statistics of HMAS data can reveal the membership of the individual's microbiome in an HMAS sample. In particular, species-level taxonomic data obtained from small-scale HMAS can be highly vulnerable to privacy risk. Minimal guidelines for HMAS data privacy are suggested, and an assessment of HMAS privacy risk using the simulation method proposed is recommended at the time of study design.}, }
@article {pmid33510238, year = {2021}, author = {Kursa, O and Tomczyk, G and Sawicka-Durkalec, A and Giza, A and Słomiany-Szwarc, M}, title = {Bacterial communities of the upper respiratory tract of turkeys.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2544}, pmid = {33510238}, issn = {2045-2322}, mesh = {Animals ; *Bacteria/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Respiratory Mucosa/*microbiology ; Turkeys/*microbiology ; }, abstract = {The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.}, }
@article {pmid30860572, year = {2020}, author = {Wang, Z and Wang, Y and Fuhrman, JA and Sun, F and Zhu, S}, title = {Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.}, journal = {Briefings in bioinformatics}, volume = {21}, number = {3}, pages = {777-790}, pmid = {30860572}, issn = {1477-4054}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Datasets as Topic ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics ; Microbiota/genetics ; }, abstract = {In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.}, }
@article {pmid34523982, year = {2021}, author = {Guan, H and Pu, Y and Liu, C and Lou, T and Tan, S and Kong, M and Sun, Z and Mei, Z and Qi, Q and Quan, Z and Zhao, G and Zheng, Y}, title = {Comparison of Fecal Collection Methods on Variation in Gut Metagenomics and Untargeted Metabolomics.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0063621}, doi = {10.1128/mSphere.00636-21}, pmid = {34523982}, issn = {2379-5042}, abstract = {Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at -80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.}, }
@article {pmid34328924, year = {2021}, author = {Fu, X and Ou, Z and Zhang, M and Meng, Y and Li, Y and Chen, Q and Jiang, J and Zhang, X and Norbäck, D and Zhao, Z and Sun, Y}, title = {Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools - Potential roles of indoor microbial amino acids and vitamin metabolites.}, journal = {The Science of the total environment}, volume = {795}, number = {}, pages = {148879}, doi = {10.1016/j.scitotenv.2021.148879}, pmid = {34328924}, issn = {1879-1026}, mesh = {*Air Pollution, Indoor/analysis ; Amino Acids ; *Asthma ; Humans ; *Microbiota ; Propionibacteriaceae ; Schools ; *Sick Building Syndrome ; Vitamins ; }, abstract = {Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multi-level linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial α-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (β-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.}, }
@article {pmid34312531, year = {2021}, author = {Wippel, K and Tao, K and Niu, Y and Zgadzaj, R and Kiel, N and Guan, R and Dahms, E and Zhang, P and Jensen, DB and Logemann, E and Radutoiu, S and Schulze-Lefert, P and Garrido-Oter, R}, title = {Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota.}, journal = {Nature microbiology}, volume = {6}, number = {9}, pages = {1150-1162}, pmid = {34312531}, issn = {2058-5276}, mesh = {Arabidopsis/microbiology/*physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Lotus/microbiology/*physiology ; *Microbiota ; Plant Roots/*microbiology/physiology ; Soil Microbiology ; *Symbiosis ; }, abstract = {Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.}, }
@article {pmid33886557, year = {2021}, author = {Hewson, I and Sewell, MA}, title = {Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three Aotearoa New Zealand asteroid species.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0241026}, pmid = {33886557}, issn = {1932-6203}, mesh = {Animals ; Densovirus/genetics/*isolation &amp; purification ; Mesomycetozoea/genetics/*isolation &amp; purification ; Metagenome ; Metagenomics ; Microbiota ; New Zealand ; Starfish/*parasitology/*virology ; }, abstract = {Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.}, }
@article {pmid33798237, year = {2021}, author = {Dizzell, S and Stearns, JC and Li, J and van Best, N and Bervoets, L and Mommers, M and Penders, J and Morrison, KM and Hutton, EK and , }, title = {Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0248924}, pmid = {33798237}, issn = {1932-6203}, support = {MOP-136811//CIHR/Canada ; IMG-143923//CIHR/Canada ; }, mesh = {Cohort Studies ; Diet ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Weaning ; }, abstract = {The first exposures to microbes occur during infancy and it is suggested that this initial colonization influences the adult microbiota composition. Despite the important role that the gut microbiome may have in health outcomes later in life, the factors that influence its development during infancy and early childhood have not been characterized fully. Guidelines about the introduction of solid foods and cessation of breastfeeding, which is thought to have a significant role in the transition to a more adult-like microbiota, are not based on microbiome research. There is even less understanding of approaches used to transition to solid food in the preterm population. The purpose of this study is to identify the impact of early life dietary events on gut microbiome community structures and function among infants born at term and pre-term. We plan to prospectively monitor the gut microbiome of infants during two critical timepoints in microbial development: the introduction of solid foods and cessation from breastmilk. A total of 35 participants from three primary observational birth cohorts (two full-term cohorts and one pre-term cohort) will be enrolled in this sub-study. Participants will be asked to collect stool samples and fill out a study diary before, during and after the introduction of solids and again during weaning from breastmilk. We will use frequent fecal sampling analyzed using 16S rRNA gene profiling, metagenomics, metabolomics, and targeted bacterial culturing to identify and characterize the microbial communities, as well as provide insight into the phenotypic characteristics and functional capabilities of the microbes present during these transitional periods of infancy. This study will provide a comprehensive approach to detailing the effects of dietary transition from breastmilk to a more adult-like solid food diet on the microbiome and in doing so will contribute to evidence-based infant nutrition guidance.}, }
@article {pmid34384948, year = {2021}, author = {Li, W and Gao, J and Zhuang, JL and Yao, GJ and Zhang, X and Liu, YD and Liu, QK and Shapleigh, JP and Ma, L}, title = {Metagenomics and metatranscriptomics uncover the microbial community associated with high S0 production in a denitrifying desulfurization granular sludge reactor.}, journal = {Water research}, volume = {203}, number = {}, pages = {117505}, doi = {10.1016/j.watres.2021.117505}, pmid = {34384948}, issn = {1879-2448}, mesh = {Bioreactors ; Denitrification ; Metagenomics ; *Microbiota ; Nitrates ; Oxidation-Reduction ; *Sewage ; Sulfides ; }, abstract = {The denitrification desulfurization process is a promising technology for elemental sulfur (S0) production from sulfide containing wastewater. However, the microbial community associated with high S0 production still is not well studied. This study describes an efficient denitrification S0 production bioreactor based on inoculation with anaerobic granular sludge. At an optimal S/N molar ratio of 7:2, 80 % of the influent sulfide was transformed to high quality elemental sulfur with a purity of 92.5% while the total inorganic nitrogen removal efficiency was stable at ∼80%. Metatranscriptomic analysis found that community expression of the gene encoding the sulfide-quinone reductase (SQR) was 10-fold greater than that of the flavocytochrome-c sulfide dehydrogenase subunit B (fccB). Moreover, the expression level of SQR was also significantly higher than the Dsr gene encoding for dissimilatory sulfate reductase, which encodes a critical S0 oxidation enzyme. Metagenomic binning analysis confirmed that sulfide-oxidizing bacteria (SOB) utilizing SQR were common in the community and most likely accounted for high S0 production. An unexpected enrichment in methanogens and high expression activity of bacteria carrying out Stickland fermentation as well as in other bacteria with reduced genomes indicated a complex community supporting stable sulfide oxidation to S0, likely aiding in performance stability. This study establishes this treatment approach as an alternative biotechnology for sulfide containing wastewater treatment and sheds light on the microbial interactions associated with high S0 production.}, }
@article {pmid34375790, year = {2021}, author = {Pan, Y and Zheng, X and Xiang, Y}, title = {Structure-function elucidation of a microbial consortium in degrading rice straw and producing acetic and butyric acids via metagenome combining 16S rDNA sequencing.}, journal = {Bioresource technology}, volume = {340}, number = {}, pages = {125709}, doi = {10.1016/j.biortech.2021.125709}, pmid = {34375790}, issn = {1873-2976}, mesh = {Butyrates ; DNA, Ribosomal ; Fermentation ; Lignin/metabolism ; Metagenome ; *Microbial Consortia ; *Oryza/metabolism ; }, abstract = {The characterized microbial consortium can efficiently degrade rice straw to produce acetic and butyric acids in high yields. The rice straw lost 86.9% in weight and degradation rates of hemicellulose, cellulose, and lignin attained were 97.1%, 86.4% and 70.3% within 12 days, respectively. During biodegradation via fermentation of rice straw, average concentrations of acetic and butyric acids reached 1570 mg/L and 1270 mg/L, accounting for 47.2% and 35.4% of the total volatile fatty acids, respectively. The consortium mainly composed of Prevotella, Cellulosilyticum, Pseudomonas, Clostridium and Ruminococcaceae, etc. Metagenomic analyses indicated that glycoside hydrolases (GHs) were the largest enzyme group with a relative abundance of 54.5%. Various lignocellulose degrading enzymes were identified in the top 30 abundant GHs, and were primarily distributed in the dominant genera (Prevotella, Cellulosilyticum and Clostridium). These results provide a new route for the commercial recycling of rice straw to produce organic acids.}, }
@article {pmid34149688, year = {2021}, author = {Pérez-Sáez, MJ and Uffing, A and Leon, J and Murakami, N and Watanabe, A and Borges, TJ and Sabbisetti, VS and Cureton, P and Kenyon, V and Keating, L and Yee, K and Fernandes Satiro, CA and Serena, G and Hildebrandt, F and Riella, CV and Libermann, TA and Wang, M and Pascual, J and Bonventre, JV and Cravedil, P and Fasano, A and Riella, LV}, title = {Immunological Impact of a Gluten-Free Dairy-Free Diet in Children With Kidney Disease: A Feasibility Study.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {624821}, pmid = {34149688}, issn = {1664-3224}, support = {K08 DK120868/DK/NIDDK NIH HHS/United States ; R01 DK076683/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Biomarkers/blood/urine ; Child ; Child, Preschool ; Cytokines/blood ; Dairy Products/*adverse effects ; *Diet, Gluten-Free/adverse effects ; Feasibility Studies ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Inflammation Mediators/blood ; Intestines/microbiology ; Male ; Nephrotic Syndrome/*congenital/diagnosis/diet therapy/immunology/microbiology ; Pilot Projects ; Proof of Concept Study ; Prospective Studies ; T-Lymphocytes, Regulatory/immunology/metabolism ; Th17 Cells/immunology/metabolism ; Time Factors ; Treatment Outcome ; Young Adult ; }, abstract = {Kidney disease affects 10% of the world population and is associated with increased mortality. Steroid-resistant nephrotic syndrome (SRNS) is a leading cause of end-stage kidney disease in children, often failing standard immunosuppression. Here, we report the results of a prospective study to investigate the immunological impact and safety of a gluten-free and dairy-free (GF/DF) diet in children with SRNS. The study was organized as a four-week summer camp implementing a strict GF/DF diet with prospective collection of blood, urine and stool in addition to whole exome sequencing WES of DNA of participants. Using flow cytometry, proteomic assays and microbiome metagenomics, we show that GF/DF diet had a major anti-inflammatory effect in all participants both at the protein and cellular level with 4-fold increase in T regulatory/T helper 17 cells ratio and the promotion of a favorable regulatory gut microbiota. Overall, GF/DF can have a significant anti-inflammatory effect in children with SRNS and further trials are warranted to investigate this potential dietary intervention in children with SRNS.}, }
@article {pmid32712295, year = {2020}, author = {Raiyani, NM and Singh, SP}, title = {Taxonomic and functional profiling of the microbial communities of Arabian Sea: A metagenomics approach.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {4361-4369}, doi = {10.1016/j.ygeno.2020.07.024}, pmid = {32712295}, issn = {1089-8646}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; *Metagenome ; Metagenomics ; *Microbiota ; Oceans and Seas ; Seawater/chemistry/*microbiology ; }, }
@article {pmid34512604, year = {2021}, author = {Liu, Y and Zheng, K and Liu, B and Liang, Y and You, S and Zhang, W and Zhang, X and Jie, Y and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {726074}, doi = {10.3389/fmicb.2021.726074}, pmid = {34512604}, issn = {1664-302X}, abstract = {Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from -20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.}, }
@article {pmid34484688, year = {2021}, author = {Mehta, S and Crane, M and Leith, E and Batut, B and Hiltemann, S and Arntzen, MØ and Kunath, BJ and Pope, PB and Delogu, F and Sajulga, R and Kumar, P and Johnson, JE and Griffin, TJ and Jagtap, PD}, title = {ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {103}, pmid = {34484688}, issn = {2046-1402}, support = {U24 CA199347/CA/NCI NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Workflow ; }, abstract = {The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.}, }
@article {pmid34454634, year = {2021}, author = {Gupta, CL and Blum, SE and Kattusamy, K and Daniel, T and Druyan, S and Shapira, R and Krifucks, O and Zhu, YG and Zhou, XY and Su, JQ and Cytryn, E}, title = {Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {178}, pmid = {34454634}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Cloaca ; Drug Resistance, Bacterial/genetics ; Escherichia coli ; Humans ; Longitudinal Studies ; *Microbiota ; Staphylococcus aureus ; }, abstract = {BACKGROUND: Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).<br><br>RESULTS: Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.<br><br>CONCLUSIONS: Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.}, }
@article {pmid34389047, year = {2021}, author = {Xiong, C and Singh, BK and He, JZ and Han, YL and Li, PP and Wan, LH and Meng, GZ and Liu, SY and Wang, JT and Wu, CF and Ge, AH and Zhang, LM}, title = {Plant developmental stage drives the differentiation in ecological role of the maize microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {171}, pmid = {34389047}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Fungi/genetics ; *Microbiota/genetics ; Plant Roots ; *Zea mays ; }, abstract = {BACKGROUND: Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.<br><br>RESULTS: Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage.<br><br>CONCLUSIONS: Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.}, }
@article {pmid34362459, year = {2021}, author = {Roth-Schulze, AJ and Penno, MAS and Ngui, KM and Oakey, H and Bandala-Sanchez, E and Smith, AD and Allnutt, TR and Thomson, RL and Vuillermin, PJ and Craig, ME and Rawlinson, WD and Davis, EA and Harris, M and Soldatos, G and Colman, PG and Wentworth, JM and Haynes, A and Barry, SC and Sinnott, RO and Morahan, G and Bediaga, NG and Smyth, GK and Papenfuss, AT and Couper, JJ and Harrison, LC and , }, title = {Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {167}, pmid = {34362459}, issn = {2049-2618}, mesh = {*Diabetes Mellitus, Type 1 ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestines ; Metagenome ; Pregnancy ; }, abstract = {BACKGROUND: The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D.<br><br>RESULTS: Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage.<br><br>CONCLUSIONS: Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means. Video abstract.}, }
@article {pmid33535583, year = {2021}, author = {Oliva, M and Mulet-Margalef, N and Ochoa-De-Olza, M and Napoli, S and Mas, J and Laquente, B and Alemany, L and Duell, EJ and Nuciforo, P and Moreno, V}, title = {Tumor-Associated Microbiome: Where Do We Stand?.}, journal = {International journal of molecular sciences}, volume = {22}, number = {3}, pages = {}, pmid = {33535583}, issn = {1422-0067}, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Carcinogenesis ; Cell Transformation, Neoplastic ; Computational Biology ; Cytoplasm/metabolism ; Disease Progression ; Dysbiosis ; Gastrointestinal Microbiome/physiology ; *Gene Expression Regulation, Bacterial ; *Gene Expression Regulation, Neoplastic ; *Gene Expression Regulation, Viral ; Humans ; Immunity ; Metagenome ; Metagenomics ; Mice ; Microbiota/*physiology ; Neoplasms/*microbiology ; RNA, Ribosomal, 16S/metabolism ; *Tumor Microenvironment ; }, abstract = {The study of the human microbiome in oncology is a growing and rapidly evolving field. In the past few years, there has been an exponential increase in the number of studies investigating associations of microbiome and cancer, from oncogenesis and cancer progression to resistance or sensitivity to specific anticancer therapies. The gut microbiome is now known to play a significant role in antitumor immune responses and in predicting the efficacy of immune-checkpoint inhibitors in cancer patients. Beyond the gut, the tumor-associated microbiome-microbe communities located either in the tumor or within its body compartment-seems to interact with the local microenvironment and the tumor immune contexture, ultimately impacting cancer progression and treatment outcome. However, pre-clinical research focusing on causality and mechanistic pathways as well as proof-of-concept studies are still needed to fully understand the potential clinical utility of microbiome in cancer patients. Moreover, there is a need for the standardization of methodology and the implementation of quality control across microbiome studies to allow for a better interpretation and greater comparability of the results reported between them. This review summarizes the accumulating evidence in the field and discusses the current and upcoming challenges of microbiome studies.}, }
@article {pmid33479326, year = {2021}, author = {Casaburi, G and Duar, RM and Brown, H and Mitchell, RD and Kazi, S and Chew, S and Cagney, O and Flannery, RL and Sylvester, KG and Frese, SA and Henrick, BM and Freeman, SL}, title = {Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1472}, pmid = {33479326}, issn = {2045-2322}, support = {S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Bifidobacterium/*genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/metabolism ; Databases, Factual ; Diet ; Drug Resistance, Bacterial/genetics ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Metagenomics/*methods ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; United States ; }, abstract = {The gut microbiome plays an important role in early life, protecting newborns from enteric pathogens, promoting immune system development and providing key functions to the infant host. Currently, there are limited data to broadly assess the status of the US healthy infant gut microbiome. To address this gap, we performed a multi-state metagenomic survey and found high levels of bacteria associated with enteric inflammation (e.g. Escherichia, Klebsiella), antibiotic resistance genes, and signatures of dysbiosis, independent of location, age, and diet. Bifidobacterium were less abundant than generally expected and the species identified, including B. breve, B. longum and B. bifidum, had limited genetic capacity to metabolize human milk oligosaccharides (HMOs), while B. infantis strains with a complete capacity for HMOs utilization were found to be exceptionally rare. Considering microbiome composition and functional capacity, this survey revealed a previously unappreciated dysbiosis that is widespread in the contemporary US infant gut microbiome.}, }
@article {pmid33123966, year = {2021}, author = {Yu, Z and Pei, Y and Zhao, S and Kakade, A and Khan, A and Sharma, M and Zain, H and Feng, P and Ji, J and Zhou, T and Wang, H and Wu, J and Li, X}, title = {Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {8}, pages = {1527-1537}, pmid = {33123966}, issn = {1573-3017}, support = {31870082//National Natural Science Foundation of China/ ; 17ZD2WA017//Gansu Science and Technology Department/ ; lzujbky-2018-it47//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Chromium/toxicity ; Metagenomics ; *Metals, Heavy ; *Microbiota ; }, abstract = {Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.}, }
@article {pmid34495150, year = {2021}, author = {Can-Herrera, LA and Gutierrez-Canul, CD and Dzul-Cervantes, MAA and Pacheco-Salazar, OF and Chi-Cortez, JD and Carbonell, LS}, title = {Identification by molecular techniques of halophilic bacteria producing important enzymes from pristine area in Campeche, Mexico.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {83}, number = {}, pages = {e246038}, doi = {10.1590/1519-6984.246038}, pmid = {34495150}, issn = {1678-4375}, mesh = {*Archaea ; Bacteria/genetics ; Mexico ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Isla Arena is located in the coordinate 20° 70´ N - 90° 45´ W, from Campeche, Mexico. In these estuaries, the ocean mixes with fresh water, and ecosystems are concentrated where petenes and pink flamingos proliferate. Crustaceans and mollusks abound in the sea. Despite its enormous marine wealth, there are no studies carried out on which halophilic microorganisms are present in these waters. In this work, the diversity and structure of the microbial community was investigated through a metagenomics approach and corroborated for sequencing of 16S rRNA genes. It was found that the phylum Fimicutes predominates with more than 50%, in almost the same proportion of the class Bacilli and with almost 41% of relative abundance of the order Bacillales. The sequencing results showed that one of the samples presented a high percentage of similarity (99.75%) using the Nucleotide BLAST program with a peculiar microorganism: Bacillus subtilis. This microorganism is one of the best characterized bacteria among the gram-positive ones. Our results demonstrate that B. subtilis can be an efficient source of proteases, lipases and cellulases, from halophilic microbial communities located in poorly explored areas.}, }
@article {pmid33836596, year = {2021}, author = {Epihov, DZ and Saltonstall, K and Batterman, SA and Hedin, LO and Hall, JS and van Breugel, M and Leake, JR and Beerling, DJ}, title = {Legume-microbiome interactions unlock mineral nutrients in regrowing tropical forests.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {11}, pages = {}, pmid = {33836596}, issn = {1091-6490}, mesh = {Acidobacteria/classification/genetics/metabolism ; Biomass ; Carbon/analysis ; Fabaceae/growth &amp; development/metabolism/*microbiology ; Ferric Compounds/metabolism ; *Forests ; Hydrogen-Ion Concentration ; Microbiota/genetics/*physiology ; Minerals/analysis/*metabolism ; Nitrogen/analysis/metabolism ; Nitrogen Fixation ; Nutrients/analysis/*metabolism ; Panama ; Phosphorus/metabolism ; Silicates/analysis/metabolism ; Soil/chemistry ; Soil Microbiology ; Symbiosis ; Trees/growth &amp; development/metabolism/microbiology ; *Tropical Climate ; }, abstract = {Legume trees form an abundant and functionally important component of tropical forests worldwide with N2-fixing symbioses linked to enhanced growth and recruitment in early secondary succession. However, it remains unclear how N2-fixers meet the high demands for inorganic nutrients imposed by rapid biomass accumulation on nutrient-poor tropical soils. Here, we show that N2-fixing trees in secondary Neotropical forests triggered twofold higher in situ weathering of fresh primary silicates compared to non-N2-fixing trees and induced locally enhanced nutrient cycling by the soil microbiome community. Shotgun metagenomic data from weathered minerals support the role of enhanced nitrogen and carbon cycling in increasing acidity and weathering. Metagenomic and marker gene analyses further revealed increased microbial potential beneath N2-fixers for anaerobic iron reduction, a process regulating the pool of phosphorus bound to iron-bearing soil minerals. We find that the Fe(III)-reducing gene pool in soil is dominated by acidophilic Acidobacteria, including a highly abundant genus of previously undescribed bacteria, Candidatus Acidoferrum, genus novus. The resulting dependence of the Fe-cycling gene pool to pH determines the high iron-reducing potential encoded in the metagenome of the more acidic soils of N2-fixers and their nonfixing neighbors. We infer that by promoting the activities of a specialized local microbiome through changes in soil pH and C:N ratios, N2-fixing trees can influence the wider biogeochemical functioning of tropical forest ecosystems in a manner that enhances their ability to assimilate and store atmospheric carbon.}, }
@article {pmid33688048, year = {2021}, author = {Ewens, SD and Gomberg, AFS and Barnum, TP and Borton, MA and Carlson, HK and Wrighton, KC and Coates, JD}, title = {The diversity and evolution of microbial dissimilatory phosphite oxidation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {11}, pages = {}, doi = {10.1073/pnas.2020024118}, pmid = {33688048}, issn = {1091-6490}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; Energy Metabolism ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/genetics ; Microbiota ; Oxidation-Reduction ; Phosphites/*metabolism ; Phylogeny ; Waste Water/microbiology ; }, abstract = {Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (E o') of -650 mV for the PO4 3-/PO3 3- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.}, }
@article {pmid33688005, year = {2021}, author = {Dmitrijeva, M and Kahlert, CR and Feigelman, R and Kleiner, RL and Nolte, O and Albrich, WC and Baty, F and von Mering, C}, title = {Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33688005}, issn = {2150-7511}, mesh = {Bacteria/*classification/*genetics/metabolism ; Cystic Fibrosis/*microbiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Longitudinal Studies ; Lung/*microbiology ; Metagenomics ; *Microbiota ; Respiratory Tract Infections ; Sputum/microbiology ; }, abstract = {In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals can colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting lineages. Routine clinical protocols, however, provide a limited overview of the colonizer populations. Therefore, a more comprehensive and precise identification and characterization of infecting lineages could assist in making corresponding decisions on treatment. Here, we describe longitudinal tracking for four cystic fibrosis patients who exhibited extreme clinical phenotypes and, thus, were selected from a pilot cohort of 11 patients with repeated sampling for more than a year. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sublineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences. Our study showcases a culture-independent shotgun metagenomics approach for longitudinal tracking of sublineage pathogen dynamics, opening up the possibility of using such methods to assist in monitoring disease progression through providing high-resolution routine characterization of the cystic fibrosis lung microbiome.IMPORTANCE Cystic fibrosis patients frequently suffer from recurring respiratory infections caused by colonizing pathogenic and commensal bacteria. Although modern therapies can sometimes alleviate respiratory symptoms by ameliorating residual function of the protein responsible for the disorder, management of chronic respiratory infections remains an issue. Here, we propose a minimally invasive and culture-independent method to monitor microbial lung content in patients with cystic fibrosis at minimal additional effort on the patient's part. Through repeated sampling and metagenomics sequencing of our selected cystic fibrosis patients, we successfully classify infecting bacterial lineages and deconvolute multiple lineage variants of the same species within a given patient. This study explores the application of modern computational methods for deconvoluting lineages in the cystic fibrosis lung microbiome, an environment known to be inhabited by a heterogeneous pathogen population that complicates management of the disorder.}, }
@article {pmid33531396, year = {2021}, author = {Gushgari-Doyle, S and Oremland, RS and Keren, R and Baesman, SM and Akob, DM and Banfield, JF and Alvarez-Cohen, L}, title = {Acetylene-Fueled Trichloroethene Reductive Dechlorination in a Groundwater Enrichment Culture.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33531396}, issn = {2150-7511}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; R01 ES024255/ES/NIEHS NIH HHS/United States ; }, mesh = {Acetylene/*metabolism ; Actinobacteria/*metabolism ; Biodegradation, Environmental ; Ethane/analogs &amp; derivatives/metabolism ; *Groundwater/analysis ; Halogenation ; Hydrocarbons, Chlorinated/metabolism ; Metagenomics ; Microbiota ; Trichloroethylene/*metabolism ; }, abstract = {In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2 IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.}, }
@article {pmid33049161, year = {2021}, author = {Khan, S and Hauptman, R and Kelly, L}, title = {Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities.}, journal = {Annual review of pharmacology and toxicology}, volume = {61}, number = {}, pages = {159-179}, doi = {10.1146/annurev-pharmtox-031620-031509}, pmid = {33049161}, issn = {1545-4304}, support = {T32 GM007288/GM/NIGMS NIH HHS/United States ; T32 AI070117/AI/NIAID NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Pharmaceutical Preparations ; }, abstract = {In the past decade of microbiome research, we have learned about numerous adverse interactions between the microbiome and medical interventions such as drugs, radiation, and surgery. What if we could alter our microbiomes to prevent these events? In this review, we discuss potential routes to mitigate microbiome adverse events, including applications from the emerging field of microbiome engineering. We highlight cases where the microbiome acts directly on a treatment, such as via differential drug metabolism, and cases where a treatment directly harms the microbiome, such as in radiation therapy. Understanding and preventing microbiome adverse events is a difficult challenge that will require a data-driven approach involving causal statistics, multiomics techniques, and a personalized means of mitigating adverse events. We propose research considerations to encourage productive work in preventing microbiome adverse events, and we highlight the many challenges and opportunities that await.}, }
@article {pmid32764209, year = {2020}, author = {Park, YM and Ha, E and Gu, KN and Shin, GY and Lee, CK and Kim, K and Kim, HJ}, title = {Host Genetic and Gut Microbial Signatures in Familial Inflammatory Bowel Disease.}, journal = {Clinical and translational gastroenterology}, volume = {11}, number = {7}, pages = {e00213}, doi = {10.14309/ctg.0000000000000213}, pmid = {32764209}, issn = {2155-384X}, mesh = {Adult ; Aged ; Colitis, Ulcerative/*genetics/immunology/microbiology ; Crohn Disease/*genetics/immunology/microbiology ; DNA, Bacterial/isolation &amp; purification ; Dysbiosis/*diagnosis/genetics/immunology/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Host Microbial Interactions/genetics/immunology ; Humans ; Male ; Medical History Taking/statistics &amp; numerical data ; Metagenomics ; Middle Aged ; Pedigree ; Polymorphism, Single Nucleotide ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Whole Exome Sequencing ; Young Adult ; }, abstract = {INTRODUCTION: The family history of inflammatory bowel disease (IBD) has been strongly associated with risk of developing IBD. This study aimed to identify the host genetic and gut microbial signatures in familial IBD.<br><br>METHODS: Genetic analyses using genome-wide single nucleotide polymorphism genotyping and whole exome sequencing were performed to calculate weighted genetic risk scores from known IBD-associated common variants and to identify rare deleterious protein-altering variants specific to patients with familial IBD in 8 Korean families that each included more than 2 affected first-degree relatives (FDRs) and their unaffected FDR(s). In parallel, gut microbial community was analyzed by 16S rRNA sequencing of stools from the sample individuals.<br><br>RESULTS: The risk of familial IBD was not well explained by the genetic burden from common IBD-risk variants, suggesting the presence of family-shared genetic and environmental disease-risk factors. We identified 17 genes (AC113554.1, ACE, AKAP17A, AKAP9, ANK2, ASB16, ASIC3, DNPH1, DUS3L, FAM200A, FZD10, LAMA5, NUTM2F, PKN1, PRR26, WDR66, and ZC3H4) that each contained rare, potentially deleterious variants transmitted to the affected FDRs in multiple families. In addition, metagenomic analyses revealed significantly different diversity of gut microbiota and identified a number of differentially abundant taxa in affected FDRs, highlighting 22 novel familial disease-associated taxa with large abundance changes and the previously reported gut dysbiosis including low alpha diversity in IBD and 16 known IBD-specific taxa.<br><br>DISCUSSION: This study identified familial IBD-associated rare deleterious variants and gut microbial dysbiosis in familial IBD.}, }
@article {pmid34415303, year = {2021}, author = {Li, H and Zhao, C and Yang, Y and Zhou, Z and Qi, J and Li, C}, title = {The Influence of Gut Microbiota on the Fecundity of Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae).}, journal = {Journal of insect science (Online)}, volume = {21}, number = {4}, pages = {}, pmid = {34415303}, issn = {1536-2442}, support = {31572010//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/isolation &amp; purification ; *Coleoptera/microbiology/physiology ; DNA, Bacterial ; Diet ; Female ; *Fertility ; Gastrointestinal Microbiome/*genetics ; Lipid Metabolism ; Male ; Metagenomics ; Ovary/growth &amp; development ; Pest Control ; RNA, Ribosomal, 16S ; Testis/growth &amp; development ; }, abstract = {The gut microbiota of insects usually plays an important role in the development and reproduction of their hosts. The fecundity of Henosepilachna vigintioctopunctata (Fabricius) varies greatly when they develop on different host plants. Whether and how the gut microbiota regulates the fecundity of H. vigintioctopunctata was unknown. To address this question, we used 16S rRNA sequencing to analyze the gut microbiomes of H. vigintioctopunctata adults fed on two host plant species (Solanum nigrum and Solanum melongena) and one artificial diet. The development of the ovaries and testes was also examined. Our results revealed that the diversity and abundance of gut microorganisms varied significantly in insects reared on different diets. The gut microbiota of H. vigintioctopunctata raised on the two host plants was similar, with Proteobacteria being the dominant phylum in both groups, whereas Firmicutes was the dominant phylum in the group reared on the artificial diet. The predominant microbiota in the S. nigrum group were Acinetobacter soli and Acinetobacter ursingii (Acinetobacter, Moraxellaceae); Moraxella osloensis (Enhydrobacter, Moraxellaceae); and Empedobacter brevis (Empedobacter, Weeksellaceae). The microbiota in this group are associated with high lipid metabolism. In addition, the beetles' ovaries and testes were more highly developed in the S. nigrum group than in the other two groups. These findings provide valuable information for elucidating the complex roles the gut microbiota play in the fecundity of H. vigintioctopunctata, and may also contribute to developing future novel control strategies involving this economically important pest.}, }
@article {pmid34091278, year = {2021}, author = {Dall'Agnol, B and McCulloch, JA and Mayer, FQ and Souza, U and Webster, A and Antunes, P and Doyle, RL and Reck, J and Ferreira, CAS}, title = {Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {5}, pages = {101746}, doi = {10.1016/j.ttbdis.2021.101746}, pmid = {34091278}, issn = {1877-9603}, mesh = {Amblyomma/*microbiology ; Animals ; Bacteria/genetics/isolation &amp; purification ; Coxiella/genetics/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Francisella/genetics/isolation &amp; purification ; Ixodidae/microbiology ; Metagenomics ; *Microbiota ; Ornithodoros/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rickettsia/genetics/isolation &amp; purification ; }, abstract = {Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.}, }
@article {pmid33577875, year = {2021}, author = {Fujimoto, K and Kimura, Y and Allegretti, JR and Yamamoto, M and Zhang, YZ and Katayama, K and Tremmel, G and Kawaguchi, Y and Shimohigoshi, M and Hayashi, T and Uematsu, M and Yamaguchi, K and Furukawa, Y and Akiyama, Y and Yamaguchi, R and Crowe, SE and Ernst, PB and Miyano, S and Kiyono, H and Imoto, S and Uematsu, S}, title = {Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation.}, journal = {Gastroenterology}, volume = {160}, number = {6}, pages = {2089-2102.e12}, doi = {10.1053/j.gastro.2021.02.013}, pmid = {33577875}, issn = {1528-0012}, mesh = {Adult ; Aged ; Bacteriophages ; Clostridioides difficile ; Enterocolitis, Pseudomembranous/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/*microbiology/virology ; Humans ; Male ; Metagenomics ; Microviridae ; Middle Aged ; Proteobacteria ; *Virome/genetics ; }, abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI). However, the overall mechanisms underlying FMT success await comprehensive elucidation, and the safety of FMT has recently become a serious concern because of the occurrence of drug-resistant bacteremia transmitted by FMT. We investigated whether functional restoration of the bacteriomes and viromes by FMT could be an indicator of successful FMT.<br><br>METHODS: The human intestinal bacteriomes and viromes from 9 patients with rCDI who had undergone successful FMT and their donors were analyzed. Prophage-based and CRISPR spacer-based host bacteria-phage associations in samples from recipients before and after FMT and in donor samples were examined. The gene functions of intestinal microorganisms affected by FMT were evaluated.<br><br>RESULTS: Metagenomic sequencing of both the viromes and bacteriomes revealed that FMT does change the characteristics of intestinal bacteriomes and viromes in recipients after FMT compared with those before FMT. In particular, many Proteobacteria, the fecal abundance of which was high before FMT, were eliminated, and the proportion of Microviridae increased in recipients. Most temperate phages also behaved in parallel with the host bacteria that were altered by FMT. Furthermore, the identification of bacterial and viral gene functions before and after FMT revealed that some distinctive pathways, including fluorobenzoate degradation and secondary bile acid biosynthesis, were significantly represented.<br><br>CONCLUSIONS: The coordinated action of phages and their host bacteria restored the recipients' intestinal flora. These findings show that the restoration of intestinal microflora functions reflects the success of FMT.}, }
@article {pmid33486428, year = {2021}, author = {Kumar, M and Kumar, A and Sahu, KP and Patel, A and Reddy, B and Sheoran, N and Krishnappa, C and Rajashekara, H and Bhagat, S and Rathour, R}, title = {Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones.}, journal = {Microbiological research}, volume = {246}, number = {}, pages = {126704}, doi = {10.1016/j.micres.2021.126704}, pmid = {33486428}, issn = {1618-0623}, mesh = {Biodiversity ; Endophytes/*classification/genetics ; Genome, Bacterial ; Genotype ; Geography ; India ; *Metagenomics ; *Microbiota ; Oryza/*microbiology ; Plant Leaves/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated influence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Acinetobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.}, }
@article {pmid33476671, year = {2021}, author = {Brand, EC and Klaassen, MAY and Gacesa, R and Vich Vila, A and Ghosh, H and de Zoete, MR and Boomsma, DI and Hoentjen, F and Horjus Talabur Horje, CS and van de Meeberg, PC and Willemsen, G and Fu, J and Wijmenga, C and van Wijk, F and Zhernakova, A and Oldenburg, B and Weersma, RK and , }, title = {Healthy Cotwins Share Gut Microbiome Signatures With Their Inflammatory Bowel Disease Twins and Unrelated Patients.}, journal = {Gastroenterology}, volume = {160}, number = {6}, pages = {1970-1985}, doi = {10.1053/j.gastro.2021.01.030}, pmid = {33476671}, issn = {1528-0012}, mesh = {Adult ; Antigens, Bacterial/biosynthesis ; Case-Control Studies ; Cross-Sectional Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Inflammatory Breast Neoplasms/*epidemiology/*microbiology ; Male ; Metagenomics ; Middle Aged ; Netherlands/epidemiology ; Phenotype ; Risk Factors ; Siderophores/biosynthesis ; Twins, Dizygotic ; Twins, Monozygotic ; Young Adult ; }, abstract = {BACKGROUND &amp; AIMS: It is currently unclear whether reported changes in the gut microbiome are cause or consequence of inflammatory bowel disease (IBD). Therefore, we studied the gut microbiome of IBD-discordant and -concordant twin pairs, which offers the unique opportunity to assess individuals at increased risk of developing IBD, namely healthy cotwins from IBD-discordant twin pairs.<br><br>METHODS: Fecal samples were obtained from 99 twins (belonging to 51 twin pairs), 495 healthy age-, sex-, and body mass index-matched controls, and 99 unrelated patients with IBD. Whole-genome metagenomic shotgun sequencing was performed. Taxonomic and functional (pathways) composition was compared among healthy cotwins, IBD-twins, unrelated patients with IBD, and healthy controls with multivariable (ie, adjusted for potential confounding) generalized linear models.<br><br>RESULTS: No significant differences were observed in the relative abundance of species and pathways between healthy cotwins and their IBD-twins (false discovery rate <0.10). Compared with healthy controls, 13, 19, and 18 species, and 78, 105, and 153 pathways were found to be differentially abundant in healthy cotwins, IBD-twins, and unrelated patients with IBD, respectively (false discovery rate <0.10). Of these, 8 (42.1%) of 19 and 1 (5.6%) of 18 species, and 37 (35.2%) of 105 and 30 (19.6%) of 153 pathways overlapped between healthy cotwins and IBD-twins, and healthy cotwins and unrelated patients with IBD, respectively. Many of the shared species and pathways have previously been associated with IBD. The shared pathways include potentially inflammation-related pathways, for example, an increase in propionate degradation and L-arginine degradation pathways.<br><br>CONCLUSIONS: The gut microbiome of healthy cotwins from IBD-discordant twin pairs displays IBD-like signatures. These IBD-like microbiome signatures might precede the onset of IBD. However, longitudinal follow-up studies are needed to infer a causal relationship.}, }
@article {pmid33466274, year = {2021}, author = {Omori, K and Miyakawa, H and Watanabe, A and Nakayama, Y and Lyu, Y and Ichikawa, N and Sasaki, H and Shibata, S}, title = {The Combined Effects of Magnesium Oxide and Inulin on Intestinal Microbiota and Cecal Short-Chain Fatty Acids.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, pmid = {33466274}, issn = {2072-6643}, mesh = {Animals ; Cecum ; Diet, High-Fat ; Fatty Acids, Volatile/*metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*drug effects ; Hydrogen-Ion Concentration ; Inulin/*pharmacology ; Lipid Metabolism/*drug effects ; Magnesium Oxide/*pharmacology ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {Constipation is a common condition that occurs in many people worldwide. While magnesium oxide (MgO) is often used as the first-line drug for chronic constipation in Japan, dietary fiber intake is also recommended. Dietary fiber is fermented by microbiota to produce short-chain fatty acids (SCFAs). SCFAs are involved in regulating systemic physiological functions and circadian rhythm. We examined the effect of combining MgO and the water-soluble dietary fiber, inulin, on cecal SCFA concentration and microbiota in mice. We also examined the MgO administration timing effect on cecal SCFAs. The cecal SCFA concentrations were measured by gas chromatography, and the microbiota was determined using next-generation sequencing. Inulin intake decreased cecal pH and increased cecal SCFA concentrations while combining MgO increased the cecal pH lowered by inulin and decreased the cecal SCFA concentrations elevated by inulin. When inulin and MgO were combined, significant changes in the microbiota composition were observed compared with inulin alone. The MgO effect on the cecal acetic acid concentration was less when administered at ZT12 than at ZT0. In conclusion, this study suggests that MgO affects cecal SCFA and microbiota during inulin feeding, and the effect on acetic acid concentration is time-dependent.}, }
@article {pmid33436440, year = {2021}, author = {Griesenauer, B and González-Beiras, C and Fortney, KR and Lin, H and Gao, X and Godornes, C and Nelson, DE and Katz, BP and Lukehart, SA and Mitjà, O and Dong, Q and Spinola, SM}, title = {Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33436440}, issn = {2150-7511}, support = {R01 AI134727/AI/NIAID NIH HHS/United States ; T32 AI007637/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Azithromycin/therapeutic use ; Child ; Clostridiales ; Haemophilus ducreyi ; Humans ; Metagenomics ; Microbiota ; Papua New Guinea/epidemiology ; Polymerase Chain Reaction ; Prospective Studies ; RNA, Ribosomal, 16S ; Skin Ulcer/*complications/drug therapy/epidemiology/*microbiology ; Streptococcus pyogenes/genetics/*isolation &amp; purification ; Treponema ; Ulcer ; Yaws/*complications/drug therapy/epidemiology/*microbiology ; }, abstract = {Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced but failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies of IU, we obtained swabs of CU lesions (n = 279) and of the skin of asymptomatic controls (AC; n = 233) from the Lihir Island cohort and characterized their microbiomes using a metagenomics approach. CU bacterial communities were less diverse than those of the AC. Using real-time multiplex PCR with pathogen-specific primers, we separated CU specimens into HD-positive (HD+), TP+, HD+TP+, and IU groups. Each CU subgroup formed a distinct bacterial community, defined by the species detected and/or the relative abundances of species within each group. Streptococcus pyogenes was the most abundant organism in IU (22.65%) and was enriched in IU compared to other ulcer groups. Follow-up samples (n = 31) were obtained from nonhealed ulcers; the average relative abundance of S. pyogenes was 30.11% in not improved ulcers and 0.88% in improved ulcers, suggesting that S. pyogenes in the not improved ulcers may be azithromycin resistant. Catonella morbi was enriched in IU that lacked S. pyogenes As some S. pyogenes and TP strains are macrolide resistant, penicillin may be the drug of choice for CU azithromycin treatment failures. Our study will aid in the design of diagnostic tests and selective therapies for CU.IMPORTANCE Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown. Given the failure of mass drug administration of azithromycin to eradicate CU, the World Health Organization recently proposed an integrated disease management strategy to control CU. Success of this strategy requires determining the unknown cause(s) of CU. By using 16S rRNA gene sequencing of swabs obtained from CU and the skin of asymptomatic children, we identified another possible cause of skin ulcers, Streptococcus pyogenes Although S. pyogenes is known to cause impetigo and cellulitis, this is the first report implicating the organism as a causal agent of CU. Inclusion of S. pyogenes into the integrated disease management plan will improve diagnostic testing and treatment of this painful and debilitating disease of children and strengthen elimination efforts.}, }
@article {pmid33432015, year = {2021}, author = {Debesa-Tur, G and Pérez-Brocal, V and Ruiz-Ruiz, S and Castillejo, A and Latorre, A and Soto, JL and Moya, A}, title = {Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {391}, pmid = {33432015}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; Case-Control Studies ; Cohort Studies ; Colorectal Neoplasms/*microbiology/pathology ; Female ; Formaldehyde/chemistry ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestinal Mucosa/*microbiology/pathology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Paraffin Embedding ; Tissue Fixation/methods ; }, abstract = {An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.}, }
@article {pmid33310084, year = {2021}, author = {Galipeau, HJ and Caminero, A and Turpin, W and Bermudez-Brito, M and Santiago, A and Libertucci, J and Constante, M and Raygoza Garay, JA and Rueda, G and Armstrong, S and Clarizio, A and Smith, MI and Surette, MG and Bercik, P and ,  and Croitoru, K and Verdu, EF}, title = {Novel Fecal Biomarkers That Precede Clinical Diagnosis of Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {160}, number = {5}, pages = {1532-1545}, doi = {10.1053/j.gastro.2020.12.004}, pmid = {33310084}, issn = {1528-0012}, support = {1715-000-001//CIHR/Canada ; 143253//CIHR/Canada ; }, mesh = {Adolescent ; Adult ; Animals ; Bacteria/drug effects/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Biomarkers/metabolism ; Case-Control Studies ; Child ; Colitis, Ulcerative/diagnosis/drug therapy/*microbiology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Germ-Free Life ; Humans ; Male ; Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Peptide Hydrolases/genetics/*metabolism ; Predictive Value of Tests ; Prospective Studies ; Protease Inhibitors/therapeutic use ; Proteolysis ; Reproducibility of Results ; Ribotyping ; Young Adult ; }, abstract = {BACKGROUND &amp; AIMS: Altered gut microbiota composition and function have been associated with inflammatory bowel diseases, including ulcerative colitis (UC), but the causality and mechanisms remain unknown.<br><br>METHODS: We applied 16S ribosomal RNA gene sequencing, shotgun metagenomic sequencing, in vitro functional assays, and gnotobiotic colonizations to define the microbial composition and function in fecal samples obtained from a cohort of healthy individuals at risk for inflammatory bowel diseases (pre-UC) who later developed UC (post-UC) and matched healthy control individuals (HCs).<br><br>RESULTS: Microbiota composition of post-UC samples was different from HC and pre-UC samples; however, functional analysis showed increased fecal proteolytic and elastase activity before UC onset. Metagenomics identified more than 22,000 gene families that were significantly different between HC, pre-UC, and post-UC samples. Of these, 237 related to proteases and peptidases, suggesting a bacterial component to the pre-UC proteolytic signature. Elastase activity inversely correlated with the relative abundance of Adlercreutzia and other potentially beneficial taxa and directly correlated with known proteolytic taxa, such as Bacteroides vulgatus. High elastase activity was confirmed in Bacteroides isolates from fecal samples. The bacterial contribution and functional significance of the proteolytic signature were investigated in germ-free adult mice and in dams colonized with HC, pre-UC, or post-UC microbiota. Mice colonized with or born from pre-UC-colonized dams developed higher fecal proteolytic activity and an inflammatory immune tone compared with HC-colonized mice.<br><br>CONCLUSIONS: We have identified increased fecal proteolytic activity that precedes the clinical diagnosis of UC and associates with gut microbiota changes. This proteolytic signature may constitute a noninvasive biomarker of inflammation to monitor at-risk populations that can be targeted therapeutically with antiproteases.}, }
@article {pmid33208514, year = {2020}, author = {Hugerth, LW and Pereira, M and Zha, Y and Seifert, M and Kaldhusdal, V and Boulund, F and Krog, MC and Bashir, Z and Hamsten, M and Fransson, E and Svarre-Nielsen, H and Schuppe-Koistinen, I and Engstrand, L}, title = {Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33208514}, issn = {2379-5042}, mesh = {Computational Biology ; Computer Simulation ; Databases, Genetic ; Female ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.}, }
@article {pmid33203758, year = {2020}, author = {Patin, NV and Peña-Gonzalez, A and Hatt, JK and Moe, C and Kirby, A and Konstantinidis, KT}, title = {The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33203758}, issn = {2150-7511}, support = {R01 AI137679/AI/NIAID NIH HHS/United States ; }, mesh = {Asymptomatic Diseases ; Bacteroidetes/genetics/*growth &amp; development ; Caliciviridae Infections/immunology/*prevention &amp; control/virology ; Disease Susceptibility ; Firmicutes/genetics/*growth &amp; development ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Norovirus/*immunology ; Proteobacteria/genetics/*growth &amp; development ; }, abstract = {Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.}, }
@article {pmid33036549, year = {2020}, author = {Gong, G and Zhou, S and Luo, R and Gesang, Z and Suolang, S}, title = {Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {302}, pmid = {33036549}, issn = {1471-2180}, support = {CARS-37//the National Beef Cattle Industrial Technology System project/ ; }, mesh = {Animals ; Bacteroidaceae/enzymology/genetics/isolation &amp; purification ; Bacteroidetes/enzymology/genetics/isolation &amp; purification ; Carbohydrate Metabolism ; Cattle ; Clostridiaceae/enzymology/genetics/isolation &amp; purification ; Esterases/classification/*genetics/isolation &amp; purification/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gene Expression ; Genetic Variation ; Glycoside Hydrolases/classification/*genetics/isolation &amp; purification/metabolism ; High-Throughput Nucleotide Sequencing ; Lignin/metabolism ; Metagenome ; *Metagenomics/methods ; Microbial Consortia/*genetics ; Polysaccharide-Lyases/classification/*genetics/isolation &amp; purification/metabolism ; Prevotella/enzymology/genetics/isolation &amp; purification ; Rumen/enzymology/*microbiology ; Ruminococcus/enzymology/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem.<br><br>RESULTS: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability.<br><br>CONCLUSIONS: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.}, }
@article {pmid32839200, year = {2021}, author = {Mokkala, K and Paulin, N and Houttu, N and Koivuniemi, E and Pellonperä, O and Khan, S and Pietilä, S and Tertti, K and Elo, LL and Laitinen, K}, title = {Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial.}, journal = {Gut}, volume = {70}, number = {2}, pages = {309-318}, doi = {10.1136/gutjnl-2020-321643}, pmid = {32839200}, issn = {1468-3288}, mesh = {Adult ; Diabetes, Gestational/*diet therapy/etiology/microbiology ; Double-Blind Method ; Female ; Fish Oils/therapeutic use ; Gastrointestinal Microbiome/*genetics ; Glucose Tolerance Test ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Obesity, Maternal/complications/*diet therapy/microbiology ; Pregnancy ; Probiotics/therapeutic use ; }, abstract = {OBJECTIVE: Gut microbiota and diet are known to contribute to human metabolism. We investigated whether the metagenomic gut microbiota composition and function changes over pregnancy are related to gestational diabetes mellitus (GDM) and can be modified by dietary supplements, fish oil and/or probiotics.<br><br>DESIGN: The gut microbiota of 270 overweight/obese women participating in a mother-infant clinical study were analysed with metagenomics approach in early (mean gestational weeks 13.9) and late (gestational weeks 35.2) pregnancy. GDM was diagnosed with a 2 hour 75 g oral glucose tolerance test.<br><br>RESULTS: Unlike women with GDM, women without GDM manifested changes in relative abundance of bacterial species over the pregnancy, particularly those receiving the fish oil + probiotics combination. The specific bacterial species or function did not predict the onset of GDM nor did it differ according to GDM status, except for the higher abundance of Ruminococcus obeum in late pregnancy in the combination group in women with GDM compared with women without GDM. In the combination group, weak decreases over the pregnancy were observed in basic bacterial housekeeping functions.<br><br>CONCLUSIONS: The specific gut microbiota species do not contribute to GDM in overweight/obese women. Nevertheless, the GDM status may disturb maternal gut microbiota flexibility and thus limit the capacity of women with GDM to respond to diet, as evidenced by alterations in gut microbiota observed only in women without GDM. These findings may be important when considering the metabolic complications during pregnancy, but further studies with larger populations are called for to verify the findings.}, }
@article {pmid32651235, year = {2021}, author = {Hu, S and Vich Vila, A and Gacesa, R and Collij, V and Stevens, C and Fu, JM and Wong, I and Talkowski, ME and Rivas, MA and Imhann, F and Bolte, L and van Dullemen, H and Dijkstra, G and Visschedijk, MC and Festen, EA and Xavier, RJ and Fu, J and Daly, MJ and Wijmenga, C and Zhernakova, A and Kurilshikov, A and Weersma, RK}, title = {Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.}, journal = {Gut}, volume = {70}, number = {2}, pages = {285-296}, pmid = {32651235}, issn = {1468-3288}, support = {R01 HG010140/HG/NHGRI NIH HHS/United States ; R01 MH115957/MH/NIMH NIH HHS/United States ; R56 MH115957/MH/NIMH NIH HHS/United States ; U01 HG009080/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptor Proteins, Signal Transducing/genetics ; Adult ; Case-Control Studies ; DNA Copy Number Variations/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Frequency/genetics ; Genetic Predisposition to Disease/*genetics ; Humans ; Inflammatory Bowel Diseases/*etiology/genetics/microbiology ; Male ; Membrane Proteins/genetics ; Metagenomics ; Middle Aged ; Quantitative Trait Loci/genetics ; Receptors, Interleukin-17/genetics ; Transcription Factors/genetics ; Vesicular Transport Proteins/genetics ; *Whole Exome Sequencing ; }, abstract = {OBJECTIVE: Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD.<br><br>DESIGN: To evaluate the impact of host genetics on the gut microbiota of patients with IBD, we combined whole exome sequencing of the host genome and whole genome shotgun sequencing of 1464 faecal samples from 525 patients with IBD and 939 population-based controls. We followed a four-step analysis: (1) exome-wide microbial quantitative trait loci (mbQTL) analyses, (2) a targeted approach focusing on IBD-associated genomic regions and protein truncating variants (PTVs, minor allele frequency (MAF) >5%), (3) gene-based burden tests on PTVs with MAF <5% and exome copy number variations (CNVs) with site frequency <1%, (4) joint analysis of both cohorts to identify the interactions between disease and host genetics.<br><br>RESULTS: We identified 12 mbQTLs, including variants in the IBD-associated genes IL17REL, MYRF, SEC16A and WDR78. For example, the decrease of the pathway acetyl-coenzyme A biosynthesis, which is involved in short chain fatty acids production, was associated with variants in the gene MYRF (false discovery rate <0.05). Changes in functional pathways involved in the metabolic potential were also observed in participants carrying rare PTVs or CNVs in CYP2D6, GPR151 and CD160 genes. These genes are known for their function in the immune system. Moreover, interaction analyses confirmed previously known IBD disease-specific mbQTLs in TNFSF15.<br><br>CONCLUSION: This study highlights that both common and rare genetic variants affecting the immune system are key factors in shaping the gut microbiota in the context of IBD and pinpoints towards potential mechanisms for disease treatment.}, }
@article {pmid34458157, year = {2021}, author = {Chen, J and Li, H and Hird, SM and Chen, MH and Xu, W and Maas, K and Cong, X}, title = {Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {671074}, pmid = {34458157}, issn = {2235-2988}, support = {K23 NR014674/NR/NINR NIH HHS/United States ; R01 NR016928/NR/NINR NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Longitudinal Studies ; Male ; Phylogeny ; Sex Characteristics ; }, abstract = {Infant gut microbiota plays a vital role in immune response, mediates neurobehavioral development and health maintenance. Studies of twins' gut microbiota found that gut microbiota composition and diversity tend to be mature and stable with increasing postnatal age (PNA). Preterm infant gut microbiome shifts dramatically when they were staying in the neonatal intensive care unit (NICU). Compositions and shifting characteristics of gut microbiota among neonatal preterm twins and triplets during their early life are still unknown, which impedes a better understanding of the mechanism underpinning neurobehavioral development and precise intervention/health of preterm neonates. This longitudinal cohort study used a twins/triplets design to investigate the interaction of genetic (e.g., male vs. female) and environmental factors influencing the development of the gut microbiome in early life. We included 39 preterm infants, 12 were Female twins/triplets (Female T/T) including 3 twins pairs and 2 triplets, 12 were male twins (Male T) including 6 twins pairs, and 15 were mixed-sex twins/triplets (Mix T/T) including 6 twins pairs and 1 triplet (8 females and 7 males) during the first four weeks of NICU stay. Weekly gut microbiota patterns between females and males were compared by linear discriminant analysis (LDA) effect size (LEfSe). Metagenomics function of gut microbiota was predicted by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Weekly function (KEGG pathways) differences between females and males were detected by using Statistical Analysis of Metagenomic Profiles (STAMP). Results found that female pairs and male pairs were significantly different in gut microbiome diversity, compositions, and predicted metabolic profiles, importantly, females and males were also significantly dissimilar within their co-twin/triplet pairs of the mixed-sex group, infants of co-twins/triplets shared more similar features than un-related infants from different twins' pair. Future research developing personalized interventions for vulnerable high-risk infants should consider sex, and the interaction of sex and environmental factors.}, }
@article {pmid33746186, year = {2021}, author = {Zhang, YZ and Jiang, DY and Zhang, C and Yang, K and Wang, HF and Xia, XW and Ding, WJ}, title = {Pathological Impact on the Phyllosphere Microbiota of Artemisia argyi by Haze.}, journal = {Journal of microbiology and biotechnology}, volume = {31}, number = {4}, pages = {510-519}, doi = {10.4014/jmb.2009.09024}, pmid = {33746186}, issn = {1738-8872}, mesh = {Air Pollution/*adverse effects ; Artemisia/*microbiology ; Bacteria/*classification/drug effects ; China ; Fungi/*classification/drug effects ; Metagenome ; *Microbiota ; Plant Leaves/microbiology ; Secondary Metabolism ; }, abstract = {The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. Artemisia argyi, a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of Nocardia, Paracoccus, Marmoricola and Knoelia from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in A. argyi were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.}, }
@article {pmid33526565, year = {2021}, author = {Santus, W and Devlin, JR and Behnsen, J}, title = {Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease.}, journal = {Infection and immunity}, volume = {89}, number = {4}, pages = {}, pmid = {33526565}, issn = {1098-5522}, support = {R01 AI143641/AI/NIAID NIH HHS/United States ; R01 DK098170/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Bacteria ; *Disease Susceptibility ; *Fungi ; *Homeostasis ; *Host Microbial Interactions/immunology ; Humans ; Immune System/immunology/metabolism ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; Microbiological Techniques ; Microbiota ; *Mycobiome ; Organ Specificity ; }, abstract = {The term "microbiota" invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. However, research from this past decade has started to complete the picture by focusing on important but largely neglected constituents of the microbiota: fungi, viruses, and archaea. The community of commensal fungi, also called the mycobiota, interacts with commensal bacteria and the host. It is thus not surprising that changes in the mycobiota have significant impact on host health and are associated with pathological conditions such as inflammatory bowel disease (IBD). In this review we will give an overview of why the mycobiota is an important research area and different mycobiota research tools. We will specifically focus on distinguishing transient and actively colonizing fungi of the oral and gut mycobiota and their roles in health and disease. In addition to correlative and observational studies, we will discuss mechanistic studies on specific cross-kingdom interactions of fungi, bacteria, and the host.}, }
@article {pmid33089329, year = {2020}, author = {Tan, JY and Wang, S and Dick, GJ and Young, VB and Sherman, DH and Burns, MA and Lin, XN}, title = {Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {12}, number = {11}, pages = {263-274}, pmid = {33089329}, issn = {1757-9708}, support = {R21 HG005077/HG/NHGRI NIH HHS/United States ; T32 GM008353/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bioreactors ; Coculture Techniques ; Gastrointestinal Microbiome ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbiological Techniques ; *Microbiota ; Microfluidics ; Multigene Family ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {While the 'unculturable' majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial 'dark matter' with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.}, }
@article {pmid32610345, year = {2021}, author = {Levade, I and Saber, MM and Midani, FS and Chowdhury, F and Khan, AI and Begum, YA and Ryan, ET and David, LA and Calderwood, SB and Harris, JB and LaRocque, RC and Qadri, F and Shapiro, BJ and Weil, AA}, title = {Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {2}, pages = {342-351}, doi = {10.1093/infdis/jiaa358}, pmid = {32610345}, issn = {1537-6613}, support = {K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI137164/AI/NIAID NIH HHS/United States ; R37 AI106878/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; R01 AI103055/AI/NIAID NIH HHS/United States ; U01 AI058935/AI/NIAID NIH HHS/United States ; T32A1070611976/AI/NIAID NIH HHS/United States ; }, mesh = {Biomarkers ; Cholera/*diagnosis/*microbiology ; Disease Susceptibility ; Gastrointestinal Microbiome ; Metagenome ; *Metagenomics/methods ; Phylogeny ; Prognosis ; ROC Curve ; Severity of Illness Index ; Vibrio cholerae/*physiology ; }, abstract = {BACKGROUND: Susceptibility to Vibrio cholerae infection is affected by blood group, age, and preexisting immunity, but these factors only partially explain who becomes infected. A recent study used 16S ribosomal RNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution.<br><br>METHODS: To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera.<br><br>RESULTS: Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism were also correlated with protection.<br><br>CONCLUSION: Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.}, }
@article {pmid32602257, year = {2021}, author = {Delbeke, H and Younas, S and Casteels, I and Joossens, M}, title = {Current knowledge on the human eye microbiome: a systematic review of available amplicon and metagenomic sequencing data.}, journal = {Acta ophthalmologica}, volume = {99}, number = {1}, pages = {16-25}, doi = {10.1111/aos.14508}, pmid = {32602257}, issn = {1755-3768}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*genetics ; Eye Infections, Bacterial/*genetics/microbiology ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Insights in the ocular surface microbiome are still at an early stage and many more questions remain unanswered compared with other human-associated microbial communities. The current knowledge on the human microbiome changed our viewpoint on bacteria and human health and significantly enhanced our understanding of human pathophysiology. Also in ocular medicine, microbiome research might impact treatment. Here, we summarize the current knowledge on ocular microbiome research with a particular focus on potential confounding factors and their effects on microbiome composition. Moreover, we present the ocular surface core microbiome based on current available data and defined it as genera present in almost half of the published control cohorts with a relative abundance of at least 1%.}, }
@article {pmid33436010, year = {2021}, author = {Liu, J and Liu, C and Yue, J}, title = {Radiotherapy and the gut microbiome: facts and fiction.}, journal = {Radiation oncology (London, England)}, volume = {16}, number = {1}, pages = {9}, pmid = {33436010}, issn = {1748-717X}, support = {81871895//National Natural Science Foundation of China/ ; 2019RC003//Young Taishan Scholars and Academic Promotion Program of Shandong First Medical University/ ; }, mesh = {Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*radiation effects ; Humans ; Neoplasms/*radiotherapy ; Prebiotics ; Probiotics/pharmacology ; Radiation Tolerance ; Radiotherapy/*adverse effects ; }, abstract = {An ever-growing body of evidence has linked the gut microbiome with both the effectiveness and the toxicity of cancer therapies. Radiotherapy is an effective way to treat tumors, although large variations exist among patients in tumor radio-responsiveness and in the incidence and severity of radiotherapy-induced side effects. Relatively little is known about whether and how the microbiome regulates the response to radiotherapy. Gut microbiota may be an important player in modulating "hot" versus "cold" tumor microenvironment, ultimately affecting treatment efficacy. The interaction of the gut microbiome and radiotherapy is a bidirectional function, in that radiotherapy can disrupt the microbiome and those disruptions can influence the effectiveness of the anticancer treatments. Limited data have shown that interactions between the radiation and the microbiome can have positive effects on oncotherapy. On the other hand, exposure to ionizing radiation leads to changes in the gut microbiome that contribute to radiation enteropathy. The gut microbiome can influence radiation-induced gastrointestinal mucositis through two mechanisms including translocation and dysbiosis. We propose that the gut microbiome can be modified to maximize the response to treatment and minimize adverse effects through the use of personalized probiotics, prebiotics, or fecal microbial transplantation. 16S rRNA sequencing is the most commonly used approach to investigate distribution and diversity of gut microbiome between individuals though it only identifies bacteria level other than strain level. The functional gut microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, as well as metabolomics. Multiple '-omic' approaches can be applied simultaneously to the same sample to obtain integrated results. That said, challenges and remaining unknowns in the future that persist at this time include the mechanisms by which the gut microbiome affects radiosensitivity, interactions between the gut microbiome and combination treatments, the role of the gut microbiome with regard to predictive and prognostic biomarkers, the need for multi "-omic" approach for in-depth exploration of functional changes and their effects on host-microbiome interactions, and interactions between gut microbiome, microbial metabolites and immune microenvironment.}, }
@article {pmid32640105, year = {2021}, author = {Van Olden, CC and Van de Laar, AW and Meijnikman, AS and Aydin, O and Van Olst, N and Hoozemans, JB and De Brauw, LM and Bruin, SC and Acherman, YIZ and Verheij, J and Pyykkö, JE and Hagedoorn, M and Sanderman, R and Bosma, NC and Tremaroli, V and Lundqvist, A and Olofsson, LE and Herrema, H and Lappa, D and Hjorth, S and Nielsen, J and Schwartz, T and Groen, AK and Nieuwdorp, M and Bäckhed, F and Gerdes, VEA}, title = {A systems biology approach to understand gut microbiota and host metabolism in morbid obesity: design of the BARIA Longitudinal Cohort Study.}, journal = {Journal of internal medicine}, volume = {289}, number = {3}, pages = {340-354}, pmid = {32640105}, issn = {1365-2796}, mesh = {Adult ; *Bariatric Surgery ; Biomarkers/metabolism ; Fatty Liver/metabolism ; Female ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; Insulin/metabolism ; Longitudinal Studies ; Male ; Middle Aged ; Netherlands ; Obesity, Morbid/*metabolism/*surgery ; Phenotype ; *Research Design ; *Systems Biology ; Triglycerides/metabolism ; }, abstract = {INTRODUCTION: Prevalence of obesity and associated diseases, including type 2 diabetes mellitus, dyslipidaemia and non-alcoholic fatty liver disease (NAFLD), are increasing. Underlying mechanisms, especially in humans, are unclear. Bariatric surgery provides the unique opportunity to obtain biopsies and portal vein blood-samples.<br><br>METHODS: The BARIA Study aims to assess how microbiota and their metabolites affect transcription in key tissues and clinical outcome in obese subjects and how baseline anthropometric and metabolic characteristics determine weight loss and glucose homeostasis after bariatric surgery. We phenotype patients undergoing bariatric surgery (predominantly laparoscopic Roux-en-Y gastric bypass), before weight loss, with biometrics, dietary and psychological questionnaires, mixed meal test (MMT) and collect fecal-samples and intra-operative biopsies from liver, adipose tissues and jejunum. We aim to include 1500 patients. A subset (approximately 25%) will undergo intra-operative portal vein blood-sampling. Fecal-samples are analyzed with shotgun metagenomics and targeted metabolomics, fasted and postprandial plasma-samples are subjected to metabolomics, and RNA is extracted from the tissues for RNAseq-analyses. Data will be integrated using state-of-the-art neuronal networks and metabolic modeling. Patient follow-up will be ten years.<br><br>RESULTS: Preoperative MMT of 170 patients were analysed and clear differences were observed in glucose homeostasis between individuals. Repeated MMT in 10 patients showed satisfactory intra-individual reproducibility, with differences in plasma glucose, insulin and triglycerides within 20% of the mean difference.<br><br>CONCLUSION: The BARIA study can add more understanding in how gut-microbiota affect metabolism, especially with regard to obesity, glucose metabolism and NAFLD. Identification of key factors may provide diagnostic and therapeutic leads to control the obesity-associated disease epidemic.}, }
@article {pmid34472853, year = {2021}, author = {Wu, X and Chauhan, A and Layton, AC and Lau Vetter, MCY and Stackhouse, BT and Williams, DE and Whyte, L and Pfiffner, SM and Onstott, TC and Vishnivetskaya, TA}, title = {Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c00802}, pmid = {34472853}, issn = {1520-5851}, abstract = {Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.}, }
@article {pmid33650794, year = {2021}, author = {Dalcin Martins, P and de Jong, A and Lenstra, WK and van Helmond, NAGM and Slomp, CP and Jetten, MSM and Welte, CU and Rasigraf, O}, title = {Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments.}, journal = {MicrobiologyOpen}, volume = {10}, number = {1}, pages = {e1175}, pmid = {33650794}, issn = {2045-8827}, mesh = {Anaerobiosis/physiology ; Bacteroidetes/growth &amp; development/*metabolism ; Bioreactors/*microbiology ; Finland ; Geologic Sediments/*microbiology ; Iron/*metabolism ; Methane/*metabolism ; Microbiota ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/metabolism ; Sweden ; Verrucomicrobia/growth &amp; development/*metabolism ; }, abstract = {Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome-assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.}, }
@article {pmid33305509, year = {2021}, author = {Alexyuk, M and Bogoyavlenskiy, A and Alexyuk, P and Moldakhanov, Y and Berezin, V and Digel, I}, title = {Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity.}, journal = {MicrobiologyOpen}, volume = {10}, number = {1}, pages = {e1142}, doi = {10.1002/mbo3.1142}, pmid = {33305509}, issn = {2045-8827}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Kazakhstan ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA ; Uzbekistan ; }, abstract = {Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.}, }
@article {pmid29895466, year = {2021}, author = {Castillo-Álvarez, F and Pérez-Matute, P and Oteo, JA and Marzo-Sola, ME}, title = {The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis.}, journal = {Neurologia (Barcelona, Spain)}, volume = {36}, number = {7}, pages = {495-503}, doi = {10.1016/j.nrl.2018.04.006}, pmid = {29895466}, issn = {1578-1968}, mesh = {Animals ; Cross-Sectional Studies ; Feces ; *Gastrointestinal Microbiome ; Humans ; Interferon beta-1b ; *Multiple Sclerosis/drug therapy ; Prevotella ; }, abstract = {INTRODUCTION: The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce.<br><br>METHODS: We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing.<br><br>RESULTS: Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group.<br><br>CONCLUSION: We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship.}, }
@article {pmid34020448, year = {2021}, author = {Koponen, KK and Salosensaari, A and Ruuskanen, MO and Havulinna, AS and Männistö, S and Jousilahti, P and Palmu, J and Salido, R and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Meric, G and Cheng, S and Inouye, M and Jain, M and Niiranen, TJ and Valsta, LM and Knight, R and Salomaa, VV}, title = {Associations of healthy food choices with gut microbiota profiles.}, journal = {The American journal of clinical nutrition}, volume = {114}, number = {2}, pages = {605-616}, pmid = {34020448}, issn = {1938-3207}, support = {R01 ES027595/ES/NIEHS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; R01ES027595/GF/NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification ; *Choice Behavior ; Diet Surveys ; *Diet, Healthy ; Female ; *Food ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; }, abstract = {BACKGROUND: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.<br><br>OBJECTIVES: To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential.<br><br>METHODS: This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.<br><br>RESULTS: Both microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10-5; P = 2.21 × 10-3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10-3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system.<br><br>CONCLUSIONS: Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.}, }
@article {pmid33739998, year = {2021}, author = {Silver, A and Perez, S and Gee, M and Xu, B and Garg, S and Will, K and Gill, A}, title = {Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0241529}, pmid = {33739998}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; Coleoptera/classification/*microbiology ; DNA/chemistry/metabolism ; Diet ; Intestines/microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types-guts, and pygidial gland secretory cells (which produce defensive compounds)-were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.}, }
@article {pmid33428153, year = {2021}, author = {Zhao, W and Ren, Z and Luo, Y and Cheng, J and Wang, J and Wang, Y and Yang, Z and Yao, X and Zhong, Z and Yang, W and Wu, X}, title = {Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer.}, journal = {Genes &amp; genomics}, volume = {43}, number = {1}, pages = {43-53}, pmid = {33428153}, issn = {2092-9293}, mesh = {Animals ; Deer/*microbiology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Metagenome ; Pneumonia/*microbiology/veterinary ; }, abstract = {BACKGROUND: The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD.<br><br>OBJECTIVE: We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia FMD.<br><br>METHODS: The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed.<br><br>RESULTS: There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p = 0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were significantly enriched in the metagenome of the bacterial pneumonia FMD.<br><br>CONCLUSION: Our results demonstrated that the gut microbiome was significantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.}, }
@article {pmid33387519, year = {2021}, author = {Mehtani, R and Roy, A and Singh, V}, title = {Gut Microbial Metagenomics in ACLF: The Causality-Association Conundrum.}, journal = {Gastroenterology}, volume = {160}, number = {6}, pages = {2205}, doi = {10.1053/j.gastro.2020.12.055}, pmid = {33387519}, issn = {1528-0012}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; }, }
@article {pmid32643435, year = {2020}, author = {Ngo, ST and Restuadi, R and McCrae, AF and Van Eijk, RP and Garton, F and Henderson, RD and Wray, NR and McCombe, PA and Steyn, FJ}, title = {Progression and survival of patients with motor neuron disease relative to their fecal microbiota.}, journal = {Amyotrophic lateral sclerosis &amp; frontotemporal degeneration}, volume = {21}, number = {7-8}, pages = {549-562}, doi = {10.1080/21678421.2020.1772825}, pmid = {32643435}, issn = {2167-9223}, mesh = {*Amyotrophic Lateral Sclerosis ; Feces ; Humans ; *Microbiota/genetics ; *Motor Neuron Disease/complications ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbiota studies have been well-investigated for neurodegenerative diseases such as Alzheimer's and Parkinson's disease, however, fewer studies have comprehensively examined the gut microbiome in Motor Neuron Disease (MND), with none examining its impact on disease prognosis. Here, we investigate MND prognosis and the fecal microbiota, using 16S rRNA case-control data from 100 individuals with extensive medical histories and metabolic measurements. We contrast the composition and diversity of fecal microbiome signatures from 49 MND and 51 healthy controls by combining current gold-standard 16S microbiome pipelines. Using stringent quality control thresholds, we conducted qualitative assessment approaches including; direct comparison of taxa, PICRUSt2 predicted metagenomics, Shannon and Chao1-index and Firmicutes/Bacteroidetes ratio. We show that the fecal microbiome of patients with MND is not significantly different from that of healthy controls that were matched by age, sex, and BMI, however there are distinct differences in Beta-diversity in some patients with MND. Weight, BMI, and metabolic and clinical features of disease in patients with MND were not related to the composition of their fecal microbiome, however, we observe a greater risk for earlier death in patients with MND with increased richness and diversity of the microbiome, and in those with greater Firmicutes to Bacteroidetes ratio. This was independent of anthropometric, metabolic, or clinical features of disease, and warrants support for further gut microbiota studies in MND. Given the disease heterogeneity in MND, and complexity of the gut microbiota, large studies are necessary to determine the detailed role of the gut microbiota and MND prognosis.}, }
@article {pmid33387530, year = {2021}, author = {Kummen, M and Thingholm, LB and Rühlemann, MC and Holm, K and Hansen, SH and Moitinho-Silva, L and Liwinski, T and Zenouzi, R and Storm-Larsen, C and Midttun, Ø and McCann, A and Ueland, PM and Høivik, ML and Vesterhus, M and Trøseid, M and Laudes, M and Lieb, W and Karlsen, TH and Bang, C and Schramm, C and Franke, A and Hov, JR}, title = {Altered Gut Microbial Metabolism of Essential Nutrients in Primary Sclerosing Cholangitis.}, journal = {Gastroenterology}, volume = {160}, number = {5}, pages = {1784-1798.e0}, doi = {10.1053/j.gastro.2020.12.058}, pmid = {33387530}, issn = {1528-0012}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/genetics/*metabolism ; Case-Control Studies ; Cholangitis, Sclerosing/blood/diagnosis/*microbiology/surgery ; Cross-Sectional Studies ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Germany ; Humans ; Liver Transplantation ; Male ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; Middle Aged ; Norway ; Phylogeny ; Progression-Free Survival ; Young Adult ; }, abstract = {BACKGROUND &amp; AIMS: To influence host and disease phenotype, compositional microbiome changes, which have been demonstrated in patients with primary sclerosing cholangitis (PSC), must be accompanied by functional changes. We therefore aimed to characterize the genetic potential of the gut microbiome in patients with PSC compared with healthy controls (HCs) and patients with inflammatory bowel disease (IBD).<br><br>METHODS: Fecal DNA from 2 cohorts (1 Norwegian and 1 German), in total comprising 136 patients with PSC (58% with IBD), 158 HCs, and 93 patients with IBD without PSC, were subjected to metagenomic shotgun sequencing, generating 17 billion paired-end sequences, which were processed using HUMAnN2 and MetaPhlAn2, and analyzed using generalized linear models and random effects meta-analyses.<br><br>RESULTS: Patients with PSC had fewer microbial genes compared with HCs (P < .0001). Compared with HCs, patients with PSC showed enrichment and increased prevalence of Clostridium species and a depletion of, for example, Eubacterium spp and Ruminococcus obeum. Patients with PSC showed marked differences in the abundance of genes related to vitamin B6 synthesis and branched-chain amino acid synthesis (Qfdr < .05). Targeted metabolomics of plasma from an independent set of patients with PSC and controls found reduced concentrations of vitamin B6 and branched-chain amino acids in PSC (P < .0001), which strongly associated with reduced liver transplantation-free survival (log-rank P < .001). No taxonomic or functional differences were detected between patients with PSC with and without IBD.<br><br>CONCLUSIONS: The gut microbiome in patients with PSC exhibits large functional differences compared with that in HCs, including microbial metabolism of essential nutrients. Alterations in related circulating metabolites associated with disease course, suggesting that microbial functions may be relevant for the disease process in PSC.}, }
@article {pmid33065016, year = {2020}, author = {De Filippis, F and Pasolli, E and Ercolini, D}, title = {Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {4932-4943.e4}, doi = {10.1016/j.cub.2020.09.063}, pmid = {33065016}, issn = {1879-0445}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Animals ; Child ; Child, Preschool ; Datasets as Topic ; Dysbiosis/*microbiology ; Faecalibacterium/genetics/*isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; Infant ; Life Style ; Macaca ; Metagenome ; Metagenomics ; Middle Aged ; Phylogeny ; *Probiotics ; Young Adult ; }, abstract = {Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.}, }
@article {pmid34160629, year = {2021}, author = {Aguirre-von-Wobeser, E and Alonso-Sánchez, A and Méndez-Bravo, A and Villanueva Espino, LA and Reverchon, F}, title = {Barks from avocado trees of different geographic locations have consistent microbial communities.}, journal = {Archives of microbiology}, volume = {203}, number = {7}, pages = {4593-4607}, pmid = {34160629}, issn = {1432-072X}, support = {CB-2014-01-242956//SEP/CONACyT/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biodiversity ; Fungi/genetics/physiology ; Metagenomics ; *Microbiota/genetics/physiology ; *Persea/microbiology ; *Plant Bark/microbiology ; Soil Microbiology ; }, abstract = {Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air, but little is known about its microbial communities. We used shotgun metagenomic sequencing to analyze the bark microbiomes of avocado trees from two orchards, and compared one of them to rhizospheric soil. It was shown that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi, and archaea, even in trees from two different locations. Bark microbial communities were distinct from rhizospheric soil, although they showed overlap in some taxa. Thus, avocado bark is a well-defined environment, providing niches for specific taxonomic groups, many of which are also found in other aerial plant tissues. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.}, }
@article {pmid33986544, year = {2021}, author = {Sun, Z and Huang, S and Zhang, M and Zhu, Q and Haiminen, N and Carrieri, AP and Vázquez-Baeza, Y and Parida, L and Kim, HC and Knight, R and Liu, YY}, title = {Challenges in benchmarking metagenomic profilers.}, journal = {Nature methods}, volume = {18}, number = {6}, pages = {618-626}, pmid = {33986544}, issn = {1548-7105}, support = {RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; }, mesh = {Benchmarking/*methods ; Computational Biology/methods ; Gene Expression Profiling ; *Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Nevertheless, benchmarking of metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that were analyzed and interpreted and clearly stating the strategy used for metagenomic profiling.}, }
@article {pmid33462508, year = {2021}, author = {Olm, MR and Crits-Christoph, A and Bouma-Gregson, K and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.}, journal = {Nature biotechnology}, volume = {39}, number = {6}, pages = {727-736}, pmid = {33462508}, issn = {1546-1696}, mesh = {*Biodiversity ; Humans ; Infant, Newborn ; *Metagenomics ; *Microbiota ; Polymorphism, Single Nucleotide ; }, abstract = {Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.}, }
@article {pmid33407663, year = {2021}, author = {Zhang, HT and Wang, H and Wu, HS and Zeng, J and Yang, Y}, title = {Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis.}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {11}, pmid = {33407663}, issn = {1743-422X}, mesh = {Adult ; Female ; Genome, Viral/genetics ; Humans ; Metagenomics ; Phylogeny ; Pregnancy ; *Pregnant Women ; Vagina/virology ; Vaginitis/*virology ; *Virome/genetics ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment.<br><br>METHODS: To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis.<br><br>RESULTS: Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups.<br><br>CONCLUSION: Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.}, }
@article {pmid34149685, year = {2021}, author = {Das, Q and Shay, J and Gauthier, M and Yin, X and Hasted, TL and Ross, K and Julien, C and Yacini, H and Kennes, YM and Warriner, K and Marcone, MF and Diarra, MS}, title = {Effects of Vaccination Against Coccidiosis on Gut Microbiota and Immunity in Broiler Fed Bacitracin and Berry Pomace.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {621803}, pmid = {34149685}, issn = {1664-3224}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Bacitracin ; Bacterial Infections/*immunology ; Bird Diseases/*immunology ; Blueberry Plants ; Cecum/*microbiology ; Chickens/*immunology ; Coccidia/*physiology ; Coccidiosis/*immunology ; Eimeria/*physiology ; Gastrointestinal Microbiome/*immunology ; Immunity, Humoral ; Lipid Metabolism ; Protozoan Vaccines/*immunology ; Vaccination ; Vaccinium macrocarpon ; }, abstract = {Feeding practices have been found to influence gut microbiota which play a major role in immunity of poultry. In the present study, changes in cecal microbiota and humoral responses resulting in the 55 ppm bacitracin (BACI), 1% each of cranberry (CP1) and wild blueberry (BP1) pomace alone or in combination (CP+BP) feeding in broiler Cobb 500 vaccinated or not against coccidiosis were investigated. In the non-vaccinated group, no significant treatment effects were observed on performance parameters. Vaccination significantly affected bird's performance parameters particularly during the growing phase from 10 to 20 days of age. In general, the prevalence of coccidiosis and necrotic enteritis (NE) was reduced by vaccination (P < 0.05). BACI-treated birds showed low intestinal lesion scores, and both CP1 and BP1 feed supplementations reduced Eimeria acervulina and Clostridium perfringens incidences similar to BACI. Vaccination induced change in serum enzymes, minerals, and lipid levels in 21-day old birds while, levels of triglyceride (TRIG) and non-esterified fatty acids (NEFA) were higher (P < 0.05) in CP1 treated non-vaccinated group than in the control. The levels of NEFA were lower in BACI- and CP1-fed birds than in the control in non-vaccinated day 28 old birds. The highest levels of all estimated three immunoglobulins (IgY, IgM, and IgA) were found in the vaccinated birds. Metagenomics analysis of the cecal bacterial community in 21-day old birds showed the presence of Firmicutes (90%), Proteobacteria (5%), Actinobacteria (2%), and Bacteroidetes (2%). In the vaccinated group, an effect of BACI was noted on Proteobacteria (P = 0.03). Vaccination and/or dietary treatments influenced the population of Lactobacillaceae, Enterobacteriaceae, Clostridiaceae, and Streptococcaceae which were among the most abundant families. Overall, this study revealed that besides their beneficial effects on performance, alike bacitracin, berry pomaces in poultry feed have profound impacts on the chicken cecal microbiota and blood metabolites that could be influenced by vaccination against coccidiosis.}, }
@article {pmid34039428, year = {2021}, author = {Amar, Y and Lagkouvardos, I and Silva, RL and Ishola, OA and Foesel, BU and Kublik, S and Schöler, A and Niedermeier, S and Bleuel, R and Zink, A and Neuhaus, K and Schloter, M and Biedermann, T and Köberle, M}, title = {Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {123}, pmid = {34039428}, issn = {2049-2618}, mesh = {*Bacteria/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Endodeoxyribonucleases ; Endoribonucleases ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; }, abstract = {BACKGROUND: The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities.<br><br>RESULTS: We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias.<br><br>CONCLUSIONS: The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.}, }
@article {pmid33404934, year = {2021}, author = {Ali, P and Chen, F and Hassan, F and Sosa, A and Khan, S and Badshah, M and Shah, AA}, title = {Bacterial community characterization of Batura Glacier in the Karakoram Range of Pakistan.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {24}, number = {2}, pages = {183-196}, pmid = {33404934}, issn = {1618-1905}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ice Cover/*microbiology ; *Microbiota ; Pakistan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4-35 °C), pH (5-12), and salinity (1-6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.}, }
@article {pmid33378284, year = {2020}, author = {Afolayan, AO and Ayeni, FA}, title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.}, journal = {Journal of infection in developing countries}, volume = {14}, number = {12}, pages = {}, doi = {10.3855/jidc.12975}, pmid = {33378284}, issn = {1972-2680}, mesh = {DNA, Bacterial ; Humans ; Metagenomics ; *Microbiota ; Nigeria ; Proteobacteria/classification/genetics ; Pseudomonas/classification/genetics ; Public Health ; RNA, Ribosomal, 16S ; Rural Population ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.<br><br>METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.<br><br>RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.<br><br>CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.}, }
@article {pmid33813595, year = {2021}, author = {Rai, A and Bhattacharjee, A}, title = {Molecular profiling of microbial community structure and their CAZymes via metagenomics, from Tsomgo lake in the Eastern Himalayas.}, journal = {Archives of microbiology}, volume = {203}, number = {6}, pages = {3135-3146}, pmid = {33813595}, issn = {1432-072X}, mesh = {*Bacteria/classification/enzymology/genetics ; *Enzymes/genetics ; India ; *Lakes/microbiology ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; *Soil Microbiology ; }, abstract = {The present study is the first of its kind which is focused on Tsomgo lake, a high-altitude lake, located in the Eastern Himalayas of Sikkim. To get a major insight into the bacterial diversity, the shotgun sequencing was carried out in Illumina platform. Our results showed that both the samples TLSS1 (soil) and TLSW1 (water), had Proteobacteria as the most abundant taxa. Cluster of Orthologous group (COG) functional category of TLSS1 has 1,46,965 predicted functions. Cluster of Orthologous Group (COG) functional category of TLSW1 has 1,34,773 predicted functions. Kyoto Encyclopedia of Gene and Genomes (KEGG) functional category of TLSS1 has 1,76,825 predicted functions, most of the sequence fall in metabolism followed by Environmental information processing function. (KEGG) functional category of TLSW1 has 1,62,696 predicted functions and it follows the same pattern as TLSS1. Our studies also provide insight into the presence of distribution of different carbohydrate-active enzymes (CAZymes) present in Tsomgo lake. We have found that in case of both the samples TLSW1 and TLSS1, GlycosylTransferases were active followed by GlycosylHydrolase. The result found, represents for the first time very important findings related to the microbial diversity and the abundance of CAZymes in Tsomgo lake one of the pristine high-altitude lakes in Sikkim.}, }
@article {pmid33606979, year = {2021}, author = {Camarillo-Guerrero, LF and Almeida, A and Rangel-Pineros, G and Finn, RD and Lawley, TD}, title = {Massive expansion of human gut bacteriophage diversity.}, journal = {Cell}, volume = {184}, number = {4}, pages = {1098-1109.e9}, pmid = {33606979}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteriophages/*genetics ; *Biodiversity ; Databases, Nucleic Acid ; *Gastrointestinal Microbiome ; Host Specificity ; Humans ; Phylogeography ; }, abstract = {Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.}, }
@article {pmid32835795, year = {2021}, author = {Villmones, HC and Halland, A and Stenstad, T and Ulvestad, E and Weedon-Fekjær, H and Kommedal, Ø}, title = {The cultivable microbiota of the human distal ileum.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {27}, number = {6}, pages = {912.e7-912.e13}, doi = {10.1016/j.cmi.2020.08.021}, pmid = {32835795}, issn = {1469-0691}, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/*isolation &amp; purification ; Bacteriological Techniques ; Female ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Male ; Middle Aged ; }, abstract = {OBJECTIVES: The existing literature on the microbiota of the ileum is inconsistent. To further characterize the microbiota, we analysed samples obtained directly from resected ileums used for urinary diversion after radical cystectomy.<br><br>METHODS: We included 150 patients with bladder cancer operated on from March 2016 to March 2019. Samples obtained by rubbing a swab against the ileal mucosa 25 cm from the ileocecal valve were cultivated at the local laboratory. Microbial colonies were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF).<br><br>RESULTS: The microbial density of the distal ileum was low. Among our samples, 79% (95% confidence interval (CI) 71%, 84%) harboured less than 1.6 × 104 cfu/mL, whereas 36% (95% CI 28%, 44%) harboured less than 1.6 × 103 cfu/mL. The flora was dominated by viridans streptococci, Candida, Actinomyces, Rothia and Lactobacillus species. Colon-related bacteria i.e. strict anaerobic bacteria, Enterobacteriales and enterococci, were recovered from 14% of the samples. Constipation was associated with increased recovery of colon-related bacteria. Antibiotic treatment prior to surgical procedures did not affect culture results. Increased age was significantly associated with more substantial fungal growth and use of proton pump inhibitors seemed to increase both bacterial and fungal growth.<br><br>CONCLUSIONS: The microbiota of the human distal ileum is sparse and differs significantly from the colonic microbiota both quantitatively and by composition. These findings contradict recent metagenomics studies based on samples collected by retrograde colonoscopy and emphasize the crucial importance of adequate sampling techniques.}, }
@article {pmid32530501, year = {2021}, author = {Alferink, LJM and Radjabzadeh, D and Erler, NS and Vojinovic, D and Medina-Gomez, C and Uitterlinden, AG and de Knegt, RJ and Amin, N and Ikram, MA and Janssen, HLA and Kiefte-de Jong, JC and Metselaar, HJ and van Duijn, CM and Kraaij, R and Darwish Murad, S}, title = {Microbiomics, Metabolomics, Predicted Metagenomics, and Hepatic Steatosis in a Population-Based Study of 1,355 Adults.}, journal = {Hepatology (Baltimore, Md.)}, volume = {73}, number = {3}, pages = {968-982}, doi = {10.1002/hep.31417}, pmid = {32530501}, issn = {1527-3350}, mesh = {Cross-Sectional Studies ; Fatty Liver/*etiology/genetics/metabolism/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenome/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Ruminococcus/metabolism ; }, abstract = {BACKGROUND AND AIMS: Previous small studies have appraised the gut microbiome (GM) in steatosis, but large-scale studies are lacking. We studied the association of the GM diversity and composition, plasma metabolites, predicted functional metagenomics, and steatosis.<br><br>APPROACH AND RESULTS: This is a cross-sectional analysis of the prospective population-based Rotterdam Study. We used 16S ribosomal RNA gene sequencing and determined taxonomy using the SILVA reference database. Alpha diversity and beta diversity were calculated using the Shannon diversity index and Bray-Curtis dissimilarities. Differences were tested across steatosis using permutational multivariate analysis of variance. Hepatic steatosis was diagnosed by ultrasonography. We subsequently selected genera using regularized regression. The functional metagenome was predicted based on the GM using Kyoto Encyclopedia of Genes and Genomes pathways. Serum metabolomics were assessed using high-throughput proton nuclear magnetic resonance. All analyses were adjusted for age, sex, body mass index, alcohol, diet, and proton-pump inhibitors. We included 1,355 participants, of whom 472 had steatosis. Alpha diversity was lower in steatosis (P = 1.1∙10-9), and beta diversity varied across steatosis strata (P = 0.001). Lasso selected 37 genera of which three remained significantly associated after adjustment (Coprococcus3: β = -65; Ruminococcus Gauvreauiigroup: β = 62; and Ruminococcus Gnavusgroup: β = 45, Q-value = 0.037). Predicted metagenome analyses revealed that pathways of secondary bile-acid synthesis and biotin metabolism were present, and D-alanine metabolism was absent in steatosis. Metabolic profiles showed positive associations for aromatic and branched chain amino acids and glycoprotein acetyls with steatosis and R. Gnavusgroup, whereas these metabolites were inversely associated with alpha diversity and Coprococcus3.<br><br>CONCLUSIONS: We confirmed, on a large-scale, the lower microbial diversity and association of Coprococcus and Ruminococcus Gnavus with steatosis. We additionally showed that steatosis and alpha diversity share opposite metabolic profiles.}, }
@article {pmid34418978, year = {2021}, author = {Christiansen, H and Heindler, FM and Hellemans, B and Jossart, Q and Pasotti, F and Robert, H and Verheye, M and Danis, B and Kochzius, M and Leliaert, F and Moreau, C and Patel, T and Van de Putte, AP and Vanreusel, A and Volckaert, FAM and Schön, I}, title = {Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {625}, pmid = {34418978}, issn = {1471-2164}, mesh = {Animals ; Genome ; Genomics ; Humans ; *Metagenomics ; *Research Design ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.<br><br>RESULTS: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.<br><br>CONCLUSIONS: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.}, }
@article {pmid33878111, year = {2021}, author = {Wille, M and Geoghegan, JL and Holmes, EC}, title = {How accurately can we assess zoonotic risk?.}, journal = {PLoS biology}, volume = {19}, number = {4}, pages = {e3001135}, pmid = {33878111}, issn = {1545-7885}, mesh = {Animals ; Biodiversity ; Disease Reservoirs/classification/statistics &amp; numerical data ; *Environmental Monitoring/methods/standards ; Host Specificity/genetics ; Humans ; Metagenomics/methods/organization &amp; administration/standards ; Phylogeny ; Risk Assessment ; Risk Factors ; Selection Bias ; *Virus Diseases/epidemiology/etiology/prevention &amp; control/transmission ; Viruses/classification/genetics/isolation &amp; purification/pathogenicity ; Zoonoses/epidemiology/*etiology/*prevention &amp; control/virology ; }, abstract = {Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic "risk assessment." Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human-animal interface may be more productive.}, }
@article {pmid32617960, year = {2021}, author = {Guk, J and Guedj, J and Burdet, C and Andremont, A and de Gunzburg, J and Ducher, A and Mentré, F}, title = {Modeling the Effect of DAV132, a Novel Colon-Targeted Adsorbent, on Fecal Concentrations of Moxifloxacin and Gut Microbiota Diversity in Healthy Volunteers.}, journal = {Clinical pharmacology and therapeutics}, volume = {109}, number = {4}, pages = {1045-1054}, doi = {10.1002/cpt.1977}, pmid = {32617960}, issn = {1532-6535}, mesh = {Adolescent ; Adsorption/physiology ; Adult ; Colon/*drug effects ; Dose-Response Relationship, Drug ; Feces/*chemistry ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Middle Aged ; Models, Biological ; Moxifloxacin/administration &amp; dosage/*pharmacokinetics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {To prevent antibiotic-induced perturbations on gut microbiota, DAV132, a novel colon-targeted adsorbent, which sequesters antibiotic residues in the lower gastrointestinal tract, was developed. We built an integrated pharmacological model of how DAV132 reduces fecal free moxifloxacin and preserves gut microbiota. We used plasma and fecal free moxifloxacin concentrations, and Shannon diversity index from 16S ribosomal RNA gene metagenomics analysis of fecal microbiota, of 143 healthy volunteers assigned randomly to receive moxifloxacin only, or with 10 DAV132 dose regimens, or to a control group. We modeled reduced fecal moxifloxacin concentrations using a transit model for DAV132 kinetics and a Michaelis-Menten model with an effect of the amount of activated charcoal on adsorption efficacy. Changes in moxifloxacin-induced perturbations on gut microbiota diversity were then quantified through a turnover model with the Emax model. With the developed model, the efficiency of pharmacokinetic antagonism and its consequences on gut microbiota diversity were quantified.}, }
@article {pmid32569375, year = {2021}, author = {Gambardella, J and Castellanos, V and Santulli, G}, title = {Standardizing translational microbiome studies and metagenomic analyses.}, journal = {Cardiovascular research}, volume = {117}, number = {3}, pages = {640-642}, pmid = {32569375}, issn = {1755-3245}, support = {R00 DK107895/DK/NIDDK NIH HHS/United States ; R01 DK123259/DK/NIDDK NIH HHS/United States ; R01 HL146691/HL/NHLBI NIH HHS/United States ; R01 DK033823/DK/NIDDK NIH HHS/United States ; }, mesh = {Metagenome ; *Metagenomics ; *Microbiota ; }, }
@article {pmid34381036, year = {2021}, author = {Stražar, M and Temba, GS and Vlamakis, H and Kullaya, VI and Lyamuya, F and Mmbaga, BT and Joosten, LAB and van der Ven, AJAM and Netea, MG and de Mast, Q and Xavier, RJ}, title = {Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4845}, pmid = {34381036}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Arginine/metabolism ; Bacteria/immunology/isolation &amp; purification/metabolism ; Cytokines/*immunology ; Diet ; Female ; Gastrointestinal Microbiome/immunology/*physiology ; Histidine/metabolism ; Humans ; Immunomodulation ; Male ; Metabolic Networks and Pathways ; Metabolome/immunology ; *Rural Population ; Socioeconomic Factors ; Tanzania ; *Urban Population ; Urbanization ; }, abstract = {The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Here, we uncover a gradient of intestinal microbial compositions from rural through urban Tanzanian, towards European samples, manifested both in relative abundance and genomic variation observed in stool metagenomics. The rural population shows increased Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 immunomodulatory microbes, which have a larger impact on circulating metabolites than non-significant microbes. Pathway effects on cytokines, notably TNF-α and IFN-γ, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila.}, }
@article {pmid33990301, year = {2021}, author = {Mota-Gutierrez, J and Ferrocino, I and Giordano, M and Suarez-Quiroz, ML and Gonzalez-Ríos, O and Cocolin, L}, title = {Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {14}, pages = {e0042521}, pmid = {33990301}, issn = {1098-5336}, mesh = {Adult ; Bacteria/genetics ; Cacao/*microbiology ; Female ; Fermentation ; Fungi/genetics ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Odorants ; Taste ; Young Adult ; }, abstract = {Microbial metabolism drives changes in the physicochemical properties and, consequently, the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function, and metabolic potential of microbial communities' present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physicochemical, microbiological, quality, and sensory analyses to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, the fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavors. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin, and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri, and Acetobacter pasteurianus were the most prevalent. Fermentation time and roasting are the most important determinants of cocoa quality, while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is urgently needed for developing fermentation protocols according to regions, countries, and cocoa varieties to guarantee safety and desirable flavor development. IMPORTANCE Monitoring the composition, structure, functionalities, and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.}, }
@article {pmid31816621, year = {2020}, author = {Paul, AA and Hoffman, KL and Hagan, JL and Sampath, V and Petrosino, JF and Pammi, M}, title = {Fungal cutaneous microbiome and host determinants in preterm and term neonates.}, journal = {Pediatric research}, volume = {88}, number = {2}, pages = {225-233}, pmid = {31816621}, issn = {1530-0447}, mesh = {Anti-Bacterial Agents/pharmacology ; CARD Signaling Adaptor Proteins/genetics ; Female ; Fungi/classification ; Genotype ; Humans ; Infant, Premature ; *Intensive Care Units, Neonatal ; Intensive Care, Neonatal ; Longitudinal Studies ; Male ; *Microbiota ; *Mycobiome ; NLR Family, Pyrin Domain-Containing 3 Protein/genetics ; Neoplasm Proteins/genetics ; Nod2 Signaling Adaptor Protein/genetics ; Polymorphism, Single Nucleotide ; Prospective Studies ; Skin/metabolism/*microbiology ; Toll-Like Receptor 4/genetics ; }, abstract = {BACKGROUND: The neonatal cutaneous mycobiome has not been characterized in preterm infants. Invasive fungal infections in preterm neonates are associated with high mortality. The immaturity of the preterm skin predisposes neonates to invasive infection by skin colonizers. We report the clinical and host determinants that influence the skin mycobiome.<br><br>METHODS: Skin swabs from the antecubital fossa, forehead, and gluteal region of 15 preterm and 15 term neonates were obtained during the first 5 weeks of life. The mycobiome was sequenced using the conserved pan-fungal ITS2 region. Blood samples were used to genotype immune modulating genes. Clinical metadata was collected to determine the clinical predictors of the abundance and diversity of the skin mycobiome.<br><br>RESULTS: The neonatal mycobiome is characterized by few taxa. Alpha diversity of the mycobiome is influenced by antibiotic exposure, the forehead body site, and the neonatal intensive care unit (NICU) environment. Beta diversity varies with mode of delivery, diet, and body site. The host determinants of the cutaneous microbiome include single-nucleotide polymorphisms in TLR4, NLRP3,CARD8, and NOD2.<br><br>CONCLUSION: The neonatal cutaneous mycobiome is composed of few genera and is influenced by clinical factors and host genetics, the understanding of which will inform preventive strategies against invasive fungal infections.}, }
@article {pmid33624266, year = {2021}, author = {Whon, TW and Shin, NR and Kim, JY and Roh, SW}, title = {Omics in gut microbiome analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {292-297}, pmid = {33624266}, issn = {1976-3794}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Metagenome ; Metagenomics ; }, abstract = {Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.}, }
@article {pmid33565054, year = {2021}, author = {Gwak, HJ and Lee, SJ and Rho, M}, title = {Application of computational approaches to analyze metagenomic data.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {233-241}, pmid = {33565054}, issn = {1976-3794}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Genome, Microbial ; Humans ; Metagenome ; *Metagenomics/methods ; Microbiota ; }, abstract = {Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of next-generation sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational methods that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed.}, }
@article {pmid33221999, year = {2020}, author = {Liu, J and Deng, XC and Li, XY and Yang, ZB and Zhang, GY and Chen, TT}, title = {Intramuscular injection of tetracycline decreased gut microbial diversity in mouse.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {31}, number = {9-12}, pages = {295-308}, doi = {10.1007/s00335-020-09852-2}, pmid = {33221999}, issn = {1432-1777}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gastrointestinal Microbiome/*drug effects ; Injections, Intramuscular ; Metagenome ; Metagenomics/methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S ; Tetracycline/administration &amp; dosage/*pharmacology ; }, abstract = {Antibiotics contribute a lot to human beings and can kill bacteria effectively. However, more and more studies show that antibiotics can disturb the intestinal microbial community. It has been widely reported that oral antibiotics can reduce the diversity of intestinal microflora, but the effect of intramuscular injection on intestinal microflora is less studied. In this study, we sequenced the intestinal microflora of mice treated with tetracycline by 16SrRNA method, and found that intramuscular injection of tetracycline (TET) can also reduce the intestinal microbial richness of mice. In addition, the results showed that within a certain range (3 mg), with the increase of TET injection concentration, the wind of intestinal microflora in mice decreased significantly. When the injection concentration reached saturation, although the amount of TET injection was increased, the degree of intestinal flora affected was not increased. The results showed that the degree of diversity decrease was in direct proportion to the amount of tetracycline injection in the saturated concentration, but not positively related to the high amount of TET injection after exceeding the saturated concentration.}, }
@article {pmid32919016, year = {2020}, author = {Zhang, H and Wang, Q and Zhao, J and Liu, S and Zhang, L and Zhao, Y and Yang, H and Sun, L}, title = {Quantitative microbiome profiling links microbial community variation to the intestine regeneration rate of the sea cucumber Apostichopus japonicus.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {5012-5020}, doi = {10.1016/j.ygeno.2020.09.017}, pmid = {32919016}, issn = {1089-8646}, mesh = {Animals ; *Gastrointestinal Microbiome ; Intestines/microbiology/physiology ; Metagenomics ; Regeneration ; Stichopus/*microbiology/*physiology ; }, abstract = {The intestinal microbiota may play important roles in regenerating intestine of the sea cucumber Apostichopus japonicus, the underlying mechanism remains unclear. In the present study, a germ-free sea cucumber model was developed, and the intestinal microbial differentiation of faster and slower regenerating A. japonicus individuals during intestine regeneration was analyzed. The results revealed that depletion of the intestinal microbiota resulted in elevated abundance of the potential key players Flavobacteriaceae and Rhodobacteraceae during intestine regeneration and thus promoted the intestine regeneration rate of A. japonicus. Metagenomic analysis revealed that the increased abundance of Flavobacteriaceae elevated the enrichment of genes associated with carbohydrate utilization, whereas the abundant Rhodobacteraceae-enriched genes were associated with polyhydroxybutyrate production. We identified microbiota abundance as a key driver of microbial community alterations, especially beneficial microbiota members, in the developing intestine of A. japonicus. This study provides new insights into the mechanism of host-microbiota interactions related to organ regeneration.}, }
@article {pmid31916894, year = {2020}, author = {Kovtun, AS and Averina, OV and Alekseeva, MG and Danilenko, VN}, title = {Antibiotic Resistance Genes in the Gut Microbiota of Children with Autistic Spectrum Disorder as Possible Predictors of the Disease.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {26}, number = {11}, pages = {1307-1320}, doi = {10.1089/mdr.2019.0325}, pmid = {31916894}, issn = {1931-8448}, mesh = {Aminoglycosides/genetics ; Anti-Bacterial Agents/therapeutic use ; Autism Spectrum Disorder/*microbiology ; Bacteria/drug effects/*genetics ; Child ; Child, Preschool ; Drug Resistance, Microbial/drug effects/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/*genetics ; Humans ; Male ; Metagenomics/methods ; Moscow ; beta-Lactams/metabolism ; }, abstract = {The gut microbiota (GM), which contains thousands of bacterial species, is a reservoir of antibiotic resistance genes (ARGs) called resistome. Early life exposure to antibiotics alters significantly the composition and function of the gut microbiota of children, which may trigger symptoms of autism spectrum disorder (ASD). This is because the GM plays an important role in the bidirectional communication between the gut and the brain and influences the brain normal functioning through multiple pathways. The goal of this article is to study the distribution of ARGs in the GM of 3- to 5-year-old healthy children and children with ASD living in Moscow, Russia. The metagenomic analysis of samples from both groups revealed differences in the signatures between them. The signatures consisted of the bacterial genera and aminoglycoside, β-lactam, macrolide, and tetracycline resistance genes that they harbored. Our results show an increase in ARGs in the resistome of the GM of children with ASD. These findings emphasize the negative influence of early-life antibiotic therapy. We found three ARGs, aac(6')-aph(2''), cepA-49, and tet(40), which could serve as markers of ASD. The additional functions carried out by the enzymes, encoded by these genes, are being discussed.}, }
@article {pmid34408730, year = {2021}, author = {Xue, CX and Lin, H and Zhu, XY and Liu, J and Zhang, Y and Rowley, G and Todd, JD and Li, M and Zhang, XH}, title = {DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {698286}, doi = {10.3389/fmicb.2021.698286}, pmid = {34408730}, issn = {1664-302X}, abstract = {Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.}, }
@article {pmid34325201, year = {2021}, author = {Wang, M and Sun, Y and Zeng, Z and Wang, Z}, title = {Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment.}, journal = {Ecotoxicology and environmental safety}, volume = {222}, number = {}, pages = {112552}, doi = {10.1016/j.ecoenv.2021.112552}, pmid = {34325201}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents ; Genes, Bacterial ; *Metagenomics ; Swine ; Virome ; Waste Water ; *Water Purification ; }, abstract = {Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.}, }
@article {pmid34051009, year = {2021}, author = {Matsushita, M and Fujita, K and Motooka, D and Hatano, K and Fukae, S and Kawamura, N and Tomiyama, E and Hayashi, Y and Banno, E and Takao, T and Takada, S and Yachida, S and Uemura, H and Nakamura, S and Nonomura, N}, title = {The gut microbiota associated with high-Gleason prostate cancer.}, journal = {Cancer science}, volume = {112}, number = {8}, pages = {3125-3135}, pmid = {34051009}, issn = {1349-7006}, support = {//Yakult Bio-Science Foundation/ ; //Japanese Urological Association/ ; }, mesh = {Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Humans ; Japan ; Male ; Middle Aged ; Neoplasm Grading ; Phylogeny ; Prostatic Neoplasms/microbiology/*pathology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We have found that intestinal bacteria and their metabolites, short-chain fatty acids (SCFAs), promote cancer growth in prostate cancer (PCa) mouse models. To clarify the association between gut microbiota and PCa in humans, we analyzed the gut microbiota profiles of men with suspected PCa. One hundred and fifty-two Japanese men undergoing prostate biopsies (96 with cancer and 56 without cancer) were included in the study and randomly divided into two cohorts: a discovery cohort (114 samples) and a test cohort (38 samples). The gut microbiota was compared between two groups, a high-risk group (men with Grade group 2 or higher PCa) and a negative + low-risk group (men with negative biopsy or Grade group 1 PCa), using 16S rRNA gene sequencing. The relative abundances of Rikenellaceae, Alistipes, and Lachnospira, all SCFA-producing bacteria, were significantly increased in high-risk group. In receiver operating characteristic curve analysis, the index calculated from the abundance of 18 bacterial genera which were selected by least absolute shrinkage and selection operator regression detected high-risk PCa in the discovery cohort with higher accuracy than the prostate specific antigen test (area under the curve [AUC] = 0.85 vs 0.74). Validation of the index in the test cohort showed similar results (AUC = 0.81 vs 0.67). The specific bacterial taxa were associated with high-risk PCa. The gut microbiota profile could be a novel useful marker for the detection of high-risk PCa and could contribute to the carcinogenesis of PCa.}, }
@article {pmid33713395, year = {2021}, author = {Gil, P and Dupuy, V and Koual, R and Exbrayat, A and Loire, E and Fall, AG and Gimonneau, G and Biteye, B and Talla Seck, M and Rakotoarivony, I and Marie, A and Frances, B and Lambert, G and Reveillaud, J and Balenghien, T and Garros, C and Albina, E and Eloit, M and Gutierrez, S}, title = {A library preparation optimized for metagenomics of RNA viruses.}, journal = {Molecular ecology resources}, volume = {21}, number = {6}, pages = {1788-1807}, doi = {10.1111/1755-0998.13378}, pmid = {33713395}, issn = {1755-0998}, support = {CuliOme/291815//Seventh Framework Programme/ ; Vmerge/613996//Seventh Framework Programme/ ; //Direction Générale de l'Alimentation/ ; }, mesh = {Animals ; *Gene Library ; Genome, Viral ; Metagenome ; *Metagenomics ; *RNA Viruses/genetics ; *Virome ; }, abstract = {Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.}, }
@article {pmid33441409, year = {2021}, author = {Fishbein, SRS and Hink, T and Reske, KA and Cass, C and Struttmann, E and Iqbal, ZH and Seiler, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33441409}, issn = {2379-5042}, support = {T32 DK077653/DK/NIDDK NIH HHS/United States ; K23 AI137321/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; R01 AT009741/AT/NCCIH NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; }, mesh = {Administration, Oral ; Adult ; Aged ; Anti-Bacterial Agents/*administration &amp; dosage/adverse effects/therapeutic use ; Clostridioides difficile/*drug effects/physiology ; Clostridium Infections/*drug therapy ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Vancomycin/*administration &amp; dosage/adverse effects/therapeutic use ; Vancomycin-Resistant Enterococci/drug effects/genetics/isolation &amp; purification ; }, abstract = {Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.)IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.}, }
@article {pmid33281177, year = {2020}, author = {Hashimoto, K and Yamazaki, F and Kohyama, N and Kawakami, Y}, title = {Analysis of Fungal Flora in the Dust of Bedding in Japanese Houses and Genetic Identification of Yeasts Isolated from the Dust.}, journal = {Biocontrol science}, volume = {25}, number = {4}, pages = {193-202}, doi = {10.4265/bio.25.193}, pmid = {33281177}, issn = {1884-0205}, mesh = {Bedding and Linens/*microbiology ; Dust/*analysis ; *Environmental Microbiology ; Fungi/*classification/*genetics/isolation &amp; purification ; Humans ; Metagenome ; Metagenomics/methods ; *Mycobiome ; }, abstract = {This study examined the fungal flora contained in the dust of bedding used in 50 houses in Japan. The result showed that the mycoflora having the largest isolation rate was yeasts, which were isolated by 42 out of 50 houses (84%), and exceeded the isolation rate of Cladosporium spp. (80%) and Aspergillus spp. (66%). In addition, the isolation rate of Alternaria, which was an important fungus causing asthma, 66% was being considered as a high isolation rate, and this result was very interesting. The isolation rate of xerophilic fungi such as Aspergillus restrictus and Wallemia often found in house dust on the floor, was not very high. Forty-one strains of yeasts isolated from each dust sample were identified, and Naganishia diffluens species complex and Filobasidium magnum had a larger number of 13 strains, respectively. Since N. diffluens was the yeasts often isolated from human skin, it was thought to be an association between the fungal skin flora and fungal flora of bed dust. Meanwhile, there was no report of isolation of F. magnum from house dust previously. To the best of our knowledge, this is the first study showing its isolation from bedding with relatively high frequency.}, }
@article {pmid33028395, year = {2020}, author = {Berggrund, M and Gustavsson, I and Aarnio, R and Lindberg, JH and Sanner, K and Wikström, I and Enroth, S and Bunikis, I and Olovsson, M and Gyllensten, U}, title = {Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2.}, journal = {Virology journal}, volume = {17}, number = {1}, pages = {147}, pmid = {33028395}, issn = {1743-422X}, mesh = {Adult ; Cervical Intraepithelial Neoplasia/diagnosis/*etiology/*microbiology ; Early Detection of Cancer ; Female ; Human papillomavirus 16/genetics/isolation &amp; purification ; Humans ; *Microbiota ; Middle Aged ; Papillomavirus Infections/diagnosis/*etiology/*microbiology ; Specimen Handling/methods ; Uterine Cervical Neoplasms/diagnosis/etiology/microbiology ; Vagina/*virology ; Vaginal Smears/*methods ; }, abstract = {BACKGROUND: The vaginal microbiota has been reported to be associated with HPV infection and cervical cancer. This study was performed to compare the vaginal microbiota at two timepoints in women performing self-sampling and had a persistent or transient HPV16 infection. The women were tested for 12 high-risk HPV (hrHPV) types but only women with single type (HPV16) were included to reduce confounding variables.<br><br>METHODS: In total 96 women were included in this study. Of these, 26 were single positive for HPV16 in the baseline test and HPV negative in the follow-up test and 38 were single positive for HPV16 in both tests and diagnosed with CIN2+ in histology. In addition, 32 women that were negative for all 12 HPV tested were included. The samples of vaginal fluid were analyzed with the Ion 16S™ Metagenomics Kit and Ion 16S™ metagenomics module within the Ion Reporter™ software.<br><br>RESULTS: K-means clustering resulted in two Lactobacillus-dominated groups, one with Lactobacillus sp. and the other specifically with Lactobacillus iners. The two remaining clusters were dominated by a mixed non-Lactobacillus microbiota. HPV negative women had lower prevalence (28%) of the non-Lactobacill dominant cluster in the baseline test, as compared to women with HPV16 infection (42%) (p value = 0.0173). Transition between clusters were more frequent in women with persistent HPV16 infection (34%) as compared in women who cleared the HPV16 infection (19%) (p value = 0.036).<br><br>CONCLUSIONS: The vaginal microbiota showed a higher rate of transitioning between bacterial profiles in women with persistent HPV16 infection as compared to women with transient infection. This indicate an instability in the microenvironment in women with persistent HPV infection and development of CIN2+.}, }
@article {pmid32966856, year = {2020}, author = {Hoque, MN and Istiaq, A and Rahman, MS and Islam, MR and Anwar, A and Siddiki, AMAMZ and Sultana, M and Crandall, KA and Hossain, MA}, title = {Microbiome dynamics and genomic determinants of bovine mastitis.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {5188-5203}, doi = {10.1016/j.ygeno.2020.09.039}, pmid = {32966856}, issn = {1089-8646}, mesh = {Animals ; Cattle ; Drug Resistance, Microbial/genetics ; Female ; Genome, Archaeal ; Genome, Bacterial ; Genome, Viral ; Mastitis, Bovine/*microbiology/virology ; Metagenomics ; Microbiota/*genetics ; Milk/microbiology ; Virulence Factors/genetics ; }, abstract = {The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can influence the pathophysiology of mastitis. We hypothesized possible dynamic shifts of microbiome composition and genomic features with different pathological conditions of mastitis (Clinical Mastitis; CM, Recurrent CM; RCM, Subclinical Mastitis; SCM). To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM, 5; RCM, 6; SCM, 4; H, 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. The WMS data mapped to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition (CM > H > RCM > SCM). Furthermore, we identified a number of microbial genomic features, including 333, 304, 183 and 50 virulence factors-associated genes (VFGs) and 48, 31, 11 and 6 antibiotic resistance genes (ARGs) in CM, RCM, SCM, and H-microbiomes, respectively. We also detected different metabolic pathway and functional genes associated with mastitis pathogenesis. Therefore, profiling microbiome dynamics in different conditions of mastitis and associated microbial genomic features contributes to developing microbiome-based diagnostics and therapeutics for bovine mastitis.}, }
@article {pmid32800611, year = {2021}, author = {Ryan, MJ and Schloter, M and Berg, G and Kostic, T and Kinkel, LL and Eversole, K and Macklin, JA and Schelkle, B and Kazou, M and Sarand, I and Singh, BK and Fischer, D and Maguin, E and Ferrocino, I and Lima, N and McClure, RS and Charles, TC and de Souza, RSC and Kiran, GS and Krug, HL and Taffner, J and Roume, H and Selvin, J and Smith, D and Rybakova, D and Sessitsch, A}, title = {Development of Microbiome Biobanks - Challenges and Opportunities.}, journal = {Trends in microbiology}, volume = {29}, number = {2}, pages = {89-92}, doi = {10.1016/j.tim.2020.06.009}, pmid = {32800611}, issn = {1878-4380}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biological Specimen Banks/*standards/trends ; Biomedical Research ; Humans ; Mammals/microbiology ; *Microbiota ; Plants/microbiology ; Preservation, Biological ; }, abstract = {The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.}, }
@article {pmid32622559, year = {2021}, author = {Khan Mirzaei, M and Xue, J and Costa, R and Ru, J and Schulz, S and Taranu, ZE and Deng, L}, title = {Challenges of Studying the Human Virome - Relevant Emerging Technologies.}, journal = {Trends in microbiology}, volume = {29}, number = {2}, pages = {171-181}, doi = {10.1016/j.tim.2020.05.021}, pmid = {32622559}, issn = {1878-4380}, mesh = {Bacteriophages/classification/*genetics/isolation &amp; purification ; Genome, Viral ; Humans ; Metagenomics/*methods/trends ; *Virome ; Viruses/classification/*genetics/isolation &amp; purification ; }, abstract = {In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.}, }
@article {pmid32448763, year = {2021}, author = {Carr, VR and Shkoporov, A and Hill, C and Mullany, P and Moyes, DL}, title = {Probing the Mobilome: Discoveries in the Dynamic Microbiome.}, journal = {Trends in microbiology}, volume = {29}, number = {2}, pages = {158-170}, doi = {10.1016/j.tim.2020.05.003}, pmid = {32448763}, issn = {1878-4380}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {There has been an explosion of metagenomic data representing human, animal, and environmental microbiomes. This provides an unprecedented opportunity for comparative and longitudinal studies of many functional aspects of the microbiome that go beyond taxonomic classification, such as profiling genetic determinants of antimicrobial resistance, interactions with the host, potentially clinically relevant functions, and the role of mobile genetic elements (MGEs). One of the most important but least studied of these aspects are the MGEs, collectively referred to as the 'mobilome'. Here we elaborate on the benefits and limitations of using different metagenomic protocols, discuss the relative merits of various sequencing technologies, and highlight relevant bioinformatics tools and pipelines to predict the presence of MGEs and their microbial hosts.}, }
@article {pmid31744351, year = {2021}, author = {Bender, JM and Li, F and Purswani, H and Capretz, T and Cerini, C and Zabih, S and Hung, L and Francis, N and Chin, S and Pannaraj, PS and Aldrovandi, G}, title = {Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome.}, journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {34}, number = {20}, pages = {3335-3343}, doi = {10.1080/14767058.2019.1684466}, pmid = {31744351}, issn = {1476-4954}, support = {K12 HD052954/HD/NICHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Intensive Care Units, Neonatal ; }, abstract = {INTRODUCTION: The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time.<br><br>MATERIALS AND METHODS: Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed.<br><br>RESULTS: A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R2 = 0.044, p = .002) but later courses did not (R2 = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome.<br><br>CONCLUSION: Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.}, }
@article {pmid34118665, year = {2021}, author = {Zhang, L and Gong, X and Wang, L and Guo, K and Cao, S and Zhou, Y}, title = {Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.}, journal = {The Science of the total environment}, volume = {791}, number = {}, pages = {148096}, doi = {10.1016/j.scitotenv.2021.148096}, pmid = {34118665}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Hydrolysis ; *Metagenomics ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sewage ; }, abstract = {Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.}, }
@article {pmid34064231, year = {2021}, author = {Alanin, KWS and Junco, LMF and Jørgensen, JB and Nielsen, TK and Rasmussen, MA and Kot, W and Hansen, LH}, title = {Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay.}, journal = {Viruses}, volume = {13}, number = {6}, pages = {}, pmid = {34064231}, issn = {1999-4915}, mesh = {Computational Biology ; Host Specificity ; *Metagenome ; *Metagenomics/methods ; Pseudomonas/*virology ; Pseudomonas Phages/classification/*physiology ; *Viral Plaque Assay/methods ; *Virome ; }, abstract = {Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas&amp;nbsp;syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.}, }
@article {pmid33509255, year = {2021}, author = {Muturi, EJ and Njoroge, TM and Dunlap, C and Cáceres, CE}, title = {Blood meal source and mixed blood-feeding influence gut bacterial community composition in Aedes aegypti.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {83}, pmid = {33509255}, issn = {1756-3305}, support = {NSF DEB 1754115//National Science Foundation/ ; }, mesh = {*Aedes/microbiology/physiology ; Animals ; Bacteria/classification ; Blood ; Chickens ; *Feeding Behavior ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Meals ; Metagenomics/methods ; Microbiota ; Mosquito Vectors/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Rabbits ; }, abstract = {BACKGROUND: The guts of blood-sucking insects host a community of bacteria that can shift dramatically in response to biotic and abiotic factors. Identifying the key factors structuring these microbial communities has important ecological and epidemiological implications.<br><br>METHODS: We used the yellow fever mosquito, Aedes aegypti, to investigate the impact of mixed blood meals on gut microbiota of vector mosquitoes. Adult females were experimentally fed on sugar or blood from chicken, rabbit or a mixture of chicken and rabbit blood, and their gut microbiota were characterized using 16S rRNA gene amplification and MiSeq sequencing.<br><br>RESULTS: The gut bacterial communities of mosquitoes fed on the three blood meal treatments clustered separately, suggesting that host species identity and mixed blood-feeding are key determinants of gut bacterial community composition in mosquitoes. Mixed blood meal had a synergistic effect on both operational taxonomic unit (OTU) richness and the Shannon diversity index, suggesting that mixed blood-feeding can offset the nutritional deficit of blood meals from certain host species. The microbial communities observed in this study were distinct from those identified from similarly fed Ae. aegypti from our previous study.<br><br>CONCLUSIONS: These findings demonstrate that vector host-feeding preferences can influence gut microbial composition and diversity, which could potentially impact pathogen acquisition and transmission by the vector. The results also demonstrate that different microenvironmental conditions within the laboratory may play an important role in structuring the microbial communities of independently reared mosquito colonies.}, }
@article {pmid33486715, year = {2021}, author = {Fadiji, AE and Ayangbenro, AS and Babalola, OO}, title = {Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach.}, journal = {Journal of applied genetics}, volume = {62}, number = {2}, pages = {339-351}, pmid = {33486715}, issn = {2190-3883}, support = {UID123634//National Research Foundation/ ; }, mesh = {Endophytes/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Nitrogen Fixation/genetics ; Plant Development ; Plant Roots/*microbiology ; Zea mays/*microbiology ; }, abstract = {To ensure food security for the ever-increasing world's population, it is important to explore other alternatives for enhancing plant productivity. This study is aimed at identifying the putative plant growth-promoting (PGP) and endophytic gene clusters in root-associated endophytic microbes from maize root and to also verify if their abundance is affected by different farming practices. To achieve this, we characterize endophytic microbiome genes involved in PGP and endophytic lifestyle inside maize root using the shotgun metagenomic approach. Our results revealed the presence of genes involved in PGP activities such as nitrogen fixation, HCN biosynthesis, siderophore, 4-hydroxybenzoate, ACC deaminase, phenazine, phosphate solubilization, butanediol, methanol utilization, acetoin, nitrogen metabolism, and IAA biosynthesis. We also identify genes involved in stress resistance such as glutathione, catalase, and peroxidase. Our results further revealed the presence of putative genes involved in endophytic behaviors such as aerotaxis, regulator proteins, motility mechanisms, flagellum biosynthesis, nitrogen regulation, regulation of carbon storage, formation of biofilm, reduction of nitric oxide, regulation of beta-lactamase resistance, type III secretion, type IV conjugal DNA, type I pilus assembly, phosphotransferase system (PTS), and ATP-binding cassette (ABC). Our study suggests a high possibility in the utilization of endophytic microbial community for plant growth promotion, biocontrol activities, and stress mitigation. Further studies in ascertaining this claim through culturing of the beneficial isolates as well as pot and field experiments are necessary.}, }
@article {pmid33063421, year = {2021}, author = {Tiew, PY and Jaggi, TK and Chan, LLY and Chotirmall, SH}, title = {The airway microbiome in COPD, bronchiectasis and bronchiectasis-COPD overlap.}, journal = {The clinical respiratory journal}, volume = {15}, number = {2}, pages = {123-133}, doi = {10.1111/crj.13294}, pmid = {33063421}, issn = {1752-699X}, support = {NMRC/Fellowship/0049/2017//Singapore Ministry of Health's National Medical Research Council under its Research Training Fellowship/ ; MOH-000141//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; }, mesh = {*Bronchiectasis ; Humans ; *Microbiota ; *Pulmonary Disease, Chronic Obstructive ; Severity of Illness Index ; }, abstract = {OBJECTIVE: To review the airway microbiome in chronic obstructive pulmonary disease (COPD), bronchiectasis and bronchiectasis-COPD overlap (BCO).<br><br>Relevant studies were selected from PubMed, Google scholar, EMBASE and Web of Science. All studies involving human microbiomes, published in the English language, and using the search terms "COPD", "Chronic Obstructive Pulmonary Disease", "Bronchiectasis", "BCO" or "Bronchiectasis and COPD overlap", AND "microbiome", "mycobiome" or "metagenomics" were included.<br><br>RESULTS: Despite variability in sampling methods and specimen types used, microbiome composition remains relatively comparable in COPD and bronchiectasis with prominence of Proteobacteria, Firmicutes and Bacteroidetes. Alterations to airway microbiomes occur in association to disease severity and/or exacerbations in COPD and bronchiectasis. Decreased alpha diversity and Haemophilus-predominant microbiomes are associated with poorer survival in COPD, while, in bronchiectasis, Pseudomonas-predominant microbiomes demonstrate high exacerbation frequency and greater symptom burden while Aspergillus-dominant mycobiome profiles associate with exacerbations. The role of the microbiome in BCO remains understudied.<br><br>CONCLUSION: Use of next-generation sequencing has revolutionised our detection and understanding of the airway microbiome in chronic respiratory diseases such as COPD and bronchiectasis. Targeted amplicon sequencing reveals important associations between the respiratory microbiome and disease outcome while metagenomics may elucidate functional pathways. How best to apply this information into patient care, monitoring and treatment, however, remains challenging and necessitates further study.}, }
@article {pmid31868094, year = {2020}, author = {Urban, RJ and Pyles, RB and Stewart, CJ and Ajami, N and Randolph, KM and Durham, WJ and Danesi, CP and Dillon, EL and Summons, JR and Singh, CK and Morrison, M and Kreber, LA and Masel, B and Miller, AL and Wright, TJ and Sheffield-Moore, M}, title = {Altered Fecal Microbiome Years after Traumatic Brain Injury.}, journal = {Journal of neurotrauma}, volume = {37}, number = {8}, pages = {1037-1051}, doi = {10.1089/neu.2019.6688}, pmid = {31868094}, issn = {1557-9042}, mesh = {Adult ; Aged ; Bacteria/genetics/metabolism ; Brain Injuries, Traumatic/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics/metabolism ; Young Adult ; }, abstract = {Patients with chronic traumatic brain injury (TBI) requiring long-term, permanent care suffer a myriad of clinical symptoms (i.e., impaired cognition, fatigue, and other conditions) that persist for years beyond the acute brain injury. In addition to these comorbid clinical symptoms, chronic TBI patients exhibit altered amino acid and hormonal profiles with distinct cytokine patterns suggesting chronic inflammation. This metabolic link suggests a role of the gut-brain axis in chronic TBI. Thus, we utilized a two-site trial to investigate the role of the gut-brain axis in comorbidities of chronic TBI. The fecal microbiome profile of 22 moderate/severe TBI patients residing in permanent care facilities in Texas and California was compared to 18 healthy age-matched control subjects working within the participating facilities. Each fecal microbiome was characterized by 16S(V4) ribosomal RNA (rRNA) gene sequencing and metagenomic genome sequencing approaches followed by confirmatory full 16S rRNA gene sequencing or focused tuf gene speciation and specific quantitative polymerase chain reaction evaluation of selected genera or species. The average chronic TBI patient fecal microbiome structure was significantly different compared to the control cohort, and these differences persisted after group stratification analysis to identify any unexpected confounders. Notably, the fecal microbiome of the chronic TBI cohort had absent or reduced Prevotella spp. and Bacteroidies spp. Conversely, bacteria in the Ruminococcaceae family were higher in abundance in TBI compared to control profiles. Previously reported hypoaminoacidemia, including significantly reduced levels of l-tryptophan, l-sarcosine, ß-alanine, and alanine, positively correlated with the reduced levels of Prevotella spp. in the TBI cohort samples compared to controls. Although the sequelae of gut-brain axis disruption after TBI is not fully understood, characterizing TBI-related alterations in the fecal microbiome may provide biomarkers and therapeutic targets to address patient morbidity.}, }
@article {pmid34387940, year = {2021}, author = {Ruscheweyh, HJ and Milanese, A and Paoli, L and Sintsova, A and Mende, DR and Zeller, G and Sunagawa, S}, title = {mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities.}, journal = {Current protocols}, volume = {1}, number = {8}, pages = {e218}, doi = {10.1002/cpz1.218}, pmid = {34387940}, issn = {2691-1299}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; Software ; }, abstract = {The mOTU profiler, or mOTUs for short, is a software tool that enables the profiling of microbial communities in terms of their taxonomic composition, relative abundance of metabolically active members, and diversity of strain populations. To this end, it maintains a database of single-copy phylogenetic marker gene sequences, which are used as a reference to which short read metagenomic and metatranscriptomic reads are mapped for the identification and quantification of microbial taxa. Here, we describe the most common use cases of the mOTU profiler in two basic protocols. Additional supporting protocols provide information on its installation and in-depth guidance on adjusting its settings for increasing or decreasing the stringency with which taxa are detected and quantified, as well as for customizing the output file format. Guidelines for understanding the profiling results are provided, along with additional information on unique features, methodological details, and the development history of the tool. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metagenomic and metatranscriptomic mOTU profiling Basic Protocol 2: Metagenomic SNV profiling Support Protocol 1: Installing mOTUs Support Protocol 2: Profiling pipeline-step by step Support Protocol 3: The mOTUs profiling routine using advanced parameters Support Protocol 4: Metagenomic SNV calling: advanced parameters.}, }
@article {pmid33547403, year = {2021}, author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M}, title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {169}, pmid = {33547403}, issn = {2399-3642}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeology ; DNA, Ancient/isolation &amp; purification ; Ecosystem ; Feces/*microbiology ; Fossils/microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/analysis/microbiology ; History, Ancient ; Humans ; Metagenomics ; Neanderthals/*microbiology ; Sequence Analysis, DNA ; Spain ; }, abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.}, }
@article {pmid32536582, year = {2021}, author = {Jian, C and Luukkonen, P and Sädevirta, S and Yki-Järvinen, H and Salonen, A}, title = {Impact of short-term overfeeding of saturated or unsaturated fat or sugars on the gut microbiota in relation to liver fat in obese and overweight adults.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {40}, number = {1}, pages = {207-216}, doi = {10.1016/j.clnu.2020.05.008}, pmid = {32536582}, issn = {1532-1983}, mesh = {Body Mass Index ; Diet, High-Fat/*adverse effects ; Dietary Sugars/administration &amp; dosage ; Eating/physiology ; Fasting/blood ; Fats, Unsaturated/administration &amp; dosage ; Fatty Acids/administration &amp; dosage ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Liver/metabolism ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*etiology ; Obesity/complications/*metabolism ; Overweight/complications/*metabolism ; }, abstract = {BACKGROUNDS &amp; AIMS: Intestinal microbiota may be causally involved in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We aimed to study the effect of short-term overfeeding on human gut microbiota in relation to baseline and overfeeding-induced liver steatosis. We also asked whether the baseline microbiota composition is associated to the overfeeding-induced increase in liver fat.<br><br>METHODS: In a randomized trial, 38 overweight and obese subjects were assigned to consume an excess of 1000 kcal/day of diets rich in either saturated fat, unsaturated fat, or simple sugars for 3 weeks. Fasting blood samples and 1H-MR spectroscopy were used for extensive clinical phenotyping as previously reported (PMID: 29844096). Fecal samples were collected for the analysis of the gut microbiota using 16S rRNA amplicon sequencing, imputed metagenomics and qPCR. Microbiota results were correlated with dietary intakes and clinical measurements before and during overfeeding.<br><br>RESULTS: The overall community structure of the microbiota remained highly stable and personalized during overfeeding based on between-sample Bray-Curtis dissimilarity, but the relative abundances of individual taxa were altered in a diet-specific manner: overfeeding saturated fat increased Proteobacteria, while unsaturated fat increased butyrate producers. Sugar overfeeding increased Lactococcus and Escherichia coli. Imputed functions of the gut microbiota were not affected by overfeeding. Several taxa affected by overfeeding significantly correlated with the changes in host metabolic markers. The baseline levels of proteobacterial family Desulfovibrionaceae, and especially genus Bilophila, were significantly associated to overfeeding-induced liver fat increase independently of the diet arm. In general, limited overlap was observed between the overfeeding-induced microbiota changes and the liver fat-associated microbiota features at baseline.<br><br>CONCLUSIONS: Our work indicates that the human gut microbiota is resilient to short-term overfeeding on community level, but specific taxa are altered on diet composition-dependent manner. Generalizable microbiota signatures directly associated with liver steatosis could not be identified. Instead, the carriage of Bilophila was identified as a potential novel risk factor for diet-induced liver steatosis in humans. Clinical trial registry number: NCT02133144 listed on NIH website: ClinicalTrials.gov.}, }
@article {pmid30815668, year = {2020}, author = {Ayling, M and Clark, MD and Leggett, RM}, title = {New approaches for metagenome assembly with short reads.}, journal = {Briefings in bioinformatics}, volume = {21}, number = {2}, pages = {584-594}, pmid = {30815668}, issn = {1477-4054}, support = {BB/M004805/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Animals ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; Microbiota/genetics ; Plants/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.}, }
@article {pmid34065683, year = {2021}, author = {Daugrois, JH and Filloux, D and Julian, C and Claude, L and Ferdinand, R and Fernandez, E and Fontes, H and Rott, PC and Roumagnac, P}, title = {Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station.}, journal = {Viruses}, volume = {13}, number = {5}, pages = {}, pmid = {34065683}, issn = {1999-4915}, mesh = {*Metagenome ; *Metagenomics/methods ; Phylogeny ; Plant Diseases/virology ; Poaceae/*virology ; Quarantine ; Saccharum/*virology ; Virion ; *Virome ; }, abstract = {Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.}, }
@article {pmid33925487, year = {2021}, author = {Nebbak, A and Monteil-Bouchard, S and Berenger, JM and Almeras, L and Parola, P and Desnues, C}, title = {Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France.}, journal = {Viruses}, volume = {13}, number = {5}, pages = {}, pmid = {33925487}, issn = {1999-4915}, mesh = {Animals ; Computational Biology/methods ; Culicidae/*virology ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Mosquito Vectors/virology ; Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Virome ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {Some mosquito species have significant public health importance given their ability to transmit major diseases to humans and animals, making them the deadliest animals in the world. Among these, the Aedes (Ae.) genus is a vector of several viruses such as Dengue, Chikungunya, and Zika viruses that can cause serious pathologies in humans. Since 2004, Ae. albopictus has been encountered in the South of France, and autochthonous cases of Dengue, Chikungunya, and Zika diseases have recently been reported, further highlighting the need for a comprehensive survey of the mosquitoes and their associated viruses in this area. Using high throughput sequencing (HTS) techniques, we report an analysis of the DNA and RNA viral communities of three mosquito species Ae. albopictus, Culex (Cx.) pipiens, and Culiseta (Cs.) longiareolata vectors of human infectious diseases in a small sub-urban city in the South of France. Results revealed the presence of a significant diversity of viruses known to infect bacteria, plants, insects, and mammals. Several novel viruses were detected, including novel members of the Rhabdoviridae, Totiviridae, Iflaviviridae, Circoviridae, and Sobemoviridae families. No sequence related to major zoonotic viruses transmitted by mosquitoes was detected. The use of HTS on arthropod vector populations is a promising strategy for monitoring the emergence and circulation of zoonoses and epizooties. This study is a contribution to the knowledge of the mosquito microbiome.}, }
@article {pmid33925168, year = {2021}, author = {François, S and Antoine-Lorquin, A and Kulikowski, M and Frayssinet, M and Filloux, D and Fernandez, E and Roumagnac, P and Froissart, R and Ogliastro, M}, title = {Characterisation of the Viral Community Associated with the Alfalfa Weevil (Hypera postica) and Its Host Plant, Alfalfa (Medicago sativa).}, journal = {Viruses}, volume = {13}, number = {5}, pages = {}, pmid = {33925168}, issn = {1999-4915}, mesh = {Agriculture ; Animals ; Biodiversity ; Ecosystem ; Medicago sativa/*parasitology/*virology ; Metagenome ; Metagenomics/methods ; Phylogeny ; Plant Diseases/virology ; *Virome ; Weevils/*virology ; }, abstract = {Advances in viral metagenomics have paved the way of virus discovery by making the exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach opens new possibilities to explore how viruses circulate between insects and plants, which may help to optimise their management. It could also lead to identifying novel entomopathogenic viral resources potentially suitable for biocontrol strategies. We sampled the larvae of a natural population of alfalfa weevils (Hypera postica), a major herbivorous pest feeding on legumes, and its host plant alfalfa (Medicago sativa). Insect and plant samples were collected from a crop field and an adjacent meadow. We characterised the diversity and abundance of viruses associated with weevils and alfalfa, and described nine putative new virus species, including four associated with alfalfa and five with weevils. In addition, we found that trophic accumulation may result in a higher diversity of plant viruses in phytophagous pests compared to host plants.}, }
@article {pmid33757515, year = {2021}, author = {Vientós-Plotts, AI and Ericsson, AC and Rindt, H and Reinero, CR}, title = {Blood cultures and blood microbiota analysis as surrogates for bronchoalveolar lavage fluid analysis in dogs with bacterial pneumonia.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {129}, pmid = {33757515}, issn = {1746-6148}, mesh = {Animals ; Bacterial Typing Techniques/methods/veterinary ; Blood Culture/*veterinary ; Bronchoalveolar Lavage Fluid/*microbiology ; DNA, Bacterial ; Dog Diseases/*blood/diagnosis/microbiology ; Dogs ; Female ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; *Microbiota ; Pneumonia, Bacterial/blood/diagnosis/microbiology/*veterinary ; RNA, Ribosomal, 16S ; Sensitivity and Specificity ; Sequence Analysis, DNA/veterinary ; }, abstract = {BACKGROUND: Diagnosis of canine bacterial pneumonia relies on airway lavage to confirm septic, suppurative inflammation, and a positive bacterial culture. Considering risks of bronchoalveolar lavage fluid (BALF) collection, minimally invasive methods like culture or next generation sequencing of blood would be appealing. In dogs with bacterial pneumonia, our study aims included (1): determining proportion of agreement between cultivable bacteria in BALF and blood (2); characterizing BALF, blood, and oropharyngeal (OP) microbiota and determining if bacteria cultured from BALF were present in these communities; and (3) comparing relatedness of microbial community composition at all three sites. Bacterial cultures were performed on BALF and blood. After DNA extraction of BALF, blood and OP, 16S rRNA amplicon libraries were generated, sequenced, and compared to a bacterial gene sequence database.<br><br>RESULTS: Disregarding one false positive, blood cultures were positive in 2/9 dogs (5 total isolates), all 5 isolates were present in BALF cultures (16 total isolates). Based on sequencing data, all sites had rich and diverse microbial communities. Comparing cultured BALF bacterial genera with sequenced taxa, all dogs had ≥1 cultured isolate present in their microbiota: cultured BALF isolates were found in microbiota of BALF (12/16), blood (7/16), and OP (6/11; only 7 dogs had OP swabs). Of 394 distinct taxa detected in BALF, these were present in 75% OP and 45% blood samples. BALF community composition was significantly different than OP (p = 0.0059) and blood (p = 0.0009).<br><br>CONCLUSIONS: Blood cultures are insensitive but specific for cultured BALF bacteria in canine bacterial pneumonia. Cultivable BALF bacteria were present in BALF, blood and OP microbiota to differing degrees.}, }
@article {pmid33225533, year = {2020}, author = {Bollmann-Giolai, A and Giolai, M and Heavens, D and Macaulay, I and Malone, J and Clark, MD}, title = {A low-cost pipeline for soil microbiome profiling.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1133}, pmid = {33225533}, issn = {2045-8827}, support = {BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA, Bacterial/*analysis/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Soil ; *Soil Microbiology ; }, abstract = {Common bottlenecks in environmental and crop microbiome studies are the consumable and personnel costs necessary for genomic DNA extraction and sequencing library construction. This is harder for challenging environmental samples such as soil, which is rich in Polymerase Chain Reaction (PCR) inhibitors. To address this, we have established a low-cost genomic DNA extraction method for soil samples. We also present an Illumina-compatible 16S and ITS rRNA gene amplicon library preparation workflow that uses common laboratory equipment. We evaluated the performance of our genomic DNA extraction method against two leading commercial soil genomic DNA kits (MoBio PowerSoil® and MP Biomedicals™ FastDNA™ SPIN) and a recently published non-commercial extraction method by Zou et al. (PLoS Biology, 15, e2003916, 2017). Our benchmarking experiment used four different soil types (coniferous, broad-leafed, and mixed forest plus a standardized cereal crop compost mix) assessing the quality and quantity of the extracted genomic DNA by analyzing sequence variants of 16S V4 and ITS rRNA amplicons. We found that our genomic DNA extraction method compares well to both commercially available genomic DNA extraction kits in DNA quality and quantity. The MoBio PowerSoil® kit, which relies on silica column-based DNA extraction with extensive washing, delivered the cleanest genomic DNA, for example, best A260:A280 and A260:A230 absorbance ratios. The MP Biomedicals™ FastDNA™ SPIN kit, which uses a large amount of binding material, yielded the most genomic DNA. Our method fits between the two commercial kits, producing both good yields and clean genomic DNA with fragment sizes of approximately 10 kb. Comparative analysis of detected amplicon sequence variants shows that our method correlates well with the two commercial kits. Here, we present a low-cost genomic DNA extraction method for soil samples that can be coupled to an Illumina-compatible simple two-step amplicon library construction workflow for 16S V4 and ITS marker genes. Our method delivers high-quality genomic DNA at a fraction of the cost of commercial kits and enables cost-effective, large-scale amplicon sequencing projects. Notably, our extracted gDNA molecules are long enough to be suitable for downstream techniques such as full gene sequencing or even metagenomics shotgun approaches using long reads (PacBio or Nanopore), 10x Genomics linked reads, and Dovetail genomics.}, }
@article {pmid33205903, year = {2020}, author = {Zhang, L and Li, C and Zhai, Y and Feng, L and Bai, K and Zhang, Z and Huang, Y and Li, T and Li, D and Li, H and Cui, P and Chen, D and Wang, H and Yang, X}, title = {Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1131}, pmid = {33205903}, issn = {2045-8827}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Age Factors ; Animals ; Basidiomycota/genetics/isolation &amp; purification ; Chlamydia/genetics/isolation &amp; purification ; Female ; Firmicutes/genetics/isolation &amp; purification ; Geography ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Neisseria gonorrhoeae/genetics/isolation &amp; purification ; Proteobacteria/genetics/isolation &amp; purification ; Ursidae ; Vagina/*microbiology ; }, abstract = {In this study, a total of 14 vaginal samples (GPV1-14) from giant pandas were analyzed. These vaginal samples were divided into two groups as per the region and age of giant pandas. All the vaginal samples were analyzed using metagenomic sequencing. As per the outcomes of metagenomic analysis, Proteobacteria (39.04%), Firmicutes (5.27%), Actinobacteria (2.94%), and Basidiomycota (2.77%) were found to be the dominant phyla in the microbiome of the vaginal samples. At the genus level, Pseudomonas (21.90%) was found to be the most dominant genus, followed by Streptococcus (3.47%), Psychrobacter (1.89%), and Proteus (1.38%). Metastats analysis of the microbial species in the vaginal samples of giant pandas from Wolong Nature Reserve, Dujiangyan and Ningbo Youngor Zoo, and Ya'an Bifengxia Nature Reserve was found to be significantly different (p < 0.05). Age groups, that is, AGE1 (5-10 years old) and AGE2 (11-16 years old), also demonstrated significantly different inter-group microbial species (p < 0.05). For the first time, Chlamydia and Neisseria gonorrhoeae were detected in giant pandas' reproductive tract. GPV3 vaginal sample (2.63%) showed highest Chlamydia content followed by GPV14 (0.91%), and GPV7 (0.62%). GPV5 vaginal sample (7.17%) showed the highest Neisseria gonorrhoeae content, followed by GPV14 (7.02%), and GPV8 (6.50%). Furthermore, we employed eggNOG, CAZy, KEGG, and NCBI databases to investigate the functional significance of giant panda's vaginal microbial community. The outcomes indicated that giant panda's vaginal microbes were involved in biological processes. The data from this study will help in improving the reproductive health of giant pandas.}, }
@article {pmid33204736, year = {2020}, author = {Huang, Y and Tang, J and Cai, Z and Zhou, K and Chang, L and Bai, Y and Ma, Y}, title = {Prevotella Induces the Production of Th17 Cells in the Colon of Mice.}, journal = {Journal of immunology research}, volume = {2020}, number = {}, pages = {9607328}, pmid = {33204736}, issn = {2314-7156}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Colon/*immunology/*metabolism/microbiology ; Cytokines/biosynthesis/blood ; Dendritic Cells/immunology/metabolism ; Gastrointestinal Microbiome/drug effects/*immunology ; Gene Expression Regulation ; Immunophenotyping ; Interleukin-17/genetics/metabolism ; Intestinal Mucosa/*immunology/*metabolism ; Lymphocyte Activation/drug effects/immunology ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Prevotella/drug effects/*immunology ; Th17 Cells/*immunology/*metabolism ; }, abstract = {Th17-mediated mucosal inflammation is related to increased Prevotella bacterial abundance. The actual involvement of Prevotella in the development and accumulation of intestinal Th17 cells at a steady state, however, remains undefined. Herein, we investigated the role of Prevotella in inducing intestinal Th17 cells in mice. Mice were treated with a combination of broad-spectrum antibiotics (including ampicillin, neomycin sulfate, vancomycin hydrochloride, and metronidazole) in their drinking water for 4 weeks and then gavaged with Prevotella for 4 weeks. After inoculation, 16S rDNA sequencing was used to verify the colonization of Prevotella in the colon of mice. The IL-17A as well as IL-17A-expressing T cells was localized and quantified by an immunofluorescence assay (IFA) of colon sections. Th17 cells in the mesenteric lymph nodes of mice were counted by flow cytometry. Systemic immune response to Prevotella colonization was evaluated based on the serum levels of IL-6, TNF-α, IL-1β, IL-17A, IL-10, IL-4, IFN-γ, and IL-2. Th17-polarizing cytokines (IL-6, TNF-α, IL-1β, and IL-2) induced by Prevotella were evaluated by stimulation of bone marrow-derived dendritic cells (BMDCs). Results revealed that after inoculation, Prevotella successfully colonized the intestine of mice and induced the production and accumulation of colonic Th17 cells in the colon. Moreover, Prevotella elevated some of the Th17-related cytokines in the serum of mice. And Th17-polarizing cytokines (IL-6 and IL-1β) produced by BMDCs were mediated mainly through the interaction between Prevotella and Toll-like receptor 2 (TLR2). In conclusion, our data suggest that Prevotella induces the production of Th17 cells in the colon of mice, thus highlighting the potential role of Prevotella in training the intestinal immune system.}, }
@article {pmid33141656, year = {2020}, author = {Parras-Moltó, M and Aguirre de Cárcer, D}, title = {A comprehensive human minimal gut metagenome extends the host's metabolic potential.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33141656}, issn = {2057-5858}, mesh = {Bacteria/*genetics/metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study analyses the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3412 genes, mapping to 1856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.}, }
@article {pmid33001022, year = {2020}, author = {Maguire, F and Jia, B and Gray, KL and Lau, WYV and Beiko, RG and Brinkman, FSL}, title = {Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands.}, journal = {Microbial genomics}, volume = {6}, number = {10}, pages = {}, pmid = {33001022}, issn = {2057-5858}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; Bacteria/*genetics ; Computer Simulation ; Genome, Bacterial/genetics ; Genomic Islands/*genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82-94 % of chromosomes could be correctly recovered and binned, only 38-44 % of GIs and 1-29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0-45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.}, }
@article {pmid32439117, year = {2020}, author = {Pammi, M and Hollister, E and Neu, J}, title = {Gut Injury and the Microbiome in Neonates.}, journal = {Clinics in perinatology}, volume = {47}, number = {2}, pages = {369-382}, doi = {10.1016/j.clp.2020.02.010}, pmid = {32439117}, issn = {1557-9840}, mesh = {Dysbiosis/*congenital/*immunology ; Enterocolitis, Necrotizing/congenital/immunology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Intestinal Diseases/*congenital/*immunology ; Risk Factors ; }, abstract = {The causes of neonatal gut injury are multifactorial and include ischemia, tissue hypoxia due to anemia, excessive inflammation, deficiency of growth factors, and food protein sensitivity. The developing intestinal microbiome plays a role in some of these forms of intestinal injury but knowledge of its relative role in each remains poorly understood. Commensal bacteria are required for normal immune development and immune tolerance. Dysbiosis in the neonatal gut that alters the patterns of commensal and pathogenic bacteria may accentuate gut injury.}, }
@article {pmid32176535, year = {2020}, author = {Haley, BJ and Kim, SW and Salaheen, S and Hovingh, E and Van Kessel, JAS}, title = {Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds.}, journal = {Foodborne pathogens and disease}, volume = {17}, number = {8}, pages = {494-503}, doi = {10.1089/fpd.2019.2768}, pmid = {32176535}, issn = {1556-7125}, mesh = {Animals ; Animals, Suckling/microbiology ; Bacteria/*classification/drug effects ; Cattle ; Dairying ; Drug Resistance, Bacterial/*genetics ; Feces/*microbiology ; Female ; Lactation ; *Microbiota ; }, abstract = {Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 100 ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10-1 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.}, }
@article {pmid34380279, year = {2021}, author = {Liang, H and Wang, F and Mu, R and Huang, J and Zhao, R and Li, X and Yu, K and Li, B}, title = {Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes.}, journal = {The Science of the total environment}, volume = {790}, number = {}, pages = {148262}, doi = {10.1016/j.scitotenv.2021.148262}, pmid = {34380279}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Lakes ; *Metagenomics ; *Microbiota ; }, abstract = {Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.}, }
@article {pmid33676490, year = {2021}, author = {Liu, Y and Liu, B and Liu, C and Hu, Y and Liu, C and Li, X and Li, X and Zhang, X and Irwin, DM and Wu, Z and Chen, Z and Jin, Q and Zhang, S}, title = {Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {112}, pmid = {33676490}, issn = {1746-6148}, support = {2016YFD0500300//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Amylases/genetics ; Animals ; Anti-Bacterial Agents ; Bacteria/*classification/drug effects ; China ; Diet/veterinary ; Dogs/*microbiology ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/*drug effects ; RNA, Ribosomal, 16S/genetics ; Starch ; Wolves/*microbiology ; }, abstract = {BACKGROUND: Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared with captive wolves. We surveyed the gut bacterial diversity of 27 domestic dogs, which were fed commercial dog food, and 31 wolves, which were fed uncooked meat, by 16S rRNA sequencing. In addition, we collected fecal samples from 5 dogs and 5 wolves for shotgun metagenomic sequencing to explore changes in the functions of their gut microbiome.<br><br>RESULTS: Differences in the abundance of core bacterial genera were observed between dogs and wolves. Together with shotgun metagenomics, the gut microbiome of dogs was found to be enriched in bacteria resistant to clinical drugs (P < 0.001), while wolves were enriched in bacteria resistant to antibiotics used in livestock (P < 0.001). In addition, a higher abundance of putative α-amylase genes (P < 0.05; P < 0.01) was observed in the dog samples.<br><br>CONCLUSIONS: Living environment of dogs and domestic wolves has led to increased numbers of bacteria with antibiotic resistance genes, with exposure to antibiotics through direct and indirect methods. In addition, the living environment of dogs has allowed the adaptation of their microbiota to a starch-rich diet. These observations align with a domestic lifestyle for domestic dogs and captive wolves, which might have consequences for public health.}, }
@article {pmid33593943, year = {2021}, author = {Andersen, SB and Schluter, J}, title = {A metagenomics approach to investigate microbiome sociobiology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {10}, pages = {}, pmid = {33593943}, issn = {1091-6490}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Sociobiology ; }, }
@article {pmid34344959, year = {2021}, author = {Rouchka, EC and Chariker, JH and Alejandro, B and Adcock, RS and Singhal, R and Ramirez, J and Palmer, KE and Lasnik, AB and Carrico, R and Arnold, FW and Furmanek, S and Zhang, M and Wolf, LA and Waigel, S and Zacharias, W and Bordon, J and Chung, D}, title = {Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15715}, pmid = {34344959}, issn = {2045-2322}, support = {P20 GM103436/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; COVID-19/*pathology/virology ; Dysbiosis/etiology ; Female ; Humans ; Interferons/*metabolism ; Male ; Metagenomics ; Microbiota/genetics ; Middle Aged ; Nasopharynx/virology ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; Respiratory System/microbiology/virology ; SARS-CoV-2/*genetics/isolation &amp; purification ; Severity of Illness Index ; Transcriptome ; Up-Regulation ; Viral Load ; }, abstract = {Key elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.}, }
@article {pmid34299675, year = {2021}, author = {Su Mun, L and Wye Lum, S and Kong Yuiin Sze, G and Hock Yoong, C and Ching Yung, K and Kah Lok, L and Gopinath, D}, title = {Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {14}, pages = {}, pmid = {34299675}, issn = {1660-4601}, mesh = {*Carcinoma, Squamous Cell ; *Head and Neck Neoplasms ; Humans ; Metagenomics ; *Microbiota ; *Mouth Neoplasms ; Squamous Cell Carcinoma of Head and Neck ; }, abstract = {The past decade has witnessed a surge in epidemiological studies that have explored the relationship between the oral microbiome and oral cancer. Owing to the diversity of the published data, a comprehensive systematic overview of the currently available evidence is critical. This review summarises the current evidence on the metagenomic studies on the oral microbiome in oral cancer. A systematic search was conducted in Medline and Embase databases to identify original studies examining the differences in the oral microbiome of oral cancer cases and controls. A total of twenty-six studies were identified that reported differences in microbial abundance between oral squamous cell carcinoma (OSCC) and controls. Although almost all the studies identified microbial dysbiosis to be associated with oral cancer, the detailed qualitative analysis did not reveal the presence/abundance of any individual bacteria or a consortium to be consistently enriched in OSCC samples across the studies. Interestingly, few studies reported a surge of periodontopathogenic taxa, especially Fusobacteria, whereas others demonstrated a depletion of commensal taxa Streptococci. Considerable heterogeneity could be identified in the parameters used for designing the studies as well as reporting the microbial data. If microbiome data needs to be translated in the future, to complement the clinical parameters for diagnosis and prognosis of oral cancer, further studies with the integration of clinical variables, adequate statistical power, reproducible methods, and models are required.}, }
@article {pmid34287529, year = {2021}, author = {Baima, DC and Carvalho, NS and Barbuti, RC and Navarro-Rodriguez, T}, title = {ASSESSMENT OF THE INTESTINAL MICROBIOTA IN ADULTS WITH EROSIVE ESOPHAGITIS.}, journal = {Arquivos de gastroenterologia}, volume = {58}, number = {2}, pages = {168-174}, doi = {10.1590/S0004-2803.202100000-29}, pmid = {34287529}, issn = {1678-4219}, mesh = {Adolescent ; Adult ; Dysbiosis ; *Esophagitis ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: The intestinal microbiota influences the appropriate function of the gastrointestinal tract. Intestinal dysbiosis may be associated with a higher risk of esophageal lesions, mainly due to changes in gastroesophageal motility patterns, elevation of intra-abdominal pressure, and increased frequency of transient relaxation of the lower esophageal sphincter.<br><br>OBJECTIVE: The aim of this study was to evaluate the intestinal microbiota in individuals with erosive esophagitis and in healthy individuals using metagenomics.<br><br>METHODS: A total of 22 fecal samples from adults aged between 18 and 60 years were included. Eleven individuals had esophagitis (eight men and three women) and 11 were healthy controls (10 men and one woman). The individuals were instructed to collect and store fecal material into a tube containing guanidine solution. The DNA of the microbiota was extracted from each fecal samples and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion Torrent PGM platform and the data were analyzed using the QIIME™ software version 1.8. Statistical analyses were performed using the Mann-Whitney non-parametric test and the ANOSIM non-parametric method based on distance matrix.<br><br>RESULTS: The alpha-diversity and beta-diversity indices were similar between the two groups, without statistically significant differences. There was no statistically significant difference in the phylum level. However, a statistically significant difference was observed in the abundance of the family Clostridiaceae (0.3% vs 2.0%, P=0.032) and in the genus Faecaliumbacterium (10.5% vs 4.5%, P=0.045) between healthy controls and esophagitis patients.<br><br>CONCLUSION: The findings suggest that reduced abundance of the genus Faecaliumbacterium and greater abundance of the family Clostridiaceae may be risk factors for the development of erosive esophagitis. Intervention in the composition of the intestinal microbiota should be considered as an adjunct to current therapeutic strategies for this clinical condition.}, }
@article {pmid33803225, year = {2021}, author = {Nieuwenhuijse, DF and Oude Munnink, BB and Koopmans, MPG}, title = {viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis Results.}, journal = {Viruses}, volume = {13}, number = {3}, pages = {}, pmid = {33803225}, issn = {1999-4915}, mesh = {Base Sequence/genetics ; Computational Biology/*methods ; Data Analysis ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/instrumentation/*methods ; Molecular Sequence Annotation/*methods ; Software ; Virome/*genetics ; }, abstract = {Experiments in which complex virome sequencing data is generated remain difficult to explore and unpack for scientists without a background in data science. The processing of raw sequencing data by high throughput sequencing workflows usually results in contigs in FASTA format coupled to an annotation file linking the contigs to a reference sequence or taxonomic identifier. The next step is to compare the virome of different samples based on the metadata of the experimental setup and extract sequences of interest that can be used in subsequent analyses. The viromeBrowser is an application written in the opensource R shiny framework that was developed in collaboration with end-users and is focused on three common data analysis steps. First, the application allows interactive filtering of annotations by default or custom quality thresholds. Next, multiple samples can be visualized to facilitate comparison of contig annotations based on sample specific metadata values. Last, the application makes it easy for users to extract sequences of interest in FASTA format. With the interactive features in the viromeBrowser we aim to enable scientists without a data science background to compare and extract annotation data and sequences from virome sequencing analysis results.}, }
@article {pmid33314800, year = {2021}, author = {Artacho, A and Isaac, S and Nayak, R and Flor-Duro, A and Alexander, M and Koo, I and Manasson, J and Smith, PB and Rosenthal, P and Homsi, Y and Gulko, P and Pons, J and Puchades-Carrasco, L and Izmirly, P and Patterson, A and Abramson, SB and Pineda-Lucena, A and Turnbaugh, PJ and Ubeda, C and Scher, JU}, title = {The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {73}, number = {6}, pages = {931-942}, doi = {10.1002/art.41622}, pmid = {33314800}, issn = {2326-5205}, support = {R01HL122593//National Institute of Allergy and Infectious Diseases/ ; K08AR073930/AR/NIAMS NIH HHS/United States ; R01AR074500/AR/NIAMS NIH HHS/United States ; }, mesh = {Administration, Oral ; Adult ; Antirheumatic Agents/metabolism/*therapeutic use ; Arthritis, Rheumatoid/*drug therapy/microbiology/physiopathology ; Bacteroidetes/genetics/metabolism ; Clostridiales/genetics/metabolism ; Cohort Studies ; Escherichia/genetics/metabolism ; Euryarchaeota/genetics/metabolism ; Female ; Firmicutes/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Machine Learning ; Male ; Metabolomics ; Metagenomics ; Methotrexate/metabolism/*therapeutic use ; Middle Aged ; Prognosis ; RNA, Ribosomal, 16S ; Shigella/genetics/metabolism ; Treatment Outcome ; }, abstract = {OBJECTIVE: Although oral methotrexate (MTX) remains the anchor drug for rheumatoid arthritis (RA), up to 50% of patients do not achieve a clinically adequate outcome. In addition, there is a lack of prognostic tools for treatment response prior to drug initiation. This study was undertaken to investigate whether interindividual differences in the human gut microbiome can aid in the prediction of MTX efficacy in new-onset RA.<br><br>METHODS: We performed 16S ribosomal RNA gene and shotgun metagenomic sequencing on the baseline gut microbiomes of drug-naive patients with new-onset RA (n = 26). Results were validated in an additional independent cohort (n = 21). To gain insight into potential microbial mechanisms, we conducted ex vivo experiments coupled with metabolomics analysis to evaluate the association between microbiome-driven MTX depletion and clinical response.<br><br>RESULTS: Our analysis revealed significant associations of the abundance of gut bacterial taxa and their genes with future clinical response (q < 0.05), including orthologs related to purine and MTX metabolism. Machine learning techniques were applied to the metagenomic data, resulting in a microbiome-based model that predicted lack of response to MTX in an independent group of patients. Finally, MTX levels remaining after ex vivo incubation with distal gut samples from pretreatment RA patients significantly correlated with the magnitude of future clinical response, suggesting a possible direct effect of the gut microbiome on MTX metabolism and treatment outcomes.<br><br>CONCLUSION: Taken together, these findings are the first step toward predicting lack of response to oral MTX in patients with new-onset RA and support the value of the gut microbiome as a possible prognostic tool and as a potential target in RA therapeutics.}, }
@article {pmid33302990, year = {2020}, author = {Chen, JC and Tyler, AD}, title = {Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data.}, journal = {Biology direct}, volume = {15}, number = {1}, pages = {29}, pmid = {33302990}, issn = {1745-6150}, mesh = {*Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*analysis ; *Supervised Machine Learning ; }, abstract = {BACKGROUND: The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets provided by the 2019 CAMDA challenge, we evaluated the influence of variable technical, analytical and machine learning approaches for result interpretation and novel source prediction.<br><br>RESULTS: Comparison between 16S rRNA amplicon and shotgun sequencing approaches as well as metagenomic analytical tools showed differences in normalized microbial abundance, especially for organisms present at low abundance. Shotgun sequence data analyzed using Kraken2 and Bracken, for taxonomic annotation, had higher detection sensitivity. As classification models are limited to labeling pre-trained origins, we took an alternative approach using Lasso-regularized multivariate regression to predict geographic coordinates for comparison. In both models, the prediction errors were much higher in Leave-1-city-out than in 10-fold cross validation, of which the former realistically forecasted the increased difficulty in accurately predicting samples from new origins. This challenge was further confirmed when applying the model to a set of samples obtained from new origins. Overall, the prediction performance of the regression and classification models, as measured by mean squared error, were comparable on mystery samples. Due to higher prediction error rates for samples from new origins, we provided an additional strategy based on prediction ambiguity to infer whether a sample is from a new origin. Lastly, we report increased prediction error when data from different sequencing protocols were included as training data.<br><br>CONCLUSIONS: Herein, we highlight the capacity of predicting sample origin accurately with pre-trained origins and the challenge of predicting new origins through both regression and classification models. Overall, this work provides a summary of the impact of sequencing technique, protocol, taxonomic analytical approaches, and machine learning approaches on the use of metagenomics for prediction of sample origin.}, }
@article {pmid33225966, year = {2020}, author = {Huang, L and Xu, C and Yang, W and Yu, R}, title = {A machine learning framework to determine geolocations from metagenomic profiling.}, journal = {Biology direct}, volume = {15}, number = {1}, pages = {27}, pmid = {33225966}, issn = {1745-6150}, mesh = {Cities ; Geography ; Humans ; *Machine Learning ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; }, abstract = {BACKGROUND: Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples' geolocations. In this paper, we present a machine learning framework to determine the geolocations from metagenomics profiling of microbial samples.<br><br>RESULTS: Our method was applied to the multi-source microbiome data from MetaSUB (The Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium for the CAMDA 2019 Metagenomic Forensics Challenge (the Challenge). The goal of the Challenge is to predict the geographical origins of mystery samples by constructing microbiome fingerprints.First, we extracted features from metagenomic abundance profiles. We then randomly split the training data into training and validation sets and trained the prediction models on the training set. Prediction performance was evaluated on the validation set. By using logistic regression with L2 normalization, the prediction accuracy of the model reaches 86%, averaged over 100 random splits of training and validation datasets.The testing data consists of samples from cities that do not occur in the training data. To predict the "mystery" cities that are not sampled before for the testing data, we first defined biological coordinates for sampled cities based on the similarity of microbial samples from them. Then we performed affine transform on the map such that the distance between cities measures their biological difference rather than geographical distance. After that, we derived the probabilities of a given testing sample from unsampled cities based on its predicted probabilities on sampled cities using Kriging interpolation. Results show that this method can successfully assign high probabilities to the true cities-of-origin of testing samples.<br><br>CONCLUSION: Our framework shows good performance in predicting the geographic origin of metagenomic samples for cities where training data are available. Furthermore, we demonstrate the potential of the proposed method to predict metagenomic samples' geolocations for samples from locations that are not in the training dataset.}, }
@article {pmid34210980, year = {2021}, author = {Wang, J and Zhang, J and Liu, W and Zhang, H and Sun, Z}, title = {Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {55}, pmid = {34210980}, issn = {2055-5008}, mesh = {Computational Biology/methods ; *Gastrointestinal Microbiome ; *Gene Expression Profiling/methods ; Gene Expression Regulation, Bacterial ; Humans ; Lactobacillus casei/*genetics ; *Metagenome ; *Metagenomics/methods ; *Transcriptome ; }, abstract = {Little is known about the replication and dynamic transcription of probiotics during their "passenger" journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.}, }
@article {pmid34112927, year = {2021}, author = {Ericsson, AC and Hart, ML and Kwan, J and Lanoue, L and Bower, LR and Araiza, R and Kent Lloyd, KC and Franklin, CL}, title = {Supplier-origin mouse microbiomes significantly influence locomotor and anxiety-related behavior, body morphology, and metabolism.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {716}, pmid = {34112927}, issn = {2399-3642}, mesh = {Animals ; Anxiety/metabolism/microbiology/physiopathology ; Behavior, Animal ; Disease Models, Animal ; Exploratory Behavior ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Locomotion ; Lymphopoiesis ; Male ; Mice/anatomy &amp; histology/*microbiology/physiology ; Mice, Inbred ICR ; }, abstract = {The mouse is the most commonly used model species in biomedical research. Just as human physical and mental health are influenced by the commensal gut bacteria, mouse models of disease are influenced by the fecal microbiome (FM). The source of mice represents one of the strongest influences on the FM and can influence the phenotype of disease models. The FM influences behavior in mice leading to the hypothesis that mice of the same genetic background from different vendors, will have different behavioral phenotypes. To test this hypothesis, colonies of CD-1 mice, rederived via embryo transfer into surrogate dams from four different suppliers, were subjected to phenotyping assays assessing behavior and physiological parameters. Significant differences in behavior, growth rate, metabolism, and hematological parameters were observed. Collectively, these findings show the profound influence of supplier-origin FMs on host behavior and physiology in healthy, genetically similar, wild-type mice maintained in identical environments.}, }
@article {pmid33986295, year = {2021}, author = {Huang, HJ and Ye, ZX and Wang, X and Yan, XT and Zhang, Y and He, YJ and Qi, YH and Zhang, XD and Zhuo, JC and Lu, G and Lu, JB and Mao, QZ and Sun, ZT and Yan, F and Chen, JP and Zhang, CX and Li, JM}, title = {Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {43}, pmid = {33986295}, issn = {2055-5008}, mesh = {Animals ; Databases, Genetic ; Hemiptera/*virology ; Host Specificity ; Insect Vectors/virology ; Metagenome ; Metagenomics/methods ; Phylogeny ; RNA Viruses/*classification/*genetics ; RNA, Viral ; *Virome ; }, abstract = {A large number of insect-specific viruses (ISVs) have recently been discovered, mostly from hematophagous insect vectors because of their medical importance, but little attention has been paid to important plant virus vectors such as the whitefly Bemisia tabaci, which exists as a complex of cryptic species. Public SRA datasets of B. tabaci and newly generated transcriptomes of three Chinese populations are here comprehensively investigated to characterize the whitefly viromes of different cryptic species. Twenty novel ISVs were confidently identified, mostly associated with a particular cryptic species while different cryptic species harbored one or more core ISVs. Microinjection experiments showed that some ISVs might cross-infect between the two invasive whitefly cryptic species, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), but others appeared to have a more restricted host range, reflecting the possibility of distinct long-term coevolution of these ISVs and whitefly hosts. Moreover, analysis of the profiles of virus-derived small-interfering RNAs indicated that some of the ISVs can successfully replicate in whitefly and the antiviral RNAi pathway of B. tabaci is actively involved in response to ISV infections. Our study provides a comprehensive analysis of the RNA virome, the distinct relationships and cross-cryptic species infectivity of ISVs in an agriculturally important insect vector.}, }
@article {pmid33963194, year = {2021}, author = {Callegari, M and Crotti, E and Fusi, M and Marasco, R and Gonella, E and De Noni, I and Romano, D and Borin, S and Tsiamis, G and Cherif, A and Alma, A and Daffonchio, D}, title = {Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {42}, pmid = {33963194}, issn = {2055-5008}, mesh = {Animals ; *Bacteria/classification/ultrastructure ; *Bees ; *Biodiversity ; *Fungi/classification/ultrastructure ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; }, abstract = {The core gut microbiome of adult honeybee comprises a set of recurring bacterial phylotypes, accompanied by lineage-specific, variable, and less abundant environmental bacterial phylotypes. Several mutual interactions and functional services to the host, including the support provided for growth, hormonal signaling, and behavior, are attributed to the core and lineage-specific taxa. By contrast, the diversity and distribution of the minor environmental phylotypes and fungal members in the gut remain overlooked. In the present study, we hypothesized that the microbial components of forager honeybees (i.e., core bacteria, minor environmental phylotypes, and fungal members) are compartmentalized along the gut portions. The diversity and distribution of such three microbial components were investigated in the context of the physico-chemical conditions of different gut compartments. We observed that changes in the distribution and abundance of microbial components in the gut are consistently compartment-specific for all the three microbial components, indicating that the ecological and physiological interactions among the host and microbiome vary with changing physico-chemical and metabolic conditions of the gut.}, }
@article {pmid33879801, year = {2021}, author = {Guo, N and Wu, Q and Shi, F and Niu, J and Zhang, T and Degen, AA and Fang, Q and Ding, L and Shang, Z and Zhang, Z and Long, R}, title = {Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {38}, pmid = {33879801}, issn = {2055-5008}, mesh = {*Acclimatization ; *Altitude ; *Animal Feed ; Animals ; Biodiversity ; Biomass ; Cattle ; Cold Temperature ; *Gastrointestinal Microbiome ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; *Seasons ; }, abstract = {Dietary selection and intake affect the survival and health of mammals under extreme environmental conditions. It has been suggested that dietary composition is a key driver of gut microbiota variation; however, how gut microbiota respond to seasonal dietary changes under extreme natural conditions remains poorly understood. Sequencing plant trnL (UAA) region and 16S rRNA gene analysis were employed to determine dietary composition and gut microbiota in freely grazing yaks on the Tibetan plateau. Dietary composition was more diverse in winter than in summer, while Gramineae and Rosaceae were consumed frequently all year. Turnover of seasonal diet and gut microbiota composition occurred consistently. Yaks shifted enterotypes in response to dietary change between warm and cold seasons to best utilize nitrogen and energy, in particular in the harsh cold season. Our findings provide insights into understanding seasonal changes of diet-microbiota linkages in the adaptation of mammals to high altitudes.}, }
@article {pmid33863892, year = {2021}, author = {Luhung, I and Uchida, A and Lim, SBY and Gaultier, NE and Kee, C and Lau, KJX and Gusareva, ES and Heinle, CE and Wong, A and Premkrishnan, BNV and Purbojati, RW and Acerbi, E and Kim, HL and Junqueira, ACM and Longford, S and Lohar, SR and Yap, ZH and Panicker, D and Koh, Y and Kushwaha, KK and Ang, PN and Putra, A and Drautz-Moses, DI and Schuster, SC}, title = {Experimental parameters defining ultra-low biomass bioaerosol analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {37}, pmid = {33863892}, issn = {2055-5008}, mesh = {Air Microbiology ; *Biomass ; *Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.}, }
@article {pmid33619330, year = {2021}, author = {Bessey, C and Neil Jarman, S and Simpson, T and Miller, H and Stewart, T and Kenneth Keesing, J and Berry, O}, title = {Passive eDNA collection enhances aquatic biodiversity analysis.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {236}, pmid = {33619330}, issn = {2399-3642}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Environmental DNA/*isolation &amp; purification ; *Environmental Monitoring/instrumentation ; Fishes/classification/*genetics ; Membranes, Artificial ; *Metagenome ; *Metagenomics ; Oceans and Seas ; Phylogeny ; }, abstract = {Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish biodiversity. Furthermore, passive eDNA collection enables greater levels of biological sampling, which increases the range of ecological questions that eDNA metabarcoding can address.}, }
@article {pmid33619320, year = {2021}, author = {Sims, TT and El Alam, MB and Karpinets, TV and Dorta-Estremera, S and Hegde, VL and Nookala, S and Yoshida-Court, K and Wu, X and Biegert, GWG and Delgado Medrano, AY and Solley, T and Ahmed-Kaddar, M and Chapman, BV and Sastry, KJ and Mezzari, MP and Petrosino, JF and Lin, LL and Ramondetta, L and Jhingran, A and Schmeler, KM and Ajami, NJ and Wargo, J and Colbert, LE and Klopp, AH}, title = {Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {237}, pmid = {33619320}, issn = {2399-3642}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Antigens, CD/metabolism ; Antigens, Differentiation, T-Lymphocyte/metabolism ; CD4-Positive T-Lymphocytes/immunology/metabolism ; *Chemoradiotherapy/adverse effects/mortality ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; Ki-67 Antigen/metabolism ; Lectins, C-Type/metabolism ; Lymphocytes, Tumor-Infiltrating/immunology/metabolism ; Middle Aged ; Prospective Studies ; Time Factors ; Treatment Outcome ; Tumor Microenvironment ; Uterine Cervical Neoplasms/immunology/microbiology/mortality/*therapy ; }, abstract = {Diversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not have adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut microbiome was independently associated with survival in cervical cancer patients receiving chemoradiation. Our study demonstrates that the diversity of gut microbiota is associated with a favorable response to chemoradiation. Additionally, compositional variation among patients correlated with short term and long-term survival. Short term survivor fecal samples were significantly enriched in Porphyromonas, Porphyromonadaceae, and Dialister, whereas long term survivor samples were significantly enriched in Escherichia Shigella, Enterobacteriaceae, and Enterobacteriales. Moreover, analysis of immune cells from cervical tumor brush samples by flow cytometry revealed that patients with a high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ over the course of radiation therapy. Modulation of the gut microbiota before chemoradiation might provide an alternative way to enhance treatment efficacy and improve treatment outcomes in cervical cancer patients.}, }
@article {pmid33606522, year = {2021}, author = {Cerro-Gálvez, E and Dachs, J and Lundin, D and Fernández-Pinos, MC and Sebastián, M and Vila-Costa, M}, title = {Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {14}, pages = {9609-9621}, doi = {10.1021/acs.est.0c07262}, pmid = {33606522}, issn = {1520-5851}, mesh = {Carbon ; *Environmental Pollutants ; Metagenomics ; *Microbiota ; Seawater ; }, abstract = {Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.}, }
@article {pmid34371435, year = {2021}, author = {Balasubramanian, VK and Joseph Maran, MI and Ramteke, D and Vijaykumar, DS and Kottarathail Rajendran, A and Ramachandran, P and Ramachandran, R}, title = {Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India.}, journal = {Marine pollution bulletin}, volume = {171}, number = {}, pages = {112786}, doi = {10.1016/j.marpolbul.2021.112786}, pmid = {34371435}, issn = {1879-3363}, abstract = {Strong conservation management needs comprehensive data on biodiversity. Rapid methods that document aquatic biodiversity or assess the health condition of an ecosystem remain scarce. Herein, we have performed a metagenomics study on environmental DNA (eDNA) collected from an urban backwater area - Muttukadu, located in the southeast coast of India. Shotgun metagenomics approach using Illumina®NextSeq500 sequencing yielded 88.4 million raw reads. The processed data was assigned as 80% prokaryotes, 0.4% eukaryotes, ~2% viruses, and ~17% remain unknown. This approach has the potential to identify small micro-eukaryote, unseen species from both estuarine and marine environments. We have identified 156 eukaryote organisms represented from 21 phyla and 112 families, including those that are of conservational significance and ecological importance. Furthermore, our data also demonstrated the presence of pathogenic microorganisms due to sewage mixing with the backwaters. Given its sensitivity, we suggest this approach for an initial assessment of biodiversity structure in an ecosystem for the biomonitoring program.}, }
@article {pmid34051218, year = {2021}, author = {Wang, H and Banerjee, N and Liang, Y and Wang, G and Hoffman, KL and Khan, MF}, title = {Gut microbiome-host interactions in driving environmental pollutant trichloroethene-mediated autoimmunity.}, journal = {Toxicology and applied pharmacology}, volume = {424}, number = {}, pages = {115597}, pmid = {34051218}, issn = {1096-0333}, support = {R01 ES016302/ES/NIEHS NIH HHS/United States ; R01 ES026887/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Autoimmunity/*drug effects ; Bacteria/*drug effects ; Drug Administration Schedule ; Environmental Pollutants/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Inflammation ; Liver/drug effects ; Mice ; Mice, Inbred Strains ; Oxidative Stress ; Spleen/drug effects ; Trichloroethylene/*toxicity ; }, abstract = {Trichloroethene (TCE), a widely used industrial solvent, is associated with the development of autoimmune diseases (ADs), including systemic lupus erythematosus and autoimmune hepatitis. Increasing evidence support a linkage between altered gut microbiome composition and the onset of ADs. However, it is not clear how gut microbiome contributes to TCE-mediated autoimmunity, and initial triggers for microbiome-host interactions leading to systemic autoimmune responses remain unknown. To achieve this, female MRL+/+ mice were treated with 0.5 mg/ml TCE for 52 weeks and fecal samples were subjected to 16S rRNA sequencing to determine the microbiome composition. TCE exposure resulted in distinct bacterial community revealed by β-diversity analysis. Notably, we observed reduction in Lactobacillaceae, Rikenellaceae and Bifidobacteriaceae families, and enrichment of Akkermansiaceae and Lachnospiraceae families after TCE exposure. We also observed significantly increased colonic oxidative stress and inflammatory markers (CD14 and IL-1β), and decreased tight junction proteins (ZO-2, occludin and claudin-3). These changes were associated with increases in serum antinuclear and anti-smooth muscle antibodies and cytokines (IL-6 and IL-12), together with increased PD1 + CD4+ T cells in TCE-exposed spleen and liver tissues. Importantly, fecal microbiota transplantation (FMT) using feces from TCE-treated mice to antibiotics-treated mice induced increased anti-dsDNA antibodies and hepatic CD4+ T cell infiltration in the recipient mice. Our studies thus delineate how imbalance in gut microbiome and mucosal redox status together with gut inflammatory response and permeability changes could be the key factors in contributing to TCE-mediated ADs. Furthermore, FMT studies provide a solid support to a causal role of microbiome in TCE-mediated autoimmunity.}, }
@article {pmid33990699, year = {2021}, author = {Rasmussen, JA and Villumsen, KR and Duchêne, DA and Puetz, LC and Delmont, TO and Sveier, H and Jørgensen, LVG and Præbel, K and Martin, MD and Bojesen, AM and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {579}, pmid = {33990699}, issn = {2399-3642}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; *Metagenome ; Mycoplasma/*genetics ; Phylogeny ; Salmonidae/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.}, }
@article {pmid33686191, year = {2021}, author = {Holmfeldt, K and Nilsson, E and Simone, D and Lopez-Fernandez, M and Wu, X and de Bruijn, I and Lundin, D and Andersson, AF and Bertilsson, S and Dopson, M}, title = {The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {307}, pmid = {33686191}, issn = {2399-3642}, mesh = {Firmicutes/growth &amp; development/virology ; Groundwater/microbiology/*virology ; Host-Pathogen Interactions ; Metagenomics ; Population Density ; Time Factors ; *Virome ; *Virus Replication ; Viruses/genetics/*growth &amp; development/metabolism ; Water Microbiology ; }, abstract = {The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.}, }
@article {pmid33022252, year = {2020}, author = {Lemon, KP}, title = {Human nasal microbiota.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {R1118-R1119}, doi = {10.1016/j.cub.2020.08.010}, pmid = {33022252}, issn = {1879-0445}, support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Infections/*microbiology ; Humans ; *Microbiota ; Nasal Cavity/*microbiology ; }, abstract = {The human nasal passages host a distinct community of microbes. Katherine P. Lemon describes this distinct community, and why it matters so much for human health.}, }
@article {pmid32531278, year = {2020}, author = {Ellegaard, KM and Suenami, S and Miyazaki, R and Engel, P}, title = {Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species.}, journal = {Current biology : CB}, volume = {30}, number = {13}, pages = {2520-2531.e7}, pmid = {32531278}, issn = {1879-0445}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Bees/*microbiology ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Species Specificity ; }, abstract = {Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.}, }
@article {pmid34361900, year = {2021}, author = {Panaiotov, S and Hodzhev, Y and Tsafarova, B and Tolchkov, V and Kalfin, R}, title = {Culturable and Non-Culturable Blood Microbiota of Healthy Individuals.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, doi = {10.3390/microorganisms9071464}, pmid = {34361900}, issn = {2076-2607}, support = {DN-01-4/16.12.2016//Bulgarian National Science Fund/ ; KP-06-DV/10-21.12.2019//Bulgarian National Science Fund/ ; }, abstract = {Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.}, }
@article {pmid34271900, year = {2021}, author = {Oliveira, SG and Nishiyama, RR and Trigo, CAC and Mattos-Guaraldi, AL and Dávila, AMR and Jardim, R and Aguiar, FHB}, title = {Core of the saliva microbiome: an analysis of the MG-RAST data.}, journal = {BMC oral health}, volume = {21}, number = {1}, pages = {351}, pmid = {34271900}, issn = {1472-6831}, mesh = {Bacteria/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Saliva ; }, abstract = {BACKGROUND: Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms.<br><br>METHODS: Projects containing the term "SALIVA", deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann-Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used.<br><br>RESULTS: The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r = - 0.78) and the lowest between Alpha and Unknown (r = - 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r = - 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter.<br><br>CONCLUSIONS: Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.}, }
@article {pmid32576522, year = {2020}, author = {Lopetuso, LR and Quagliariello, A and Schiavoni, M and Petito, V and Russo, A and Reddel, S and Del Chierico, F and Ianiro, G and Scaldaferri, F and Neri, M and Cammarota, G and Putignani, L and Gasbarrini, A}, title = {Towards a disease-associated common trait of gut microbiota dysbiosis: The pivotal role of Akkermansia muciniphila.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {52}, number = {9}, pages = {1002-1010}, doi = {10.1016/j.dld.2020.05.020}, pmid = {32576522}, issn = {1878-3562}, mesh = {Akkermansia/physiology ; Case-Control Studies ; Dysbiosis/metabolism/*physiopathology ; Feces/*microbiology ; Gastrointestinal Diseases/metabolism/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestinal Mucosa/*metabolism/microbiology ; Permeability ; Phenotype ; }, abstract = {BACKGROUND: Gut microbiota exerts a crucial role in gastrointestinal (GI) and extra-intestinal (EI) disorders. In this context, Akkermansia muciniphila is pivotal for the maintenance of host health and has been correlated with several disorders.<br><br>AIM: To explore the potential role of A. muciniphila as common dysbiotic marker linked to the disease status.<br><br>METHODS: A cohort of patients affected by GI and EI disorders was enrolled and compared to healthy controls (CTRLs). A targeted-metagenomics approach combined to unsupervised cluster and machine learning (ML) analyses provided microbiota signatures.<br><br>RESULTS: Microbiota composition was associated to disease phenotype, therapies, diet and anthropometric features, identifying phenotype and therapies as the most impacting variables on microbiota ecology. Unsupervised cluster analyses identified one cluster composed by the majority of patients. DESeq2 algorithm identified ten microbial discriminatory features of patients and CTRLs clusters. Among these microbes, Akkermansia muciniphila resulted the discriminating ML node between patients and CTRLs, independently of specific GI/EI disease or confounding effects. A. muciniphila decrease represented a transversal signature of gut microbiota alteration, showing also an inverse correlation with α-diversity.<br><br>CONCLUSION: Overall, A. muciniphila decline may have a crucial role in affecting microbial ecology and in discriminating patients from healthy subjects. Its grading may be considered as a gut dysbiosis feature associated to disease-related microbiota profile.}, }
@article {pmid32350078, year = {2020}, author = {Call, L and Molina, T and Stoll, B and Guthrie, G and Chacko, S and Plat, J and Robinson, J and Lin, S and Vonderohe, C and Mohammad, M and Kunichoff, D and Cruz, S and Lau, P and Premkumar, M and Nielsen, J and Fang, Z and Olutoye, O and Thymann, T and Britton, R and Sangild, P and Burrin, D}, title = {Parenteral lipids shape gut bile acid pools and microbiota profiles in the prevention of cholestasis in preterm pigs.}, journal = {Journal of lipid research}, volume = {61}, number = {7}, pages = {1038-1051}, pmid = {32350078}, issn = {1539-7262}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK094616/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Cholestasis/complications/*metabolism/*microbiology ; *Lipid Metabolism ; *Microbiota ; Parenteral Nutrition ; Premature Birth/*metabolism/*microbiology ; Swine ; }, abstract = {Multi-component lipid emulsions, rather than soy-oil emulsions, prevent cholestasis by an unknown mechanism. Here, we quantified liver function, bile acid pools, and gut microbial and metabolite profiles in premature parenterally fed pigs given a soy-oil lipid emulsion, Intralipid (IL), a multi component lipid emulsion, SMOFlipid (SMOF), a novel emulsion with a modified fatty-acid composition [experimental emulsion (EXP)], or a control enteral diet (ENT) for 22 days. We assayed serum cholestasis markers, measured total bile acid levels in plasma, liver, and gut contents, and analyzed colonic bacterial 16S rRNA gene sequences and metabolomic profiles. Serum cholestasis markers (i.e., bilirubin, bile acids, and γ-glutamyl transferase) were highest in IL-fed pigs and normalized in those given SMOF, EXP, or ENT. Gut bile acid pools were lowest in the IL treatment and were increased in the SMOF and EXP treatments and comparable to ENT. Multiple bile acids, especially their conjugated forms, were higher in the colon contents of SMOF and EXP than in IL pigs. The colonic microbial communities of SMOF and EXP pigs had lower relative abundance of several gram-positive anaerobes, including Clostridrium XIVa, and higher abundance of Enterobacteriaceae than those of IL and ENT pigs. Differences in lipid and microbial-derived compounds were also observed in colon metabolite profiles. These results indicate that multi-component lipid emulsions prevent cholestasis and restore enterohepatic bile flow in association with gut microbial and metabolomic changes. We conclude that sustained bile flow induced by multi-component lipid emulsions likely exerts a dominant effect in reducing bile acid-sensitive gram-positive bacteria.}, }
@article {pmid32320134, year = {2020}, author = {Bieker, VC and Sánchez Barreiro, F and Rasmussen, JA and Brunier, M and Wales, N and Martin, MD}, title = {Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1206-1219}, doi = {10.1111/1755-0998.13174}, pmid = {32320134}, issn = {1755-0998}, support = {//NTNU/ ; }, mesh = {Alternaria ; Ambrosia ; Arabidopsis ; Fungi/genetics ; *Microbiota ; Museums ; *Plants/genetics/microbiology ; Sequence Analysis, DNA ; }, abstract = {Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.}, }
@article {pmid31242511, year = {2020}, author = {Faucher, MA and Greathouse, KL and Hastings-Tolsma, M and Padgett, RN and Sakovich, K and Choudhury, A and Sheikh, A and Ajami, NJ and Petrosino, JF}, title = {Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study.}, journal = {American journal of perinatology}, volume = {37}, number = {11}, pages = {1160-1172}, doi = {10.1055/s-0039-1692715}, pmid = {31242511}, issn = {1098-8785}, support = {Baylor University, Baylor College of Medicine, and Baylor Research Institution-Project//30300146/International ; }, mesh = {Adult ; African Americans ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, rRNA ; Gestational Weight Gain/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Obesity ; Pilot Projects ; Pregnancy ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; *Weight Gain ; Young Adult ; }, abstract = {OBJECTIVE: This study determines the differences in the distal gut and vaginal microbiome in African American (AA) women by prepregnancy body mass index and gestational weight gain (GWG) comparing women with and without obesity and by obesity class.<br><br>STUDY DESIGN: We prospectively sampled the vaginal and distal gut microbiome in pregnant AA women at two time points during pregnancy. Samples were analyzed using high-throughput sequencing of the V4 region of the 16S ribosomal ribonucleic acid gene.<br><br>RESULTS: Distinct differences in vaginal and distal gut α-diversity were observed at time point 1 between women with and without obesity by total GWG. Significant differences in distal gut β-diversity were also found at time point 1 in obese women by GWG. Within the Bacteroides genus, a significant association was observed by total GWG among obese women which was absent in nonobese women. Women with class III obesity who experienced low GWG had the lowest abundance of distal gut Bacteroides and appreciably higher relative abundance of a consortia of vaginal taxa including Atopobium, Gardnerella, Prevotella, and Sneathia.<br><br>CONCLUSION: These results contribute new evidence showing that GWG in combination with obesity and obesity class is associated with an altered distal gut and vaginal composition early in pregnancy among AA women.}, }
@article {pmid34225233, year = {2021}, author = {Borsetto, C and Raguideau, S and Travis, E and Kim, DW and Lee, DH and Bottrill, A and Stark, R and Song, L and Cha, CJ and Pearson, J and Quince, C and Singer, AC and Wellington, EMH}, title = {Impact of sulfamethoxazole on a riverine microbiome.}, journal = {Water research}, volume = {201}, number = {}, pages = {117382}, doi = {10.1016/j.watres.2021.117382}, pmid = {34225233}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Genes, Bacterial ; *Microbiota ; Rivers ; *Sulfamethoxazole ; Waste Water ; }, abstract = {The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment (6 kg) with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L-1) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.}, }
@article {pmid34186487, year = {2021}, author = {Wilson, BC and Butler, ÉM and Grigg, CP and Derraik, JGB and Chiavaroli, V and Walker, N and Thampi, S and Creagh, C and Reynolds, AJ and Vatanen, T and O'Sullivan, JM and Cutfield, WS}, title = {Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial.}, journal = {EBioMedicine}, volume = {69}, number = {}, pages = {103443}, doi = {10.1016/j.ebiom.2021.103443}, pmid = {34186487}, issn = {2352-3964}, mesh = {Administration, Oral ; Adult ; Bacteroides/pathogenicity ; Cesarean Section/*adverse effects ; Fecal Microbiota Transplantation/adverse effects/*methods ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/etiology/*microbiology/prevention &amp; control ; Male ; Vagina/*microbiology ; }, abstract = {BACKGROUND: Birth by caesarean section (CS) is associated with aberrant gut microbiome development and greater disease susceptibility later in life. We investigated whether oral administration of maternal vaginal microbiota to infants born by CS could restore their gut microbiome development in a pilot single-blinded, randomised placebo-controlled trial (Australian New Zealand Clinical Trials Registry, ACTRN12618000339257).<br><br>METHODS: Pregnant women scheduled for a CS underwent comprehensive antenatal pathogen screening. At birth, healthy neonates were randomised to receive a 3 ml solution of either maternal vaginal microbes (CS-seeded, n = 12) or sterile water (CS-placebo, n = 13). Vaginally-born neonates were used as the reference control (VB, n = 22). Clinical assessments occurred within the first 2 h of birth, and at 1 month and 3 months of age. Infant stool samples and maternal vaginal extracts from CS women underwent shotgun metagenomic sequencing. The primary outcome was gut microbiome composition at 1 month of age. Secondary outcomes included maternal strain engraftment, functional potential of the gut microbiome, anthropometry, body composition, and adverse events.<br><br>FINDINGS: Despite the presence of viable microbial cells within transplant solutions, there were no observed differences in gut microbiome composition or functional potential between CS-seeded and CS-placebo infants at 1 month or 3 months of age. Both CS groups displayed the characteristic signature of low Bacteroides abundance, which contributed to a number of biosynthesis pathways being underrepresented when compared with VB microbiomes. Maternal vaginal strain engraftment was rare. Vaginal seeding had no observed effects on anthropometry or body composition. There were no serious adverse events associated with treatment.<br><br>INTERPRETATION: Our pilot findings question the value of vaginal seeding given that oral administration of maternal vaginal microbiota did not alter early gut microbiome development in CS-born infants. The limited colonisation of maternal vaginal strains suggest that other maternal sources, such as the perianal area, may play a larger role in seeding the neonatal gut microbiome.<br><br>FUNDING: Health Research Council of New Zealand, A Better Start - National Science Challenge.}, }
@article {pmid33894059, year = {2021}, author = {Sun, J and Chen, YL and Ding, YC and Zhong, H and Wu, M and Liu, ZH and Ge, LP}, title = {Deposition of resistant bacteria and resistome through FMT in germ-free piglets.}, journal = {Letters in applied microbiology}, volume = {73}, number = {2}, pages = {187-196}, doi = {10.1111/lam.13490}, pmid = {33894059}, issn = {1472-765X}, support = {cstc2019jxjl80019//Chongqing Scientific Research Institute Performance Incentive and Guidance Special Project/ ; 21509(20227)//Chongqing Basic Scientific Research/ ; 20206//the Key R &amp; D Project in Agriculture and Animal Husbandries of Rongchang/ ; }, mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/*drug effects ; Biodiversity ; DNA, Bacterial ; Drug Resistance, Multiple, Bacterial/*genetics ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; Interspersed Repetitive Sequences ; Metagenomics ; Swine ; Virulence Factors/*genetics ; }, abstract = {Faecal microbiota transplantation (FMT) has received considerable attention in recent years due to its remarkable efficacy in restoring a normal gut microbiome. Here, we established the groups of post-FMT recipient piglets using germ-free piglets during early life to characterize the colonization of gut microbiota composition and the enrichment of resistance gene acquisition. By metagenomic analysis, we identified 115 bacterial phyla and 2111 bacterial genera that were acquired by the FMT recipients. We found that early-life microbial colonization and the spread of resistomes in recipient piglets were age dependent. A total of 425, 425 and 358 AR genes primarily belonging to 114, 114 and 102 different types were detected in the donors, post-FMT recipients in the FMT-3D group and post-FMT recipients in the FMT-15D group respectively. Genes that encoded tetracycline, macrolide and chloramphenicol resistance proteins were the most dominant AR genes, and the results corresponded with the exposure of antibiotic consumption at farm. Bacteroides, Escherichia, Clostridium, Parabacteroides, Treponema, Lactobacillus and Enterococcus were significantly correlated with the distribution of AR genes. More importantly, the relative abundance of AR genes was positively correlated with the levels of mobile genetic elements. Our results indicate that early-life microbial colonization can persistently shape the gut microbiota and antibiotic resistome.}, }
@article {pmid33803228, year = {2021}, author = {Marter, P and Huang, S and Brinkmann, H and Pradella, S and Jarek, M and Rohde, M and Bunk, B and Petersen, J}, title = {Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33803228}, issn = {2073-4425}, mesh = {Cyanobacteria/*genetics ; Genome, Bacterial/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.}, }
@article {pmid33148818, year = {2020}, author = {Garner, RE and Gregory-Eaves, I and Walsh, DA}, title = {Sediment Metagenomes as Time Capsules of Lake Microbiomes.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33148818}, issn = {2379-5042}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/virology ; Bacteriophages/genetics ; Canada ; Genetic Variation ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria ("Candidatus Nanopelagicales") and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.}, }
@article {pmid34346741, year = {2021}, author = {Breitkreuz, C and Heintz-Buschart, A and Buscot, F and Wahdan, SFM and Tarkka, M and Reitz, T}, title = {Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0027821}, doi = {10.1128/Spectrum.00278-21}, pmid = {34346741}, issn = {2165-0497}, abstract = {Computational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (β-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems. IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.}, }
@article {pmid34336713, year = {2021}, author = {Caddey, B and De Buck, J}, title = {Meta-Analysis of Bovine Digital Dermatitis Microbiota Reveals Distinct Microbial Community Structures Associated With Lesions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {685861}, pmid = {34336713}, issn = {2235-2988}, mesh = {Animals ; Cattle ; *Cattle Diseases ; *Digital Dermatitis ; Metagenomics ; *Microbiota ; Treponema/genetics ; }, abstract = {Bovine digital dermatitis (DD) is a significant cause of infectious lameness and economic losses in cattle production across the world. There is a lack of a consensus across different 16S metagenomic studies on DD-associated bacteria that may be potential pathogens of the disease. The goal of this meta-analysis was to identify a consistent group of DD-associated bacteria in individual DD lesions across studies, regardless of experimental design choices including sample collection and preparation, hypervariable region sequenced, and sequencing platform. A total of 6 studies were included in this meta-analysis. Raw sequences and metadata were identified on the NCBI sequence read archive and European nucleotide archive. Bacterial community structures were investigated between normal skin and DD skin samples. Random forest models were generated to classify DD status based on microbial composition, and to identify taxa that best differentiate DD status. Among all samples, members of Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were consistently identified in the majority of DD lesions, and were the best genera at differentiating DD lesions from normal skin. Individual study and 16S hypervariable region sequenced had significant influence on final DD lesion microbial composition (P < 0.05). These findings indicate that members of Treponema, Mycoplasma, Porphyromonas, and/or Fusobacterium may have significant roles in DD pathogenesis, and should be studied further in respect to elucidating DD etiopathogenic mechanisms and developing more effective treatment and mitigation strategies.}, }
@article {pmid34330336, year = {2021}, author = {Hiseni, P and Rudi, K and Wilson, RC and Hegge, FT and Snipen, L}, title = {HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {165}, pmid = {34330336}, issn = {2049-2618}, mesh = {*Gastrointestinal Microbiome/genetics ; Genome, Human ; Humans ; *Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes.<br><br>RESULTS: We screened > 5,700 healthy human gut metagenomes for the containment of > 490,000 publicly available prokaryotic genomes sourced from RefSeq and the recently announced UHGG collection. This resulted in a pool of > 381,000 genomes that were subsequently scored and ranked based on their prevalence in the healthy human metagenomes. The genomes were then clustered at a 97.5% sequence identity resolution, and cluster representatives (30,691 in total) were retained to comprise the HumGut collection. Using the Kraken2 software for classification, we find superior performance in the assignment of metagenomic reads, classifying on average 94.5% of the reads in a metagenome, as opposed to 86% with UHGG and 44% when using standard Kraken2 database. A coarser HumGut collection, consisting of genomes dereplicated at 95% sequence identity-similar to UHGG, classified 88.25% of the reads. HumGut, half the size of standard Kraken2 database and directly comparable to the UHGG size, outperforms them both.<br><br>CONCLUSIONS: The HumGut collection contains > 30,000 genomes clustered at a 97.5% sequence identity resolution and ranked by human gut prevalence. We demonstrate how metagenomes from IBD-patients map equally well to this collection, indicating this reference is relevant also for studies well outside the metagenome reference set used to obtain HumGut. All data and metadata, as well as helpful code, are available at http://arken.nmbu.no/~larssn/humgut/ . Video Abstract.}, }
@article {pmid34198177, year = {2021}, author = {Uke, A and Nakazono-Nagaoka, E and Chuah, JA and Zain, NA and Amir, HG and Sudesh, K and Abidin, NZHAZ and Hashim, Z and Kosugi, A}, title = {Effect of decomposing oil palm trunk fibers on plant growth and soil microbial community composition.}, journal = {Journal of environmental management}, volume = {295}, number = {}, pages = {113050}, doi = {10.1016/j.jenvman.2021.113050}, pmid = {34198177}, issn = {1095-8630}, mesh = {Biomass ; Humans ; *Microbiota ; *Saccharum ; Soil ; Soil Microbiology ; *Trichoderma ; }, abstract = {Oil palm trunks (OPT) are logged for replantation and the fiber residues are disposed of into the palm plantation area. The fiber residues are expected to increase soil fertility through recycling of carbon and minerals via fiber decomposition. This study investigated the effects of OPT fiber disposal and other lignocellulosic biomass on plant growth and microbial diversity in the soil environment. Four treatment plots were tested: (A) soil+OPT fiber (1:20), (B) soil+sugarcane bagasse (1:20), (C) soil+cellulose powder (1:20), and (D) unamended soil as a negative control. Low plant height, decreased chlorophyll content, and low biomass was observed in corn grown on soil mixed with OPT fiber, cellulose, and sugarcane bagasse, when compared with those of the control. The plants grown with OPT fiber were deficient in total nitrogen and magnesium when compared with those without fiber amendment, which suggested that nitrogen and minerals in soil might be taken up by changing microflora because of the OPT fibers presence. To confirm differences in the soil microflora, metagenomics analysis was performed on untreated soil and soil from each lignocellulose treatment. The microflora of soils mixed with OPT fiber, cellulose and sugarcane bagasse revealed substantial increases in bacteria such as families Cytophagaceae and Oscillospiraceae, and two major fungal genera, Trichoderma and Trichocladium, that are involved in lignocellulose degradation. OPT fiber resulted in a drastic increase in the ratios and amounts of Trichocladium in the soil when compared with those of cellulose and sugarcane bagasse. These results indicate that unregulated disposal of OPT fiber into plantation areas could result in nutrient loss from soil by increasing the abundance of microorganisms involved in lignocellulose decomposition.}, }
@article {pmid33039712, year = {2020}, author = {Li, X and Lin, Y and Li, X and Xu, X and Zhao, Y and Xu, L and Gao, Y and Li, Y and Tan, Y and Qian, P and Huang, H}, title = {Tyrosine supplement ameliorates murine aGVHD by modulation of gut microbiome and metabolome.}, journal = {EBioMedicine}, volume = {61}, number = {}, pages = {103048}, pmid = {33039712}, issn = {2352-3964}, mesh = {Acute Disease ; Animals ; Biodiversity ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; *Dietary Supplements ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Graft vs Host Disease/diagnosis/*etiology/*metabolism/therapy ; Intestinal Mucosa ; Mass Spectrometry/methods ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Tyrosine/*administration &amp; dosage ; }, abstract = {BACKGROUND: Microbial communities and their metabolic components in the gut are of vital importance for immune homeostasis and have an influence on the susceptibility of the host to a number of immune-mediated diseases like acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about the functional connections between microbiome and metabolome in aGVHD due to the complexity of the gastrointestinal environment.<br><br>METHOD: Initially, gut microbiota and fecal metabolic phenotype in aGVHD murine models were unleashed by performing 16S ribosomal DNA gene sequencing and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based metabolomics.<br><br>FINDINGS: The group with aGVHD experienced a significant drop in Lachnospiraceae_unclassified but an increase in the relative abundance of Clostridium XI, Clostridium XIVa and Enterococcus. Meanwhile, a lower content of tyrosine was observed in the gut of aGVHD mice. The correlation analysis revealed that tyrosine-related metabolites were inversely correlated with Clostridium XIVa, besides, Blautia and Enterococcus also displayed the negative tendency in aGVHD condition. Apart from exploring the importance and function of tyrosine, different tyrosine diets were offered to mice during transplantation. Additional tyrosine supplements can improve overall survival, ameliorate symptoms at the early stage of aGVHD and change the structure and composition of gut microbiota and fecal metabolic phenotype. In addition, aGVHD mice deprived from tyrosine displayed worse manifestations than the vehicle diet group.<br><br>INTERPRETATION: The results demonstrated the roles and mechanisms of gut microbiota, indispensable metabolites and tyrosine in the progression of aGVHD, which can be an underlying biomarker for aGVHD diagnosis and treatment.<br><br>FUNDING: This research was funded by the International Cooperation and Exchange Program (81520108002), the National Key R&amp;D Program of China, Stem Cell and Translation Research (2018YFA0109300), National Natural Science Foundation of China (81670169, 81670148, 81870080 and 91949115) and Natural Science Foundation of Zhejiang Province (LQ19H080006).}, }
@article {pmid33039709, year = {2020}, author = {Huang, X and Hong, X and Wang, J and Sun, T and Yu, T and Yu, Y and Fang, J and Xiong, H}, title = {Metformin elicits antitumour effect by modulation of the gut microbiota and rescues Fusobacterium nucleatum-induced colorectal tumourigenesis.}, journal = {EBioMedicine}, volume = {61}, number = {}, pages = {103037}, pmid = {33039709}, issn = {2352-3964}, mesh = {Animals ; Biomarkers ; *Cell Transformation, Neoplastic/drug effects ; Colonic Neoplasms/*etiology/*metabolism/pathology ; Disease Models, Animal ; Fusobacterium Infections/*complications/microbiology ; Fusobacterium nucleatum/*physiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/metabolism/pathology ; Metagenome ; Metagenomics/methods ; Metformin/*pharmacology ; Mice ; Mice, Transgenic ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {BACKGROUND: The effect of metformin on gut microbiota has been reported, but whether metformin can suppress colorectal cancer (CRC) by affecting gut microbiota composition and rescue F. nucleatum-induced tumourigenicity remains unclear.<br><br>METHODS: To identify microbiota associated with both CRC occurrence and metformin treatment, first, we reanalyzed the gut microbiome of our previous data on two human cohorts of normal and CRC individuals. Subsequently, we summarized microbiota altered by metformin from published literatures. Several taxa, including Fusobacterium, were associated with both CRC occurrence and metformin treatment. We investigated the effect of metformin on APCMin/+ mice given with or without F. nucleatum. 16S rRNA gene sequencing was performed.<br><br>FINDINGS: We summarized 131 genera altered by metformin from 18 published literatures. Five genera reported to be changed by metformin, including Bacteroides, Streptococcus, Achromobacter, Alistipes and Fusobacterium, were associated with CRC in both of our human cohorts. Metformin relieved the symptoms caused by F. nucleatum administration in APCMin/+ mice, and showed promise in suppressing intestinal tumour formation and rescuing F. nucleatum-induced tumourigenicity. Administration of F. nucleatum and/or metformin had effect on gut microbiome structure, composition and functions of APCMin/+ mice.<br><br>INTERPRETATION: This study pioneers in predicting critical CRC-associated taxa contributing to the antitumour effect of metformin, and correlating gut microbiome with the antitumour effect of metformin in experimental animals. We presented a basis for future investigations into metformin's potential effect on suppressing F. nucleatum-induced tumor formation in vivo.<br><br>FUNDING: This work was supported by grants from the National Natural Science Foundation of China (31701250).}, }
@article {pmid32791981, year = {2020}, author = {Yan, Y and Nguyen, LH and Franzosa, EA and Huttenhower, C}, title = {Strain-level epidemiology of microbial communities and the human microbiome.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {71}, pmid = {32791981}, issn = {1756-994X}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; R24DK110499//NIH NIDDK/International ; C10674/A27140//Cancer Research UK Grand Challenge Initiative/International ; }, mesh = {*Biodiversity ; Disease Susceptibility ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and "culturomics" technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.}, }
@article {pmid32620143, year = {2020}, author = {Creswell, R and Tan, J and Leff, JW and Brooks, B and Mahowald, MA and Thieroff-Ekerdt, R and Gerber, GK}, title = {High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {59}, pmid = {32620143}, issn = {1756-994X}, support = {1R01GM130777/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bayes Theorem ; Biodiversity ; Computational Biology/methods ; *Diet ; Feces/microbiology ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; *Metagenome ; *Metagenomics/methods ; Models, Theoretical ; Polysaccharides/*metabolism ; Software ; }, abstract = {BACKGROUND: Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds as therapeutics.<br><br>METHODS: We investigated the effect of two chemically distinct glycans (fructooligosaccharides and polydextrose) through three clinical studies conducted with 80 healthy volunteers. Stool samples, collected at dense temporal resolution (~ 4 times per week over 10 weeks) and analyzed using shotgun metagenomic sequencing, enabled detailed characterization of participants' microbiomes. For analyzing the microbiome time-series data, we developed MC-TIMME2 (Microbial Counts Trajectories Infinite Mixture Model Engine 2.0), a purpose-built computational tool based on nonparametric Bayesian methods that infer temporal patterns induced by perturbations and groups of microbes sharing these patterns.<br><br>RESULTS: Overall microbiome structure as well as individual taxa showed rapid, consistent, and durable alterations across participants, regardless of compound dose or the order in which glycans were consumed. Significant changes also occurred in the abundances of microbial carbohydrate utilization genes in response to polydextrose, but not in response to fructooligosaccharides. Using MC-TIMME2, we produced detailed, high-resolution temporal maps of the microbiota in response to glycans within and across microbiomes.<br><br>CONCLUSIONS: Our findings indicate that dietary glycans cause reproducible, dynamic, and differential alterations to the community structure of the human microbiome.}, }
@article {pmid34081399, year = {2021}, author = {Kumar, N and Hitch, TCA and Haller, D and Lagkouvardos, I and Clavel, T}, title = {MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes.}, journal = {Microbial biotechnology}, volume = {14}, number = {4}, pages = {1757-1770}, pmid = {34081399}, issn = {1751-7915}, support = {395357507//Deutsche Forschungsgemeinschaft/ ; 403224013//Deutsche Forschungsgemeinschaft/ ; SFB 1371//Deutsche Forschungsgemeinschaft/ ; SFB 1382//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bacteria/genetics ; Computational Biology ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Environmental and host-associated microbial communities are complex ecosystems, of which many members are still unknown. Hence, it is challenging to study community dynamics and important to create model systems of reduced complexity that mimic major community functions. Therefore, we developed MiMiC, a computational approach for data-driven design of simplified communities from shotgun metagenomes. We first built a comprehensive database of species-level bacterial and archaeal genomes (n = 22 627) consisting of binary (presence/absence) vectors of protein families (Pfam = 17 929). MiMiC predicts the composition of minimal consortia using an iterative scoring system based on maximal match-to-mismatch ratios between this database and the Pfam binary vector of any input metagenome. Pfam vectorization retained enough resolution to distinguish metagenomic profiles between six environmental and host-derived microbial communities (n = 937). The calculated number of species per minimal community ranged between 5 and 11, with MiMiC selected communities better recapitulating the functional repertoire of the original samples than randomly selected species. The inferred minimal communities retained habitat-specific features and were substantially different from communities consisting of most abundant members. The use of a mixture of known microbes revealed the ability to select 23 of 25 target species from the entire genome database. MiMiC is open source and available at https://github.com/ClavelLab/MiMiC.}, }
@article {pmid33754037, year = {2021}, author = {Zhong, M and Xiong, Y and Zhao, J and Gao, Z and Ma, J and Wu, Z and Song, Y and Hong, X}, title = {Candida albicans disorder is associated with gastric carcinogenesis.}, journal = {Theranostics}, volume = {11}, number = {10}, pages = {4945-4956}, pmid = {33754037}, issn = {1838-7640}, support = {26398D0016/TW/FIC NIH HHS/United States ; }, mesh = {Aged ; Aspergillus ; Basidiomycota ; *Candida albicans ; Candida glabrata ; *Carcinogenesis ; Carcinoma/*microbiology/pathology ; China ; DNA, Ribosomal/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Hypocreales ; Male ; Metagenomics ; Middle Aged ; Mycobiome/*genetics ; Penicillium ; Sordariales ; Stomach/microbiology ; Stomach Neoplasms/*microbiology/pathology ; }, abstract = {Background: Bacterial infection is associated with gastric carcinogenesis. However, the relationship between nonbacterial components and gastric cancer (GC) has not been fully explored. We aimed to characterize the fungal microbiome in GC. Methods: We performed ITS rDNA gene analysis in cancer lesions and adjacent noncancerous tissues of 45 GC cases from Shenyang, China. Obtaining the OTUs and combining effective grouping, we carried out species identifications, alpha and beta diversity analyses, and FUNGuild functional annotation. Moreover, differences were compared and tested between groups to better investigate the composition and ecology of fungi associated with GC and find fungal indicators. Results: We observed significant gastric fungal imbalance in GC. Principal component analysis revealed separate clusters for the GC and control groups, and Venn diagram analysis indicated that the GC group showed a lower OTU abundance than the control. At the genus level, the abundances of 15 fungal biomarkers distinguished the GC group from the control, of which Candida (p = 0.000246) and Alternaria (p = 0.00341) were enriched in GC, while Saitozyma (p = 0.002324) and Thermomyces (p = 0.009158) were decreased. Combining the results of Welch's t test and Wilcoxon rank sum test, Candida albicans (C. albicans) was significantly elevated in GC. The species richness Krona pie chart further revealed that C. albicans occupied 22% and classified GC from the control with an area under the receiver operating curve (AUC) of 0.743. Random forest analysis also confirmed that C. albicans could serve as a biomarker with a certain degree of accuracy. Moreover, compared with that of the control, the alpha diversity index was significantly reduced in the GC group. The Jaccard distance index and the Bray abundance index of the PCoA clarified separate clusters between the GC and control groups at the species level (p = 0.00051). Adonis (PERMANOVA) analysis and ANOVA showed that there were significant differences in fungal structure among groups (p = 0.001). Finally, FUNGuild functional classification predicted that saprotrophs were the most abundant taxa in the GC group. Conclusions: This study revealed GC-associated mycobiome imbalance characterized by an altered fungal composition and ecology and demonstrated that C. albicans can be a fungal biomarker for GC. With the significant increase of C. albicans in GC, the abundance of Fusicolla acetilerea, Arcopilus aureus, Fusicolla aquaeductuum were increased, while Candida glabrata, Aspergillus montevidensis, Saitozyma podzolica and Penicillium arenicola were obviously decreased. In addition, C. albicans may mediate GC by reducing the diversity and richness of fungi in the stomach, contributing to the pathogenesis of GC.}, }
@article {pmid33668840, year = {2021}, author = {Raethong, N and Nakphaichit, M and Suratannon, N and Sathitkowitchai, W and Weerapakorn, W and Keawsompong, S and Vongsangnak, W}, title = {Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33668840}, issn = {2073-4425}, mesh = {Adult ; Bacteria/*classification/genetics/isolation &amp; purification ; Carbohydrate Metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; Thailand ; Whole Genome Sequencing/*methods ; Young Adult ; }, abstract = {The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.}, }
@article {pmid32971520, year = {2021}, author = {Watts, AM and West, NP and Zhang, P and Smith, PK and Cripps, AW and Cox, AJ}, title = {The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls.}, journal = {International archives of allergy and immunology}, volume = {182}, number = {2}, pages = {94-105}, doi = {10.1159/000510536}, pmid = {32971520}, issn = {1423-0097}, mesh = {Adult ; Biodiversity ; Biomarkers ; Case-Control Studies ; *Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Rhinitis, Allergic/blood/diagnosis/*etiology ; Young Adult ; }, abstract = {INTRODUCTION: Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers.<br><br>OBJECTIVE: To compare the gut microbiome composition between adult AR sufferers and controls.<br><br>METHODS: Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences.<br><br>RESULTS: Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, p = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (p = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (p = 0.006). An increased abundance of Parabacteroides (p = 0.008) and a reduced abundance of Oxalobacter (p = 0.001) and Clostridiales (p = 0.005) were also observed in the AR cohort compared to the CG.<br><br>CONCLUSION: Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.}, }
@article {pmid34332366, year = {2021}, author = {Font-Verdera, F and Liébana, R and Aldeguer-Riquelme, B and Gangloff, V and Santos, F and Viver, T and Rosselló-Móra, R}, title = {Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {5}, pages = {126231}, doi = {10.1016/j.syapm.2021.126231}, pmid = {34332366}, issn = {1618-0984}, abstract = {The anaerobic hypersaline sediments of an ephemeral pond from the S'Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.}, }
@article {pmid32955994, year = {2020}, author = {Mohamed, I and Zakeer, S and Azab, M and Hanora, A}, title = {Changes in Vaginal Microbiome in Pregnant and Nonpregnant Women with Bacterial Vaginosis: Toward Microbiome Diagnostics?.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {10}, pages = {602-614}, doi = {10.1089/omi.2020.0096}, pmid = {32955994}, issn = {1557-8100}, mesh = {Case-Control Studies ; Disease Management ; Disease Susceptibility ; Female ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Pregnancy ; Pregnancy Complications, Infectious/*diagnosis/*microbiology ; Vagina/*microbiology ; Vaginosis, Bacterial/*diagnosis/*microbiology ; }, abstract = {Bacterial vaginosis (BV) is highly common, adversely affecting the health of millions of women. New therapeutic targets and diagnostics are urgently needed for BV. Microbiome research offers new prospects in this context. We report here original findings on changes in the vaginal microbiome in pregnant and nonpregnant women with BV. Reproductive age women were recruited for this study after a clinical examination. The total sample (N = 33) included four study groups: (1) healthy nonpregnant women (n = 9), (2) nonpregnant women with symptomatic BV (n = 11), (3) healthy pregnant women without BV (n = 6), and (4) pregnant women with symptomatic BV (N = 7). The vaginal microbiota in healthy women was less diverse, with dominance of a single genus, Lactobacillus. Six major phyla appeared upon taxonomic analysis of the bacterial sequences: Firmicutes, Actinobacteria, Proteobacteria, Tenericutes, Bacteroidetes, and Fusobacteria. For instance, Firmicutes had a significantly higher abundance (98.3%) in the nonpregnant healthy group and 94.3% in pregnant healthy group, compared with nonpregnant (49.7%) and pregnant (67%) women with BV (p = 0.003). Moreover, women with BV had significant increases in representation of Actinobacteria, Fusobacteria, and Bacteroidetes (p = 0.0003, 0.004, and 0.01, respectively). Although the Lactobacillus genus was predominant in healthy women, Gardnerella, Atopobium, Sneathia, and Prevotella significantly increased in nonpregnant women with BV (p = 0.001, 0.014, 0.004, and 0.012, respectively). Dysbiosis of Lactobacillus in pregnant women with BV was accompanied by increased prevalence of the Streptococcus genus. These findings contribute new insights toward microbiome diagnostics and therapeutics innovation in BV.}, }
@article {pmid32907488, year = {2020}, author = {Sibai, M and Altuntaş, E and Yıldırım, B and Öztürk, G and Yıldırım, S and Demircan, T}, title = {Microbiome and Longevity: High Abundance of Longevity-Linked Muribaculaceae in the Gut of the Long-Living Rodent Spalax leucodon.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {10}, pages = {592-601}, doi = {10.1089/omi.2020.0116}, pmid = {32907488}, issn = {1557-8100}, mesh = {Animals ; Bacteroidetes ; Biodiversity ; Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Longevity ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; Spalax/*microbiology/*physiology ; }, abstract = {With a world population living longer as well as marked disparities in life expectancy, understanding the determinants of longevity is one of the priority research agendas in 21st century life sciences. To this end, the blind mole-rat (Spalax leucodon), a subterranean mammalian, has emerged as an exceptional model organism due to its astonishing features such as remarkable longevity, hypoxia and hypercapnia tolerance, and cancer resistance. The microbiome has been found to be a vital parameter for cellular physiology and it is safe to assume that it has an impact on life expectancy. Although the unique characteristics of Spalax make it an ideal experimental model for longevity research, there is limited knowledge of the bacterial composition of Spalax microbiome, which limits its in-depth utilization. In this study, using 16S rRNA amplicon sequencing, we report the gut and skin bacterial structure of Spalax for the first time. The diversity between fecal and skin samples was manifested in the distant clustering, as revealed by beta diversity analysis. Importantly, the longevity-linked Muribaculaceae bacterial family was found to be the dominating bacterial taxa in Spalax fecal samples. These new findings contribute toward further development of Spalax as a model for longevity research and potential linkages between microbiome composition and longevity.}, }
@article {pmid32882233, year = {2020}, author = {Zamora-Briseño, JA and Cerqueda-García, D and Hernández-Velázquez, IM and Rivera-Bustamante, R and Huchín-Mian, JP and Briones-Fourzán, P and Lozano-Álvarez, E and Rodríguez-Canul, R}, title = {Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1.}, journal = {Journal of invertebrate pathology}, volume = {176}, number = {}, pages = {107457}, doi = {10.1016/j.jip.2020.107457}, pmid = {32882233}, issn = {1096-0805}, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; DNA Viruses/*physiology ; Female ; *Gastrointestinal Microbiome ; Male ; Palinuridae/*microbiology/virology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sex Factors ; }, abstract = {The spiny lobster Panulirus argus (Latreille, 1804) is currently affected by an unenveloped, icosahedral, DNA virus termed Panulirus argus virus 1 (PaV1), a virulent and pathogenic virus that produces a long-lasting infection that alters the physiology and behaviour of heavily infected lobsters. Gut-associated microbiota is crucial for lobster homeostasis and well-being, but pathogens could change microbiota composition affecting its function. In PaV1 infection, the changes of gut-associated microbiota are yet to be elucidated. In the present study, we used high-throughput 16S rRNA sequencing technology to compare the bacterial microbiota in intestines of healthy and heavily PaV1-infected male and female juveniles of spiny lobsters P. argus captured in Puerto Morelos Reef lagoon, Quintana Roo, Mexico. We found that basal gut-associated microbiota composition showed a sex-dependent bias, with females being enriched in amplicon sequence variants (ASVs) assigned to Sphingomonas, while males were enriched in the genus Candidatus Hepatoplasma and Aliiroseovarius genera. Moreover, the alpha diversity of microbiota decreased in PaV1-infected lobsters. A significant increase of the genus Candidatus Bacilloplasma was observed in infected lobsters, as well as a significant decrease in Nesterenkonia, Caldalkalibacillus, Pseudomonas, Cetobacterium and Phyllobacterium. We also observed an alteration in the abundances of Vibrio species. Results from this study suggest that PaV1 infection impacts intestinal microbiota composition in Panulirus argus in a sex-dependent manner.}, }
@article {pmid32758003, year = {2020}, author = {Elsaeed, E and Enany, S and Hanora, A and Fahmy, N}, title = {Comparative Metagenomic Screening of Aromatic Hydrocarbon Degradation and Secondary Metabolite-Producing Genes in the Red Sea, the Suez Canal, and the Mediterranean Sea.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {9}, pages = {541-550}, doi = {10.1089/omi.2020.0070}, pmid = {32758003}, issn = {1557-8100}, mesh = {Aquatic Organisms/genetics/metabolism ; Databases, Genetic ; Ecosystem ; Hydrocarbons, Aromatic/*metabolism ; Indian Ocean ; Mediterranean Sea ; *Metagenome ; *Metagenomics/methods/standards ; *Microbiota/genetics ; Seawater ; *Secondary Metabolism ; *Water Microbiology ; Water Pollution ; }, abstract = {Marine and ecosystem pollution due to oil spills can be addressed by identifying the aromatic hydrocarbon (HC)-degrading microorganisms and their responsible genes for biodegradation. Moreover, screening for genes coding for secondary metabolites is invaluable for drug discovery. We report here, the first metagenomic study investigating the shotgun metagenome of the Suez Canal water sampled at Ismailia city concerning its aromatic HC degradation potential in comparison to the seawater sampled at Halayeb city at the Red Sea and Sallum city at the Mediterranean Sea. Moreover, for an in-depth understanding of marine biotechnology applications, we screened for the polyketide synthases (PKSs) and nonribosomal peptide synthetase (NRPS) domains in those three metagenomes. By mapping against functional protein databases, we found that 13, 6, and 3 gene classes from the SEED database; 2, 1, and 3 gene classes from the EgGNOG; and 5, 4, and 2 genes from the InterPro2GO database were identified to be differentially abundant among Halayeb, Ismailia, and Sallum metagenomes, respectively. Also, Halayeb metagenome in the Red Sea reported the highest number of PKS domains showing higher potential in secondary metabolite production in addition to the oil degradation potential.}, }
@article {pmid34192637, year = {2021}, author = {Li, P and Li, K and Xu, P and Liu, X and Pu, Y}, title = {Treatment of wastewater with high carbon-to-nitrogen ratio using a waterfall aeration biofilm reactor combined with sequencing batch reactor: Microbial community structure and metabolism analysis.}, journal = {Bioresource technology}, volume = {337}, number = {}, pages = {125450}, doi = {10.1016/j.biortech.2021.125450}, pmid = {34192637}, issn = {1873-2976}, mesh = {Biofilms ; Bioreactors ; Carbon ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Waste Water ; }, abstract = {A low-cost and high-efficiency waterfall aeration biofilm reactor (WABR) combined with a sequencing batch reactor (SBR) was established to treat wastewater with a C/N ratio of 50. Three WABR-SBR systems with different fillers were used. In the stable operation phase, the removal efficiency of chemical oxygen demand was R1 (approximately 99%), R2 (97-99%), and R3 (96-99%); the effluent concentration of NH4+-N was 0.5 mg/L without nitrite or nitrate accumulation. High-throughput 16S rRNA sequencing revealed that the dominant phyla in the microbial community structure were Proteobacteria, Bacteroidetes, and Planctomycetes. Quantitative PCR was used to quantify the nitrification and denitrification gene expressions (Nitrobacter, nirS, and nirK) to evaluate the simultaneous nitrification and denitrification processes. Both anammox and denitrifying bacteria were abundant. Metagenomic annotation of genes that revealed the metabolic pathways of carbohydrates, amino acids, and the two dominant enzymes (GH and GT) provide valuable information for microbial ecology analysis.}, }
@article {pmid33973044, year = {2021}, author = {Fadiji, AE and Kanu, JO and Babalola, OO}, title = {Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach.}, journal = {Archives of microbiology}, volume = {203}, number = {6}, pages = {3605-3613}, pmid = {33973044}, issn = {1432-072X}, support = {UID123634//National Research Foundation/ ; }, mesh = {Crops, Agricultural/*microbiology ; Metagenomics ; *Microbiota ; *Rhizosphere ; *Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Understanding the functions carried out by rhizosphere microbiomes will further explore their importance in biotechnological improvement and agricultural sustainability. This study presents one of the foremost attempts to understand the functional diversity of the rhizosphere microbiome in mono-cropping and crop rotation farming sites using shotgun metagenomic techniques. We hypothesized that the functional diversity would vary in the cropping sites and more abundant in the rotational cropping site. Hence, we carried out complete DNA extraction from the bulk and rhizospheric soils associated with maize plant cultivated on the mono-cropping farm (LT and LTc) and the crop rotation farm (VD and VDc), respectively, and sequenced employing shotgun approach. Using the SEED subsystem, our result revealed that a total of 24 functional categories dominated the rotational cropping site, while four functional categories dominated the mono-cropping sites. Alpha diversity assessment showed that no significant difference (p > 0.05) was observed across the cropping sites, while beta diversity assessment revealed a significant difference. Going by the high abundance of functional groups observed in the samples from the crop rotational site, it is evident that cropping systems influenced the functions of soil microbiomes. Worthy of note is the high abundance of unknown functions associated with these maize rhizosphere microbiomes. This is an indication that there are still some under-investigated functional genes associated with the maize rhizosphere microbiome. It is, therefore, imperative that further studies explore these functional genes for their agricultural and biotechnological potentials.}, }
@article {pmid33770071, year = {2021}, author = {Pavlova, YS and Paez-Espino, D and Morozov, AY and Belalov, IS}, title = {Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.}, journal = {PLoS computational biology}, volume = {17}, number = {3}, pages = {e1008841}, pmid = {33770071}, issn = {1553-7358}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bacteriophages/genetics ; CRISPR-Cas Systems/*genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics/immunology ; DNA, Intergenic/genetics ; DNA, Viral/genetics ; Metagenome/*genetics ; Metagenomics ; *Models, Genetic ; }, abstract = {Understanding CRISPR-Cas systems-the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks-is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical 'rich-get-richer' mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.}, }
@article {pmid33713805, year = {2021}, author = {An, J and McDowell, A and Kim, YK and Kim, TB}, title = {Extracellular vesicle-derived microbiome obtained from exhaled breath condensate in patients with asthma.}, journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology}, volume = {126}, number = {6}, pages = {729-731}, doi = {10.1016/j.anai.2021.02.030}, pmid = {33713805}, issn = {1534-4436}, mesh = {Asthma/*microbiology ; Bacteria/classification/genetics ; *Breath Tests ; Exhalation ; Extracellular Vesicles/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics ; *Microbiota ; }, }
@article {pmid33609707, year = {2021}, author = {Psonis, N and Antoniou, A and Karameta, E and Darriba, D and Stamatakis, A and Lymberakis, P and Poulakakis, N}, title = {The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics.}, journal = {Molecular phylogenetics and evolution}, volume = {159}, number = {}, pages = {107121}, doi = {10.1016/j.ympev.2021.107121}, pmid = {33609707}, issn = {1095-9513}, mesh = {Animals ; Balkan Peninsula ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetics, Population ; Genomics ; Lizards/*classification ; Metagenomics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of "P. tauricus" consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of "P. erhardii" comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis' species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.}, }
@article {pmid33307384, year = {2021}, author = {Ghemrawi, M and Torres, AR and Duncan, G and Colwell, R and Dadlani, M and McCord, B}, title = {The genital microbiome and its potential for detecting sexual assault.}, journal = {Forensic science international. Genetics}, volume = {51}, number = {}, pages = {102432}, doi = {10.1016/j.fsigen.2020.102432}, pmid = {33307384}, issn = {1878-0326}, mesh = {Adult ; Aged ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Penis/*microbiology ; Pilot Projects ; Sequence Analysis, DNA ; *Sex Offenses ; Skin/microbiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Since its inception, the Human Microbiome Project (HMP) has provided key discoveries that can be applied to forensics, in addition to those of obvious medical value. Whether for postmortem interval estimation, geolocation, or human identification, there are many applications of the microbiome as an investigative lead for forensic casework. The human skin microbiome has shown great potential for use in studies of transfer and human identification, however there has been little focus on the genital microbiome, in particular penile skin which differs from other body sites. Our preliminary data on both the penile and vaginal microbiome demonstrates potential value in cases of sexual assault. In this study we describe genital microbial signatures based on the analysis of five male and five female genital samples and compare these results to those from longitudinal studies. Selected taxa, e.g., Gardnerella, Lactobacilli, Finegoldia, Peptoniphilus, and Anaerococci, are shown to be candidate constituents of the genital microbiome that merit investigation for use in sexual assault casework.}, }
@article {pmid34294041, year = {2021}, author = {Andrade, BGN and Goris, T and Afli, H and Coutinho, FH and Dávila, AMR and Cuadrat, RRC}, title = {Putative mobilized colistin resistance genes in the human gut microbiome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {220}, pmid = {34294041}, issn = {1471-2180}, abstract = {BACKGROUND: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.<br><br>RESULTS: A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.<br><br>CONCLUSION: This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.}, }
@article {pmid34210038, year = {2021}, author = {Olshan, KL and Zomorrodi, AR and Pujolassos, M and Troisi, J and Khan, N and Fanelli, B and Kenyon, V and Fasano, A and Leonard, MM}, title = {Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, pmid = {34210038}, issn = {2072-6643}, support = {K23 DK122127/DK/NIDDK NIH HHS/United States ; R01 DK104344/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Case-Control Studies ; Celiac Disease/diet therapy/*microbiology ; Cross-Sectional Studies ; *Diet, Gluten-Free ; Female ; Glutens/metabolism ; Humans ; Infant, Newborn ; *Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; Milk, Human/*microbiology ; Prospective Studies ; }, abstract = {The intestinal microbiome may trigger celiac disease (CD) in individuals with a genetic disposition when exposed to dietary gluten. Research demonstrates that nutrition during infancy is crucial to the intestinal microbiome engraftment. Very few studies to date have focused on the breast milk composition of subjects with a history of CD on a gluten-free diet. Here, we utilize a multi-omics approach with shotgun metagenomics to analyze the breast milk microbiome integrated with metabolome profiling of 36 subjects, 20 with CD on a gluten-free diet and 16 healthy controls. These analyses identified significant differences in bacterial and viral species/strains and functional pathways but no difference in metabolite abundance. Specifically, three bacterial strains with increased abundance were identified in subjects with CD on a gluten-free diet of which one (Rothia mucilaginosa) has been previously linked to autoimmune conditions. We also identified five pathways with increased abundance in subjects with CD on a gluten-free diet. We additionally found four bacterial and two viral species/strains with increased abundance in healthy controls. Overall, the differences observed in bacterial and viral species/strains and in functional pathways observed in our analysis may influence microbiome engraftment in neonates, which may impact their future clinical outcomes.}, }
@article {pmid33901182, year = {2021}, author = {He, X and Yin, Q and Zhou, L and Meng, L and Hu, W and Li, F and Li, Y and Han, K and Zhang, S and Fu, S and Zhang, X and Wang, J and Xu, S and Zhang, Y and He, Y and Dong, M and Shen, X and Zhang, Z and Nie, K and Liang, G and Ma, X and Wang, H}, title = {Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region, China.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {4}, pages = {e0009381}, pmid = {33901182}, issn = {1935-2735}, mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; High-Throughput Nucleotide Sequencing ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Mosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently.<br><br>METHODS: Mosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes.<br><br>RESULTS: A total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes.<br><br>CONCLUSION: Viral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.}, }
@article {pmid33820988, year = {2021}, author = {Tourancheau, A and Mead, EA and Zhang, XS and Fang, G}, title = {Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.}, journal = {Nature methods}, volume = {18}, number = {5}, pages = {491-498}, pmid = {33820988}, issn = {1548-7105}, support = {R01 GM128955/GM/NIGMS NIH HHS/United States ; R35 GM139655/GM/NIGMS NIH HHS/United States ; R56 HG011095/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; DNA Methylation/*physiology ; DNA, Bacterial/*genetics ; Gastrointestinal Microbiome ; Genome, Bacterial ; Metagenome ; Metagenomics/*methods ; Mice ; *Nanopore Sequencing ; }, abstract = {Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco (https://github.com/fanglab/nanodisco), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it to individual bacteria and the mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes and identifying misassembled metagenomic contigs.}, }
@article {pmid34294039, year = {2021}, author = {Zhang, Z and Zhang, L}, title = {METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs.}, journal = {BMC bioinformatics}, volume = {22}, number = {Suppl 10}, pages = {378}, pmid = {34294039}, issn = {1471-2105}, support = {HKBU 22201419//Early Career Scheme/ ; IRCMS/19-20/D02//Hong Kong Baptist University/ ; 2019A1515011046//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Algorithms ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented contigs into clusters to represent microbial genomes based on contigs' nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Contigs can be linked by sequence overlap (assembly graph) or by the paired-end reads aligned to them (PE graph), where the linked contigs have high chance to be derived from the same clusters.<br><br>RESULTS: We developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and PE graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends. METAMVGL learns the two graphs' weights automatically and predicts the contig labels in a uniform multi-view label propagation framework. In experiments, we observed METAMVGL made use of significantly more high-confidence edges from the combined graph and linked dead ends to the main graph. It also outperformed many state-of-the-art contig binning algorithms, including MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and GraphBin on the metagenomic sequencing data from simulation, two mock communities and Sharon infant fecal samples.<br><br>CONCLUSIONS: Our findings demonstrate METAMVGL outstandingly improves the short contig binning and outperforms the other existing contig binning tools on the metagenomic sequencing data from simulation, mock communities and infant fecal samples.}, }
@article {pmid34281625, year = {2021}, author = {Zhong, ZP and Tian, F and Roux, S and Gazitúa, MC and Solonenko, NE and Li, YF and Davis, ME and Van Etten, JL and Mosley-Thompson, E and Rich, VI and Sullivan, MB and Thompson, LG}, title = {Glacier ice archives nearly 15,000-year-old microbes and phages.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {160}, pmid = {34281625}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Ice Cover ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination.<br><br>RESULTS: We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants.<br><br>CONCLUSIONS: Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally. Video Abstract.}, }
@article {pmid34265247, year = {2021}, author = {Brito, IL}, title = {The comings and goings of the healthy human gut microbiota.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {7}, pages = {1163-1164}, doi = {10.1016/j.chom.2021.06.011}, pmid = {34265247}, issn = {1934-6069}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {SNP-level analysis of 5,000+ metagenomic samples enabled Hildebrand and colleagues (2021) to identify human gut microbiota by their dispersal strategies in this issue of Cell Host &amp; Microbe. This brings us a step closer in understanding how microbial communities are formed and maintained and also hints at ways in which microbiomes can be manipulated to improve human health.}, }
@article {pmid34202675, year = {2021}, author = {Jo, Y and Back, CG and Kim, KH and Chu, H and Lee, JH and Moh, SH and Cho, WK}, title = {Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34202675}, issn = {1422-0067}, support = {120085-3//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; NRF-2018R1D1A1B07043597//National Research Foundation of Korea/ ; }, mesh = {Bacteria/classification/genetics ; Computational Biology/methods ; Garlic/*microbiology ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Organ Specificity ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.}, }
@article {pmid34202141, year = {2021}, author = {Yuan, X and Zhang, X and Liu, X and Dong, Y and Yan, Z and Lv, D and Wang, P and Li, Y}, title = {Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34202141}, issn = {1422-0067}, support = {31871971//National Natural Science Foundation of China/ ; 31772503//National Natural Science Foundation of China/ ; }, mesh = {Analysis of Variance ; Animals ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Host-Parasite Interactions ; Lepidoptera/*microbiology ; Metagenomics/methods ; Plants/parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.}, }
@article {pmid33744869, year = {2021}, author = {Kurup, K and Matyi, S and Giles, CB and Wren, JD and Jones, K and Ericsson, A and Raftery, D and Wang, L and Promislow, D and Richardson, A and Unnikrishnan, A}, title = {Calorie restriction prevents age-related changes in the intestinal microbiota.}, journal = {Aging}, volume = {13}, number = {5}, pages = {6298-6329}, pmid = {33744869}, issn = {1945-4589}, support = {S10 OD021562/OD/NIH HHS/United States ; T32 AG052363/AG/NIA NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; R21 AG062894/AG/NIA NIH HHS/United States ; K01 AG056655/AG/NIA NIH HHS/United States ; R01 AG045693/AG/NIA NIH HHS/United States ; P30 AG013280/AG/NIA NIH HHS/United States ; R01 AG049494/AG/NIA NIH HHS/United States ; }, mesh = {Aging ; Animals ; *Caloric Restriction ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Mice, Inbred C57BL ; }, abstract = {The effect of calorie restriction (CR) on the microbiome, fecal metabolome, and colon transcriptome of adult and old male mice was compared. Life-long CR increased microbial diversity and the Bacteroidetes/Firmicutes ratio and prevented the age-related changes in the microbiota, shifting it to a younger microbial and fecal metabolite profile in both C57BL/6JN and B6D2F1 mice. Old mice fed CR were enriched in the Rikenellaceae, S24-7 and Bacteroides families. The changes in the microbiome that occur with age and CR were initiated in the cecum and further modified in the colon. Short-term CR in adult mice had a minor effect on the microbiome but a major effect on the transcriptome of the colon mucosa. These data suggest that CR has a major impact on the physiological status of the gastrointestinal system, maintaining it in a more youthful state, which in turn could result in a more diverse and youthful microbiome.}, }
@article {pmid33686248, year = {2021}, author = {Konishi, T and Kusakabe, S and Hino, A and Inamoto, K and Yoshifuji, K and Kiridoshi, Y and Takeshita, K and Sasajima, S and Toya, T and Igarashi, A and Najima, Y and Kobayashi, T and Doki, N and Motooka, D and Nakamura, S and Suyama, M and Suda, W and Shiota, A and Atarashi, K and Hattori, M and Honda, K and Yokota, T and Ohashi, K and Shibayama, H and Fukushima, K and Kakihana, K}, title = {Low diversity of gut microbiota in the early phase of post-bone marrow transplantation increases the risk of chronic graft-versus-host disease.}, journal = {Bone marrow transplantation}, volume = {56}, number = {7}, pages = {1728-1731}, pmid = {33686248}, issn = {1476-5365}, support = {JP19ek0510021//Japan Agency for Medical Research and Development (AMED)/ ; JP20gm0010003//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Bone Marrow Transplantation/adverse effects ; *Gastrointestinal Microbiome ; *Graft vs Host Disease/etiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Microbiota ; }, }
@article {pmid33671370, year = {2021}, author = {Daliri, EB and Ofosu, FK and Chelliah, R and Lee, BH and Oh, DH}, title = {Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies.}, journal = {Biomolecules}, volume = {11}, number = {2}, pages = {}, pmid = {33671370}, issn = {2218-273X}, mesh = {Algorithms ; Animals ; *Gastrointestinal Microbiome ; *Genome ; Humans ; Inflammation ; Mass Spectrometry ; Metabolomics/*methods ; Microbiological Techniques ; Molecular Biology/methods ; Phylogeny ; *Proteome ; Proteomics/*methods ; *Transcriptome ; }, abstract = {The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.}, }
@article {pmid33670496, year = {2021}, author = {Hernandez-Baixauli, J and Puigbò, P and Torrell, H and Palacios-Jordan, H and Ripoll, VJR and Caimari, A and Del Bas, JM and Baselga-Escudero, L and Mulero, M}, title = {A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats.}, journal = {Biomolecules}, volume = {11}, number = {2}, pages = {}, pmid = {33670496}, issn = {2218-273X}, support = {TECNOMIFOOD//Centro para el Desarrollo Tecnológico Industrial/ ; }, mesh = {Animals ; Coumaric Acids/metabolism ; Dysbiosis/*metabolism/*microbiology ; Gastrointestinal Microbiome/*physiology ; Lipid Metabolism/physiology ; Male ; Metabolomics/methods ; Obesity/*metabolism/*microbiology ; Phenylalanine/metabolism ; Pilot Projects ; Rats ; Rats, Wistar ; }, abstract = {Obesity is one of the most incident and concerning disease worldwide. Definite strategies to prevent obesity and related complications remain elusive. Among the risk factors of the onset of obesity, gut microbiota might play an important role in the pathogenesis of the disease, and it has received extensive attention because it affects the host metabolism. In this study, we aimed to define a metabolic profile of the segregated obesity-associated gut dysbiosis risk factor. The study of the metabolome, in an obesity-associated gut dysbiosis model, provides a relevant way for the discrimination on the different biomarkers in the obesity onset. Thus, we developed a model of this obesity risk factors through the transference of gut microbiota from obese to non-obese male Wistar rats and performed a subsequent metabolic analysis in the receptor rats. Our results showed alterations in the lipid metabolism in plasma and in the phenylalanine metabolism in urine. In consequence, we have identified metabolic changes characterized by: (1) an increase in DG:34:2 in plasma, a decrease in hippurate, (2) an increase in 3-HPPA, and (3) an increase in o-coumaric acid. Hereby, we propose these metabolites as a metabolic profile associated to a segregated dysbiosis state related to obesity disease.}, }
@article {pmid33217332, year = {2021}, author = {Münch, PC and Franzosa, EA and Stecher, B and McHardy, AC and Huttenhower, C}, title = {Identification of Natural CRISPR Systems and Targets in the Human Microbiome.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {1}, pages = {94-106.e4}, pmid = {33217332}, issn = {1934-6069}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics/metabolism ; Bacteriophages/genetics/physiology ; CRISPR-Associated Proteins/genetics ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gastrointestinal Microbiome/genetics ; Gene Ontology ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Metagenome ; Methylation ; Microbiota/*genetics ; Mouth/microbiology ; Viral Proteins/genetics/metabolism ; Virus Physiological Phenomena ; }, abstract = {Many bacteria resist invasive DNA by incorporating sequences into CRISPR loci, which enable sequence-specific degradation. CRISPR systems have been well studied from isolate genomes, but culture-independent metagenomics provide a new window into their diversity. We profiled CRISPR loci and cas genes in the body-wide human microbiome using 2,355 metagenomes, yielding functional and taxonomic profiles for 2.9 million spacers by aligning the spacer content to each sample's metagenome and corresponding gene families. Spacer and repeat profiles agree qualitatively with those from isolate genomes but expand their diversity by approximately 13-fold, with the highest spacer load present in the oral microbiome. The taxonomy of spacer sequences parallels that of their source community, with functional targets enriched for viral elements. When coupled with cas gene systems, CRISPR-Cas subtypes are highly site and taxon specific. Our analysis provides a comprehensive collection of natural CRISPR-cas loci and targets in the human microbiome.}, }
@article {pmid32353491, year = {2021}, author = {Abdel-Aziz, MI and Brinkman, P and Vijverberg, SJH and Neerincx, AH and Riley, JH and Bates, S and Hashimoto, S and Kermani, NZ and Chung, KF and Djukanovic, R and Dahlén, SE and Adcock, IM and Howarth, PH and Sterk, PJ and Kraneveld, AD and Maitland-van der Zee, AH and , }, title = {Sputum microbiome profiles identify severe asthma phenotypes of relative stability at 12 to 18 months.}, journal = {The Journal of allergy and clinical immunology}, volume = {147}, number = {1}, pages = {123-134}, doi = {10.1016/j.jaci.2020.04.018}, pmid = {32353491}, issn = {1097-6825}, mesh = {Asthma/*microbiology ; Female ; Follow-Up Studies ; Humans ; Male ; *Microbiota ; Middle Aged ; Severity of Illness Index ; Specimen Handling ; Sputum/*microbiology ; Time Factors ; }, abstract = {BACKGROUND: Asthma is a heterogeneous disease characterized by distinct phenotypes with associated microbial dysbiosis.<br><br>OBJECTIVES: Our aim was to identify severe asthma phenotypes based on sputum microbiome profiles and assess their stability after 12 to 18 months. A further aim was to evaluate clusters' robustness after inclusion of an independent cohort of patients with mild-to-moderate asthma.<br><br>METHODS: In this longitudinal multicenter cohort study, sputum samples were collected for microbiome profiling from a subset of the Unbiased Biomarkers in Prediction of Respiratory Disease Outcomes adult patient cohort at baseline and after 12 to 18 months of follow-up. Unsupervised hierarchical clustering was performed by using the Bray-Curtis β-diversity measure of microbial profiles. For internal validation, partitioning around medoids, consensus cluster distribution, bootstrapping, and topological data analysis were applied. Follow-up samples were studied to evaluate within-patient clustering stability in patients with severe asthma. Cluster robustness was evaluated by using an independent cohort of patients with mild-to-moderate asthma.<br><br>RESULTS: Data were available for 100 subjects with severe asthma (median age 55 years; 42% males). Two microbiome-driven clusters were identified; they were characterized by differences in asthma onset, smoking status, residential locations, percentage of blood and/or sputum neutrophils and macrophages, lung spirometry results, and concurrent asthma medications (all P values < .05). The cluster 2 patients displayed a commensal-deficient bacterial profile that was associated with worse asthma outcomes than those of the cluster 1 patients. Longitudinal clusters revealed high relative stability after 12 to 18 months in those with severe asthma. Further inclusion of an independent cohort of 24 patients with mild-to-moderate asthma was consistent with the clustering assignments.<br><br>CONCLUSION: Unbiased microbiome-driven clustering revealed 2 distinct robust phenotypes of severe asthma that exhibited relative overtime stability. This suggests that the sputum microbiome may serve as a biomarker for better characterizing asthma phenotypes.}, }
@article {pmid33233349, year = {2020}, author = {Santiago-Rodriguez, TM and Garoutte, A and Adams, E and Nasser, W and Ross, MC and La Reau, A and Henseler, Z and Ward, T and Knights, D and Petrosino, JF and Hollister, EB}, title = {Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33233349}, issn = {2073-4425}, mesh = {Bacteria/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Viruses/*genetics ; }, abstract = {Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.}, }
@article {pmid32691605, year = {2021}, author = {Maki, KA and Kazmi, N and Barb, JJ and Ames, N}, title = {The Oral and Gut Bacterial Microbiomes: Similarities, Differences, and Connections.}, journal = {Biological research for nursing}, volume = {23}, number = {1}, pages = {7-20}, doi = {10.1177/1099800420941606}, pmid = {32691605}, issn = {1552-4175}, mesh = {Bacteria/classification/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Microbiota/genetics ; Mouth/*microbiology ; Nursing Research ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: The oral cavity is associated with local and systemic diseases, although oral samples are not as commonly studied as fecal samples in microbiome research. There is a gap in understanding between the similarities and differences in oral and gut microbiomes and how they may influence each other. Methods: A scoping literature review was conducted comparing oral and gut microbiome communities in healthy humans. Results: Ten manuscripts met inclusion criteria and were examined. The oral microbiome sites demonstrated great variance in differential bacterial abundance and the oral microbiome had higher alpha diversity as compared to the gut microbiome. Studies using 16S rRNA sequencing analysis resulted in overall community differences between the oral and gut microbiomes when beta diversity was analyzed. Shotgun metagenomics sequencing increased taxonomic resolution to strain level (intraspecies) and demonstrated a greater percentage of shared taxonomy and oral bacterial translocation to the gut microbiome community. Discussion: The oral and gut microbiome bacterial communities may be more similar than earlier research has suggested, when species strain is analyzed through shotgun metagenomics sequencing. The association between oral health and systemic diseases has been widely reported but many mechanisms underlying this relationship are unknown. Although future research is needed, the oral microbiome may be a novel interventional target through its downstream effects on the gut microbiome. As nurse scientists are experts in symptom characterization and phenotyping of patients, they are also well posed to lead research on the connection of the oral microbiome to the gut microbiome in health and disease.}, }
@article {pmid32648469, year = {2021}, author = {Shibata, K and Ogai, K and Ogura, K and Urai, T and Aoki, M and Arisandi, D and Takahashi, N and Okamoto, S and Sanada, H and Sugama, J}, title = {Skin Physiology and its Microbiome as Factors Associated with the Recurrence of Pressure Injuries.}, journal = {Biological research for nursing}, volume = {23}, number = {1}, pages = {75-81}, doi = {10.1177/1099800420941100}, pmid = {32648469}, issn = {1552-4175}, mesh = {Aged ; Aged, 80 and over ; Epidermis/physiology ; Female ; Humans ; Japan/epidemiology ; Long-Term Care/statistics &amp; numerical data ; Male ; *Microbiota ; Pressure Ulcer/*microbiology/nursing/*pathology ; Prospective Studies ; Recurrence ; Skin/*microbiology/pathology ; *Skin Physiological Phenomena ; }, abstract = {BACKGROUND: Preventing recurrent pressure injuries (RPIs) is one of the important challenges faced in healthcare, but the risk factors of RPIs have not been fully revealed. This study aims to explore factors associated with RPIs, by focusing on skin physiology and its microbiome as local factors crucial for the health of healed tissue after pressure injury healing.<br><br>METHODS: This prospective observational study was conducted in a long-term care facility in Japan with patients whose PIs had healed within 1 month. Skin physiology was evaluated by stratum corneum (SC) hydration, pH, and transepidermal water loss. Skin bacteria was collected by tape stripping, followed by 16S ribosomal RNA-based metagenomics analysis. These parameters were evaluated every two weeks over a period of six weeks.<br><br>RESULTS: A total of 30 patients were included in this study, and 8 patients (26.7%) had an RPI within 6 weeks. In this study, significantly lower SC hydration and a higher rate of Staphylococcus species on the healed site were found in the RPI group.<br><br>DISCUSSION: A high rate of RPIs (about one in four) points out the necessity of a further care strategy on the healed PIs. Lower skin hydration and/or the increase in Staphylococcus bacteria may have a potential to be used as a biomarker for the prediction of RPIs, or may be an intervention point for the prevention of RPIs by, for example, skin cleansing with moisturizing care.}, }
@article {pmid32603623, year = {2020}, author = {New, FN and Brito, IL}, title = {What Is Metagenomics Teaching Us, and What Is Missed?.}, journal = {Annual review of microbiology}, volume = {74}, number = {}, pages = {117-135}, doi = {10.1146/annurev-micro-012520-072314}, pmid = {32603623}, issn = {1545-3251}, support = {R01 DK093595/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Computational Biology/methods/standards ; High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environmental samples. In the future, improvements and innovation in technology and methodology will lead to lowered costs. Data integration using multiple technological platforms will lead to a better understanding of how to harness metagenomes. Subsequently, we will be able not only to characterize complex microbiomes but also to manipulate communities to achieve prosperous outcomes for health, agriculture, and environmental sustainability.}, }
@article {pmid34287254, year = {2021}, author = {Agrawal, R and Ajami, NJ and Malhotra, S and Chen, L and White, DL and Sharafkhaneh, A and Hoffman, KL and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study.}, journal = {Clocks &amp; sleep}, volume = {3}, number = {3}, pages = {387-397}, doi = {10.3390/clockssleep3030025}, pmid = {34287254}, issn = {2624-5175}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 0000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer Organization/ ; CIN13-413//the Houston Veterans Affairs Health Services Research Center of Innovations/ ; R01CA172880/CA/NCI NIH HHS/United States ; CX001430.//U.S. Department of Veterans Affairs/ ; }, abstract = {We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6-8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.}, }
@article {pmid32975580, year = {2020}, author = {Bhattacharya, S and Roy, C and Mandal, S and Sarkar, J and Rameez, MJ and Mondal, N and Mapder, T and Chatterjee, S and Pyne, P and Alam, M and Haldar, PK and Roy, R and Fernandes, S and Peketi, A and Chakraborty, R and Mazumdar, A and Ghosh, W}, title = {Aerobic microbial communities in the sediments of a marine oxygen minimum zone.}, journal = {FEMS microbiology letters}, volume = {367}, number = {19}, pages = {}, pmid = {32975580}, issn = {1574-6968}, mesh = {Aerobiosis ; Aquatic Organisms/*metabolism ; Bacteria/classification/*metabolism ; Geologic Sediments/*microbiology ; Microbiota/*physiology ; Oceans and Seas ; Oxygen/*metabolism ; }, abstract = {The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15-30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 107 (g sediment)-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided with all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates' genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.}, }
@article {pmid31665423, year = {2020}, author = {Sanjar, F and Weaver, AJ and Peacock, TJ and Nguyen, JQ and Brandenburg, KS and Leung, KP}, title = {Identification of Metagenomics Structure and Function Associated With Temporal Changes in Rat (Rattus norvegicus) Skin Microbiome During Health and Cutaneous Burn.}, journal = {Journal of burn care &amp; research : official publication of the American Burn Association}, volume = {41}, number = {2}, pages = {347-358}, doi = {10.1093/jbcr/irz165}, pmid = {31665423}, issn = {1559-0488}, mesh = {Animals ; Biopsy ; Burns/*genetics/*microbiology ; Disease Models, Animal ; Male ; *Metagenome ; *Microbiota ; Rats ; Rats, Sprague-Dawley ; Skin/*microbiology ; Time Factors ; }, abstract = {The cutaneous skin microbiome is host to a vast ensemble of resident microbes that provide essential capabilities including protection of skin barrier integrity and modulation of the host immune response. Cutaneous burn-injury promotes alteration of cutaneous and systemic immune response that can affect both commensal and pathogenic microbes. A cross-sectional study of a limited number of burn patients revealed a difference in the bacteriome of burned versus control participants. Temporal changes of the skin microbiome during health and cutaneous burn-injury remains largely unknown. Furthermore, how this microbial shift relates to community function in the collective metagenome remain elusive. Due to cost considerations and reduced healing time, rodents are frequently used in burn research, despite inherent physiological differences between rodents and human skin. Using a rat burn model, a longitudinal study was conducted to characterize the rat skin bacterial residents and associated community functions in states of health (n = 30) (sham-burned) and when compromised by burn-injury (n = 24). To address the knowledge gap, traumatic thermal injury and disruption of cutaneous surface is associated with genus-level changes in the microbiota, reduced bacterial richness, and altered representation of bacterial genes and associated predicted functions across different skin microbial communities. These findings demonstrate that, upon burn-injury, there is a shift in diversity of the skin's organismal assemblages, yielding a core microbiome that is distinct at the genome and functional level. Moreover, deviations from the core community correlate with temporal changes post-injury and community transition from the state of cutaneous health to disease (burn-injury).}, }
@article {pmid33671794, year = {2021}, author = {Kazarina, A and Petersone-Gordina, E and Kimsis, J and Kuzmicka, J and Zayakin, P and Griškjans, Ž and Gerhards, G and Ranka, R}, title = {The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33671794}, issn = {2073-4425}, mesh = {Adolescent ; Adult ; Archaeology ; Body Remains ; Burial ; Child ; DNA, Ancient/analysis ; DNA, Bacterial/*genetics ; Dental Calculus/genetics/*microbiology ; Dental Plaque/genetics/*microbiology ; Female ; Humans ; Latvia/epidemiology ; Male ; Metagenome/genetics ; Microbiota/*genetics ; Middle Aged ; Soil Microbiology ; Young Adult ; }, abstract = {Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.}, }
@article {pmid33109755, year = {2020}, author = {Oliverio, AM and Bissett, A and McGuire, K and Saltonstall, K and Turner, BL and Fierer, N}, title = {The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {33109755}, issn = {2150-7511}, mesh = {Bacteria/classification/*metabolism ; Ecosystem ; Forests ; Metagenome ; Metagenomics ; Microbial Consortia ; Nitrogen/metabolism ; Phosphorus/*metabolism ; *Soil Microbiology ; }, abstract = {Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.}, }
@article {pmid33024037, year = {2020}, author = {Vuillemin, A and Vargas, S and Coskun, ÖK and Pockalny, R and Murray, RW and Smith, DC and D'Hondt, S and Orsi, WD}, title = {Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {33024037}, issn = {2150-7511}, mesh = {Atlantic Ocean ; Bacteria/*classification/metabolism ; Ecosystem ; Geologic Sediments/*microbiology ; *Metagenome ; Microbial Viability ; *Microbiota ; Phylogeny ; Time Factors ; }, abstract = {How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum "Candidatus Atribacteria," which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. "Ca. Atribacteria" dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing "Ca. Atribacteria" also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD+ Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor "Ca Atribacteria," as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the "Ca Atribacteria" can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments.IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum "Candidatus Atribacteria" dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that "Ca Atribacteria" can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.}, }
@article {pmid32738030, year = {2020}, author = {Yuan, Z and Ye, X and Zhu, L and Zhang, N and An, Z and Zheng, WJ}, title = {Virome assembly and annotation in brain tissue based on next-generation sequencing.}, journal = {Cancer medicine}, volume = {9}, number = {18}, pages = {6776-6790}, pmid = {32738030}, issn = {2045-7634}, support = {R01 AG066749/AG/NIA NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; }, mesh = {Brain/pathology/*virology ; Brain Neoplasms/pathology/*virology ; Case-Control Studies ; Contig Mapping ; Databases, Nucleic Acid ; Glioblastoma/pathology/*virology ; *High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Picornaviridae/*genetics ; RNA, Viral/genetics ; RNA-Seq ; Retroviridae/*genetics ; Virome/*genetics ; }, abstract = {The glioblastoma multiforme (GBM) is one of the deadliest tumors. It has been speculated that virus plays a role in GBM but the evidences are controversy. Published researches are mainly limited to studies on the presence of human cytomegalovirus (HCMV) in GBM. No comprehensive assessment of the brain virome, the collection of viral material in the brain, based on recently sequenced data has been performed. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from eight projects in the SRA database by a tested and comprehensive assembly approach. The annotation of the assembled contigs showed that most viral sequences in the brain belong to the viral family Retroviridae. In some GBM samples, we also detected full genome sequence of a novel picornavirus recently discovered in invertebrates. Unlike previous reports, our study did not detect herpes virus such as HCMV in GBM from the data we used. However, some contigs that cannot be annotated with any known genes exhibited antibody epitopes in their sequences. These findings provide several avenues for potential cancer therapy: the newly discovered picornavirus could be a starting point to engineer novel oncolytic virus; and the exhibited antibody epitopes could be a source to explore potential drug targets for immune cancer therapy. By characterizing the virosphere in GBM and normal brain at a global level, the results from this study strengthen the link between GBM and viral infection which warrants the further investigation.}, }
@article {pmid32205368, year = {2020}, author = {Vorobev, A and Dupouy, M and Carradec, Q and Delmont, TO and Annamalé, A and Wincker, P and Pelletier, E}, title = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.}, journal = {Genome research}, volume = {30}, number = {4}, pages = {647-659}, pmid = {32205368}, issn = {1549-5469}, mesh = {Biodiversity ; Computational Biology/*methods ; Eukaryota/classification/*genetics ; *Gene Expression Profiling/methods ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; Plankton/classification/*genetics ; *Transcriptome ; }, abstract = {Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.}, }
@article {pmid33360047, year = {2021}, author = {Pastor-Villaescusa, B and Plaza-Díaz, J and Egea-Zorrilla, A and Leis, R and Bueno, G and Hoyos, R and Vázquez-Cobela, R and Latorre, M and Cañete, MD and Caballero-Villarraso, J and Gil, Á and Cañete, R and Aguilera, CM}, title = {Evaluation of the gut microbiota after metformin intervention in children with obesity: A metagenomic study of a randomized controlled trial.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {134}, number = {}, pages = {111117}, doi = {10.1016/j.biopha.2020.111117}, pmid = {33360047}, issn = {1950-6007}, mesh = {Adolescent ; Age Factors ; Bacteria/*drug effects/genetics/growth &amp; development ; Child ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hypoglycemic Agents/*therapeutic use ; Intestines/*microbiology ; Life Style ; Male ; *Metagenome ; *Metagenomics ; Metformin/*therapeutic use ; Pediatric Obesity/diagnosis/*drug therapy/microbiology ; Spain ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND: Metformin, a first-line oral antidiabetic agent that has shown promising results in terms of treating childhood and adolescent obesity, might influence the composition of the gut microbiota. We aimed to evaluate whether the gut microbiota of non-diabetic children with obesity changes after a metformin intervention.<br><br>METHODS: The study was a multicenter and double-blind randomized controlled trial in 160 children with obesity. Children were randomly assigned to receive either metformin (1 g/day) or placebo for 6 months in combination with healthy lifestyle recommendations in both groups. Then, we conducted a metagenomic analysis in a subsample obtained from 33 children (15 metformin, 18 placebo). A linear mixed-effects model (LMM) was used to determine the abundance changes from baseline to six months according to treatment. To analyze the data by clusters, a principal component analysis was performed to understand whether lifestyle habits have a different influence on the microbiota depending on the treatment group.<br><br>RESULTS: Actinobacteria abundance was higher after placebo treatment compared with metformin. However, the interaction time x treatment just showed a trend to be significant (4.6% to 8.1% after placebo vs. 3.8 % to 2.6 % after metformin treatment, p = 0.055). At genus level, only the abundance of Bacillus was significantly higher after the placebo intervention compared with metformin (2.5% to 5.7% after placebo vs. 1.5 % to 0.8 % after metformin treatment, p = 0.044). Furthermore, different ensembles formed by Firmicutes, Bacteroidetes, and Verrucomicrobia were found according to the interventions under a similar food consumption.<br><br>CONCLUSION: Further studies with a large sample size controlled by lifestyle patterns are required in obese children and adolescents to clarify whether metformin might trigger gut microbiota alterations.<br><br>TRIAL REGISTRATION: Registered on the European Clinical Trials Database (EudraCT, ID: 2010-023061-21) on 14 November 2011.}, }
@article {pmid33113351, year = {2020}, author = {Gálvez, EJC and Iljazovic, A and Amend, L and Lesker, TR and Renault, T and Thiemann, S and Hao, L and Roy, U and Gronow, A and Charpentier, E and Strowig, T}, title = {Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.}, journal = {Cell host &amp; microbe}, volume = {28}, number = {6}, pages = {838-852.e6}, doi = {10.1016/j.chom.2020.09.012}, pmid = {33113351}, issn = {1934-6069}, mesh = {Animals ; DNA, Bacterial ; *Gastrointestinal Microbiome ; Genetic Loci ; Genome, Bacterial ; Glycoside Hydrolases/genetics ; Glycosyltransferases/genetics ; Humans ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Phylogeny ; Polysaccharides/*metabolism ; Prevotella/classification/*growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S ; Transcriptome ; Vegans ; Whole Genome Sequencing ; Xylans/*metabolism ; }, abstract = {Prevotella spp. are a dominant bacterial genus within the human gut. Multiple Prevotella spp. co-exist in some individuals, particularly those consuming plant-based diets. Additionally, Prevotella spp. exhibit variability in the utilization of diverse complex carbohydrates. To investigate the relationship between Prevotella competition and diet, we isolated Prevotella species from the mouse gut, analyzed their genomes and transcriptomes in vivo, and performed competition experiments between species in mice. Diverse dominant Prevotella species compete for similar metabolic niches in vivo, which is linked to the upregulation of specific polysaccharide utilization loci (PULs). Complex plant-derived polysaccharides are required for Prevotella spp. expansion, with arabinoxylans having a prominent impact on species abundance. The most dominant Prevotella species encodes a specific tandem-repeat trsusC/D PUL that enables arabinoxylan utilization and is conserved in human Prevotella copri strains, particularly among those consuming a vegan diet. These findings suggest that efficient (arabino)xylan-utilization is a factor contributing to Prevotella dominance.}, }
@article {pmid32979836, year = {2020}, author = {Thijssen, M and Tacke, F and Beller, L and Deboutte, W and Yinda, KC and Nevens, F and Laleman, W and Van Ranst, M and Pourkarim, MR}, title = {Clinical relevance of plasma virome dynamics in liver transplant recipients.}, journal = {EBioMedicine}, volume = {60}, number = {}, pages = {103009}, pmid = {32979836}, issn = {2352-3964}, mesh = {Adult ; Aged ; Antiviral Agents/pharmacology/therapeutic use ; Coinfection ; Computational Biology/methods ; Female ; Humans ; Liver Transplantation/*adverse effects/methods ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Phylogeny ; *Transplant Recipients ; Viremia/diagnosis/*etiology ; *Virome ; Virus Diseases/diagnosis/drug therapy/*etiology ; }, abstract = {BACKGROUND: The role of the microbiome in liver transplantation (LT) outcome has received a growing interest in the past decades. In contrast to bacteria, the role of endogenous viral communities, known as the virome, is poorly described. Here, we applied a viral metagenomic approach to study the dynamic evolution of circulating viruses in the plasma of LT recipients and its effect on the clinical course of patients.<br><br>METHODS: Patients chronically infected with hepatitis B virus (HBV) that received a LT due to endstage liver disease were included in this study. Longitudinal plasma samples were collected pre- and post-LT. Intact viral particles were isolated and sequenced on an Illumina HiSeq 2500 platform. Short read libraries were analysed with an in-house bioinformatics pipeline. Key endpoints were the dynamics of viral families and post-LT complications.<br><br>FINDINGS: The initiation of immunosuppression induced a bloom of the Anelloviridae that dominated the post-LT plasma virome. A variety of post-LT complication were observed. Nephrotoxicity was reported in 38% of the patients and was associated with a high abundance of anelloviruses. Besides nephrotoxicity, 16 (67%) patients experienced flares of viral or bacterial infections in post-transplant follow-up. These flares were recognized by an increased burden of anelloviruses (p < 0.05). Interestingly, no mortality was observed in patients infected with human pegivirus.<br><br>INTERPRETATION: These findings suggest a diagnostic potential for the Anelloviridae family in post-LT complications. Furthermore, the impact of human pegivirus infection on post-transplant survival should be further investigated.<br><br>FUNDING: This trial was supported by Gilead Sciences grant number BE-2017-000133.}, }
@article {pmid32907957, year = {2020}, author = {Brugger, SD and Eslami, SM and Pettigrew, MM and Escapa, IF and Henke, MT and Kong, Y and Lemon, KP}, title = {Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {32907957}, issn = {2379-5042}, support = {R01 DC013554/DC/NIDCD NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Carnobacteriaceae/genetics/*physiology ; Child, Preschool ; Genomics ; Humans ; Infant ; *Microbial Interactions ; *Microbiota ; Nasopharynx/*microbiology ; Pneumococcal Infections/microbiology ; Staphylococcus aureus/genetics/physiology ; Streptococcus pneumoniae/genetics/physiology ; }, abstract = {Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro, whereas robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together. D. pigrum l-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into D. pigrum's functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.IMPORTANCE Staphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureus in vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.}, }
@article {pmid32907949, year = {2020}, author = {Ramírez, AL and Colmant, AMG and Warrilow, D and Huang, B and Pyke, AT and McMahon, JL and Meyer, DB and Graham, RMA and Jennison, AV and Ritchie, SA and van den Hurk, AF}, title = {Metagenomic Analysis of the Virome of Mosquito Excreta.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {32907949}, issn = {2379-5042}, support = {1044698/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aedes/*virology ; Animals ; Arboviruses/classification/isolation &amp; purification ; Australia ; Culex/*virology ; Feces/*virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Insect Viruses/*classification/isolation &amp; purification ; Metagenomics ; Virome/*genetics ; }, abstract = {Traditional screening for arboviruses in mosquitoes requires a priori knowledge and the utilization of appropriate assays for their detection. Mosquitoes can also provide other valuable information, including unexpected or novel arboviruses, nonarboviral pathogens ingested from hosts they feed on, and their own genetic material. Metagenomic analysis using next-generation sequencing (NGS) is a rapidly advancing technology that allows us to potentially obtain all this information from a mosquito sample without any prior knowledge of virus, host, or vector. Moreover, it has been recently demonstrated that pathogens, including arboviruses and parasites, can be detected in mosquito excreta by molecular methods. In this study, we investigated whether RNA viruses could be detected in mosquito excreta by NGS. Excreta samples were collected from Aedes vigilax and Culex annulirostris experimentally exposed to either Ross River or West Nile viruses and from field mosquitoes collected across Queensland, Australia. Total RNA was extracted from the excreta samples, reverse transcribed to cDNA, and sequenced using the Illumina NextSeq 500 platform. Bioinformatic analyses from the generated reads demonstrate that mosquito excreta provide sufficient RNA for NGS, allowing the assembly of near-full-length viral genomes. We detected Australian Anopheles totivirus, Wuhan insect virus 33, and Hubei odonate virus 5 and identified seven potentially novel viruses closely related to members of the order Picornavirales (2/7) and to previously described, but unclassified, RNA viruses (5/7). Our results suggest that metagenomic analysis of mosquito excreta has great potential for virus discovery and for unbiased arbovirus surveillance in the near future.IMPORTANCE When a mosquito feeds on a host, it ingests not only its blood meal but also an assortment of microorganisms that are present in the blood, thus acting as an environmental sampler. By using specific tests, it is possible to detect arthropod-borne viruses (arboviruses) like dengue and West Nile viruses in mosquito excreta. Here, we explored the use of next-generation sequencing (NGS) for unbiased detection of RNA viruses present in excreta from experimentally infected and field-collected mosquitoes. We have demonstrated that mosquito excreta provide a suitable template for NGS and that it is possible to recover and assemble near-full-length genomes of both arboviruses and insect-borne viruses, including potentially novel ones. These results importantly show the direct practicality of the use of mosquito excreta for NGS, which in the future could be used for virus discovery, environmental virome sampling, and arbovirus surveillance.}, }
@article {pmid32848005, year = {2020}, author = {Bobay, LM and Wissel, EF and Raymann, K}, title = {Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32848005}, issn = {2379-5042}, support = {R01 GM132137/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Bees/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; *High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; *Metagenome ; Metagenomics ; Phylogeny ; Symbiosis ; }, abstract = {Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.}, }
@article {pmid32727857, year = {2020}, author = {Auchtung, JM and Preisner, EC and Collins, J and Lerma, AI and Britton, RA}, title = {Identification of Simplified Microbial Communities That Inhibit Clostridioides difficile Infection through Dilution/Extinction.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32727857}, issn = {2379-5042}, support = {R01 AI123278/AI/NIAID NIH HHS/United States ; R33 AI121522/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Animals ; Clostridioides difficile/*classification/*physiology ; Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Microbiological Techniques/*methods ; Middle Aged ; }, abstract = {The gastrointestinal microbiome plays an important role in limiting susceptibility to infection with Clostridioides difficile To better understand the ecology of bacteria important for C. difficile colonization resistance, we developed an experimental platform to simplify complex communities of fecal bacteria through dilution and rapidly screen for their ability to resist C. difficile colonization after challenge, as measured by >100-fold reduction in levels of C. difficile in challenged communities. We screened 76 simplified communities diluted from cultures of six fecal donors and identified 24 simplified communities that inhibited C. difficile colonization in vitro Sequencing revealed that simplified communities were composed of 19 to 67 operational taxonomic units (OTUs) and could be partitioned into four distinct community types. One simplified community could be further simplified from 56 to 28 OTUs through dilution and retain the ability to inhibit C. difficile We tested the efficacy of seven simplified communities in a humanized microbiota mouse model. We found that four communities were able to significantly reduce the severity of the initial C. difficile infection and limit susceptibility to disease relapse. Analysis of fecal microbiomes from treated mice demonstrated that simplified communities accelerated recovery of indigenous bacteria and led to stable engraftment of 19 to 22 OTUs from simplified communities. Overall, the insights gained through the identification and characterization of these simplified communities increase our understanding of the microbial dynamics of C. difficile infection and recovery.IMPORTANCE Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and a significant health care burden. Fecal microbiota transplantation is highly effective at treating recurrent C. difficile disease; however, uncertainties about the undefined composition of fecal material and potential long-term unintended health consequences remain. These concerns have motivated studies to identify new communities of microbes with a simpler composition that will be effective at treating disease. This work describes a platform for rapidly identifying and screening new simplified communities for efficacy in treating C. difficile infection. Four new simplified communities of microbes with potential for development of new therapies to treat C. difficile disease are identified. While this platform was developed and validated to model infection with C. difficile, the underlying principles described in the paper could be easily modified to develop therapeutics to treat other gastrointestinal diseases.}, }
@article {pmid32574649, year = {2020}, author = {Van Borm, S and Fu, Q and Winand, R and Vanneste, K and Hakhverdyan, M and Höper, D and Vandenbussche, F}, title = {Evaluation of a commercial exogenous internal process control for diagnostic RNA virus metagenomics from different animal clinical samples.}, journal = {Journal of virological methods}, volume = {283}, number = {}, pages = {113916}, doi = {10.1016/j.jviromet.2020.113916}, pmid = {32574649}, issn = {1879-0984}, mesh = {Animals ; Feces/virology ; High-Throughput Nucleotide Sequencing/methods ; Mengovirus/genetics/isolation &amp; purification ; Metagenomics/*methods ; RNA Virus Infections/*diagnosis/*virology ; RNA Viruses/genetics/*isolation &amp; purification ; RNA, Viral/genetics/isolation &amp; purification ; Sensitivity and Specificity ; Swine ; Swine Diseases/virology ; Virome ; }, abstract = {Metagenomic next generation sequencing (mNGS) is increasingly recognized as an important complementary tool to targeted human and animal infectious disease diagnostics. It is, however, sensitive to biases and errors that are currently not systematically evaluated by the implementation of quality controls (QC) for the diagnostic use of mNGS. We evaluated a commercial reagent (Mengovirus extraction control kit, CeraamTools, bioMérieux) as an exogenous internal control for mNGS. It validates the integrity of reagents and workflow, the efficient isolation of viral nucleic acids and the absence of inhibitors in individual samples (verified using a specific qRT-PCR). Moreover, it validates the efficient generation of viral sequence data in individual samples (verified by normalized mengoviral read counts in the metagenomic analysis). We show that when using a completely random metagenomics workflow: (1) Mengovirus RNA can be reproducibly detected in different animal sample types (swine feces and sera, wild bird cloacal swabs), except for tissue samples (swine lung); (2) the Mengovirus control kit does not contain other contaminating viruses that may affect metagenomic experiments (using a cutoff of minimum 1 Kraken classified read per million (RPM)); (3) the addition of 2.17 × 106Mengovirus copies/mL of sample does not affect the virome composition of pig fecal samples or wild bird cloacal swab samples; (4) Mengovirus Cq values (using as cutoff the upper limit of the 99 % confidence interval of Cq values for a given sample matrix) allow the identification of samples with poor viral RNA extraction or high inhibitor load; (5) Mengovirus normalized read counts (cutoff RPM > 1) allow the identification of samples where the viral sequences are outcompeted by host or bacterial target sequences in the random metagenomic workflow. The implementation of two QC testing points, a first one after RNA extraction (Mengoviral qRT-PCR) and a second one after metagenomic data analysis provide valuable information for the validation of individual samples and results. Their implementation in addition to external controls validating runs or experiments should be carefully considered for a given sample type and workflow.}, }
@article {pmid34272286, year = {2021}, author = {Osvatic, JT and Wilkins, LGE and Leibrecht, L and Leray, M and Zauner, S and Polzin, J and Camacho, Y and Gros, O and van Gils, JA and Eisen, JA and Petersen, JM and Yuen, B}, title = {Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {29}, pages = {}, doi = {10.1073/pnas.2104378118}, pmid = {34272286}, issn = {1091-6490}, abstract = {In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.}, }
@article {pmid34266351, year = {2021}, author = {Khattab, AR and Farag, MA}, title = {Marine and terrestrial endophytic fungi: a mine of bioactive xanthone compounds, recent progress, limitations, and novel applications.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-28}, doi = {10.1080/07388551.2021.1940087}, pmid = {34266351}, issn = {1549-7801}, abstract = {Endophytic fungi are a kind of fungi that colonizes living plant tissues presenting a myriad of microbial adaptations that have been developed in such a hidden environment. Owing to its large diversity and particular habituation, they present a golden mine for research in the field of drug discovery. Endophytic fungal communities possess unique biocatalytic machinery that furnishes a myriad of complex natural product scaffolds. Xanthone compounds are examples of endophytic secondary metabolic products with pronounced biological activity to include: antioxidant, antimicrobial, anti-inflammatory, antithrombotic, antiulcer, choleretic, diuretic, and monoamine oxidase inhibiting activity.The current review compiles the recent progress made on the microbiological production of xanthones using fungal endophytes obtained from both marine and terrestrial origins, with comparisons being made among both natural resources. The biosynthesis of xanthones in endophytic fungi is outlined along with its decoding enzymes. Biotransformation reactions reported to be carried out using different endophytic microbial models are also outlined for xanthones structural modification purposes and the production of novel molecules.A promising application of novel computational tools is presented as a future direction for the goal of optimizing microbial xanthones production to include establishing metabolic pathway databases and the in silico analysis of microbial interactions. Metagenomics methods and related bioinformatics platforms are highlighted as unexplored tools for the biodiversity analysis of endophytic microbial communities that are difficult to be cultured.}, }
@article {pmid33754165, year = {2021}, author = {Del Chierico, F and Manco, M and Gardini, S and Guarrasi, V and Russo, A and Bianchi, M and Tortosa, V and Quagliariello, A and Shashaj, B and Fintini, D and Putignani, L}, title = {Fecal microbiota signatures of insulin resistance, inflammation, and metabolic syndrome in youth with obesity: a pilot study.}, journal = {Acta diabetologica}, volume = {58}, number = {8}, pages = {1009-1022}, pmid = {33754165}, issn = {1432-5233}, support = {600932//European Commission (FP7 Information Communication Technologies Programme)/ ; }, mesh = {Adolescent ; Bacteria/classification/genetics ; Biomarkers/blood ; Child ; Feces/*microbiology ; Female ; Glucose Intolerance/microbiology ; Humans ; Hypertension/microbiology ; Inflammation/*microbiology ; Insulin Resistance/*physiology ; Male ; Metabolic Syndrome/*microbiology ; Metagenomics ; Microbiota/*physiology ; *Obesity/complications ; Pilot Projects ; RNA, Ribosomal, 16S/analysis ; Risk Factors ; Triglycerides/blood ; }, abstract = {AIMS: To identify fecal microbiota profiles associated with metabolic abnormalities belonging to the metabolic syndrome (MS), high count of white blood cells (WBCs) and insulin resistance (IR).<br><br>METHODS: Sixty-eight young patients with obesity were stratified for percentile distribution of MS abnormalities. A MS risk score was defined as low, medium, and high MS risk. High WBCs were defined as a count ≥ 7.0 103/µL; severe obesity as body mass index Z-score ≥ 2 standard deviations; IR as homeostatic assessment model algorithm of IR (HOMA) ≥ 3.7. Stool samples were analyzed by 16S rRNA-based metagenomics.<br><br>RESULTS: We found reduced bacterial richness of fecal microbiota in patients with IR and high diastolic blood pressure (BP). Distinct microbial markers were associated to high BP (Clostridium and Clostridiaceae), low high-density lipoprotein cholesterol (Lachnospiraceae, Gemellaceae, Turicibacter), and high MS risk (Coriobacteriaceae), WBCs (Bacteroides caccae, Gemellaceae), severe obesity (Lachnospiraceae), and impaired glucose tolerance (Bacteroides ovatus and Enterobacteriaceae). Conversely, taxa such as Faecalibacterium prausnitzii, Parabacterodes, Bacteroides caccae, Oscillospira, Parabacterodes distasonis, Coprococcus, and Haemophilus parainfluenzae were associated to low MS risk score, triglycerides, fasting glucose and HOMA-IR, respectively. Supervised multilevel analysis grouped clearly "variable" patients based on the MS risk.<br><br>CONCLUSIONS: This was a proof-of-concept study opening the way at the identification of fecal microbiota signatures, precisely associated with cardiometabolic risk factors in young patients with obesity. These evidences led us to infer, while some gut bacteria have a detrimental role in exacerbating metabolic risk factors some others are beneficial ameliorating cardiovascular host health.}, }
@article {pmid33549667, year = {2021}, author = {Ariaeenejad, S and Kavousi, K and Mamaghani, ASA and Motahar, SFS and Nedaei, H and Salekdeh, GH}, title = {In-silico discovery of bifunctional enzymes with enhanced lignocellulose hydrolysis from microbiota big data.}, journal = {International journal of biological macromolecules}, volume = {177}, number = {}, pages = {211-220}, doi = {10.1016/j.ijbiomac.2021.02.014}, pmid = {33549667}, issn = {1879-0003}, mesh = {Animals ; Big Data ; Biomass ; Cellulase/metabolism ; Cellulose/metabolism ; Endo-1,4-beta Xylanases/metabolism ; Hydrogen-Ion Concentration ; Hydrolysis ; Lignin/*metabolism ; Metagenome/physiology ; Metagenomics/methods ; Microbiota/*physiology ; Oryza/metabolism ; Polysaccharides/metabolism ; Rumen/metabolism ; Temperature ; Thermodynamics ; }, abstract = {Due to the importance of using lignocellulosic biomass, it is always important to find an effective novel enzyme or enzyme cocktail or fusion enzymes. Identification of bifunctional enzymes through a metagenomic approach is an efficient method for converting agricultural residues and a beneficial way to reduce the cost of enzyme cocktail and fusion enzyme production. In this study, a novel stable bifunctional cellulase/xylanase, PersiCelXyn1 was identified from the rumen microbiota by the multi-stage in-silico screening pipeline and computationally assisted methodology. The enzyme exhibited the optimal activity at pH 5 and 50°C. Analyzing the enzyme activity at extreme temperature, pH, long-term storage, and presence of inhibitors and metal ions, confirmed the stability of the bifunctional enzyme under harsh conditions. Hydrolysis of the rice straw by PersiCelXyn1 showed its capability to degrade both cellulose and hemicellulose polymers. Also, the enzyme improved the degradation of various biomass substrates after 168 h of hydrolysis. Our results demonstrated the power of the multi-stage in-silico screening to identify bifunctional enzymes from metagenomic big data for effective bioconversion of lignocellulosic biomass.}, }
@article {pmid32862246, year = {2021}, author = {Starke, R and Pylro, VS and Morais, DK}, title = {16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {535-539}, pmid = {32862246}, issn = {1432-184X}, support = {18-25706S//Grantová Agentura České Republiky/ ; 20-02022Y//Grantová Agentura České Republiky/ ; }, mesh = {Gene Dosage ; Gene Library ; Metagenome/genetics ; Metagenomics/*standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.}, }
@article {pmid32638044, year = {2021}, author = {Lukoseviciute, L and Lebedeva, J and Kuisiene, N}, title = {Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {110-121}, pmid = {32638044}, issn = {1432-184X}, mesh = {Acidobacteria/genetics ; Actinobacteria/genetics ; Bacteria/classification/*genetics/metabolism ; Caves/*microbiology ; Chloroflexi/genetics ; Firmicutes/genetics ; Geologic Sediments/*microbiology ; Georgia (Republic) ; Metagenome/genetics ; Microbiota/genetics ; Peptide Synthases/*genetics ; Polyketide Synthases/*genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Secondary Metabolism/*genetics ; Soil Microbiology ; }, abstract = {Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.}, }
@article {pmid34264153, year = {2021}, author = {Gilroy, R}, title = {Spotlight on the Avian Gut Microbiome: Fresh Opportunities in Discovery.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/03079457.2021.1955826}, pmid = {34264153}, issn = {1465-3338}, abstract = {Chickens represent a globally ubiquitous food animal underpinning many aspects of human nutrition and health. Consumption of chicken meat continues to surge, representing a cheaper, healthier, low carbon alternative to other livestock meats. Despite this importance, we are still unable to define what lives within the chicken gut microbiome. This complex community bridges poultry diet, health and productivity as well as providing a reservoir for zoonotic pathogens. Even with decades of intensive study we are still discovering novel microbial species within this environment, each of which having the potential to provide an avenue for commercial microbiome modulation. The chicken gut truly represents an exhilarating challenge in turning new-found knowledge into new-won power to improve the health and wealth of poultry and people.}, }
@article {pmid34256809, year = {2021}, author = {Chen, P and Zhou, H and Huang, Y and Xie, Z and Zhang, M and Wei, Y and Li, J and Ma, Y and Luo, M and Ding, W and Cao, J and Jiang, T and Nan, P and Fang, J and Li, X}, title = {Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {207}, pmid = {34256809}, issn = {1474-760X}, support = {2018YFC0310600//National Key Research and Development Program of China/ ; 31771412//National Natural Science Foundation of China/ ; KFJ-BRP-009//Biological Resources Programme from Chinese Academy of Sciences/ ; }, abstract = {BACKGROUND: The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.<br><br>RESULTS: We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts' nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat.<br><br>CONCLUSION: Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.}, }
@article {pmid33849075, year = {2021}, author = {Arif, M and Zhang, C and Li, X and Güngör, C and Çakmak, B and Arslantürk, M and Tebani, A and Özcan, B and Subaş, O and Zhou, W and Piening, B and Turkez, H and Fagerberg, L and Price, N and Hood, L and Snyder, M and Nielsen, J and Uhlen, M and Mardinoglu, A}, title = {iNetModels 2.0: an interactive visualization and database of multi-omics data.}, journal = {Nucleic acids research}, volume = {49}, number = {W1}, pages = {W271-W276}, pmid = {33849075}, issn = {1362-4962}, support = {RC2 HG005805/HG/NHGRI NIH HHS/United States ; P50 GM076547/GM/NIGMS NIH HHS/United States ; P30 ES017885/ES/NIEHS NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; *Databases, Factual ; *Gastrointestinal Microbiome ; Gene Regulatory Networks ; Humans ; *Metabolomics ; *Metagenomics ; Middle Aged ; Mouth/*microbiology ; Neoplasms/genetics ; Non-alcoholic Fatty Liver Disease/blood/microbiology ; *Proteomics ; Software ; }, abstract = {It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.}, }
@article {pmid33270378, year = {2021}, author = {Gatcliffe, C and Rao, A and Brigger, M and Dimmock, D and Hansen, C and Montgomery, J and Schlaberg, R and Coufal, NG and Farnaes, L}, title = {Metagenomic sequencing and evaluation of the host response in the pediatric aerodigestive population.}, journal = {Pediatric pulmonology}, volume = {56}, number = {2}, pages = {516-524}, doi = {10.1002/ppul.25198}, pmid = {33270378}, issn = {1099-0496}, mesh = {Bronchoalveolar Lavage Fluid/immunology/microbiology ; Child ; Child, Preschool ; Deglutition Disorders/immunology/*microbiology ; Female ; Host Microbial Interactions ; Humans ; Immunity ; Infant ; Male ; Metagenomics ; Microbiota/genetics ; Mouth/microbiology ; Respiratory Aspiration/immunology/*microbiology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {OBJECTIVES: To assess the diagnostic utility of metagenomic sequencing in pediatric aerodigestive clinic patients being evaluated for chronic aspiration. We hypothesize that using a metagenomics platform will aid in the identification of microbes not found on standard culture.<br><br>STUDY DESIGN AND METHODS: Twenty-four children referred to an aerodigestive clinic were enrolled in a prospective, single-site, cross-sectional cohort study. At the time of clinical evaluation under anesthesia, two samples were obtained: an upper airway sample and a sample from bronchoalveolar lavage (BAL). Samples were sent for routine culture and analyzed using Explify® Respiratory, a CLIA Laboratory Developed Test which identifies respiratory commensals and pathogens through RNA and DNA sequencing. Since RNA was sequenced in the course of the metagenomic analysis to identify organisms (RNA viruses and bacteria), the sequencing approach also captured host derived messenger RNA during sample analysis. This incidentally obtained host transcriptomic data were analyzed to evaluate the host immune response. The results of these studies were correlated with the clinical presentation of the research subjects.<br><br>RESULTS: In 10 patients, organisms primarily associated with oral flora were identified in the BAL. Standard culture was negative in three patients where clinical metagenomics led to a result with potential clinical significance. Transcriptomic data correlated with the presence or absence of dysphagia as identified on prior videofluoroscopic evaluation of swallowing.<br><br>CONCLUSIONS: Clinical metagenomics allows for simultaneous analysis of the microbiota and the host immune response from BAL samples. As the technologies in this field continue to advance, such testing may improve the diagnostic evaluation of patients with suspected chronic aspiration.}, }
@article {pmid33215702, year = {2021}, author = {Akinola, SA and Ayangbenro, AS and Babalola, OO}, title = {The diverse functional genes of maize rhizosphere microbiota assessed using shotgun metagenomics.}, journal = {Journal of the science of food and agriculture}, volume = {101}, number = {8}, pages = {3193-3201}, doi = {10.1002/jsfa.10948}, pmid = {33215702}, issn = {1097-0010}, support = {UID123634//National Research Foundation South Africa/ ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Metagenomics ; Microbiota ; Nitrogen Fixation ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Zea mays/*growth &amp; development/microbiology ; }, abstract = {BACKGROUND: The geographical diversification in chemical, biological and physical properties of plant biospheres instigates heterogenicity in the proliferation of important soil microbiome. Controlling functions and structure of plant rhizosphere from a better understanding and prediction of a plant's immediate environment will help assess plant-microbe interplay, improve the productivity of plant ecosystems and improve plant response to adverse soil conditions. Here we characterized functional genes of the microbial community of maize rhizosphere using a culture-independent method.<br><br>RESULTS: Our metadata showed microbial genes involved in nitrogen fixation, phosphate solubilization, quorum sensing molecules, trehalose, siderophore production, phenazine biosynthesis protein, daunorubicin resistance, acetoin, 1-aminocyclopropane-1-carboxylate deaminase, 4-hydroxybenzoate, disease control and stress-reducing genes (superoxidase dismutase, catalase, peroxidase, etc.). β-Diversity showed that there is a highly significant difference between most of the genes mined from rhizosphere soil samples and surrounding soils.<br><br>CONCLUSIONS: The high relative abundance of stress-reducing genes mined from this study showed that the sampling sites harbor not only important plant-beneficial organisms but also a hotspot for developing bio-fertilizers. Nevertheless, since most of these organisms are unculturable, mapping cultivation strategies for their growth could make them readily available as bio-inoculants and possible biotechnological applications in the future. © 2020 Society of Chemical Industry.}, }
@article {pmid32434845, year = {2020}, author = {Evans, JT and Denef, VJ}, title = {To Dereplicate or Not To Dereplicate?.}, journal = {mSphere}, volume = {5}, number = {3}, pages = {}, pmid = {32434845}, issn = {2379-5042}, mesh = {*Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; *Software ; }, abstract = {Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences. We show that (i) published data sets contain a large fraction of MAGs sharing >99% average nucleotide identity, (ii) different software packages and parameters used to resolve this redundancy remove very different numbers of MAGs, and (iii) the removal of closely related genomes leads to losses of population-specific auxiliary genes. Finally, we highlight some approaches that can infer strain-specific dynamics across a sample series without dereplication.}, }
@article {pmid32343490, year = {2020}, author = {Estaki, M and Jiang, L and Bokulich, NA and McDonald, D and González, A and Kosciolek, T and Martino, C and Zhu, Q and Birmingham, A and Vázquez-Baeza, Y and Dillon, MR and Bolyen, E and Caporaso, JG and Knight, R}, title = {QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.}, journal = {Current protocols in bioinformatics}, volume = {70}, number = {1}, pages = {e100}, doi = {10.1002/cpbi.100}, pmid = {32343490}, issn = {1934-340X}, support = {UL1 TR001442/TR/NCATS NIH HHS/United States ; }, mesh = {Biodiversity ; *Databases as Topic ; Linear Models ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug-ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses-e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta-analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data Support Protocol: Further microbiome analyses.}, }
@article {pmid34251746, year = {2021}, author = {Garrido-Sanz, L and Senar, MÀ and Piñol, J}, title = {Relative species abundance estimation in artificial mixtures of insects using mito-metagenomics and a correction factor for the mitochondrial DNA copy number.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13464}, pmid = {34251746}, issn = {1755-0998}, abstract = {Mito-metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high-throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within-species estimation) but failed to estimate the RSA within a single sample (across-species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single-species libraries and the lengths of the whole genomes and mitogenomes.}, }
@article {pmid34246242, year = {2021}, author = {Kameoka, S and Motooka, D and Watanabe, S and Kubo, R and Jung, N and Midorikawa, Y and Shinozaki, NO and Sawai, Y and Takeda, AK and Nakamura, S}, title = {Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {527}, pmid = {34246242}, issn = {1471-2164}, support = {18K08431//Ministry of Education, Culture, Sports, Science and Technology/ ; 172107106//Ministry of Internal Affairs and Communications/ ; JP18gm1010005//Japan Agency for Medical Research and Development/ ; }, mesh = {Benchmarking ; *Gastrointestinal Microbiome/genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol.<br><br>RESULTS: QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data.<br><br>CONCLUSIONS: These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.}, }
@article {pmid34193290, year = {2021}, author = {Huang, S and Jiang, S and Huo, D and Allaband, C and Estaki, M and Cantu, V and Belda-Ferre, P and Vázquez-Baeza, Y and Zhu, Q and Ma, C and Li, C and Zarrinpar, A and Liu, YY and Knight, R and Zhang, J}, title = {Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {151}, pmid = {34193290}, issn = {2049-2618}, support = {T32 OD017863/NH/NIH HHS/United States ; K08 DK102902/NH/NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; DP1-AT010885/AT/NCCIH NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; P30 DK120515, P30 DK063491, and UL1 TR001442/DK/NIDDK NIH HHS/United States ; R01AI141529, R01HD093761, R01AG067744/NH/NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; 31701577//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bifidobacterium ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; *Probiotics ; Zebrafish ; }, abstract = {BACKGROUND: Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.<br><br>RESULTS: We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10-70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.<br><br>CONCLUSIONS: Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans. Video abstract.}, }
@article {pmid34133435, year = {2021}, author = {Hardmeier, I and Aeberhard, N and Qi, W and Schoenbaechler, K and Kraettli, H and Hatt, JM and Fraefel, C and Kubacki, J}, title = {Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0252534}, pmid = {34133435}, issn = {1932-6203}, mesh = {Adenoviridae/classification/genetics ; Animals ; Chiroptera/classification/*virology ; Disease Reservoirs/virology ; Feces/*virology ; Genetic Variation ; Genome, Viral/genetics ; Hepevirus/classification/genetics ; Humans ; Metagenomics/*methods ; Middle East Respiratory Syndrome Coronavirus/classification/genetics ; Phylogeny ; Rotavirus/classification/genetics ; Sequence Analysis, DNA/methods ; Switzerland ; Virome/*genetics ; Viruses/classification/*genetics ; Zoonoses/*virology ; }, abstract = {Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.}, }
@article {pmid33660141, year = {2021}, author = {Krishnamoorthy, A and Gupta, A and Sar, P and Maiti, MK}, title = {Metagenomics of two gnotobiotically grown aromatic rice cultivars reveals genotype-dependent and tissue-specific colonization of endophytic bacterial communities attributing multiple plant growth promoting traits.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {37}, number = {4}, pages = {59}, pmid = {33660141}, issn = {1573-0972}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Endophytes/classification/isolation &amp; purification/*physiology ; *Genotype ; *Germ-Free Life ; High-Throughput Nucleotide Sequencing ; Indoleacetic Acids ; *Metagenomics ; Microbiota/*physiology ; Nitrogen Fixation ; Oryza/growth &amp; development/*microbiology ; *Phenotype ; *Plant Development ; Plant Roots/microbiology ; Plant Shoots/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.}, }
@article {pmid33184266, year = {2020}, author = {Zhuang, W and Yu, X and Hu, R and Luo, Z and Liu, X and Zheng, X and Xiao, F and Peng, Y and He, Q and Tian, Y and Yang, T and Wang, S and Shu, L and Yan, Q and Wang, C and He, Z}, title = {Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {52}, pmid = {33184266}, issn = {2055-5008}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; DNA, Ribosomal Spacer/genetics ; Fungal Proteins/*genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; Wetlands ; }, abstract = {Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56-74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.}, }
@article {pmid32787773, year = {2020}, author = {Khurana, H and Singh, DN and Singh, A and Singh, Y and Lal, R and Negi, RK}, title = {Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {249}, pmid = {32787773}, issn = {1471-2180}, support = {NBAIM/AMAAS/2017-20/GF/1a//National Bureau of Agriculturally Important Microorganisms/International ; }, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification/pathogenicity ; Bacterial Proteins/genetics ; *Drug Resistance, Bacterial ; Endangered Species ; Fishes/*microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome.<br><br>RESULTS: The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens.<br><br>CONCLUSIONS: Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.}, }
@article {pmid32703080, year = {2020}, author = {Ammer-Herrmenau, C and Pfisterer, N and Weingarten, MF and Neesse, A}, title = {The microbiome in pancreatic diseases: Recent advances and future perspectives.}, journal = {United European gastroenterology journal}, volume = {8}, number = {8}, pages = {878-885}, pmid = {32703080}, issn = {2050-6414}, mesh = {Biomarkers/analysis ; DNA, Bacterial/analysis/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Intestinal Mucosa/immunology/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota/genetics/*immunology ; Pancreas/immunology/*microbiology/pathology ; Pancreatic Neoplasms/diagnosis/immunology/*microbiology ; Pancreatitis/diagnosis/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human microbiota exerts multiple physiological functions such as the regulation of metabolic and inflammatory processes. High-throughput sequencing techniques such as next-generation sequencing have become widely available in preclinical and clinical settings and have exponentially increased our knowledge about the microbiome and its interaction with host cells and organisms. There is now emerging evidence that microorganisms also contribute to inflammatory and neoplastic diseases of the pancreas. This review summarizes current clinical and translational microbiome studies in acute and chronic pancreatitis as well as pancreatic cancer and provides evidence that the microbiome has a high potential for biomarker discovery. Furthermore, the intestinal and pancreas-specific microbiome may also become an integrative part of diagnostic and therapeutic approaches of pancreatic diseases in the near future.}, }
@article {pmid32665016, year = {2020}, author = {Le Bastard, Q and Chapelet, G and Birgand, G and Hillmann, BM and Javaudin, F and Hayatgheib, N and Bourigault, C and Bemer, P and De Decker, L and Batard, E and Lepelletier, D and Montassier, E}, title = {Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases.}, journal = {Antimicrobial resistance and infection control}, volume = {9}, number = {1}, pages = {107}, pmid = {32665016}, issn = {2047-2994}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Carrier State/microbiology ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/enzymology/*genetics ; Enterobacteriaceae Infections/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Nursing Homes/*statistics &amp; numerical data ; *Transcriptome ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: The prevalence of extended beta-lactamase producing Enterobacteriaceae (ESBL-E) has been constantly increasing over the last few decades. These microorganisms that have acquired broad antibiotic resistance are now common human pathogens. Changes in the gut microbiome, induced by antibiotics or other drugs, enable expansion of these microorganisms, but the mechanisms are not yet fully understood.<br><br>OBJECTIVES: The main objective was to identify specific bacteria and functional pathways and genes characterizing the gut microbiome of nursing home residents carrying ESBL-E, using metagenomics.<br><br>SUBJECTS AND METHODS: We included 144 residents living in two different nursing homes. All fecal samples were screened for ESBL-E and gut microbiome was characterized using shallow shotgun metagenomic DNA sequencing.<br><br>RESULTS: Ten nursing home residents were colonized by ESBL-E, namely Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae species, and were compared to non-carriers. We found that ESBL-E carriers had an alteration in within-sample diversity. Using a bootstrap algorithm, we found that the gut microbiome of ESBL-E carriers was depleted in butyrate-producing species, enriched in succinate-producing species and enriched in pathways involved in intracellular pH homeostasis compared to non-carriers individuals. Several energy metabolism pathways were overrepresented in ESBL-E carriers suggesting a greater ability to metabolize multiple microbiota and mucus layer-derived nutrients.<br><br>CONCLUSIONS: The gut microbiome of ESBL-E carriers in nursing homes harbors specific taxonomic and functional characteristics, conferring an environment that enables Enterobacteriaceae expansion. Here we describe new functional features associated with ESBL-E carriage that could help us to elucidate the complex interactions leading to colonization persistence in the human gut microbiota.}, }
@article {pmid32602643, year = {2020}, author = {Mahadevan, P and Middlebrooks, ML}, title = {Bacterial diversity in the clarki ecotype of the photosynthetic sacoglossan, Elysia crispata.}, journal = {MicrobiologyOpen}, volume = {9}, number = {9}, pages = {e1098}, pmid = {32602643}, issn = {2045-8827}, mesh = {Amino Acids/metabolism ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Carbohydrate Metabolism ; Ecotype ; Gastropoda/classification/metabolism/*microbiology ; Lipid Metabolism ; Metabolic Networks and Pathways ; Metabolome ; *Microbiota ; Nucleotides/metabolism ; Photosynthesis ; Phylogeny ; Symbiosis ; }, abstract = {Few studies have examined the bacterial communities associated with photosynthetic sacoglossan sea slugs. In this study, we determined the bacterial diversity in the clarki ecotype, Elysia crispata using 16S rRNA sequencing. Computational analysis using QIIME2 revealed variability between individual samples, with the Spirochaetes and Bacteroidetes phyla dominating most samples. Tenericutes and Proteobacteria were also found, among other phyla. Computational metabolic profiling of the bacteria revealed a variety of metabolic pathways involving carbohydrate metabolism, lipid metabolism, nucleotide metabolism, and amino acid metabolism. Although associated bacteria may be involved in mutually beneficial metabolic pathways, there was a high degree of variation in the bacterial community of individual slugs. This suggests that many of these relationships are likely opportunistic rather than obligate and that many of these bacteria may live commensally providing no major benefit to the slugs.}, }
@article {pmid32505584, year = {2021}, author = {Raita, Y and Toivonen, L and Schuez-Havupalo, L and Karppinen, S and Waris, M and Hoffman, KL and Camargo, CA and Peltola, V and Hasegawa, K}, title = {Maturation of nasal microbiota and antibiotic exposures during early childhood: a population-based cohort study.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {27}, number = {2}, pages = {283.e1-283.e7}, doi = {10.1016/j.cmi.2020.05.033}, pmid = {32505584}, issn = {1469-0691}, mesh = {Age Factors ; Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Bacteria/*classification/drug effects/genetics/isolation &amp; purification ; Child, Preschool ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Finland ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Microbiota/drug effects ; Neural Networks, Computer ; Nose/drug effects/*microbiology ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {OBJECTIVES: Little is known about maturation of the airway microbiota during early childhood and the consequences of early-life antibiotic exposure.<br><br>METHODS: In a population-based birth cohort of 902 healthy Finnish children, we applied deep neural network models to investigate the relationship between the nasal microbiota (measured by 16S rRNA gene sequencing at up to three time points) and child age during the first 24 months. We also performed stratified analyses according to antibiotic exposure during the age period 0-2 months.<br><br>RESULTS: The dense deep neural network analysis successfully modelled the relationship between 232 bacterial genera and child age with a mean absolute error of 4.3 (95%CI 4.0-4.7) months. Similarly, the recurrent neural network analysis also successfully modelled the relationship between 215 genera and child age with a mean absolute error of 0.45 (95%CI 0.42-0.47) months. Among the genera, Staphylococcus spp. and members of the Corynebacteriaceae decreased with age, while Dolosigranulum and Moraxella increased with age in the first 2 years of life (all false discovery rate (FDR) = 0.001). In children without early-life antibiotic exposure, Dolosigranulum increased with age (FDR = 0.001). By contrast, in those with early-life antibiotic exposure, Haemophilus increased with age (FDR = 0.002).<br><br>CONCLUSIONS: In this prospective birth cohort of healthy children, we demonstrated the development of the nasal microbiota, with shifts in specific genera constituting maturation, in the first 2 years of life. Antibiotic exposures during early infancy were related to different age-discriminatory bacteria.}, }
@article {pmid33164148, year = {2020}, author = {Mandal, R and Cano, R and Davis, CD and Hayashi, D and Jackson, SA and Jones, CM and Lampe, JW and Latulippe, ME and Lin, NJ and Lippa, KA and Piotrowski, P and Da Silva, SM and Swanson, KS and Wishart, DS}, title = {Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {16}, number = {11}, pages = {119}, pmid = {33164148}, issn = {1573-3890}, support = {R01 GM120519/GM/NIGMS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; R44 GM134710/GM/NIGMS NIH HHS/United States ; T34 GM007821/GM/NIGMS NIH HHS/United States ; }, mesh = {Diet ; Feces/chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; }, abstract = {INTRODUCTION: To date, there has been little effort to develop standards for metabolome-based gut microbiome measurements despite the significant efforts toward standard development for DNA-based microbiome measurements.<br><br>OBJECTIVES: The National Institute of Standards and Technology (NIST), The BioCollective (TBC), and the North America Branch of the International Life Sciences Institute (ILSI North America) are collaborating to extend NIST's efforts to develop a Human Whole Stool Reference Material for the purpose of method harmonization and eventual quality control.<br><br>METHODS: The reference material will be rationally designed for adequate quality assurance and quality control (QA/QC) for underlying measurements in the study of the impact of diet and nutrition on functional aspects of the host gut microbiome and relationships of those functions to health. To identify which metabolites deserve priority in their value assignment, NIST, TBC, and ILSI North America jointly conducted a workshop on September 12, 2019 at the NIST campus in Gaithersburg, Maryland. The objective of the workshop was to identify metabolites for which evidence indicates relevance to health and disease and to decide on the appropriate course of action to develop a fit-for-purpose reference material.<br><br>RESULTS: This document represents the consensus opinions of workshop participants and co-authors of this manuscript, and provides additional supporting information. In addition to developing general criteria for metabolite selection and a preliminary list of proposed metabolites, this paper describes some of the strengths and limitations of this initiative given the current state of microbiome research.<br><br>CONCLUSIONS: Given the rapidly evolving nature of gut microbiome science and the current state of knowledge, an RM (as opposed to a CRM) measured for multiple metabolites is appropriate at this stage. As the science evolves, the RM can evolve to match the needs of the research community. Ultimately, the stool RM may exist in sequential versions. Beneficial to this evolution will be a clear line of communication between NIST and the stakeholder community to ensure alignment with current scientific understanding and community needs.}, }
@article {pmid33148984, year = {2020}, author = {Smibert, OC and Trubiano, JA and Slavin, MA and Kwong, JC}, title = {An infectious diseases perspective on the microbiome and allogeneic stem cell transplant.}, journal = {Current opinion in infectious diseases}, volume = {33}, number = {6}, pages = {426-432}, doi = {10.1097/QCO.0000000000000683}, pmid = {33148984}, issn = {1473-6527}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Communicable Diseases/epidemiology/*microbiology ; Gastrointestinal Microbiome ; Graft vs Host Disease/epidemiology/microbiology ; Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Metagenomics ; *Microbiota ; Observational Studies as Topic ; Prospective Studies ; Stem Cell Transplantation/*adverse effects ; T-Lymphocytes, Regulatory/metabolism ; }, abstract = {PURPOSE OF REVIEW: The gut microbiome presents a novel source of diagnostic and therapeutic potential to modify post allogeneic stem cell transplant complications. There is an explosion of interest in microbiome research, mostly in the form of single-centre prospective time-series cohorts utilizing a variety of sampling frequencies and metagenomic technologies to sequence the microbiome. The purpose of this review is to summarize important recent publications and contextualize them within what has already been described in this rapidly growing field.<br><br>RECENT FINDING: Results from observational human cohort and animal transplant models add to the growing body of evidence that the microbiome modulates the immunopathogenesis of posttransplant complications. This is particularly the case for recipients of grafts replete with T cells where the evidence that acute graft-versus-host disease is mediated by anaerobic commensal-associated short-chain fatty acids, which interact with mucosa-associated (CD4FOXP3) T-regulatory cells.<br><br>SUMMARY: Future human research into the role of the microbiome in allogeneic stem transplant should incorporate rigorous and considered experimental design in addition to next-generation sequencing technology to better portray microbiome functional potential and active gene expression. In combination with host immune phenotyping, which would facilitate a robust understanding of the host--microbiome interaction that is required before meaningful translation into clinical diagnostics and therapeutics can be expected.}, }
@article {pmid32742640, year = {2020}, author = {Wagner, J and Kancherla, J and Braccia, D and Matsumara, J and Felix, V and Crabtree, J and Mahurkar, A and Corrada Bravo, H}, title = {Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {601}, pmid = {32742640}, issn = {2046-1402}, support = {R01 GM114267/GM/NIGMS NIH HHS/United States ; U54 DK102556/DK/NIDDK NIH HHS/United States ; }, mesh = {*Data Analysis ; Data Interpretation, Statistical ; Humans ; *Microbiota ; Research Design ; }, abstract = {The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual's health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource.}, }
@article {pmid34014265, year = {2021}, author = {Quiza, L and Tremblay, J and Greer, CW and Hemmingsen, SM and St-Arnaud, M and Pozniak, CJ and Yergeau, E}, title = {Rhizosphere shotgun metagenomic analyses fail to show differences between ancestral and modern wheat genotypes grown under low fertilizer inputs.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {6}, pages = {}, doi = {10.1093/femsec/fiab071}, pmid = {34014265}, issn = {1574-6941}, mesh = {Fertilizers ; Genotype ; Metagenome ; *Microbiota ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; }, abstract = {It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast to our hypothesis, there was no significant difference in the global rhizosphere metagenomes of the different genotypes, and this held true when focusing the analyses on specific taxonomic or functional categories of genes. Some genes were significantly more abundant in the rhizosphere of one genotype or another, but they comprised only a small portion of the total genes identified and did not affect the global rhizosphere metagenomes. Our study shows for the first time that the rhizosphere metagenome of wheat is stable across a wide variety of genotypes when growing under nutrient poor conditions.}, }
@article {pmid33810508, year = {2021}, author = {Liu, J and He, X and Sun, J and Ma, Y}, title = {A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33810508}, issn = {1422-0067}, support = {2017ZY14//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/*genetics ; Metagenome ; Metagenomics ; *Microbial Consortia ; Plant Roots/microbiology ; Populus/*genetics/*microbiology ; *Rhizosphere ; Soil ; Soil Microbiology ; Trees/genetics ; }, abstract = {Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.}, }
@article {pmid33428003, year = {2021}, author = {Demirci, H and Kurt-Gur, G and Ordu, E}, title = {Microbiota profiling and screening of the lipase active halotolerant yeasts of the olive brine.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {37}, number = {2}, pages = {23}, pmid = {33428003}, issn = {1573-0972}, mesh = {Ascomycota/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Candida/metabolism ; Food Microbiology ; Hydrogen-Ion Concentration ; Hydrolysis ; Lipase/*metabolism ; *Microbiota ; Olive Oil ; Saccharomycetales ; Salt Tolerance/*physiology ; *Salts ; Sequence Analysis ; Sodium Chloride ; Yeasts/genetics/*metabolism ; }, abstract = {Searching for novel enzymes that could be active in organic solvents has become an area of interest in recent years. Olive brine naturally provides a suitable environment for the survival of halophilic and acidophilic microorganisms and the resulting genome is thought to be a gene source for determining the halophilic and acidophilic proteins that are active in a non-aqueous organic solvent medium, and so it has been used in several biotechnological and industrial applications. In this study, microbial analysis of natural, cracked green olive brine from the southern region of Turkey has been made by next-generation sequencing of the brine metagenome for the first time in the literature. The number of reads assigned to fungal operational taxonomic units was the highest percentage (73.04%) with the dominant representation of Ascomycota phylum (99% of fungi). Bacterial OTU was 3.56% of the reads and Proteobacteria phylum was 65% of the reads. The lipase production capacity of the yeasts that were grown on the media containing elevated concentrations of NaCl (1-3 M) was determined on a Rhodamine B-including medium. Molecular identification of the selected yeasts was performed and 90% of sequenced yeasts had a high level of similarity with Candida diddensiae, whereas 10% showed similarity to Candida boidinii. The hydrolytic lipase activities using olive oil were analyzed and both yeasts showed cell-bound lipase activity at pH 3.0.}, }
@article {pmid32746888, year = {2020}, author = {Calgaro, M and Romualdi, C and Waldron, L and Risso, D and Vitulo, N}, title = {Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {191}, pmid = {32746888}, issn = {1474-760X}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; 1U01CA230551/CA/NCI NIH HHS/United States ; 2U24CA180996/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, RNA ; Single-Cell Analysis ; *Statistics as Topic ; }, abstract = {BACKGROUND: The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.<br><br>RESULTS: We compare methods developed for single-cell and bulk RNA-seq, and specifically for microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, concordance, power, and correct identification of differentially abundant genera. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing.<br><br>CONCLUSIONS: The multivariate and compositional methods developed specifically for microbiome analysis did not outperform univariate methods developed for differential expression analysis of RNA-seq data. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner.}, }
@article {pmid34223947, year = {2021}, author = {Jiao, L and Kourkoumpetis, T and Hutchinson, D and Ajami, NJ and Hoffman, K and White, DL and Graham, DY and Hair, C and Shah, R and Kanwal, F and Jarbrink-Sehgal, M and Husain, N and Hernaez, R and Hou, J and Cole, R and Velez, M and Ketwaroo, G and Kramer, J and El-Serag, HB and Petrosino, JF}, title = {Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34223947}, issn = {1432-184X}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 000//Gillson Longenbaugh Foundation/ ; 000//Golfers Against Cancer/ ; R01CA172880//Division of Cancer Prevention, National Cancer Institute/ ; CX001430//Office of Academic Affiliations, Department of Veterans Affairs/ ; CIN13-413//Office of Academic Affiliations, Department of Veterans Affairs/ ; P30 DK56338/DK/NIDDK NIH HHS/United States ; }, abstract = {Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.}, }
@article {pmid34204939, year = {2021}, author = {Zampieri, A and Babbucci, M and Carraro, L and Milan, M and Fasolato, L and Cardazzo, B}, title = {Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {6}, pages = {}, pmid = {34204939}, issn = {2304-8158}, support = {C26C18000030004//Dipartimenti di Eccellenza/ ; CARD_SID18_01//Department of Comparative Biomedicine and Food Science/ ; ID 10062983//PORFESR/ ; }, abstract = {Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.}, }
@article {pmid34177841, year = {2021}, author = {Selari, PJRG and Olchanheski, LR and Ferreira, AJ and Paim, TDP and Calgaro Junior, G and Claudio, FL and Alves, EM and Santos, DC and Araújo, WL and Silva, FG}, title = {Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {661410}, pmid = {34177841}, issn = {1664-302X}, abstract = {The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.}, }
@article {pmid34176489, year = {2021}, author = {Berry, ASF and Pierdon, MK and Misic, AM and Sullivan, MC and O'Brien, K and Chen, Y and Murray, SJ and Ramharack, LA and Baldassano, RN and Parsons, TD and Beiting, DP}, title = {Remodeling of the maternal gut microbiome during pregnancy is shaped by parity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {146}, pmid = {34176489}, issn = {2049-2618}, support = {4100068710//Commonwealth Universal Research Enhancement (CURE) program/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Parity ; Pregnancy ; *Premature Birth ; Prevotella ; Swine ; Treponema ; }, abstract = {BACKGROUND: The maternal microbiome has emerged as an important factor in gestational health and outcome and is associated with risk of preterm birth and offspring morbidity. Epidemiological evidence also points to successive pregnancies-referred to as maternal parity-as a risk factor for preterm birth, infant mortality, and impaired neonatal growth. Despite the fact that both the maternal microbiome and parity are linked to maternal-infant health, the impact of parity on the microbiome remains largely unexplored, in part due to the challenges of studying parity in humans.<br><br>RESULTS: Using synchronized pregnancies and dense longitudinal monitoring of the microbiome in pigs, we describe a microbiome trajectory during pregnancy and determine the extent to which parity modulates this trajectory. We show that the microbiome changes reproducibly during gestation and that this remodeling occurs more rapidly as parity increases. At the time of parturition, parity was linked to the relative abundance of several bacterial species, including Treponema bryantii, Lactobacillus amylovorus, and Lactobacillus reuteri. Strain tracking carried out in 18 maternal-offspring "quadrads"-each consisting of one mother sow and three piglets-linked maternal parity to altered levels of Akkermansia muciniphila, Prevotella stercorea, and Campylobacter coli in the infant gut 10 days after birth.<br><br>CONCLUSIONS: Collectively, these results identify parity as an important environmental factor that modulates the gut microbiome during pregnancy and highlight the utility of a swine model for investigating the microbiome in maternal-infant health. In addition, our data show that the impact of parity extends beyond the mother and is associated with alterations in the community of bacteria that colonize the offspring gut early in life. The bacterial species we identified as parity-associated in the mother and offspring have been shown to influence host metabolism in other systems, raising the possibility that such changes may influence host nutrient acquisition or utilization. These findings, taken together with our observation that even subtle differences in parity are associated with microbiome changes, underscore the importance of considering parity in the design and analysis of human microbiome studies during pregnancy and in infants. Video abstract.}, }
@article {pmid34162081, year = {2021}, author = {Kaur, I and Gaur, VK and Regar, RK and Roy, A and Srivastava, PK and Gaur, R and Manickam, N and Barik, SK}, title = {Plants exert beneficial influence on soil microbiome in a HCH contaminated soil revealing advantage of microbe-assisted plant-based HCH remediation of a dumpsite.}, journal = {Chemosphere}, volume = {280}, number = {}, pages = {130690}, doi = {10.1016/j.chemosphere.2021.130690}, pmid = {34162081}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Hexachlorocyclohexane/analysis ; *Microbiota ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Persistence of hexachlorocyclohexane (HCH) pesticide is a major problem for its disposal. Soil microflora plays an important role in remediating contaminated sites. Keeping concepts of microbial- and phyto-remediation together, the difference between soil microflora with and without association of HCH accumulating plant species was studied. Metagenomic analysis among the non-plant soil (BS) (∑HCH 434.19 mg/g), rhizospheric soil of shrubs (RSS) (∑HCH 157.31 mg/g), and rhizospheric soil of trees (RSD) (∑HCH 105.39 mg/g) revealed significant differences in microbial communities. Shrubs and trees occurred at a long-term dumpsite accumulated α- and β- HCH residues. Plant rhizospheric soils exhibited high richness and evenness with higher diversity indices compared to the non-plant soil. Order Rhizobiales was most abundant in all soils and Streptomycetales was absent in the BS soil. Proteobacteria and Ascomycota were highest in BS soil, while Actinobacteria was enriched in both the plant rhizospheric soil samples. In BS soil, Pseudomonas, Sordaria, Caulobacter, Magnetospirillum, Rhodospirillum were abundant. While, genera Actinoplanes, Streptomyces, Bradyrhizobium, Rhizobium, Azospirillum, Agrobacterium are abundant in RSD soil. Selected plants have accumulated HCH residues from soil and exerted positive impacts on soil microbial communities in HCH contaminated site. This study advocates microbe-assisted plant-based bioremediation strategy to remediate HCH contamination.}, }
@article {pmid34154658, year = {2021}, author = {West, PT and Peters, SL and Olm, MR and Yu, FB and Gause, H and Lou, YC and Firek, BA and Baker, R and Johnson, AD and Morowitz, MJ and Hettich, RL and Banfield, JF}, title = {Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {142}, pmid = {34154658}, issn = {2049-2618}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Candida parapsilosis/genetics ; *Candidiasis ; Humans ; Infant ; Infant, Newborn ; Microbial Sensitivity Tests ; *Microbiota ; Proteomics ; Transcriptome ; }, abstract = {BACKGROUND: Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context.<br><br>RESULTS: Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition.<br><br>CONCLUSIONS: The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes. Video abstract.}, }
@article {pmid34152440, year = {2021}, author = {Schmidt, BM and Erb-Downward, J and Ranjan, P and Dickson, R}, title = {Metagenomics to Identify Pathogens in Diabetic Foot Ulcers and the Potential Impact for Clinical Care.}, journal = {Current diabetes reports}, volume = {21}, number = {8}, pages = {26}, pmid = {34152440}, issn = {1539-0829}, mesh = {Adult ; *Diabetes Mellitus ; *Diabetic Foot ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Wound Healing ; }, abstract = {PURPOSE OF REVIEW: Diabetes mellitus may affect every third adult American by 2050, and about one-third will develop a diabetic foot ulcer (DFU) during their lifetime. The current standard of care results in healing of less than 50% of all DFUs. Many individuals with DFU develop limb-threatening infection which place them at risk for additional morbidity and mortality. We review research associated with culture-independent next-generation sequencing techniques pertaining to diabetic foot ulcers and their potential for clinical application.<br><br>RECENT FINDINGS: Diabetic foot ulcers are a growing problem and clinicians are limited by their reliance on conventional culture. Metagenomic sequencing technology provides an unparalleled viewpoint of the polymicrobial constituency of DFU. The microbiome techniques used to study the microbial constituency of DFU may offer insight to improve care for these patients, but without standardized approaches in research based on real-world clinical practices, a significant knowledge gap will remain.}, }
@article {pmid34150671, year = {2021}, author = {Townsend, EM and Kelly, L and Muscatt, G and Box, JD and Hargraves, N and Lilley, D and Jameson, E}, title = {The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {643214}, pmid = {34150671}, issn = {2235-2988}, support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria ; *Bacteriophages ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Virome ; }, abstract = {The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.}, }
@article {pmid34149649, year = {2021}, author = {Morrison, MD and Thissen, JB and Karouia, F and Mehta, S and Urbaniak, C and Venkateswaran, K and Smith, DJ and Jaing, C}, title = {Investigation of Spaceflight Induced Changes to Astronaut Microbiomes.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {659179}, pmid = {34149649}, issn = {1664-302X}, abstract = {The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts' time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts' saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts' time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut's microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.}, }
@article {pmid34130621, year = {2021}, author = {Glickman, C and Hendrix, J and Strong, M}, title = {Simulation study and comparative evaluation of viral contiguous sequence identification tools.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {329}, pmid = {34130621}, issn = {1471-2105}, mesh = {*Bacteriophages/genetics ; Genome, Viral/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota ; *Viruses/genetics ; }, abstract = {BACKGROUND: Viruses, including bacteriophages, are important components of environmental and human associated microbial communities. Viruses can act as extracellular reservoirs of bacterial genes, can mediate microbiome dynamics, and can influence the virulence of clinical pathogens. Various targeted metagenomic analysis techniques detect viral sequences, but these methods often exclude large and genome integrated viruses. In this study, we evaluate and compare the ability of nine state-of-the-art bioinformatic tools, including Vibrant, VirSorter, VirSorter2, VirFinder, DeepVirFinder, MetaPhinder, Kraken 2, Phybrid, and a BLAST search using identified proteins from the Earth Virome Pipeline to identify viral contiguous sequences (contigs) across simulated metagenomes with different read distributions, taxonomic compositions, and complexities.<br><br>RESULTS: Of the tools tested in this study, VirSorter achieved the best F1 score while Vibrant had the highest average F1 score at predicting integrated prophages. Though less balanced in its precision and recall, Kraken2 had the highest average precision by a substantial margin. We introduced the machine learning tool, Phybrid, which demonstrated an improvement in average F1 score over tools such as MetaPhinder. The tool utilizes machine learning with both gene content and nucleotide features. The addition of nucleotide features improves the precision and recall compared to the gene content features alone.Viral identification by all tools was not impacted by underlying read distribution but did improve with contig length. Tool performance was inversely related to taxonomic complexity and varied by the phage host. For instance, Rhizobium and Enterococcus phages were identified consistently by the tools; whereas, Neisseria prophage sequences were commonly missed in this study.<br><br>CONCLUSION: This study benchmarked the performance of nine state-of-the-art bioinformatic tools to identify viral contigs across different simulation conditions. This study explored the ability of the tools to identify integrated prophage elements traditionally excluded from targeted sequencing approaches. Our comprehensive analysis of viral identification tools to assess their performance in a variety of situations provides valuable insights to viral researchers looking to mine viral elements from publicly available metagenomic data.}, }
@article {pmid34118976, year = {2021}, author = {Xie, F and Jin, W and Si, H and Yuan, Y and Tao, Y and Liu, J and Wang, X and Yang, C and Li, Q and Yan, X and Lin, L and Jiang, Q and Zhang, L and Guo, C and Greening, C and Heller, R and Guan, LL and Pope, PB and Tan, Z and Zhu, W and Wang, M and Qiu, Q and Li, Z and Mao, S}, title = {An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {137}, pmid = {34118976}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Phylogeny ; Ruminants ; }, abstract = {BACKGROUND: Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.<br><br>RESULTS: Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.<br><br>CONCLUSIONS: Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. Video abstract.}, }
@article {pmid34117246, year = {2021}, author = {Lloréns-Rico, V and Vieira-Silva, S and Gonçalves, PJ and Falony, G and Raes, J}, title = {Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3562}, pmid = {34117246}, issn = {2041-1723}, mesh = {Benchmarking/*methods ; Classification ; Computational Biology/*methods ; Dysbiosis/microbiology ; Electronic Data Processing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Selection Bias ; }, abstract = {While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.}, }
@article {pmid34110473, year = {2021}, author = {Rivera, AJ and Tyx, RE}, title = {Microbiology of the American Smokeless Tobacco.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {12}, pages = {4843-4853}, pmid = {34110473}, issn = {1432-0614}, mesh = {Carcinogens ; Humans ; Metagenomics ; *Microbiota ; Tobacco ; *Tobacco, Smokeless ; United States ; }, abstract = {Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.}, }
@article {pmid34108585, year = {2021}, author = {Yoshitake, K and Kimura, G and Sakami, T and Watanabe, T and Taniuchi, Y and Kakehi, S and Kuwata, A and Yamaguchi, H and Kataoka, T and Kawachi, M and Ikeo, K and Tan, E and Igarashi, Y and Ohtsubo, M and Watabe, S and Suzuki, Y and Asakawa, S and Ishino, S and Tashiro, K and Ishino, Y and Kobayashi, T and Mineta, K and Gojobori, T}, title = {Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12222}, pmid = {34108585}, issn = {2045-2322}, abstract = {Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird's-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.}, }
@article {pmid34100638, year = {2021}, author = {Wei, ST and Chen, YL and Wu, YW and Wu, TY and Lai, YL and Wang, PH and Ismail, W and Lee, TH and Chiang, YR}, title = {Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0035821}, doi = {10.1128/mSystems.00358-21}, pmid = {34100638}, issn = {2379-5077}, support = {AS-CDA-110-L13//Academia Sinica/ ; MOST 109-2221-E-001-002//Ministry of Science and Technology, Taiwan (MOST)/ ; MOST 110-2222-E-008-002//Ministry of Science and Technology, Taiwan (MOST)/ ; }, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase-key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively-are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.}, }
@article {pmid34090540, year = {2021}, author = {Callahan, BJ and Grinevich, D and Thakur, S and Balamotis, MA and Yehezkel, TB}, title = {Ultra-accurate microbial amplicon sequencing with synthetic long reads.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {130}, pmid = {34090540}, issn = {2049-2618}, support = {R35 GM133745/GM/NIGMS NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge.<br><br>METHODS: Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads.<br><br>RESULTS: LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens.<br><br>CONCLUSIONS: The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.}, }
@article {pmid34090519, year = {2021}, author = {Wilkins, D and Tong, X and Leung, MHY and Mason, CE and Lee, PKH}, title = {Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {129}, pmid = {34090519}, issn = {2049-2618}, support = {R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {Bayes Theorem ; Hong Kong ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days.<br><br>RESULTS: Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied.<br><br>CONCLUSIONS: These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.}, }
@article {pmid34079525, year = {2021}, author = {Sisk-Hackworth, L and Ortiz-Velez, A and Reed, MB and Kelley, ST}, title = {Compositional Data Analysis of Periodontal Disease Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {617949}, pmid = {34079525}, issn = {1664-302X}, abstract = {Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic libraries, have greatly expanded our understanding of PD biodiversity, identified novel PD microbial associations, and shown that PD biodiversity increases with pocket depth. NGS studies have also found PD communities to be highly host-specific in terms of both biodiversity and the response of microbial communities to periodontal treatment. As with most microbiome work, the majority of PD microbiome studies use standard data normalization procedures that do not account for the compositional nature of NGS microbiome data. Here, we apply recently developed compositional data analysis (CoDA) approaches and software tools to reanalyze multiomics (16S, metagenomics, and metabolomics) data generated from previously published periodontal disease studies. CoDA methods, such as centered log-ratio (clr) transformation, compensate for the compositional nature of these data, which can not only remove spurious correlations but also allows for the identification of novel associations between microbial features and disease conditions. We validated many of the studies' original findings, but also identified new features associated with periodontal disease, including the genera Schwartzia and Aerococcus and the cytokine C-reactive protein (CRP). Furthermore, our network analysis revealed a lower connectivity among taxa in deeper periodontal pockets, potentially indicative of a more "random" microbiome. Our findings illustrate the utility of CoDA techniques in multiomics compositional data analysis of the oral microbiome.}, }
@article {pmid34071172, year = {2021}, author = {Chukwuma, OB and Rafatullah, M and Tajarudin, HA and Ismail, N}, title = {Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {34071172}, issn = {2075-1729}, support = {1001/PTEKIND/8011044//Universiti Sains Malaysia/ ; }, abstract = {Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.}, }
@article {pmid34069990, year = {2021}, author = {Ansorge, R and Birolo, G and James, SA and Telatin, A}, title = {Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.}, journal = {International journal of molecular sciences}, volume = {22}, number = {10}, pages = {}, pmid = {34069990}, issn = {1422-0067}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1//UK Research and Innovation/ ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Metadata ; Metagenomics/*statistics &amp; numerical data ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.}, }
@article {pmid34069916, year = {2021}, author = {Izawa, K and Okamoto-Shibayama, K and Kita, D and Tomita, S and Saito, A and Ishida, T and Ohue, M and Akiyama, Y and Ishihara, K}, title = {Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {10}, pages = {}, pmid = {34069916}, issn = {1422-0067}, support = {18K09559//Japan Society for Promotion of Science/ ; 45//MEXT Private University Research Branding Project/ ; }, mesh = {Adult ; Aged ; Bacteria/genetics ; Dental Plaque/genetics/*microbiology ; Dysbiosis/genetics ; Female ; Gingiva/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Japan/epidemiology ; Male ; Metagenome ; Microbiota/genetics ; Middle Aged ; Periodontal Pocket/genetics/microbiology ; Periodontitis/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Periodontitis is an inflammation of tooth-supporting tissues, which is caused by bacteria in the subgingival plaque (biofilm) and the host immune response. Traditionally, subgingival pathogens have been investigated using methods such as culturing, DNA probes, or PCR. The development of next-generation sequencing made it possible to investigate the whole microbiome in the subgingival plaque. Previous studies have implicated dysbiosis of the subgingival microbiome in the etiology of periodontitis. However, details are still lacking. In this study, we conducted a metagenomic analysis of subgingival plaque samples from a group of Japanese individuals with and without periodontitis. In the taxonomic composition analysis, genus Bacteroides and Mycobacterium demonstrated significantly different compositions between healthy sites and sites with periodontal pockets. The results from the relative abundance of functional gene categories, carbohydrate metabolism, glycan biosynthesis and metabolism, amino acid metabolism, replication and repair showed significant differences between healthy sites and sites with periodontal pockets. These results provide important insights into the shift in the taxonomic and functional gene category abundance caused by dysbiosis, which occurs during the progression of periodontal disease.}, }
@article {pmid34053518, year = {2021}, author = {Franciosa, I and Ferrocino, I and Giordano, M and Mounier, J and Rantsiou, K and Cocolin, L}, title = {Specific metagenomic asset drives the spontaneous fermentation of Italian sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {144}, number = {}, pages = {110379}, doi = {10.1016/j.foodres.2021.110379}, pmid = {34053518}, issn = {1873-7145}, mesh = {Fermentation ; Food Microbiology ; Italy ; *Lactobacillus ; *Metagenomics ; }, abstract = {Metagenomics is a powerful tool to study and understand the microbial dynamics that occur during food fermentation and allows to close the link between microbial diversity and final sensory characteristics. Each food matrix can be colonized by different microbes, but also by different strains of the same species. In this study, using an innovative integrated approach combining culture-dependent method with a shotgun sequencing, we were able to show how strain-level biodiversity could influence the quality characteristics of the final product. The attention was placed on a model food fermentation process: Salame Piemonte, a Protected Geographical Indication (PGI) Italian fermented sausage. Three independent batches produced in February, March and May 2018 were analysed. The sausages were manufactured, following the production specification, in a local meat factory in the area of Turin (Italy) without the use of starter cultures. A pangenomic approach was applied in order to identify and evaluate the lactic acid bacteria (LAB) population driving the fermentation process. It was observed that all batches were characterized by the presence of few LAB species, namely Pediococcus pentosaceus, Latilactobacillus curvatus and Latilactobacillus sakei. Sausages from the different batches were different when the volatilome was taken into consideration, and a strong association between quality attributes and strains present was determined. In particular, different strains of L. sakei, showing heterogeneity at genomic level, colonized the meat at the beginning of each production and deeply influenced the fermentation process by distinctive metabolic pathways that affected the fermentation process and the final sensory aspects.}, }
@article {pmid34050180, year = {2021}, author = {Xu, L and Dong, Z and Chiniquy, D and Pierroz, G and Deng, S and Gao, C and Diamond, S and Simmons, T and Wipf, HM and Caddell, D and Varoquaux, N and Madera, MA and Hutmacher, R and Deutschbauer, A and Dahlberg, JA and Guerinot, ML and Purdom, E and Banfield, JF and Taylor, JW and Lemaux, PG and Coleman-Derr, D}, title = {Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3209}, pmid = {34050180}, issn = {2041-1723}, support = {P42 ES007373/ES/NIEHS NIH HHS/United States ; }, mesh = {Acclimatization ; Actinobacteria/genetics/*metabolism ; Crop Production ; *Droughts ; Food Security ; Iron/*metabolism ; Metagenomics/methods ; Microbiota/*physiology ; Plant Roots/microbiology ; RNA-Seq ; Rhizosphere ; Soil Microbiology ; Sorghum/microbiology/*physiology ; Stress, Physiological ; }, abstract = {Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome's response to drought and may inform efforts to improve plant drought tolerance to increase food security.}, }
@article {pmid34050176, year = {2021}, author = {Behsaz, B and Bode, E and Gurevich, A and Shi, YN and Grundmann, F and Acharya, D and Caraballo-Rodríguez, AM and Bouslimani, A and Panitchpakdi, M and Linck, A and Guan, C and Oh, J and Dorrestein, PC and Bode, HB and Pevzner, PA and Mohimani, H}, title = {Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3225}, pmid = {34050176}, issn = {2041-1723}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Amino Acid Sequence/genetics ; Anti-Bacterial Agents/biosynthesis/*isolation &amp; purification ; Biological Products/*isolation &amp; purification/metabolism ; Computational Biology/*methods ; Datasets as Topic ; Drug Discovery/*methods ; Humans ; Mass Spectrometry ; Metabolic Networks and Pathways/genetics ; Metabolomics/methods ; Metagenomics/methods ; Microbiota/genetics ; Multigene Family ; Peptide Biosynthesis ; Peptide Synthases/genetics/metabolism ; Peptides/genetics/*isolation &amp; purification/metabolism ; Soil Microbiology ; }, abstract = {Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.}, }
@article {pmid34044757, year = {2021}, author = {Guo, J and Pang, E and Song, H and Lin, K}, title = {A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {282}, pmid = {34044757}, issn = {1471-2105}, mesh = {*Algorithms ; Genome ; *Genomics ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.<br><br>RESULTS: We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (< 50 bp) for highly similar samples, which can be validated by simulated datasets. Moreover, we demonstrated that cSupB can adapt to the complex cycle structure.<br><br>CONCLUSIONS: Although the solution is made suitable for increasingly complex genome graphs by relaxing the constraint, the directed acyclic graph, the motif cSupB and the cSupB method can be extended to any colored directed acyclic graph. We anticipate that our method will facilitate the analysis of individual haplotype variants and population genomic diversity. We have developed a C + + program for implementing our method that is available at https://github.com/eggleader/cSupB .}, }
@article {pmid34039416, year = {2021}, author = {Leung, MHY and Tong, X and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Gohli, J and Green, DC and Hernandez, MT and Kelly, FJ and Levy, S and Mason-Buck, G and Nieto-Caballero, M and Syndercombe-Court, D and Udekwu, K and Young, BG and Mason, CE and Dybwad, M and Lee, PKH}, title = {Characterization of the public transit air microbiome and resistome reveals geographical specificity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {112}, pmid = {34039416}, issn = {2049-2618}, support = {R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; U01 DA053941/DA/NIDA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; }, mesh = {Bacteria/genetics ; Geography ; Hong Kong ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.<br><br>RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.<br><br>CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.}, }
@article {pmid34037469, year = {2021}, author = {Fulci, V and Carissimi, C and Laudadio, I}, title = {COVID-19 and Preparing for Future Ecological Crises: Hopes from Metagenomics in Facing Current and Future Viral Pandemic Challenges.}, journal = {Omics : a journal of integrative biology}, volume = {25}, number = {6}, pages = {336-341}, doi = {10.1089/omi.2021.0058}, pmid = {34037469}, issn = {1557-8100}, abstract = {The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak demonstrates the potential of coronaviruses, especially bat-derived beta coronaviruses to rapidly escalate to a global pandemic that has caused deaths in the order of several millions already. The huge efforts put in place by the scientific community to address this emergency have disclosed how the implementation of new technologies is crucial in the prepandemic period to timely face future ecological crises. In this context, we argue that metagenomics and new approaches to understanding ecosystems and biodiversity offer veritable prospects to innovate therapeutics and diagnostics against novel and existing infectious agents. We discuss the opportunities and challenges associated with the science of metagenomics, specifically with an eye to inform and prevent future ecological crises and pandemics that are looming on the horizon in the 21st century.}, }
@article {pmid34037156, year = {2021}, author = {Valença, IN and Santos, RBD and Peronni, KC and Sauvage, V and Vandenbogaert, M and Caro, V and Silva Junior, WAD and Covas, DT and Silva-Pinto, AC and Laperche, S and Kashima, S and Slavov, SN}, title = {Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {63}, number = {}, pages = {e40}, pmid = {34037156}, issn = {1678-9946}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Seroepidemiologic Studies ; Virome ; *beta-Thalassemia/genetics ; }, abstract = {To date, blood banks apply routine diagnosis to a specific spectrum of transfusion-transmitted viruses. Even though this measure is considered highly efficient to control their transmission, the threat imposed by emerging viruses is increasing globally, which can impact transfusion safety, especially in the light of the accelerated viral discovery by novel sequencing technologies. One of the most important groups of patients, who may indicate the presence of emerging viruses in the field of blood transfusion, is the group of individuals who receive multiple transfusions due to hereditary hemoglobinopathies. It is possible that they harbor unknown or unsuspected parenterally-transmitted viruses. In order to elucidate this, nucleic acids from 30 patients with beta-thalassemia were analyzed by Illumina next-generation sequencing and bioinformatics analysis. Three major viral families: Anelloviridae, Flaviviridae and Hepadnaviridae were identified. Among them, anelloviruses were the most representative, being detected with high number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C), Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV and HCV detection was expected due to the high seroprevalence in patients with beta thalassemia. Our results do not confirm the presence of emerging or unsuspected viruses threatening the transfusion safety at present, but can be used to actively search for viruses that threaten blood transfusion safety. We believe that the application of viral metagenomics in multiple-transfused patients is highly useful to monitor possible viral transfusion threats and for the annotation of their virome composition.}, }
@article {pmid34034165, year = {2021}, author = {Wu, X and Liu, P and Wegner, CE and Luo, Y and Xiao, KQ and Cui, Z and Zhang, F and Liesack, W and Peng, J}, title = {Deciphering microbial mechanisms underlying soil organic carbon storage in a wheat-maize rotation system.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147798}, doi = {10.1016/j.scitotenv.2021.147798}, pmid = {34034165}, issn = {1879-1026}, mesh = {Agriculture ; *Carbon ; Fertilizers/analysis ; Manure ; RNA, Ribosomal, 16S ; Rotation ; *Soil ; Soil Microbiology ; Triticum ; Zea mays ; }, abstract = {A link between microbial life history strategies and soil organic carbon storage in agroecosystems is presumed, but largely unexplored at the gene level. We aimed to elucidate whether and how differential organic material amendments (manure versus peat-vermiculite) affect, relative to sole chemical fertilizer application, the link between microbial life history strategies and soil organic carbon storage in a wheat-maize rotation field experiment. To achieve this goal, we combined bacterial 16S rRNA gene and fungal ITS amplicon sequencing, metagenomics and the assembly of genomes. Fertilizer treatments had a significantly greater effect on microbial community composition than aggregate size, with soil available phosphorus and potassium being the most important community-shaping factors. Limitation in labile carbon was linked to a K-selected oligotrophic life history strategy (Gemmatimonadetes, Acidobacteria) under sole chemical fertilizer application; defined by a significant enrichment of genes involved in resource acquisition, polymer hydrolysis, and competition. By contrast, excess of labile carbon promoted an r-selected copiotrophic life history strategy (Cytophagales, Bacillales, Mortierellomycota) under manure treatment; defined by a significant enrichment of genes involved in cellular growth. A distinct life history strategy was not observed under peat-vermiculite treatment, but rather a mix of both K-selected (Acidobacteria) and r-selected (Actinobacteria, Mortierellomycota) microorganisms. Compared to sole chemical fertilizer application, soil organic carbon storage efficiency was significantly increased by 26.5% and 50.0% under manure and peat-vermiculite treatments, respectively. Taken together, our results highlight the importance of organic material amendments, but in particular a one-time peat-vermiculite application, to promote soil organic carbon storage as a potential management strategy for sustainable agriculture.}, }
@article {pmid34030239, year = {2021}, author = {Qiao, L and Liu, X and Zhang, S and Zhang, L and Li, X and Hu, X and Zhao, Q and Wang, Q and Yu, C}, title = {Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach.}, journal = {The Science of the total environment}, volume = {779}, number = {}, pages = {146502}, doi = {10.1016/j.scitotenv.2021.146502}, pmid = {34030239}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Farms ; Gold ; Metagenomics ; *Metals, Heavy/analysis ; *Microbiota ; *Soil Pollutants/analysis ; }, abstract = {Metal mining has caused the accumulation of waste mine tailing dumps from abandoned mines. The pollution of farmlands surrounding metal tailings by heavy metals has been a long-recognized problem. However, the distribution of antibiotic resistance genes (ARGs) in tailings and the main factors influencing this distribution have rarely been reported. In this study, a metagenomics approach was used to investigate the microbial community and ARGs present in farmland surrounding gold tailings in northern China. The results showed that the main pollutants in the farmland were As, Pb, and Cd. Proteobacteria and Actinobacteria were the dominant phyla of microbes in farmlands surrounding gold tailings. A total of 75 ARGs with 327 ARG subtypes were detected in soil samples. Macrolide-, lincosaminide-, and streptogramin B resistant genes accounted for the majority of ARGs in this study, and Actinobacteria, Proteobacteria, and Acidobacteria were the hosts of most ARGs. Partial least squares path modeling revealed that the microbial community was the most influential driver moderating the distribution of soil ARGs near tailings, and heavy metals have direct and partially indirect effects on these ARGs. In contrast to previous analyses of ARGs, our study found that mobile gene elements had a minimal impact on ARGs. Overall, this study presents a complete ARG survey that sheds light on the distribution and fate of ARGs under heavy metal contamination in farmland around gold tailings.}, }
@article {pmid34029816, year = {2021}, author = {Ramírez-Fernández, L and Orellana, LH and Johnston, ER and Konstantinidis, KT and Orlando, J}, title = {Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147693}, doi = {10.1016/j.scitotenv.2021.147693}, pmid = {34029816}, issn = {1879-1026}, mesh = {Animals ; Antarctic Regions ; *Metagenome ; Metagenomics ; *Microbiota ; Nitrous Oxide ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; }, abstract = {Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.}, }
@article {pmid34029658, year = {2021}, author = {Nodari, R and Drancourt, M and Barbieri, R}, title = {Paleomicrobiology of the human digestive tract: A review.}, journal = {Microbial pathogenesis}, volume = {157}, number = {}, pages = {104972}, doi = {10.1016/j.micpath.2021.104972}, pmid = {34029658}, issn = {1096-1208}, mesh = {Gastrointestinal Tract ; Humans ; *Metagenomics ; *Microbiota ; }, abstract = {The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.}, }
@article {pmid34022966, year = {2021}, author = {Matheus Carnevali, PB and Lavy, A and Thomas, AD and Crits-Christoph, A and Diamond, S and Méheust, R and Olm, MR and Sharrar, A and Lei, S and Dong, W and Falco, N and Bouskill, N and Newcomer, ME and Nico, P and Wainwright, H and Dwivedi, D and Williams, KH and Hubbard, S and Banfield, JF}, title = {Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {121}, pmid = {34022966}, issn = {2049-2618}, mesh = {Carbon ; *Microbiota/genetics ; Nitrogen ; Rivers ; *Soil ; }, abstract = {BACKGROUND: Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.<br><br>RESULTS: We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.<br><br>CONCLUSIONS: The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change. Video abstract.}, }
@article {pmid34006865, year = {2021}, author = {Tierney, BT and Tan, Y and Kostic, AD and Patel, CJ}, title = {Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2907}, pmid = {34006865}, issn = {2041-1723}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Cluster Analysis ; Colorectal Neoplasms/genetics/microbiology ; Computational Biology/*methods ; Diabetes Mellitus, Type 2/genetics/microbiology ; Firmicutes/genetics/physiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/genetics/microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Phylogeny ; Species Specificity ; }, abstract = {We propose microbiome disease "architectures": linking >1 million microbial features (species, pathways, and genes) to 7 host phenotypes from 13 cohorts using a pipeline designed to identify associations that are robust to analytical model choice. Here, we quantify conservation and heterogeneity in microbiome-disease associations, using gene-level analysis to identify strain-specific, cross-disease, positive and negative associations. We find coronary artery disease, inflammatory bowel diseases, and liver cirrhosis to share gene-level signatures ascribed to the Streptococcus genus. Type 2 diabetes, by comparison, has a distinct metagenomic signature not linked to any one specific species or genus. We additionally find that at the species-level, the prior-reported connection between Solobacterium moorei and colorectal cancer is not consistently identified across models-however, our gene-level analysis unveils a group of robust, strain-specific gene associations. Finally, we validate our findings regarding colorectal cancer and inflammatory bowel diseases in independent cohorts and identify that features inversely associated with disease tend to be less reproducible than features enriched in disease. Overall, our work is not only a step towards gene-based, cross-disease microbiome diagnostic indicators, but it also illuminates the nuances of the genetic architecture of the human microbiome, including tension between gene- and species-level associations.}, }
@article {pmid34006626, year = {2021}, author = {Hwang, Y and Rahlff, J and Schulze-Makuch, D and Schloter, M and Probst, AJ}, title = {Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {34006626}, issn = {2379-5077}, abstract = {Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.}, }
@article {pmid34006335, year = {2021}, author = {Nearing, JT and Comeau, AM and Langille, MGI}, title = {Identifying biases and their potential solutions in human microbiome studies.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {113}, pmid = {34006335}, issn = {2049-2618}, support = {2016-05039//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (CA)/ ; }, mesh = {Bias ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Specimen Handling ; }, abstract = {Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases. Video abstract.}, }
@article {pmid33986253, year = {2021}, author = {Ma, S and Zhang, F and Zhou, F and Li, H and Ge, W and Gan, R and Nie, H and Li, B and Wang, Y and Wu, M and Li, D and Wang, D and Wang, Z and You, Y and Huang, Z}, title = {Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19.}, journal = {Signal transduction and targeted therapy}, volume = {6}, number = {1}, pages = {191}, pmid = {33986253}, issn = {2059-3635}, support = {31825008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31422014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872117//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; *Bacteria/classification/genetics/growth &amp; development ; COVID-19/*microbiology ; Female ; Humans ; Male ; *Metagenomics ; *Microbiota ; Middle Aged ; Oropharynx/*microbiology ; *SARS-CoV-2 ; }, abstract = {COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients, 29 influenza B patients, and 28 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium, Rothia, and Streptococcus. Based on the relative abundance of the oropharyngeal microbiome, we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889, in which Veillonella was identified as the most prominent biomarker for COVID-19 group. Several members of the genus Veillonella, especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients, were also overrepresented in the BALF of COVID-19 patients, indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients. We also found the increased ratios of Klebsiella sp., Acinetobacter sp., and Serratia sp. were correlated with both disease severity and elevated systemic inflammation markers (neutrophil-lymphocyte ratio, NLR), suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response. Moreover, the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism. In addition, all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group, and were significantly enriched in critical cases. In conclusion, we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.}, }
@article {pmid33968595, year = {2021}, author = {Shet, SA and Garg, S}, title = {Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics.}, journal = {3 Biotech}, volume = {11}, number = {5}, pages = {252}, pmid = {33968595}, issn = {2190-572X}, abstract = {Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure.<br><br>Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-021-02809-5.}, }
@article {pmid33962692, year = {2021}, author = {Mayneris-Perxachs, J and Cardellini, M and Hoyles, L and Latorre, J and Davato, F and Moreno-Navarrete, JM and Arnoriaga-Rodríguez, M and Serino, M and Abbott, J and Barton, RH and Puig, J and Fernández-Real, X and Ricart, W and Tomlinson, C and Woodbridge, M and Gentileschi, P and Butcher, SA and Holmes, E and Nicholson, JK and Pérez-Brocal, V and Moya, A and Clain, DM and Burcelin, R and Dumas, ME and Federici, M and Fernández-Real, JM}, title = {Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {104}, pmid = {33962692}, issn = {2049-2618}, support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; MR/M501797/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Iron ; Mice ; *Non-alcoholic Fatty Liver Disease ; Obesity ; }, abstract = {BACKGROUND: The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear.<br><br>RESULTS: Here, we applied an integrative systems medicine approach (faecal metagenomics, plasma and urine metabolomics, hepatic transcriptomics) in 2 well-characterised human cohorts of subjects with obesity (discovery n = 49 and validation n = 628) and an independent cohort formed by both individuals with and without obesity (n = 130), combined with in vitro and animal models. Serum ferritin levels, as a markers of liver iron stores, were positively associated with liver fat accumulation in parallel with lower gut microbial gene richness, composition and functionality. Specifically, ferritin had strong negative associations with the Pasteurellaceae, Leuconostocaceae and Micrococcaea families. It also had consistent negative associations with several Veillonella, Bifidobacterium and Lactobacillus species, but positive associations with Bacteroides and Prevotella spp. Notably, the ferritin-associated bacterial families had a strong correlation with iron-related liver genes. In addition, several bacterial functions related to iron metabolism (transport, chelation, heme and siderophore biosynthesis) and NAFLD (fatty acid and glutathione biosynthesis) were also associated with the host serum ferritin levels. This iron-related microbiome signature was linked to a transcriptomic and metabolomic signature associated to the degree of liver fat accumulation through hepatic glucose metabolism. In particular, we found a consistent association among serum ferritin, Pasteurellaceae and Micrococcacea families, bacterial functions involved in histidine transport, the host circulating histidine levels and the liver expression of GYS2 and SEC24B. Serum ferritin was also related to bacterial glycine transporters, the host glycine serum levels and the liver expression of glycine transporters. The transcriptomic findings were replicated in human primary hepatocytes, where iron supplementation also led to triglycerides accumulation and induced the expression of lipid and iron metabolism genes in synergy with palmitic acid. We further explored the direct impact of the microbiome on iron metabolism and liver fact accumulation through transplantation of faecal microbiota into recipient's mice. In line with the results in humans, transplantation from 'high ferritin donors' resulted in alterations in several genes related to iron metabolism and fatty acid accumulation in recipient's mice.<br><br>CONCLUSIONS: Altogether, a significant interplay among the gut microbiome, iron status and liver fat accumulation is revealed, with potential significance for target therapies. Video abstract.}, }
@article {pmid33953314, year = {2021}, author = {Melkonian, C and Fillinger, L and Atashgahi, S and da Rocha, UN and Kuiper, E and Olivier, B and Braster, M and Gottstein, W and Helmus, R and Parsons, JR and Smidt, H and van der Waals, M and Gerritse, J and Brandt, BW and Röling, WFM and Molenaar, D and van Spanning, RJM}, title = {High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {530}, pmid = {33953314}, issn = {2399-3642}, abstract = {A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.}, }
@article {pmid33946648, year = {2021}, author = {Ferrulli, A and Drago, L and Gandini, S and Massarini, S and Bellerba, F and Senesi, P and Terruzzi, I and Luzi, L}, title = {Deep Transcranial Magnetic Stimulation Affects Gut Microbiota Composition in Obesity: Results of Randomized Clinical Trial.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33946648}, issn = {1422-0067}, support = {RF-2011-02349303//Ministero della Salute/ ; Ricerca Corrente//IRCCS Multimedica/ ; }, mesh = {Adult ; Aged ; Autonomic Nervous System/physiopathology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics/isolation &amp; purification ; Double-Blind Method ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Male ; Middle Aged ; Models, Biological ; Norepinephrine/blood ; Obesity/*microbiology/physiopathology/*therapy ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Transcranial Magnetic Stimulation/*methods ; Weight Loss ; Young Adult ; }, abstract = {Growing evidence highlights the crucial role of gut microbiota in affecting different aspects of obesity. Considering the ability of deep transcranial magnetic stimulation (dTMS) to modulate the cortical excitability, the reward system, and, indirectly, the autonomic nervous system (ANS), we hypothesized a potential role of dTMS in affecting the brain-gut communication pathways, and the gut microbiota composition in obesity. In a hospital setting, 22 subjects with obesity (5 M, 17 F; 44.9 ± 2.2 years; BMI 37.5 ± 1.0 kg/m2) were randomized into three groups receiving 15 sessions (3 per week for 5 weeks) of high frequency (HF), low frequency (LF) dTMS, or sham stimulation. Fecal samples were collected at baseline and after 5 weeks of treatment. Total bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool Mini Kit (Qiagen, Italy) and analyzed by a metagenomics approach (Ion Torrent Personal Genome Machine). After 5 weeks, a significant weight loss was found in HF (HF: -4.1 ± 0.8%, LF: -1.9 ± 0.8%, sham: -1.3 ± 0.6%, p = 0.042) compared to LF and sham groups, associated with a decrease in norepinephrine compared to baseline (HF: -61.5 ± 15.2%, p < 0.01; LF: -31.8 ± 17.1%, p < 0.05; sham: -35.8 ± 21.0%, p > 0.05). Furthermore, an increase in Faecalibacterium (+154.3% vs. baseline, p < 0.05) and Alistipes (+153.4% vs. baseline, p < 0.05) genera, and a significant decrease in Lactobacillus (-77.1% vs. baseline, p < 0.05) were found in HF. Faecalibacterium variations were not significant compared to baseline in the other two groups (LF: +106.6%, sham: +27.6%; p > 0.05) as well as Alistipes (LF: -54.9%, sham: -15.1%; p > 0.05) and Lactobacillus (LF: -26.0%, sham: +228.3%; p > 0.05) variations. Norepinephrine change significantly correlated with Bacteroides (r2 = 0.734; p < 0.05), Eubacterium (r2 = 0.734; p < 0.05), and Parasutterella (r2 = 0.618; p < 0.05) abundance variations in HF. In conclusion, HF dTMS treatment revealed to be effective in modulating gut microbiota composition in subjects with obesity, reversing obesity-associated microbiota variations, and promoting bacterial species representative of healthy subjects with anti-inflammatory properties.}, }
@article {pmid33942283, year = {2021}, author = {VanWallendael, A and Alvarez, M and Franks, SJ}, title = {Patterns of population genomic diversity in the invasive Japanese knotweed species complex.}, journal = {American journal of botany}, volume = {108}, number = {5}, pages = {857-868}, doi = {10.1002/ajb2.1653}, pmid = {33942283}, issn = {1537-2197}, mesh = {*Fallopia japonica ; Genetic Variation ; Genotype ; *Introduced Species ; Metagenomics ; North America ; }, abstract = {PREMISE: Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity.<br><br>METHODS: We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids.<br><br>RESULTS: Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex.<br><br>CONCLUSIONS: The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.}, }
@article {pmid33941275, year = {2021}, author = {Altabtbaei, K and Maney, P and Ganesan, SM and Dabdoub, SM and Nagaraja, HN and Kumar, PS}, title = {Anna Karenina and the subgingival microbiome associated with periodontitis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {97}, pmid = {33941275}, issn = {2049-2618}, support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; }, mesh = {*Aggressive Periodontitis ; Cross-Sectional Studies ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associations from those common to all three forms of periodontitis has hampered biomarker discovery. Therefore, we aimed to map the genomic content of, and the biological pathways encoded by, the microbiomes associated with these clinical phenotypes. We also estimated the extent to which these biomes are governed by the Anna Karenina principle (AKP), which states that eubiotic communities are similar between individuals while disease-associated communities are highly individualized.<br><br>METHODS: We collected subgingival plaque from 25 periodontally healthy individuals and diseased sites of 59 subjects with stage 3 periodontitis and used shotgun metagenomics to characterize the aggregate of bacterial genes.<br><br>RESULTS: Beta-dispersion metrics demonstrated that AKP was most evident in CP, followed by GAP and LAP. We discovered broad dysbiotic signatures spanning the three phenotypes, with over-representation of pathways that facilitate life in an oxygen-poor, protein- and heme-rich, pro-oxidant environment and enhance capacity for attachment and biofilm formation. Phenotype-specific indicators were more readily evident in LAP microbiome than GAP or CP. Genes that enable acetate-scavenging lifestyle, utilization of alternative nutritional sources, oxidative and nitrosative stress responses, and siderophore production were unique to LAP. An attenuation of virulence-related functionalities and stress response from LAP to GAP to CP was apparent. We also discovered that clinical phenotypes of disease resolved variance in the microbiome with greater clarity than the newly established grading system. Importantly, we observed that one third of the metagenome of LAP is unique to this phenotype while GAP shares significant functional and taxonomic features with both LAP and CP, suggesting either attenuation of an aggressive disease or an early-onset chronic disease.<br><br>CONCLUSION: Within the limitations of a small sample size and a cross-sectional study design, the distinctive features of the microbiomes associated with LAP and CP strongly persuade us that these are discrete disease entities, while calling into question whether GAP is a separate disease, or an artifact induced by cross-sectional study designs. Further studies on phenotype-specific microbial genes are warranted to explicate their role in disease etiology. Video Abstract.}, }
@article {pmid33927711, year = {2021}, author = {Griggs, RG and Steenwerth, KL and Mills, DA and Cantu, D and Bokulich, NA}, title = {Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {673810}, pmid = {33927711}, issn = {1664-302X}, abstract = {Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.}, }
@article {pmid33927454, year = {2021}, author = {Bae, J and Cho, HW and Jung, H and Park, J and Yun, S and Ha, S and Lee, Y and Kim, TJ}, title = {Changes in Intestinal Microbiota Due to the Expanded Polystyrene Diet of Mealworms (Tenebrio molitor).}, journal = {Indian journal of microbiology}, volume = {61}, number = {2}, pages = {130-136}, pmid = {33927454}, issn = {0046-8991}, abstract = {Expanded polystyrene (EPS), which is difficult to decompose, is usually buried or incinerated, causing the natural environment to be contaminated with microplastics and environmental hormones. Digestion of EPS by mealworms has been identified as a possible biological solution to the problem of pollution, but the complete degradation mechanism of EPS is not yet known. Intestinal microorganisms play a significant role in the degradation of EPS by mealworms, and relatively few other EPS degradation microorganisms are currently known. This study observed significant differences in the intestinal microbiota of mealworms according to the dietary results of metagenomics analysis and biodiversity indices. We have proposed two new candidates of EPS-degrading bacteria, Cronobacter sakazakii and Lactococcus garvieae, which increased significantly in the EPS feeding group population. The population change and the new two bacteria will help us understand the biological mechanism of EPS degradation and develop practical EPS degradation methods.}, }
@article {pmid33925672, year = {2021}, author = {Altomare, A and Del Chierico, F and Rocchi, G and Emerenziani, S and Nuglio, C and Putignani, L and Angeletti, S and Lo Presti, A and Ciccozzi, M and Russo, A and Cocca, S and Ribolsi, M and Muscaritoli, M and Cicala, M and Guarino, MPL}, title = {Association between Dietary Habits and Fecal Microbiota Composition in Irritable Bowel Syndrome Patients: A Pilot Study.}, journal = {Nutrients}, volume = {13}, number = {5}, pages = {}, pmid = {33925672}, issn = {2072-6643}, support = {WFR GR-2011-02350817//Ministero della Salute (Italy)/ ; Italy, 201905_genetica_putignani to LP//RC Ministry of Health (Ministero della Salute, Italy)/ ; }, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Diet/*methods/statistics &amp; numerical data ; Feces/*microbiology ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*microbiology/physiopathology ; Male ; Middle Aged ; Pilot Projects ; }, abstract = {Intestinal dysbiosis seems to play a role in the pathophysiology of irritable bowel syndrome (IBS). The present pilot study aimed to elucidate the association between nutrient intake and Mediterranean diet (MD) adherence with IBS symptoms and gut microbiota in IBS patients. The nutrient intake of 28 IBS patients and 21 controls was assessed through a food diary, the reference intake ranges (RIs) for energy-yielding macronutrients and the MD serving score (MDSS) index. MD adherence and nutrients intake were compared to IBS symptoms and fecal microbiota, obtained by 16S rRNA targeted-metagenomics. In IBS patients MDSS index was altered compared to controls (p < 0.01). IBS patients with low-MD score reported severe abdominal pain and higher flatulence point-scales. Through Linear discriminant analysis effect size (LEfSe), Erysipelotrichaceae were detected as a microbial biomarker in IBS patients with altered RIs for macronutrients intake, compared to controls. Lactobacillaceae and Lactobacillus were associated to an altered carbohydrates intake in IBS patients, while specific taxonomic biomarkers, such as Aldercreuzia, Mogibacteriaceae, Rikenellaceae, Parabacteroides and F. prausnitzii were associated with an adequate intake of nutrient in these patients. This study supports an association between dietary patterns and gut microbial biomarkers in IBS patients. Further investigations are needed to clarify these connections.}, }
@article {pmid33923841, year = {2021}, author = {van der Linde, C and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Swann, JR and Costabile, A}, title = {An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {33923841}, issn = {1420-3049}, mesh = {*Chlorella ; Enterobacteriaceae/classification/genetics ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; RNA, Ribosomal, 16S ; }, abstract = {The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by1H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.}, }
@article {pmid33923593, year = {2021}, author = {Fulci, V and Stronati, L and Cucchiara, S and Laudadio, I and Carissimi, C}, title = {Emerging Roles of Gut Virome in Pediatric Diseases.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33923593}, issn = {1422-0067}, mesh = {Celiac Disease/microbiology/*virology ; Child ; Diabetes Mellitus, Type 1/microbiology/*virology ; Diarrhea/microbiology/*virology ; Humans ; Inflammatory Bowel Diseases/microbiology/*virology ; Intestinal Mucosa/microbiology/*virology ; Metagenome ; *Virome ; }, abstract = {In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.}, }
@article {pmid33921772, year = {2021}, author = {Park, DH and Kim, JW and Park, HJ and Hahm, DH}, title = {Comparative Analysis of the Microbiome across the Gut-Skin Axis in Atopic Dermatitis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33921772}, issn = {1422-0067}, support = {NRF-2020R1A4A1018598//National Research Foundation of Korea/ ; }, mesh = {Animals ; Dermatitis, Atopic/*microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metagenomics ; Skin/microbiology ; }, abstract = {Atopic dermatitis (AD) is a refractory and relapsing skin disease with a complex and multifactorial etiology. Various congenital malformations and environmental factors are thought to be involved in the onset of the disease. The etiology of the disease has been investigated, with respect to clinical skin symptoms and systemic immune response factors. A gut microbiome-mediated connection between emotional disorders such as depression and anxiety, and dermatologic conditions such as acne, based on the comorbidities of these two seemingly unrelated disorders, has long been hypothesized. Many aspects of this gut-brain-skin integration theory have recently been revalidated to identify treatment options for AD with the recent advances in metagenomic analysis involving powerful sequencing techniques and bioinformatics that overcome the need for isolation and cultivation of individual microbial strains from the skin or gut. Comparative analysis of microbial clusters across the gut-skin axis can provide new information regarding AD research. Herein, we provide a historical perspective on the modern investigation and clinical implications of gut-skin connections in AD in terms of the integration between the two microbial clusters.}, }
@article {pmid33919845, year = {2021}, author = {Thompson, HJ and Levitt, JO and McGinley, JN and Chandler, P and Guenther, PM and Huybrechts, I and Playdon, MC}, title = {Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure.}, journal = {Nutrients}, volume = {13}, number = {4}, pages = {}, pmid = {33919845}, issn = {2072-6643}, support = {5R00CA218694-03/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Algorithms ; Chronic Disease/prevention &amp; control ; Diet Surveys/*methods/statistics &amp; numerical data ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; *Phytochemicals ; Plants, Edible/*chemistry ; }, abstract = {The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.}, }
@article {pmid33915727, year = {2021}, author = {Jia, B and Park, D and Chun, BH and Hahn, Y and Jeon, CO}, title = {Diet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33915727}, issn = {1422-0067}, support = {2017M3C1B5019250//National Research Foundation of Korea/ ; 2018R1A5A1025077//National Research Foundation of Korea/ ; }, mesh = {Amidohydrolases/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; *Diet, Ketogenic ; *Gastrointestinal Microbiome ; Humans ; Hyperphagia/*microbiology ; Metagenomics ; }, abstract = {The metabolism of bile acid by the gut microbiota is associated with host health. Bile salt hydrolases (BSHs) play a crucial role in controlling microbial bile acid metabolism. Herein, we conducted a comparative study to investigate the alterations in the abundance of BSHs using data from three human studies involving dietary interventions, which included a ketogenetic diet (KD) versus baseline diet (BD), overfeeding diet (OFD) versus underfeeding diet, and low-carbohydrate diet (LCD) versus BD. The KD increased BSH abundance compared to the BD, while the OFD and LCD did not change the total abundance of BSHs in the human gut. BSHs can be classified into seven clusters; Clusters 1 to 4 are relatively abundant in the gut. In the KD cohort, the levels of BSHs from Clusters 1, 3, and 4 increased significantly, whereas there was no notable change in the levels of BSHs from the clusters in the OFD and LCD cohorts. Taxonomic studies showed that members of the phyla Bacteroidetes, Firmicutes, and Actinobacteria predominantly produced BSHs. The KD altered the community structure of BSH-active bacteria, causing an increase in the abundance of Bacteroidetes and decrease in Actinobacteria. In contrast, the abundance of BSH-active Bacteroidetes decreased in the OFD cohort, and no significant change was observed in the LCD cohort. These results highlight that dietary patterns are associated with the abundance of BSHs and community structure of BSH-active bacteria and demonstrate the possibility of manipulating the composition of BSHs in the gut through dietary interventions to impact human health.}, }
@article {pmid33910647, year = {2021}, author = {Tourlousse, DM and Narita, K and Miura, T and Sakamoto, M and Ohashi, A and Shiina, K and Matsuda, M and Miura, D and Shimamura, M and Ohyama, Y and Yamazoe, A and Uchino, Y and Kameyama, K and Arioka, S and Kataoka, J and Hisada, T and Fujii, K and Takahashi, S and Kuroiwa, M and Rokushima, M and Nishiyama, M and Tanaka, Y and Fuchikami, T and Aoki, H and Kira, S and Koyanagi, R and Naito, T and Nishiwaki, M and Kumagai, H and Konda, M and Kasahara, K and Ohkuma, M and Kawasaki, H and Sekiguchi, Y and Terauchi, J}, title = {Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {95}, pmid = {33910647}, issn = {2049-2618}, mesh = {DNA ; Humans ; *Metagenomics ; *Microbiota/genetics ; Reference Standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.<br><br>RESULTS: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories.<br><br>CONCLUSIONS: The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.}, }
@article {pmid33902743, year = {2021}, author = {Cabello-Yeves, PJ and Callieri, C and Picazo, A and Mehrshad, M and Haro-Moreno, JM and Roda-Garcia, JJ and Dzhembekova, N and Slabakova, V and Slabakova, N and Moncheva, S and Rodriguez-Valera, F}, title = {The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {5}, pmid = {33902743}, issn = {2524-6372}, support = {CGL2016-76273-p//Ministerio de Ciencia, Innovación y Universidades/ ; PROMETEO/2019/009//Conselleria d'Educació, Investigació, Cultura i Esport/ ; APOSTD/2019/009//Conselleria d'Educació, Investigació, Cultura i Esport/ ; D01-230/06.12.2018//Bulgarian Academy of Sciences/ ; }, abstract = {BACKGROUND: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level.<br><br>RESULTS: We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of "dark matter" streamlined genomes of largely unpredictable ecology.<br><br>CONCLUSIONS: The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.}, }
@article {pmid33884825, year = {2021}, author = {Cheng, S and Lu, P and Feng, QY}, title = {[Distribution of Antibiotic Resistance Genes and Microbial Communities in a Fishery Reclamation Mining Subsidence Area].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {5}, pages = {2541-2549}, doi = {10.13227/j.hjkx.202009166}, pmid = {33884825}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Fisheries ; Genes, Bacterial/genetics ; *Microbiota/genetics ; }, abstract = {The widespread use of antibiotics in the aquaculture industry has caused antibiotic resistance genes (ARGs) pollution. Metagenomics technology was used to detect and analyze the relative abundance of ARGs and microbial community structure in a fishery reclamation mining subsidence area. A total of 29 ARGs were detected, and bacA had the highest relative abundance in all the samples, reaching 1.96×10-5-1.19×10-4. The relative abundance of sulfonamide and tetracycline ARGs in sediments was relatively high and the relative abundance of multidrug ARGs in well water was relatively high. Proteobacteria was the most dominant bacterial phylum in all the samples, and Chloroflexi and Euryarchaeota were relatively abundant in the sediments. Thiobacillus was the most dominant bacterial genus in the sediments, and Acinetobacter and Pseudomonas were the dominant bacterial genera in the well water. The correlation analysis between the ARGs and microorganisms showed that the genera and ARGs were mainly correlated to a moderate degree, and multiple genera had significant positive correlations with ARGs. The distribution of ARGs was affected by the structure of the microbial community. The sediments and well water in the fishery reclamation mining subsidence area were both contaminated by ARGs, and corresponding control measures should be strengthened to protect the regional environment.}, }
@article {pmid33875193, year = {2021}, author = {Xiao, M and Huang, T and Xu, Y and Peng, Z and Liu, Z and Guan, Q and Xie, M and Xiong, T}, title = {Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation.}, journal = {Food microbiology}, volume = {98}, number = {}, pages = {103573}, doi = {10.1016/j.fm.2020.103573}, pmid = {33875193}, issn = {1095-9998}, mesh = {Brassica/metabolism/*microbiology ; China ; Enterobacteriaceae/classification/genetics/*isolation &amp; purification/*metabolism ; Fermentation ; Fermented Foods and Beverages/*microbiology ; Food Microbiology ; Lactobacillaceae/classification/genetics/*isolation &amp; purification/metabolism ; Metagenomics ; *Microbiota ; Transcriptome ; Vegetables/metabolism/*microbiology ; }, abstract = {Chinese Sichuan Paocai (CSP) is one of the world's best-known fermented vegetables with a large presence in the Chinese market. The dynamic microbial community is the main contributor to Paocai fermentation. However, little is known about the ecological distribution and functional importance of these community members. In this study, metatranscriptomics was used to comprehensively explore the active microbial community members and key transcripts with significant functions in the Paocai fermentation process. Enterobacter, Leuconostoc, and Lactobacillus dominated the three-fermentation stages (Pre-, Mid- and Lat-), respectively. Carbon metabolism was the most abundant pathway. GH (glycoside hydrolase) and GT (lycosyl transferase) were the two most highly expressed carbohydrate-active enzymes. The most highly differentially expressed genes were grouped in the biosynthesis of amino acids, followed by glycolysis. Meta-pathways in the Sichuan Paocai fermentation ecosystem were reconstructed, Lactobacillaceae and Enterobacteriaceae were the two most important metabolic contributors. In addition, the nrfA and nirB were two genes referred to distinct nitrite reductase enzymes and 9 specialized genes, such as eclo, ron and ent were expressed to produce autoinducer 2 (AI-2) kinase in response to population density. The present study revealed functional enzymes and meta-pathways of the active microbial communities, which provide a deeper understanding of their contribution to CSP products.}, }
@article {pmid33869074, year = {2021}, author = {Xiao, S and Zhang, G and Jiang, C and Liu, X and Wang, X and Li, Y and Cheng, M and Lv, H and Xian, F and Guo, X and Tan, Y}, title = {Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {605825}, pmid = {33869074}, issn = {2235-2988}, mesh = {Dysbiosis ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Psoriasis ; RNA, Ribosomal, 16S/genetics ; Vascular Endothelial Growth Factor A ; }, abstract = {Background: Increasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.<br><br>Objectives: To comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.<br><br>Methods: DNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.<br><br>Results: Compared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.<br><br>Conclusions: A clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.}, }
@article {pmid33868800, year = {2021}, author = {Gilroy, R and Ravi, A and Getino, M and Pursley, I and Horton, DL and Alikhan, NF and Baker, D and Gharbi, K and Hall, N and Watson, M and Adriaenssens, EM and Foster-Nyarko, E and Jarju, S and Secka, A and Antonio, M and Oren, A and Chaudhuri, RR and La Ragione, R and Hildebrand, F and Pallen, MJ}, title = {Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10941}, pmid = {33868800}, issn = {2167-8359}, abstract = {Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.<br><br>Results: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.<br><br>Conclusions: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.}, }
@article {pmid33868230, year = {2021}, author = {Liu, F and Xu, X and Chao, L and Chen, K and Shao, A and Sun, D and Hong, Y and Hu, R and Jiang, P and Zhang, N and Xiao, Y and Yan, F and Feng, N}, title = {Alteration of the Gut Microbiome in Chronic Kidney Disease Patients and Its Association With Serum Free Immunoglobulin Light Chains.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {609700}, pmid = {33868230}, issn = {1664-3224}, mesh = {Biomarkers ; Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Glomerular Filtration Rate ; Humans ; Immunoglobulin Light Chains/*blood ; Kidney Function Tests ; Male ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Renal Insufficiency, Chronic/*blood/diagnosis/*etiology ; Severity of Illness Index ; }, abstract = {Objectives: Gut dysbiosis is associated with chronic kidney disease (CKD), and serum free immunoglobulin light chains (FLCs) are biomarkers for CKD. This study aims to assess the CKD gut microbiome and to determine its impact on serum FLC levels.<br><br>Methods: To control for confounders, 100 patients and sex- and age-matched healthy controls (HCs) were recruited. The gut microbiome was assessed by sequencing 16S rRNA gene V3-V4 hypervariable regions. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was applied to infer functional metabolic pathways. When observing group differences in the microbiome and predicted metabolic pathways, demographic confounders were adjusted using binary logistic regression; when examining impacts of the gut microbiome and metabolic pathways on serum FLCs, factors influencing FLC levels were adjusted using multiple regression.<br><br>Results: Principal coordinate analysis revealed a significantly different bacterial community between the CKD and HC groups (P < 0.05). After adjusting for confounders, lower Chao 1, observed species and Shannon indices based on binary logistic regression predicted CKD prevalence. Actinobacteria, Alistipes, Bifidobacterium and Bifidobacterium longum enrichment, upregulation of metabolic pathways of bacterial toxin, chloroalkane and chloroalkene degradation, and Staphylococcus aureus infection also predicted CKD prevalence (P < 0.05). Furthermore, depletion of Actinobacteria and Bifidobacterium and reduced chloroalkane and chloroalkene degradation predicted high levels of FLC λ (P < 0.05).<br><br>Conclusions: Gut dysbiosis in CKD patients was confirmed by controlling for confounders in the present study. Additionally, the association between gut dysbiosis and FLC λ levels demonstrates the existence of crosstalk between the microbiome and immune response in CKD.}, }
@article {pmid33863919, year = {2021}, author = {Larkin, AA and Garcia, CA and Garcia, N and Brock, ML and Lee, JA and Ustick, LJ and Barbero, L and Carter, BR and Sonnerup, RE and Talley, LD and Tarran, GA and Volkov, DL and Martiny, AC}, title = {High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {107}, pmid = {33863919}, issn = {2052-4463}, support = {T32AI141346//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NA10OAR4320143//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; U8R1SE3-PRF//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; U8R1SE3-PRF//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; OCE-1437015//National Science Foundation (NSF)/ ; OCE-1046297//National Science Foundation (NSF)/ ; OCE-1559002//National Science Foundation (NSF)/ ; OCE-1848576//National Science Foundation (NSF)/ ; OCE-1948842//National Science Foundation (NSF)/ ; }, mesh = {Genomic Library ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Oceans and Seas ; Seawater/*microbiology ; }, abstract = {Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or "Bio-GO-SHIP." One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.}, }
@article {pmid33859184, year = {2021}, author = {Couch, CE and Stagaman, K and Spaan, RS and Combrink, HJ and Sharpton, TJ and Beechler, BR and Jolles, AE}, title = {Diet and gut microbiome enterotype are associated at the population level in African buffalo.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2267}, pmid = {33859184}, issn = {2041-1723}, support = {BB/L011085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Buffaloes/*microbiology/physiology ; Communicable Diseases/epidemiology/microbiology/*veterinary ; DNA, Bacterial/isolation &amp; purification ; Feces/microbiology ; Feeding Behavior/*physiology ; Firmicutes/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*immunology ; Incidence ; Metagenomics ; Phylogeny ; Planococcaceae/genetics/isolation &amp; purification ; Prevalence ; RNA, Ribosomal, 16S/genetics ; South Africa/epidemiology ; Symbiosis/immunology ; }, abstract = {Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.}, }
@article {pmid33858103, year = {2021}, author = {Zeng, H and Xu, H and Liu, G and Wei, Y and Zhang, J and Shi, H}, title = {Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {125143}, doi = {10.1016/j.jhazmat.2021.125143}, pmid = {33858103}, issn = {1873-3336}, mesh = {Bacteria/genetics ; *Manihot ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Plant Roots ; Rhizosphere ; Soil Microbiology ; }, abstract = {The most common environmental pollutants such as cadmium (Cd), glyphosate and tetracycline have led to profoundly adverse impacts on plant productivity. However, how tropical crops such as cassava sense these pollutants via roots and how rhizosphere microbiome interacts with the host and pollutants remain largely unknown. In this study, we found these stresses significantly inhibited plant growth and triggered cell damage in a dosage-dependent manner, and the toxic effect on redox homeostasis was correlated with antioxidant metabolism. Using metagenomics technique, we found the rhizosphere microbiomes dynamically altered as the dose of these stresses increased. We also identified stressor-associated metagenome-assembled genomes and microbial metabolic pathways as well as mobile genetic elements in the rhizosphere microbiomes. Next, a co-occurrence network of both physiological and microbiome features was constructed to explore how these pollutants derived oxidative damage through the microbiome succession. Notably, phyllosphere transplantation of Agrobacterium tumefaciens or Pseudomonas stutzeri can significantly alleviate the negative effects of stresses on cassava growth and redox homeostasis. Collectively, this study demonstrated the dynamics of rhizosphere bacterial microbiome of cassava under three common environmental stresses, and A. tumefaciens and P. stutzeri could be developed as potential beneficial bacteria to alleviate Cd, glyphosate and tetracycline-triggered damage to cassava.}, }
@article {pmid33853691, year = {2021}, author = {Zuo, T and Liu, Q and Zhang, F and Yeoh, YK and Wan, Y and Zhan, H and Lui, GCY and Chen, Z and Li, AYL and Cheung, CP and Chen, N and Lv, W and Ng, RWY and Tso, EYK and Fung, KSC and Chan, V and Ling, L and Joynt, G and Hui, DSC and Chan, FKL and Chan, PKS and Ng, SC}, title = {Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {91}, pmid = {33853691}, issn = {2049-2618}, mesh = {*COVID-19 ; Child, Preschool ; DNA ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA ; SARS-CoV-2 ; Virome ; }, abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.<br><br>METHODS: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.<br><br>RESULTS: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.<br><br>CONCLUSIONS: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19. Video Abstract.}, }
@article {pmid33850115, year = {2021}, author = {Raes, EJ and Karsh, K and Sow, SLS and Ostrowski, M and Brown, MV and van de Kamp, J and Franco-Santos, RM and Bodrossy, L and Waite, AM}, title = {Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2213}, pmid = {33850115}, issn = {2041-1723}, mesh = {Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Biodiversity ; Ecology ; Genes, Bacterial/*genetics ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Metagenomics/*methods ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thermodynamics ; }, abstract = {Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.}, }
@article {pmid33845910, year = {2021}, author = {Restrepo, L and Domínguez-Borbor, C and Bajaña, L and Betancourt, I and Rodríguez, J and Bayot, B and Reyes, A}, title = {Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus).}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {88}, pmid = {33845910}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Microbiota ; Necrosis ; *Penaeidae ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Survivors ; Vibrio ; *Vibrio parahaemolyticus/genetics ; }, abstract = {BACKGROUND: Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use probiotics in order to limit the detrimental effects of AHNPD, we evaluated the effect of the ILI strain, a Vibrio sp. bacterium and efficient shrimp probiotic, using metabarcoding (16S rRNA gene) on the gastrointestinal microbiota of shrimp after being challenged with AHPND-causing V. parahaemolyticus.<br><br>RESULTS: We showed how the gastrointestinal microbiome of shrimp varied between healthy and infected organisms. Nevertheless, a challenge of working with AHPND-causing Vibrio pathogens and Vibrio-related bacteria as probiotics is the potential risk of the probiotic strain becoming pathogenic. Consequently, we evaluated whether ILI strain can acquire the plasmid pV-AHPND via horizontal transfer and further cause the disease in shrimp. Conjugation assays were performed resulting in a high frequency (70%) of colonies harboring the pv-AHPND. However, no shrimp mortality was observed when transconjugant colonies of the ILI strain were used in a challenge test using healthy shrimp. We sequenced the genome of the ILI strain and performed comparative genomics analyses using AHPND and non-AHPND Vibrio isolates. Using available phylogenetic and phylogenomics analyses, we reclassified the ILI strain as Vibrio diabolicus. In summary, this work represents an effort to study the role that probiotics play in the normal gastrointestinal shrimp microbiome and in AHPND-infected shrimp, showing that the ILI probiotic was able to control pathogenic bacterial populations in the host's gastrointestinal tract and stimulate the shrimp's survival. The identification of probiotic bacterial species that are effective in the host's colonization is important to promote animal health and prevent disease.<br><br>CONCLUSIONS: This study describes probiotic bacteria capable of controlling pathogenic populations of bacteria in the shrimp gastrointestinal tract. Our work provides new insights into the complex dynamics between shrimp and the changes in the microbiota. It also addresses the practical application of probiotics to solve problems with pathogens that cause high mortality-rate in shrimp farming around the world. Video Abstract.}, }
@article {pmid33841399, year = {2021}, author = {Xia, C and Jiang, C and Li, W and Wei, J and Hong, H and Li, J and Feng, L and Wei, H and Xin, H and Chen, T}, title = {A Phase II Randomized Clinical Trial and Mechanistic Studies Using Improved Probiotics to Prevent Oral Mucositis Induced by Concurrent Radiotherapy and Chemotherapy in Nasopharyngeal Carcinoma.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {618150}, pmid = {33841399}, issn = {1664-3224}, mesh = {Animals ; Chemoradiotherapy/*adverse effects/methods ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; Duration of Therapy ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Nasopharyngeal Neoplasms/*complications/therapy ; Probiotics/*therapeutic use ; Rats ; Severity of Illness Index ; Stomatitis/diagnosis/*etiology/*therapy ; Treatment Outcome ; }, abstract = {Earlier evidence has proven that probiotic supplements can reduce concurrent chemoradiotherapy (CCRT)-induced oral mucositis (OM) in nasopharyngeal cancer (NPC). The incidence of severe OM (grade 3 or higher) was the primary endpoint in this study. We first enrolled 85 patients with locally advanced NPC who were undergoing CCRT. Of them, 77 patients were finally selected and randomized (1:1) to receive either a probiotic cocktail or placebo. To investigate the protective effects and the mechanism of probiotic cocktail treatment on OM induced by radiotherapy and chemotherapy, we randomly divided the rats into the control (C) group, the model (M) group, and the probiotic (P) group. After treatment, samples from the tongue, blood, and fecal and proximal colon tissues on various days (7th, 14th, and 21st days) were collected and tested for the inflammatory response, cell apoptosis, intestinal permeability, and intestinal microbial changes. We found that patients taking the probiotic cocktail showed significantly lower OM. The values of the incidence of 0, 1, 2, 3, and 4 grades of OM in the placebo group and in the probiotic cocktail group were reported to be 0, 14.7, 38.2, 32.4, and 14.7% and 13.9, 36.1, 25, 22.2, and 2.8%, respectively. Furthermore, patients in the probiotic cocktail group showed a decrease in the reduction rate of CD3+ T cells (75.5% vs. 81%, p < 0.01), CD4+ T cells (64.53% vs. 79.53%, p < 0.01), and CD8+ T cells (75.59 vs. 62.36%, p < 0.01) compared to the placebo group. In the rat model, the probiotic cocktail could ameliorate the severity of OM, decrease the inflammatory response, cause cell apoptosis and intestinal permeability, and restore the structure of gut microbiota to normalcy. In conclusion, the modified probiotic cocktail significantly reduces the severity of OM by enhancing the immune response of patients with NPC and modifying the structure of gut microbiota. Clinical Trial Registration: The Clinical Trial Registration should be the NCT03112837.}, }
@article {pmid33837467, year = {2021}, author = {Kaushik, R and Pandit, MK and Meyerson, LA and Chaudhari, DS and Sharma, M and Dhotre, D and Shouche, YS}, title = {Contrasting Composition, Diversity and Predictive Metabolic Potential of the Rhizobacterial Microbiomes Associated with Native and Invasive Prosopis Congeners.}, journal = {Current microbiology}, volume = {78}, number = {5}, pages = {2051-2060}, pmid = {33837467}, issn = {1432-0991}, mesh = {*Microbiota ; *Prosopis ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Invasive plants are known to alter the soil microbial communities; however, the effects of co-occurring native and invasive congeners on the soil bacterial diversity and their predictive metabolic profiles are not known. Here, we compared the rhizosphere bacterial communities of invasive Prosopis juliflora and its native congener Prosopis cineraria using high-throughput sequencing of the 16S rRNA gene. Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram revealed significant variation in the communities of these co-occurring Prosopis species. Additionally, Canonical Correspondence Analysis (CCA) based on microbial communities in addition to the soil physiochemical parameters viz. soil pH, electrical conductivity, moisture content and sampling depth showed ~ 80% of the variation in bacterial communities of the rhizosphere and control soil. We observed that Proteobacteria was the predominant phylum of P. juliflora rhizosphere and the control soil, while P. cineraria rhizosphere was dominated by Cyanobacteria. Notably, the invasive P. juliflora rhizosphere showed an enhanced abundance of bacterial phyla like Actinobacteria, Chloroflexi, Firmicutes and Acidobacteria compared to the native P. cineraria as well as the control soil. Predictive metagenomics revealed that the bacterial communities of the P. juliflora rhizosphere had a higher abundance of pathways involved in antimicrobial biosynthesis and degradation, suggesting probable exposure to enemy attack and an active response mechanism to counter it as compared to native P. cineraria. Interestingly, the higher antimicrobial biosynthesis predicted in the invasive rhizosphere microbiome is further corroborated by the fact that the bacterial isolates purified from the rhizosphere of P. juliflora belonged to genera like Streptomyces, Isoptericola and Brevibacterium from the phylum Actinobacteria, which are widely reported for their antibiotic production ability. In conclusion, our results demonstrate that the co-occurring native and invasive Prosopis species have significantly different rhizosphere bacterial communities in terms of composition, diversity and their predictive metabolic potentials. In addition, the rhizosphere microbiome of invasive Prosopis proffers it a fitness advantage and influences invasion success of the species.}, }
@article {pmid33837203, year = {2021}, author = {Das, S and Bernasconi, E and Koutsokera, A and Wurlod, DA and Tripathi, V and Bonilla-Rosso, G and Aubert, JD and Derkenne, MF and Mercier, L and Pattaroni, C and Rapin, A and von Garnier, C and Marsland, BJ and Engel, P and Nicod, LP}, title = {A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2126}, pmid = {33837203}, issn = {2041-1723}, mesh = {Adult ; Allografts/immunology/microbiology ; Bacteria/genetics/immunology/isolation &amp; purification/pathogenicity ; Bacterial Load/immunology ; Bacteriological Techniques ; Bronchoalveolar Lavage Fluid/microbiology ; Bronchoscopy ; DNA, Bacterial/isolation &amp; purification ; Female ; Graft Rejection/diagnosis/immunology/*microbiology ; Humans ; Immune Tolerance ; Longitudinal Studies ; Lung/immunology/*microbiology ; Lung Transplantation/*adverse effects ; Male ; Metagenomics ; Microbiota/genetics/*immunology ; Middle Aged ; Pneumonia, Bacterial/diagnosis/immunology/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.}, }
@article {pmid33831764, year = {2021}, author = {Pandit, PR and Kumar, R and Kumar, D and Patel, Z and Pandya, L and Kumar, M and Joshi, C}, title = {Deciphering the black box of microbial community of common effluent treatment plant through integrated metagenomics: Tackling industrial effluent.}, journal = {Journal of environmental management}, volume = {289}, number = {}, pages = {112448}, doi = {10.1016/j.jenvman.2021.112448}, pmid = {33831764}, issn = {1095-8630}, mesh = {Bacteria/genetics ; Metagenome ; *Metagenomics ; *Microbiota ; Waste Water ; }, abstract = {Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.}, }
@article {pmid33823666, year = {2021}, author = {Dong, F and Kuo, HC and Chen, GL and Wu, F and Shan, PF and Wang, J and Chen,  and Lei, FM and Hung, CM and Liu, Y and Yang, XJ}, title = {Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl (Pavo muticus).}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1948}, pages = {20210073}, doi = {10.1098/rspb.2021.0073}, pmid = {33823666}, issn = {1471-2954}, mesh = {Animals ; Climate Change ; Ecosystem ; Extinction, Biological ; *Genome ; Humans ; *Metagenomics ; }, abstract = {Both anthropogenic impacts and historical climate change could contribute to population decline and species extinction, but their relative importance is still unclear. Emerging approaches based on genomic, climatic and anthropogenic data provide a promising analytical framework to address this question. This study applied such an integrative approach to examine potential drivers for the endangerment of the green peafowl (Pavo muticus). Several demographic reconstructions based on population genomes congruently retrieved a drastic population declination since the mid-Holocene. Furthermore, a comparison between historical and modern genomes suggested genetic diversity decrease during the last 50 years. However, climate-based ecological niche models predicted stationary general range during these periods and imply the little impact of climate change. Further analyses suggested that human disturbance intensities were negatively correlated with the green peafowl's effective population sizes and significantly associated with its survival status (extirpation or persistence). Archaeological and historical records corroborate the critical role of humans, leaving the footprint of low genomic diversity and high inbreeding in the survival populations. This study sheds light on the potential deep-time effects of human disturbance on species endangerment and offers a multi-evidential approach in examining underlying forces for population declines.}, }
@article {pmid33820995, year = {2021}, author = {Mac Aogáin, M and Narayana, JK and Tiew, PY and Ali, NABM and Yong, VFL and Jaggi, TK and Lim, AYH and Keir, HR and Dicker, AJ and Thng, KX and Tsang, A and Ivan, FX and Poh, ME and Oriano, M and Aliberti, S and Blasi, F and Low, TB and Ong, TH and Oliver, B and Giam, YH and Tee, A and Koh, MS and Abisheganaden, JA and Tsaneva-Atanasova, K and Chalmers, JD and Chotirmall, SH}, title = {Integrative microbiomics in bronchiectasis exacerbations.}, journal = {Nature medicine}, volume = {27}, number = {4}, pages = {688-699}, pmid = {33820995}, issn = {1546-170X}, support = {SCAF/17/03/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Bronchiectasis/*microbiology/virology ; Disease Progression ; Humans ; Metagenomics ; Microbial Interactions/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion (https://integrative-microbiomics.ntu.edu.sg). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.}, }
@article {pmid33819653, year = {2021}, author = {Zhang, Z and Wan, J and Liu, L and Ye, M and Jiang, X}, title = {Metagenomics reveals functional profiling of microbial communities in OCP contaminated sites with rapeseed oil and tartaric acid biostimulation.}, journal = {Journal of environmental management}, volume = {289}, number = {}, pages = {112515}, doi = {10.1016/j.jenvman.2021.112515}, pmid = {33819653}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Humans ; Metagenomics ; *Microbiota ; Rapeseed Oil ; Soil Microbiology ; *Soil Pollutants/analysis ; Tartrates ; }, abstract = {Organochlorine pesticides (OCPs) contaminated sites pose great threats to both human health and environmental safety. Targeted bioremediation in these regions largely depends on microbial diversity and activity. This study applied metagenomics to characterize the microbial communities and functional groups composition features during independent or simultaneous rapeseed oil and tartaric acid applications, as well as the degradation kinetics of OCPs. Results showed that: the degradation rates of α-chlordane, β-chlordane and mirex were better when (0.50% w/w) rapeseed oil and (0.05 mol L-1) tartaric acid were applied simultaneously than singular use, yielding removal rates of 56.4%, 53.9%, and 49.4%, respectively. Meanwhile, bio-stimulation facilitated microbial enzyme (catalase/superoxide dismutase/peroxidase) activity in soils significantly, promoting the growth of dominant bacterial communities. Classification at phylum level showed that the relative abundance of Proteobacteria was significantly increased (p < 0.05). Network analysis showed that bio-stimulation substantially increased the dominant bacterial community's proportion, especially Proteobacteria. The functional gene results illustrated that bio-stimulation facilitated total relative abundance of degradation genes, phosphorus, carbon, nitrogen, sulfur metabolic genes, and iron transporting genes (p < 0.05). In metabolic pathways, functional genes related to methanogenesis and ammonia generation were markedly upregulated, indicating that bio-stimulation promoted the transformation of metabolic genes, such as carbon and nitrogen. This research is conducive to exploring the microbiological response mechanisms of bio-stimulation in indigenous flora, which may provide technical support for assessing the microbial ecological remediation outcomes of bio-stimulation in OCP contaminated sites.}, }
@article {pmid33816323, year = {2021}, author = {Even, G and Lokmer, A and Rodrigues, J and Audebert, C and Viscogliosi, E and Ségurel, L and Chabé, M}, title = {Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {533528}, pmid = {33816323}, issn = {2235-2988}, mesh = {Adult ; *Blastocystis/genetics ; *Entamoeba/genetics ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis, the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural "traditional" populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae, Coprococcus and Butyrivibrio) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba-negative and Entamoeba-positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis, our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.}, }
@article {pmid33810955, year = {2021}, author = {Tian, R and Liu, H and Feng, S and Wang, H and Wang, Y and Wang, Y and Liang, L and Xu, H and Xing, H and Zhang, S}, title = {Gut microbiota dysbiosis in stable coronary artery disease combined with type 2 diabetes mellitus influences cardiovascular prognosis.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {31}, number = {5}, pages = {1454-1466}, doi = {10.1016/j.numecd.2021.01.007}, pmid = {33810955}, issn = {1590-3729}, mesh = {Aged ; Bacteria/drug effects/growth &amp; development/*metabolism ; Biomarkers/blood ; Case-Control Studies ; Clostridiales/growth &amp; development/metabolism ; Coronary Artery Disease/blood/diagnosis/*microbiology ; Diabetes Mellitus, Type 2/blood/diagnosis/drug therapy/*microbiology ; Dysbiosis ; Female ; *Gastrointestinal Microbiome/drug effects ; Host-Pathogen Interactions ; Humans ; Hypoglycemic Agents/therapeutic use ; Intestines/*microbiology ; Male ; Metabolomics ; Metagenomics ; Metformin/therapeutic use ; Middle Aged ; Prognosis ; Prospective Studies ; }, abstract = {BACKGROUND AND AIMS: Host-microbiota interactions involving metabolic pathways have been linked to the pathogenesis of atherosclerotic disease and type 2 diabetes. As stable coronary artery disease (SCAD) patients combined with type 2 diabetes have significantly increased risk for cardiac event, we focused on elucidating the role of microbiota affecting cardiometabolic disease development.<br><br>METHODS AND RESULTS: We used multi-omics analyses (metagenomics and metabolomics) of fecal and serum samples from a prospective cohort including stable coronary artery disease combined with diabetes mellitus (SCAD + T2DM, n = 38), SCAD (n = 71), and healthy control (HC, n = 55). We linked microbiome features to disease severity in a three-pronged association analysis and identified prognostic bacterial biomarkers. We identified that bacterial and metabolic signatures varied significantly between SCAD and SCAD + T2DM groups. SCAD + T2DM individuals were characterized by increased levels of aromatic amino acids and carbohydrates, which correlate with a gut microbiome with enriched biosynthetic potential. Our study also addressed how metformin may confound gut dysbiosis and increase the potential for nitrogen metabolism. In addition, we found that specific bacterial taxa Ruminococcus torques [HR: 2.363 (08-4.56), P = 0.03] was predictive of cardiac survival outcomes.<br><br>CONCLUSION: Overall, our study identified relationships between features of the gut microbiota (GM) and circulating metabolites, providing a new direction for future studies aiming to understand the host-GM interplay in atherosclerotic cardiovascular pathogenesis.}, }
@article {pmid33810609, year = {2021}, author = {Uchida, F and Oh, S and Shida, T and Suzuki, H and Yamagata, K and Mizokami, Y and Bukawa, H and Tanaka, K and Shoda, J}, title = {Effects of Exercise on the Oral Microbiota and Saliva of Patients with Non-Alcoholic Fatty Liver Disease.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {7}, pages = {}, pmid = {33810609}, issn = {1660-4601}, mesh = {Bacteria/genetics ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; *Non-alcoholic Fatty Liver Disease ; Saliva ; }, abstract = {Exercise can be hypothesized to play an important role in non-alcoholic fatty liver disease (NAFLD) treatment by changing the oral bacterial flora and in the mechanism underlying periodontal disease. We performed salivary component analysis before and after an exercise regimen, and genome analysis of the oral bacterial flora to elucidate the underlying mechanism. Obese middle-aged men with NAFLD and periodontal disease were allocated to 12-week exercise (n = 49) or dietary restriction (n = 21) groups. We collected saliva to compare the oral microflora; performed predictive analysis of metagenomic functions; and, measured the salivary immunoglobulin A, cytokine, bacterial lipopolysaccharide (LPS), and lactoferrin concentrations. The exercise group showed improvements in the clinical indices of oral environment. Salivary component analysis revealed significant reductions in LPS, and lactoferrin during the exercise regimen. Diversity analysis of oral bacterial flora revealed higher alpha- and beta-diversity after the exercise regimen. Analysis of the microbial composition revealed that the numbers of Campylobacter (+83.9%), Corynebacterium (+142.3%), Actinomyces (+75.9%), and Lautropia (+172.9%) were significantly higher, and that of Prevotella (-28.3%) was significantly lower. The findings suggest that an exercise regimen improves the oral environment of NAFLD patients by increasing the diversity of the oral microflora and reducing the number of periodontal bacteria that produce LPS and its capability.}, }
@article {pmid33809267, year = {2021}, author = {Lee, SY and Yuk, HG and Ko, SG and Cho, SG and Moon, GS}, title = {Gut Microbiome Prolongs an Inhibitory Effect of Korean Red Ginseng on High-Fat-Diet-Induced Mouse Obesity.}, journal = {Nutrients}, volume = {13}, number = {3}, pages = {}, pmid = {33809267}, issn = {2072-6643}, support = {Not relevant//Korean Society of Ginseng/ ; }, mesh = {Animals ; Blood Glucose/analysis ; Diet, High-Fat/*adverse effects ; Fluorescent Antibody Technique ; *Gastrointestinal Microbiome/genetics/physiology ; Insulin/blood ; Leptin/blood ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/microbiology/pathology ; *Panax ; Pancreas/pathology ; Phytotherapy/*methods ; Plant Extracts/*therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although the anti-obesity effect of Korean red ginseng (Panax ginseng Meyer) has been revealed, its underlying mechanisms are not clearly understood. Here, we demonstrate an involvement of gut microbiome in the inhibitory effect of Korean red ginseng on high-fat-diet (HFD)-induced mouse obesity, and further provides information on the effects of saponin-containing red ginseng extract (SGE) and saponin-depleted red ginseng extract (GE). Mice were fed with either SGE or GE every third day for one month, and their food intakes, fat weights, plasma glucose, and insulin and leptin levels were measured. Immunofluorescence assays were conducted to measure pancreatic islet size. Stools from the mice were subjected to metagenomic analysis. Both SGE and GE attenuated HFD-induced gain of body weight, reducing HFD-induced increase of food intakes and fat weights. They also reduced HFD-increased plasma glucose, insulin, and leptin levels, decreased both fasting and postprandial glucose concentrations, and improved both insulin resistance and glucose intolerance. Immunofluorescence assays revealed that they blocked HFD-induced increase of pancreatic islet size. Our pyrosequencing of the 16S rRNA gene V3 region from stools revealed that both SGE and GE modulated HFD-altered composition of gut microbiota. Therefore, we conclude that Korean red ginseng inhibits HFD-induced obesity and diabetes by altering gut microbiome.}, }
@article {pmid33807914, year = {2021}, author = {Litvinova, EA and Bets, VD and Feofanova, NA and Gvozdeva, OV and Achasova, KM and Alperina, EL and Kozhevnikova, EN}, title = {Dietary Fucose Affects Macrophage Polarization and Reproductive Performance in Mice.}, journal = {Nutrients}, volume = {13}, number = {3}, pages = {}, pmid = {33807914}, issn = {2072-6643}, support = {0259-2019-0004-C-01//Governmental project/ ; 0538-2019-0005//Budgetary funding for basic scientific research/ ; 18-015-00329//Russian Foundation for Basic Research/ ; 19-015-00169//Russian Foundation for Basic Research/ ; 20-64-47020//Russian Science Foundation/ ; 20-74-10022//Russian Science Foundation/ ; }, mesh = {Animals ; *Dietary Supplements ; Embryo Implantation/drug effects ; Female ; Fucose/*adverse effects ; Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/drug effects ; Macrophage Activation/*drug effects ; Macrophages/drug effects ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mucin-2/*metabolism ; Mucus/drug effects ; Pregnancy ; Reproduction/*drug effects ; }, abstract = {Intestinal mucus protects epithelial and immune cells from the gut resident microorganisms, and provides growth-promoting factors as mucus-derived O-glycans for beneficial bacteria. A lack of intestinal protective mucus results in changes in the commensal microflora composition, mucosal immune system reprogramming, and inflammation. Previous work has shown that fucose, the terminal glycan chain component of the intestinal glycoprotein Mucin2, and fucoidan polysaccharides have an anti-inflammatory effect in some mouse models of colitis. This study evaluates the effect of fucose on reproductive performance in heterozygous mutant Muc2 female mice. We found that even though Muc2+/- females are physiologically indistinguishable from C57Bl/6 mice, they have a significantly reduced reproductive performance upon dietary fucose supplementation. Metagenomic analysis reveals that the otherwise healthy wild-type siblings of Muc2-/- animals have reduced numbers of some of the intestinal commensal bacterial species, compared to C57BL/6 mice. We propose that the changes in beneficial microflora affect the immune status in Muc2+/- mice, which causes implantation impairment. In accordance with this hypothesis, we find that macrophage polarization during pregnancy is impaired in Muc2+/- females upon addition of fucose. Metabolic profiling of peritoneal macrophages from Muc2+/- females reveals their predisposition towards anaerobic glycolysis in favor of oxidative phosphorylation, compared to C57BL/6-derived cells. In vitro experiments on phagocytosis activity and mitochondrial respiration suggest that fucose affects oxidative phosphorylation in a genotype-specific manner, which might interfere with implantation depending on the initial status of macrophages. This hypothesis is further confirmed in BALB/c female mice, where fucose caused pregnancy loss and opposed implantation-associated M2 macrophage polarization. Taken together, these data suggest that intestinal microflora affects host immunity and pregnancy outcome. At the same time, dietary fucose might act as a differential regulator of macrophage polarization during implantation, depending on the immune status of the host.}, }
@article {pmid33805379, year = {2021}, author = {Su, H and Xiao, Z and Yu, K and Zhang, Q and Lu, C and Wang, G and Wang, Y and Liang, J and Huang, W and Huang, X and Wei, F}, title = {High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33805379}, issn = {1422-0067}, support = {42030502//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 41706158//National Natural Science Foundation of China/ ; AD19245121//Science and Technology Project of Guangxi/ ; AD17129019//Science and Technology Project of Guangxi/ ; AD17129063//Science and Technology Project of Guangxi/ ; AA17204074//Science and Technology Project of Guangxi/ ; AA18242026//Major Research Project of Guangxi for Science and Technology/ ; 2018GXNSFBA281101//Natural Science Foundation of Guangxi Province/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*enzymology/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; beta-Glucosidase/*genetics/metabolism ; }, abstract = {β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.}, }
@article {pmid33796482, year = {2021}, author = {Chen, Z and Cheng, H and Cai, Z and Wei, Q and Li, J and Liang, J and Zhang, W and Yu, Z and Liu, D and Liu, L and Zhang, Z and Wang, K and Yang, L}, title = {Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {637018}, pmid = {33796482}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial ; *Empyema, Pleural/drug therapy ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Identification of the offending organism and appropriate antimicrobial therapy are crucial for treating empyema. Diagnosis of empyema is largely obscured by the conventional bacterial cultivation and PCR process that has relatively low sensitivity, leading to limited understanding of the etiopathogenesis, microbiology, and role of antibiotics in the pleural cavity. To expand our understanding of its pathophysiology, we have carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure. Our results showed that the variation of microbiota in the pleural effusion is generally stratified, not continuous. There are two distinct microbiome clusters observed in the forty-five samples: HA-SA type and LA-SA type. The categorization is mostly driven by species composition: HA-SA type is marked by Staphylococcus aureus as the core species, with other enriched 6 bacteria and 3 fungi, forming a low diversity and highly stable microbial community; whereas the LA-SA type has a more diverse microbial community with a distinct set of bacterial species that are assumed to be the oral origin. The microbial community does not shape the dominant antibiotic resistance classes which were common in the two types, while the increase of microbial diversity was correlated with the increase in antibiotic resistance genes. The existence of well-balanced microbial symbiotic states might respond differently to pathogen colonization and drug intake. This study provides a deeper understanding of the pathobiology of pleural empyema and suggests that potential resistance genes may hinder the antimicrobial therapy of empyema.}, }
@article {pmid33795009, year = {2021}, author = {Stamboulian, M and Li, S and Ye, Y}, title = {Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {80}, pmid = {33795009}, issn = {2049-2618}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Peptides/genetics ; Proteomics ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: A few recent large efforts significantly expanded the collection of human-associated bacterial genomes, which now contains thousands of entities including reference complete/draft genomes and metagenome assembled genomes (MAGs). These genomes provide useful resource for studying the functionality of the human-associated microbiome and their relationship with human health and diseases. One application of these genomes is to provide a universal reference for database search in metaproteomic studies, when matched metagenomic/metatranscriptomic data are unavailable. However, a greater collection of reference genomes may not necessarily result in better peptide/protein identification because the increase of search space often leads to fewer spectrum-peptide matches, not to mention the drastic increase of computation time. Video Abstract METHODS: Here, we present a new approach that uses two steps to optimize the use of the reference genomes and MAGs as the universal reference for human gut metaproteomic MS/MS data analysis. The first step is to use only the high-abundance proteins (HAPs) (i.e., ribosomal proteins and elongation factors) for metaproteomic MS/MS database search and, based on the identification results, to derive the taxonomic composition of the underlying microbial community. The second step is to expand the search database by including all proteins from identified abundant species. We call our approach HAPiID (HAPs guided metaproteomics IDentification).<br><br>RESULTS: We tested our approach using human gut metaproteomic datasets from a previous study and compared it to the state-of-the-art reference database search method MetaPro-IQ for metaproteomic identification in studying human gut microbiota. Our results show that our two-steps method not only performed significantly faster but also was able to identify more peptides. We further demonstrated the application of HAPiID to revealing protein profiles of individual human-associated bacterial species, one or a few species at a time, using metaproteomic data.<br><br>CONCLUSIONS: The HAP guided profiling approach presents a novel effective way for constructing target database for metaproteomic data analysis. The HAPiID pipeline built upon this approach provides a universal tool for analyzing human gut-associated metaproteomic data.}, }
@article {pmid33791245, year = {2021}, author = {Li, A and Li, T and Gao, X and Yan, H and Chen, J and Huang, M and Wang, L and Yin, D and Li, H and Ma, R and Zeng, Q and Ding, S}, title = {Gut Microbiome Alterations in Patients With Thyroid Nodules.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {643968}, pmid = {33791245}, issn = {2235-2988}, mesh = {Adult ; Butyrates ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Humans ; Metagenomics ; *Thyroid Nodule ; }, abstract = {Thyroid nodules are found in nearly half of the adult population. Accumulating evidence suggests that the gut microbiota plays an important role in thyroid metabolism, yet the association between gut microbiota capacity, thyroid nodules, and thyroid function has not been studied comprehensively. We performed a gut microbiome genome-wide association study in 196 patients with thyroid nodules and 283 controls by using whole-genome shotgun sequencing. We found that participants with high-grade thyroid nodules have decreased number of gut microbial species and gene families compared with those with lower grade nodules and controls. There are also significant alterations in the overall microbial composition in participants with high-grade thyroid nodules. The gut microbiome in participants with high-grade thyroid nodules is characterized by greater amino acid degradation and lower butyrate production. The relative abundances of multiple butyrate producing microbes are reduced in patients with high-grade thyroid nodules and the relative abundances of L-histidine metabolism pathways are associated with thyrotropin-releasing hormone. Our study describes the gut microbiome characteristics in thyroid nodules and a gut-thyroid link and highlight specific gut microbiota as a potential therapeutic target to regulate thyroid metabolism.}, }
@article {pmid33791236, year = {2021}, author = {Fitzgerald, CB and Shkoporov, AN and Upadrasta, A and Khokhlova, EV and Ross, RP and Hill, C}, title = {Probing the "Dark Matter" of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {616918}, pmid = {33791236}, issn = {2235-2988}, mesh = {*Bacteriophages/genetics ; DNA, Viral/genetics ; Gastrointestinal Tract ; Humans ; *Metagenomics ; Virome ; }, abstract = {Recent years have been marked by the growing interest towards virulent and temperate bacteriophage populations inhabiting the human lower gastrointestinal tract - the gut phageome. A number of studies demonstrated high levels of specificity and temporal stability of individual gut phageomes, as well as their specific alterations in disease cohorts, in parallel with changes in the bacteriome. It has been speculated that phages might have an active role in shaping the taxonomic composition and functional properties of the human gut bacteriome. An overwhelming majority of gut bacteriophages, however, remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. They are often referred to as "the viral dark matter". A possible breakthrough in understanding of the phageome can only become possible when a significant proportion of the "the viral dark matter" is identified and linked to bacterial hosts. Here, we describe a method that enables rapid discovery and host-linking of novel bacteriophages in the gut via a combination of serial enrichment cultures and shotgun metagenomics of viral DNA. Using this approach dozens of novel and previously known bacteriophages were detected, including the ones infecting difficult-to-culture anaerobic bacteria. The majority of phages failed to produce lysis and propagate on host cultures in traditional assays. The newly identified phages include representatives of Siphoviridae, Myoviridae, Podoviridae, and crAss-like viruses, infecting diverse bacterial taxa of Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia and Proteobacteria phyla. The proposed new method has a potential for high-throughput screening applications for mass discovery of new phages in different environments.}, }
@article {pmid33790294, year = {2021}, author = {Singleton, CM and Petriglieri, F and Kristensen, JM and Kirkegaard, RH and Michaelsen, TY and Andersen, MH and Kondrotaite, Z and Karst, SM and Dueholm, MS and Nielsen, PH and Albertsen, M}, title = {Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2009}, pmid = {33790294}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Bioreactors/microbiology ; Denmark ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5S/genetics ; Sewage/*microbiology ; Waste Water/microbiology ; Water Purification/methods ; }, abstract = {Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.}, }
@article {pmid33786001, year = {2021}, author = {Sehli, S and Allali, I and Chahboune, R and Bakri, Y and Al Idrissi, N and Hamdi, S and Nejjari, C and Amzazi, S and Ghazal, H}, title = {Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients.}, journal = {Bioinformatics and biology insights}, volume = {15}, number = {}, pages = {1177932221999428}, pmid = {33786001}, issn = {1177-9322}, abstract = {Over the last decade, it has become increasingly apparent that the microbiome is a central component in human well-being and illness. However, to establish innovative therapeutic methods, it is crucial to learn more about the microbiota. Thereby, the area of metagenomics and associated bioinformatics methods and tools has become considerable in the study of the human microbiome biodiversity. The application of these metagenomics approaches to studying the gut microbiome in COVID-19 patients could be one of the promising areas of research in the fight against the SARS-CoV-2 infection and disparity. Therefore, understanding how the gut microbiome is affected by or could affect the SARS-CoV-2 is very important. Herein, we present an overview of approaches and methods used in the current published studies on COVID-19 patients and the gut microbiome. The accuracy of these researches depends on the appropriate choice and the optimal use of the metagenomics bioinformatics platforms and tools. Interestingly, most studies reported that COVID-19 patients' microbiota are enriched with opportunistic microorganisms. The choice and use of appropriate computational tools and techniques to accurately investigate the gut microbiota is therefore critical in determining the appropriate microbiome profile for diagnosis and the most reliable antiviral or preventive microbial composition.}, }
@article {pmid33783596, year = {2021}, author = {Zhao, H}, title = {The human microbiome and genetic disease: towards the integration of metagenomic and multi-omics data.}, journal = {Human genetics}, volume = {140}, number = {5}, pages = {701-702}, pmid = {33783596}, issn = {1432-1203}, mesh = {Data Analysis ; Genetic Diseases, Inborn/*microbiology ; Humans ; Metagenomics ; *Microbiota ; }, }
@article {pmid33781870, year = {2021}, author = {Gayathri, KV and Aishwarya, S and Kumar, PS and Rajendran, UR and Gunasekaran, K}, title = {Metabolic and molecular modelling of zebrafish gut biome to unravel antimicrobial peptides through metagenomics.}, journal = {Microbial pathogenesis}, volume = {154}, number = {}, pages = {104862}, doi = {10.1016/j.micpath.2021.104862}, pmid = {33781870}, issn = {1096-1208}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Escherichia coli ; *Gastrointestinal Microbiome ; *Metagenomics ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Pore Forming Cytotoxic Proteins ; Pseudomonas aeruginosa ; Zebrafish ; }, abstract = {Recently efforts have been taken for unravelling mysteries between host-microbe interactions in gut microbiome studies of model organisms through metagenomics. Co-existence and the co-evolution of the microorganisms is the significant cause of the growing antimicrobial menace. There needs a novel approach to develop potential antimicrobials with capabilities to act directly on the resistant microbes with reduced side effects. One such is to tap them from the natural resources, preferably the gut of the most closely related animal model. In this study, we employed metagenomics approaches to identify the large taxonomic genomes of the zebra fish gut. About 256 antimicrobial peptides were identified using gene ontology predictions from Macrel and Pubseed servers. Upon the property predictions, the top 10 antimicrobial peptides were screened based on their action against many resistant bacterial species, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, E. coli, and Bacillus cereus. Metabolic modelling and flux balance analysis (FBA) were computed to conclude the antibiotic such as tetracycline, cephalosporins, puromycin, neomycin biosynthesis pathways were adopted by the microbiome as protection strategies. Molecular modelling strategies, including molecular docking and dynamics, were performed to estimate the antimicrobial peptides' binding against the target-putative nucleic acid binding lipoprotein and confirm stable binding. One specific antimicrobial peptide with the sequence "MPPYLHEIQPHTASNCQTELVIKL" showed promising results with 53% hydrophobic residues and a net charge +2.5, significant for the development of antimicrobial peptides. The said peptide also showed promising interactions with the target protein and expressed stable binding with docking energy of -429.34 kcal/mol and the average root mean square deviation of 1 A0. The study is a novel approach focusing on tapping out potential antimicrobial peptides to be developed against most resistant bacterial species.}, }
@article {pmid33781869, year = {2021}, author = {Yu, S and Xiong, Y and Fu, Y and Chen, G and Zhu, H and Mo, X and Wu, D and Xu, J}, title = {Shotgun metagenomics reveals significant gut microbiome features in different grades of acute pancreatitis.}, journal = {Microbial pathogenesis}, volume = {154}, number = {}, pages = {104849}, doi = {10.1016/j.micpath.2021.104849}, pmid = {33781869}, issn = {1096-1208}, mesh = {Acute Disease ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Pancreatitis ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) has a broad spectrum of severity and is associated with considerable morbidity and mortality. Dysbiosis of gut microbiota may be associated with AP severity.<br><br>AIMS: We aimed to evaluate the composition and functional effects of gut microbiota in different grades of AP severity.<br><br>METHODS: We carried out shotgun metagenomic sequencing on rectal swab samples from three patients with mild acute pancreatitis (MAP), three with moderately severe acute pancreatitis (MSAP), three with severe acute pancreatitis (SAP) and three normal control persons (NOR). Differences analysis in gut microbiota composition and functional enrichment was performed.<br><br>RESULTS: Gut microbiota in AP patients was characterized by decreased species richness. The most representative gut microbiota in mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP), and severe acute pancreatitis (SAP) was Streptococcus, Escherichia-coli, and Enterococcus, respectively. Each of the three AP-associated genera could differentiate AP from healthy control population. Representative pathways associated with the glutathione metabolism, lipopolysaccharide biosynthesis, and amino acid metabolism (valine, leucine and isoleucine degradation) were enriched in MAP, MSAP, and SAP, respectively.<br><br>CONCLUSIONS: The study shows a potential association of gut microbiome composition and function to the progression of AP severity.}, }
@article {pmid33781324, year = {2021}, author = {Snipen, L and Angell, IL and Rognes, T and Rudi, K}, title = {Reduced metagenome sequencing for strain-resolution taxonomic profiles.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {79}, pmid = {33781324}, issn = {2049-2618}, mesh = {Humans ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data.<br><br>RESULTS: We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time.<br><br>CONCLUSION: We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.}, }
@article {pmid33780842, year = {2021}, author = {Jiang, X and Liu, W and Xu, H and Cui, X and Li, J and Chen, J and Zheng, B}, title = {Characterizations of heavy metal contamination, microbial community, and resistance genes in a tailing of the largest copper mine in China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {280}, number = {}, pages = {116947}, doi = {10.1016/j.envpol.2021.116947}, pmid = {33780842}, issn = {1873-6424}, mesh = {China ; Copper ; Environmental Monitoring ; *Metals, Heavy/analysis ; *Microbiota ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Copper mine tailings are causing great environmental concern nowadays due to their high contents of heavy metals. These hazards may release to air, water, and soil, posing great threat to the living organisms in the surroundings. In the present work, we profiled the heavy metal contents, microbiome and resistome of a mine tailing in Dexing Copper Mine, which is the largest open-pit copper mine in China. A total of 39.75 Gb clean data was generated by metagenomics sequencing and taxonomy analysis revealed Actinobacteria, Proteobacteria, Acidobacteria, Euryarchaeota, and Nitrospirae as the most abundant phylum in this tailing. In general, 76 heavy metal resistance genes (HMRGs) and 194 antimicrobial resistance genes (ARGs) were identified with merA and rpoB2 as the most abundant HMRG and ARG, respectively. We also compared the differences of heavy metal concentrations among the six sampling sites in the same tailing and found that significant differences exited in copper and zinc. Hierarchical cluster analysis showed that the samples from the six sampling sites were clustering in two groups based on heavy metal concentrations. Accordingly, clustering based on microbial composition and relative abundances of resistance genes exhibited the same clustering pattern, indicating a possible shaping influence of heavy metals on the microbiome and resistome in this tailing. Our work presented heavy metal contents, microbial composition and resistance genes in a copper mine tailing of the largest copper mine in China, and these data will of great use in the surveillance, maintenance, and remediation of this tailing.}, }
@article {pmid33775256, year = {2021}, author = {Zhao, Y and Federico, A and Faits, T and Manimaran, S and Segrè, D and Monti, S and Johnson, WE}, title = {animalcules: interactive microbiome analytics and visualization in R.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {76}, pmid = {33775256}, issn = {2049-2618}, support = {R01 GM127430/GM/NIGMS NIH HHS/United States ; U01 CA220413/CA/NCI NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data.<br><br>RESULTS: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface.<br><br>CONCLUSIONS: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract.}, }
@article {pmid33775067, year = {2021}, author = {Dunaj, J and Drewnowska, J and Moniuszko-Malinowska, A and Swiecicka, I and Pancewicz, S}, title = {First metagenomic report of Borrelia americana and Borrelia carolinensis in Poland - a preliminary study.}, journal = {Annals of agricultural and environmental medicine : AAEM}, volume = {28}, number = {1}, pages = {49-55}, doi = {10.26444/aaem/118134}, pmid = {33775067}, issn = {1898-2263}, mesh = {Animals ; Dermacentor/*microbiology ; Francisella/classification/genetics/isolation &amp; purification ; Genome, Bacterial ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Poland ; Pseudomonas/classification/isolation &amp; purification ; Sphingomonas/classification/genetics/isolation &amp; purification ; Spirochaetales/classification/*genetics/isolation &amp; purification ; }, abstract = {INTRODUCTION AND OBJECTIVE: Ixodes ricinus (I. ricinus) and Dermacentor reticulatus (D. reticulatus) are the most common ticks in Poland. These ticks contain many bacteria, which compose a microbiome with potential impact on humans. The aim of the study was to discover the microbiome of ticks in Poland.<br><br>MATERIAL AND METHODS: Ticks were collected in The Protected Landscape Area of the Bug and Nurzec Valley, Poland, in 2016-2018 by flagging. They were cleaned in 70% ethanol and damaged in mortar with PBS (without Ca2+ and Mg2+ ions). DNA was extracted from the homogenates with spin columns kits, and used as a matrix in end-point PCR for bacterial 16S rRNA fragments amplifications, and further for next generation sequencing (NGS) by ILLUMINA.<br><br>RESULTS: In 22 ticks (3 I. ricinus and 19 D. reticulatus) 38 microorganisms were detected. The most common were Francisella hispaniensis and Francisella novicida. In 17 ticks, Sphingomonas oligophenolica, and in 12 Rickettsia aeshlimanii were found. In 2, I. ricinus specific DNA of Borrelia americana and Borrelia carolinensis were found. In one female, D. reticulatus Anaplasma phagocytophilum and Anaplasma centrale were found. Pseudomonas lutea and Ps. moraviensis were detected in 9 and 8 ticks, respectively.<br><br>CONCLUSIONS: Polish ticks microbiome contains not only well-known tick-borne pathogens, but also other pathogenic microorganisms. For the first time in Poland, Borrelia americana and Borrelia carolinensis in I. ricinus collected from the environment were detected. The dominant pathogenic microorganisms for humans were Francisella spp. and Rickettsia spp., and non-pathogenic - Sphingomonas oligophenolica. Knowledge of a tick microbiome might be useful in tick-borne biocontrol and tick-borne diseases prevention.}, }
@article {pmid33774727, year = {2021}, author = {Wani, GA and Khan, MA and Dar, MA and Shah, MA and Reshi, ZA}, title = {Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {106}, number = {5}, pages = {727-733}, pmid = {33774727}, issn = {1432-0800}, support = {PDF/20l8/001689//DST-SERB, Govt. of India/ ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; *Water Quality ; }, abstract = {Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologies were used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating the full variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniques for the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.}, }
@article {pmid33773355, year = {2021}, author = {Li, H and Fu, J and Hu, S and Li, Z and Qu, J and Wu, Z and Chen, S}, title = {Comparison of the effects of acetic acid bacteria and lactic acid bacteria on the microbial diversity of and the functional pathways in dough as revealed by high-throughput metagenomics sequencing.}, journal = {International journal of food microbiology}, volume = {346}, number = {}, pages = {109168}, doi = {10.1016/j.ijfoodmicro.2021.109168}, pmid = {33773355}, issn = {1879-3460}, mesh = {Acetic Acid/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Bread/*microbiology ; Fermentation ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Lactobacillales/classification/genetics/*isolation &amp; purification/metabolism ; Metagenomics ; Triticum/metabolism/microbiology ; Yeasts/classification/genetics/isolation &amp; purification ; }, abstract = {Knowledge of the effects of various strains of acetic acid bacteria (AAB) on sourdough remains limited. In this study, the diversity of microbial taxa in sourdoughs fermented by different starters was assessed and their functional capacity was evaluated via high-throughput metagenomics sequencing. Results showed that Erwinia (29.43%), Pantoea (45.89%), and Enterobacter (9.16%) were predominant in the blank CK treatment. Lactobacillus (91.40%), Saccharomyces (6.13%), as well as the AAB genus Acetobacter (0.61%) were the dominant microbial genera in the sourdoughs started by yeast and a strain of lactic acid bacteria (YL treatment). By contrast, the dominant genera in the sourdoughs started by yeasts and various LAB and AAB strains (YLA treatment) were Komagataeibacter (0.39%) except for the inoculated Lactobacillus (68.37%), Acetobacter (20.17%), and Saccharomyces (8.31%) species. Functional prediction of these changes in microbial community and diversity revealed that various metabolism-related pathways, including alanine, aspartate, and glutamate metabolism (21.95%), as well as amino acid biosynthesis (19.14%), were predominant in the sourdoughs started by yeast and an AAB strain (YA treatment). Moreover, arginine biosynthesis (11.65%) were the dominant pathways in the YL treatment. The fermented dough added with sourdoughs started with yeast + AAB and yeast + AAB + LAB strains had substantially higher contents (more than 48.58% in total) of essential amino acids than the dough added with sourdoughs started with yeast + LAB strain. These results demonstrated that amino acid biosynthesis has a beneficial effect on sourdoughs inoculated with an AAB strain.}, }
@article {pmid33766942, year = {2021}, author = {Levin, D and Raab, N and Pinto, Y and Rothschild, D and Zanir, G and Godneva, A and Mellul, N and Futorian, D and Gal, D and Leviatan, S and Zeevi, D and Bachelet, I and Segal, E}, title = {Diversity and functional landscapes in the microbiota of animals in the wild.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6539}, pages = {}, doi = {10.1126/science.abb5352}, pmid = {33766942}, issn = {1095-9203}, mesh = {Animals ; Animals, Wild/classification/*microbiology/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Toxins/metabolism ; Behavior, Animal ; Biodiversity ; Databases, Nucleic Acid ; Diet ; Ecosystem ; Falkland Islands ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Host Microbial Interactions ; Israel ; Madagascar ; *Metagenome ; Metagenomics ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; Queensland ; Uganda ; }, abstract = {Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.}, }
@article {pmid33746944, year = {2021}, author = {Berlinberg, AJ and Regner, EH and Stahly, A and Brar, A and Reisz, JA and Gerich, ME and Fennimore, BP and Scott, FI and Freeman, AE and Kuhn, KA}, title = {Multi 'Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {587119}, pmid = {33746944}, issn = {1664-3224}, support = {R01 AR075033/AR/NIAMS NIH HHS/United States ; T32 AR007534/AR/NIAMS NIH HHS/United States ; U01 AI130830/AI/NIAID NIH HHS/United States ; }, mesh = {Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; Dysbiosis ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Humans ; *Intestines ; Metabolic Networks and Pathways ; *Metabolomics ; *Metagenomics/methods ; Spondylitis, Ankylosing/*etiology/pathology ; Tryptophan/*metabolism ; }, abstract = {Intestinal microbial dysbiosis, intestinal inflammation, and Th17 immunity are all linked to the pathophysiology of spondyloarthritis (SpA); however, the mechanisms linking them remain unknown. One potential hypothesis suggests that the dysbiotic gut microbiome as a whole produces metabolites that influence human immune cells. To identify potential disease-relevant, microbiome-produced metabolites, we performed metabolomics screening and shotgun metagenomics on paired colon biopsies and fecal samples, respectively, from subjects with axial SpA (axSpA, N=21), Crohn's disease (CD, N=27), and Crohn's-axSpA overlap (CD-axSpA, N=12), as well as controls (HC, N=24). Using LC-MS based metabolomics of 4 non-inflamed pinch biopsies of the distal colon from subjects, we identified significant alterations in tryptophan pathway metabolites, including an expansion of indole-3-acetate (IAA) in axSpA and CD-axSpA compared to HC and CD and indole-3-acetaldehyde (I3Ald) in axSpA and CD-axSpA but not CD compared to HC, suggesting possible specificity to the development of axSpA. We then performed shotgun metagenomics of fecal samples to characterize gut microbial dysbiosis across these disease states. In spite of no significant differences in alpha-diversity among the 4 groups, our results confirmed differences in gene abundances of numerous enzymes involved in tryptophan metabolism. Specifically, gene abundance of indolepyruvate decarboxylase, which generates IAA and I3Ald, was significantly elevated in individuals with axSpA while gene abundances in HC demonstrated a propensity towards tryptophan synthesis. Such genetic changes were not observed in CD, again suggesting disease specificity for axSpA. Given the emerging role of tryptophan and its metabolites in immune function, altogether these data indicate that tryptophan metabolism into I3Ald and then IAA is one mechanism by which the gut microbiome potentially influences the development of axSpA.}, }
@article {pmid33741611, year = {2021}, author = {Palermo, CN and Shea, DW and Short, SM}, title = {Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {11}, pages = {}, pmid = {33741611}, issn = {1098-5336}, mesh = {Lakes/*virology ; Metagenome ; Ontario ; *Virome ; Viruses/classification/*isolation &amp; purification ; }, abstract = {Inspired by recent discoveries of the prevalence of large viruses in the environment, we reassessed the longstanding approach of filtering water through small-pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 data sets derived from <0.45-μm- and >0.45-μm-size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family, we observed highly diverse and distinct virus communities in the >0.45-μm-size fractions, whereas the <0.45-μm-size fractions were composed primarily of Caudovirales The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions, with higher relative abundances of cyanophages in the >0.45-μm-size fractions, potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, were detected exclusively in the often-disregarded >0.45-μm-size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions, suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of double-stranded DNA (dsDNA) viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing.IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller-size "free-virus" fraction. Our study demonstrates that analysis of virus communities using only the smaller-size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger->0.45-μm-size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data show that examining only the smaller-size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.}, }
@article {pmid33736375, year = {2021}, author = {Macedo, G and van Veelen, HPJ and Hernandez-Leal, L and van der Maas, P and Heederik, D and Mevius, D and Bossers, A and Schmitt, H}, title = {Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application.}, journal = {The Science of the total environment}, volume = {770}, number = {}, pages = {145399}, doi = {10.1016/j.scitotenv.2021.145399}, pmid = {33736375}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; *Manure ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; }, abstract = {Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.}, }
@article {pmid33724519, year = {2021}, author = {Kang, WN and Jin, L and Fu, KY and Guo, WC and Li, GQ}, title = {A switch of microbial flora coupled with ontogenetic niche shift in Leptinotarsa decemlineata.}, journal = {Archives of insect biochemistry and physiology}, volume = {107}, number = {1}, pages = {e21782}, doi = {10.1002/arch.21782}, pmid = {33724519}, issn = {1520-6327}, support = {32072416//The National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification ; Coleoptera/*microbiology/physiology ; Ecosystem ; Genes, Bacterial ; Larva/microbiology/physiology ; Metagenomics/methods ; Metamorphosis, Biological ; *Microbiota/genetics ; Pupa/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In Leptinotarsa decemlineata, a final-instar wandering larva typically undergoes an ontogenetic niche shift (ONS), from potato plant during the foraging stage to its pupation site below ground. Using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we determined the hypothesis that the L. decemlineata pupae harbor stage-specific bacteria to meet the physiological requirements for underground habitat. We identified 34 bacterial phyla, comprising 73 classes, 208 orders, 375 families, and 766 genera in the collected specimens. Microbes across phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were enriched in the pupae, while those in the phylum Proteobacteria, Tenericutes, Firmicutes, and Bacteroidetes dominated in the larvae and adults. A total of 18 genera, including Blastococcus, Corynebacterium_1, Gordonia, Microbacterium, Nocardia, Nocardioides, Rhodococcus, Solirubrobacter, Tsukamurella, Enterococcus, Acinetobacter, Escherichia_Shigella, Lysobacter, Pseudomonas, and Stenotrophomonas, were specifically distributed in pupae. Moreover, soil sterilizing removed a major portion of bacteria in pupae. Specifically, both Enterococcus and Pseudomonas were eliminated in the soil sterilizing and antibiotic-fed beetle groups. Furthermore, the pupation rate and fresh pupal weight were similar, whereas the emergence rate and adult weight were decreased in the antibiotic-fed beetles, compared with controls. The results demonstrate that a switch of bacterial communities occurs in the pupae; the pupal-specific bacteria genera are mainly originated from soil; this bacterial biodiversity improves pupa performance in soil. Our results provide new insight into the evolutionary fitness of L. decemlineata to different environmental niches.}, }
@article {pmid33717447, year = {2021}, author = {Meucci, S and Schulte, L and Zimmermann, HH and Stoof-Leichsenring, KR and Epp, L and Bronken Eidesen, P and Herzschuh, U}, title = {Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses.}, journal = {Ecology and evolution}, volume = {11}, number = {5}, pages = {2173-2193}, pmid = {33717447}, issn = {2045-7758}, abstract = {Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.}, }
@article {pmid33714730, year = {2021}, author = {Zhang, X and Yang, Y and Zhang, F and Yu, J and Sun, W and Wang, R and Wu, C}, title = {Traditional Chinese medicines differentially modulate the gut microbiota based on their nature (Yao-Xing).}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {85}, number = {}, pages = {153496}, doi = {10.1016/j.phymed.2021.153496}, pmid = {33714730}, issn = {1618-095X}, mesh = {Animals ; Drugs, Chinese Herbal/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Male ; Medicine, Chinese Traditional ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Property theory is a unique principle guiding traditional Chinese medicine (TCM) that classifies various TCMs into four natures (hot, warm, cool, and cold) to reflect their medical actions on the human body. Despite successful application for thousands of years, characterizing the nature of medical TCMs by modern physiological indicators remains a challenge.<br><br>PURPOSE: In this study, we investigated the potential relationship between the nature of TCMs and their modulation of the gut microbiota.<br><br>STUDY DESIGN: We selected twelve TCMs with hot, warm, cool, or cold natures that possess antidiarrheal effects. Their aqueous extracts were orally administered to C57BL/6 mice at a clinical dose for 4 weeks. The gut microbiota was measured by 16S rRNA-based metagenomics, and the correlation between microbial composition/function and TCM nature was analyzed.<br><br>RESULTS: Antidiarrheal TCMs with different natures showed distinct impacts on the gut microbiota. Hot-natured TCMs had no influence on the gut microbiota, warm-natured TCMs had a moderate influence, cool-natured TCMs had a strong influence, and cold-natured TCMs substantially changed the structure of the gut microbial community. The abundance of Anaerotruncus, Tyzzerella and Ruminiclostridium steadily increased, while that of Ruminococcaceae_UCG-010, Parasutterella and Bifidobacterium continuously decreased as the herbal nature turned from cold to hot. Microbiome functional prediction for Cluster of Orthologous Groups (COG) of proteins and Kyoto Encyclopedia of Genes and Genomes (KEGG) categories showed that colder TCMs imposed a stronger influence on microbial functional repertoires. Specifically, the abundance of ABC transporters, key bacterial proteins involved in nutrient absorption and drug resistance, was gradually decreased by colder TCMs.<br><br>CONCLUSION: Our results demonstrated that the nature of TCMs could be reflected by their modulation of gut microbes. Cold TCMs may exert their antidiarrheal effects, at least partially, by modulating the gut microbiota, while hot TCMs may alleviate dysentery in other ways.}, }
@article {pmid33713107, year = {2021}, author = {Kim, J and Jiang, S and Wang, Y and Xiao, G and Xie, Y and Liu, DJ and Li, Q and Koh, A and Zhan, X}, title = {MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data.}, journal = {G3 (Bethesda, Md.)}, volume = {11}, number = {4}, pages = {}, pmid = {33713107}, issn = {2160-1836}, support = {R01 GM126479/GM/NIGMS NIH HHS/United States ; R01 HG008983/HG/NHGRI NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; R01 GM115473/GM/NIGMS NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; P50 CA070907/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {In microbiome research, metagenomic sequencing generates enormous amounts of data. These data are typically classified into taxa for taxonomy analysis, or into genes for functional analysis. However, a joint analysis where the reads are classified into taxa-specific genes is often overlooked. To enable the analysis of this biologically meaningful feature, we developed a novel bioinformatic toolkit, MetaPrism, which can analyze sequence reads for a set of joint taxa/gene analyses to: 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) compare the abundances between groups; and 4) build prediction models for clinical outcome. We illustrated these functions using a published microbiome metagenomics dataset from patients treated with immune checkpoint inhibitor therapy and showed the joint features can serve as potential biomarkers to predict therapeutic responses. MetaPrism is a toolkit for joint taxa and gene analysis. It offers biological insights on the taxa-specific genes on top of the taxa-alone or gene-alone analysis. MetaPrism is open-source software and freely available at https://github.com/jiwoongbio/MetaPrism. The example script to reproduce the manuscript is also provided in the above code repository.}, }
@article {pmid33708211, year = {2021}, author = {Shen, S and Prame Kumar, K and Wen, SW and Shim, R and Wanrooy, BJ and Stanley, D and Moore, RJ and Van, TTH and Robert, R and Hickey, MJ and Wong, CHY}, title = {Deficiency of Dietary Fiber Modulates Gut Microbiota Composition, Neutrophil Recruitment and Worsens Experimental Colitis.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {619366}, pmid = {33708211}, issn = {1664-3224}, mesh = {Animals ; Biomarkers ; Cell Adhesion ; Chemotaxis, Leukocyte/*immunology ; Colitis/*etiology/metabolism/pathology ; Dextran Sulfate/adverse effects ; Diet ; Dietary Fiber/*deficiency ; Disease Models, Animal ; Endothelial Cells ; *Gastrointestinal Microbiome ; Leukocyte Count ; Male ; Metagenomics/methods ; Mice ; Neutrophil Infiltration/*immunology ; RNA, Ribosomal, 16S ; }, abstract = {Ulcerative colitis is an inflammatory disease of the colon that is associated with colonic neutrophil accumulation. Recent evidence indicates that diet alters the composition of the gut microbiota and influences host-pathogen interactions. Specifically, bacterial fermentation of dietary fiber produces metabolites called short-chain fatty acids (SCFAs), which have been shown to protect against various inflammatory diseases. However, the effect of fiber deficiency on the key initial steps of inflammation, such as leukocyte-endothelial cell interactions, is unknown. Moreover, the impact of fiber deficiency on neutrophil recruitment under basal conditions and during inflammation in vivo is unknown. Herein, we hypothesized that a fiber-deficient diet promotes an inflammatory state in the colon at baseline and predisposes the host to more severe colitis pathology. Mice fed a no-fiber diet for 14 days showed significant changes in the gut microbiota and exhibited increased neutrophil-endothelial interactions in the colonic microvasculature. Although mice fed a no-fiber diet alone did not have observable colitis-associated symptoms, these animals were highly susceptible to low dose (0.5%) dextran sodium sulphate (DSS)-induced model of colitis. Supplementation of the most abundant SCFA, acetate, prevented no-fiber diet-mediated enrichment of colonic neutrophils and colitis pathology. Therefore, dietary fiber, possibly through the actions of acetate, plays an important role in regulating neutrophil recruitment and host protection against inflammatory colonic damage in an experimental model of colitis.}, }
@article {pmid33706240, year = {2021}, author = {DeBofsky, A and Xie, Y and Challis, JK and Jain, N and Brinkmann, M and Jones, PD and Giesy, JP}, title = {Responses of juvenile fathead minnow (Pimephales promelas) gut microbiome to a chronic dietary exposure of benzo[a]pyrene.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {278}, number = {}, pages = {116821}, doi = {10.1016/j.envpol.2021.116821}, pmid = {33706240}, issn = {1873-6424}, mesh = {Animals ; Benzo(a)pyrene/toxicity ; *Cyprinidae ; Dietary Exposure ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The microbiome has been described as an additional host "organ" with well-established beneficial roles. However, the effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. To determine effects of benzo[a]pyrene (BaP), a model persistent organic pollutant, on structural shifts of gut microbiome in juvenile fathead minnows (Pimephales promelas), fish were exposed ad libitum in the diet to concentrations of 1, 10, 100, or 1000 μg BaP g-1 food, in addition to a vehicle control, for two weeks. To determine the link between exposure to BaP and changes in the microbial community, concentrations of metabolites of BaP were measured in fish bile and 16S rRNA amplicon sequencing was used to evaluate the microbiome. Exposure to BaP only reduced alpha-diversity at the greatest exposure concentrations. However, it did alter community composition assessed as differential abundance of taxa and reduced network complexity of the microbial community in all exposure groups. Results presented here illustrate that environmentally-relevant concentrations of BaP can alter the diversity of the gut microbiome and community network connectivity.}, }
@article {pmid33705534, year = {2021}, author = {Lim, SJ and Davis, B and Gill, D and Swetenburg, J and Anderson, LC and Engel, AS and Campbell, BJ}, title = {Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab042}, pmid = {33705534}, issn = {1574-6941}, mesh = {Animals ; Bacteria ; *Bivalvia ; Gills ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes and their environment.}, }
@article {pmid33689954, year = {2021}, author = {Hitch, TCA and Afrizal, A and Riedel, T and Kioukis, A and Haller, D and Lagkouvardos, I and Overmann, J and Clavel, T}, title = {Recent advances in culture-based gut microbiome research.}, journal = {International journal of medical microbiology : IJMM}, volume = {311}, number = {3}, pages = {151485}, doi = {10.1016/j.ijmm.2021.151485}, pmid = {33689954}, issn = {1618-0607}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Gut microbes affect the physiology of their hosts. Studying their diversity and functions is thus of utmost importance as it will open new avenues towards the discovery of new biomolecules and the treatment of diseases. Gut microbiome research is currently boosted by the unification of metagenomics, which has dominated the field in the last two decades, and cultivation, which is experiencing a renaissance. Each of these approaches has advantages and drawbacks that can be overcome if used synergistically. In this brief article, we summarize recent literature and own studies on the cultivation of gut microbes, provide a succinct status quo of cultured fractions and collections of isolates, and give short opinions on challenges and next steps to take.}, }
@article {pmid33689953, year = {2021}, author = {Podlesny, D and Fricke, WF}, title = {Strain inheritance and neonatal gut microbiota development: A meta-analysis.}, journal = {International journal of medical microbiology : IJMM}, volume = {311}, number = {3}, pages = {151483}, doi = {10.1016/j.ijmm.2021.151483}, pmid = {33689953}, issn = {1618-0607}, mesh = {Adolescent ; Adult ; Cesarean Section ; Child ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Metagenome ; *Microbiota ; Pregnancy ; }, abstract = {As many inflammatory and metabolic disorders have been associated with structural deficits of the human gut microbiota, the principles and mechanisms that govern its initialization and development are of considerable scientific interest and clinical relevance. However, our current understanding of the developing gut microbiota dynamics remains incomplete. We carried out a large-scale, comprehensive meta-analysis of over 1900 available metagenomic shotgun samples from neonates, infants, adolescents, and their families, using our recently introduced SameStr program for strain-level microbiota profiling and the detection of microbial strain transfer and persistence. We found robust associations between fecal microbiota composition and age, as well as delivery mode, which was measurable for up to two years of life. C-section was associated with increased relative abundances of non-gut species and delayed transition from a predominantly oxygen-tolerant to intolerant microbial community. Unsupervised networks based on shared strain profiles generated family-specific clusters connecting infants, their siblings, parents and grandparents and, in one case, suggested strain transfer between neonates from the same hospital ward, but could also be used to identify potentially mislabeled metagenome samples. Vaginally delivered newborns shared more strains with their mothers than C-section infants, but strain sharing was reduced if mothers underwent antibiotic treatment. Shared strains persisted in infants throughout the first year of life and belonged to the same bacterial species as strains that were shared between adults and their parents. Irrespective of delivery type, older children shared strains with their mothers and fathers and, into adulthood, could be accurately distinguished from unrelated sample pairs. Prominent fecal commensal bacteria were both among frequently transferred (e.g. Bacteroides and Sutterella) and newly acquired taxa (e.g. Blautia, Faecalibacterium, and Ruminococcus). Our meta-analysis presents a more detailed and comprehensive picture of the highly dynamic neonatal and infant fecal microbiota development than previous studies and presents evidence for taxonomic and functional compositional differences early in life between infants born naturally or by C-section, which persist well into adolescence.}, }
@article {pmid33685682, year = {2021}, author = {Choi, Y and Park, E and Kim, S and Ha, J and Oh, H and Kim, Y and Lee, Y and Seo, Y and Kang, J and Lee, S and Lee, H and Yoon, Y and Choi, KH}, title = {Fermented milk with Lactobacillus curvatus SMFM2016-NK alleviates periodontal and gut inflammation, and alters oral and gut microbiota.}, journal = {Journal of dairy science}, volume = {104}, number = {5}, pages = {5197-5207}, doi = {10.3168/jds.2020-19625}, pmid = {33685682}, issn = {1525-3198}, mesh = {Animals ; *Gastrointestinal Microbiome ; Inflammation/veterinary ; Lactobacillus ; Milk ; *Probiotics ; Rats ; *Rodent Diseases ; }, abstract = {This study aimed to analyze the effect of milk fermented with Lactobacillus curvatus SMFM2016-NK on periodontal diseases and gut health in a rat model. To improve the effect of Lb. curvatus SMFM2016-NK-fermented milk administration for relieving periodontitis, the periodontitis rat models were treated with the following for 4 wk: 10% skim milk (normal), periodontitis + 10% skim milk (negative control), periodontitis + Lactobacillus rhamnosus GG-fermented milk (positive control), and periodontitis + Lb. curvatus SMFM2016-NK-fermented milk (PD+LCFM). Transcriptional analysis of inflammatory cytokines [tumor necrosis factor α (TNF-α), IL-1β, IL-6, and IL-10] was performed via quantitative reverse-transcription PCR. The changes in the oral and gut microbiomes after administering Lb. curvatus SMFM2016-NK-fermented milk were analyzed with metagenomics sequencing using DNA extracted from the oral gingival tissues and feces from the cecum of the rat models. After treatment with Lb. curvatus SMFM2016-NK-fermented milk, the relative gene expression levels of TNFA and IL1B in the gingiva decreased in the PD+LCFM group compared with those in the negative control group. In the oral microbiome, the proportion of the phylum Proteobacteria in the PD+LCFM group was lower than that in the negative control after treatment with Lb. curvatus SMFM2016-NK-fermented milk. For the effect in the gut, the relative gene expression levels of inflammatory cytokines in the colon between the normal and negative control groups were not different; however, the expression levels of TNFA and IL1B in the PD+LCFM and positive control groups, respectively, were lower than those in the negative control group. The composition and diversity of the gut microbiome differed among normal, periodontitis, and Lb. curvatus SMFM2016-NK-fermented milk treatment groups. These results indicate that Lb. curvatus SMFM2016-NK-fermented milk could alleviate periodontal and gut inflammation and change oral and gut microbiota.}, }
@article {pmid33683127, year = {2021}, author = {Mehta, S and Kumar, P and Crane, M and Johnson, JE and Sajulga, R and Nguyen, DDA and McGowan, T and Arntzen, MØ and Griffin, TJ and Jagtap, PD}, title = {Updates on metaQuantome Software for Quantitative Metaproteomics.}, journal = {Journal of proteome research}, volume = {20}, number = {4}, pages = {2130-2137}, doi = {10.1021/acs.jproteome.0c00960}, pmid = {33683127}, issn = {1535-3907}, mesh = {Mass Spectrometry ; Metagenomics ; *Microbiota ; *Proteomics ; Software ; }, abstract = {metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.}, }
@article {pmid33681975, year = {2021}, author = {Keller, AG and Apprill, A and Lebaron, P and Robbins, J and Romano, TA and Overton, E and Rong, Y and Yuan, R and Pollara, S and Whalen, KE}, title = {Characterizing the culturable surface microbiomes of diverse marine animals.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, pmid = {33681975}, issn = {1574-6941}, support = {R21 AI119311/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.}, }
@article {pmid33680988, year = {2021}, author = {Wang, L and Yu, X and Xu, X and Ming, J and Wang, Z and Gao, B and Xing, Y and Zhou, J and Fu, J and Liu, T and Liu, X and Garstka, MA and Wang, X and Ji, Q}, title = {The Fecal Microbiota Is Already Altered in Normoglycemic Individuals Who Go on to Have Type 2 Diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {598672}, pmid = {33680988}, issn = {2235-2988}, mesh = {Case-Control Studies ; Clostridiales ; *Diabetes Mellitus, Type 2 ; Humans ; *Microbiota ; Porphyromonas ; Veillonella ; }, abstract = {Objective: Mounting evidence has suggested a link between gut microbiome characteristics and type 2 diabetes (T2D). To determine whether these alterations occur before the impairment of glucose regulation, we characterize gut microbiota in normoglycemic individuals who go on to develop T2D.<br><br>Methods: We designed a nested case-control study, and enrolled individuals with a similar living environment. A total of 341 normoglycemic individuals were followed for 4 years, including 30 who developed T2D, 33 who developed prediabetes, and their matched controls. Fecal samples (developed T2D, developed prediabetes and controls: n=30, 33, and 63, respectively) collected at baseline underwent metagenomics sequencing.<br><br>Results: Compared with matched controls, individuals who went on to develop T2D had lower abundances of Bifidobacterium longum, Coprobacillus unclassified, and Veillonella dispar and higher abundances of Roseburia hominis, Porphyromonas bennonis, and Paraprevotella unclassified. The abundance of Bifidobacterium longum was negatively correlated with follow-up blood glucose levels. Moreover, the microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of carbohydrate metabolism, methane metabolism, amino acid metabolism, fatty acid metabolism, and membrane transport were changed between the two groups.<br><br>Conclusions: We found that fecal microbiota of healthy individuals who go on to develop T2D had already changed when they still were normoglycemic. These alterations of fecal microbiota might provide insights into the development of T2D and a new perspective for identifying individuals at risk of developing T2D.}, }
@article {pmid33675403, year = {2021}, author = {Arumugam, M and Sundararaju, S and Jagadesan, S and Gunasekaran, P and Rajendhran, J}, title = {Metagenomic Analysis of Microbial Community Affiliated with Termitarium Reveals High Lignocellulolytic Potential.}, journal = {Current microbiology}, volume = {78}, number = {4}, pages = {1551-1565}, pmid = {33675403}, issn = {1432-0991}, support = {No.012/RUSA/MKU/2020-2021//MKU-RUSA/ ; }, mesh = {Bacteria/genetics ; Bacteroidetes/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Termitarium (nest of termites) is a rich source of microbial populations whose resources remain untapped to date. Using the metagenomic sequencing approach, we generated 38 GB sequences comprising 808,386 contigs (896 MB) with a maximum contig size of 470 kb. The taxonomic profile obtained by BLAST against the NCBI NR database and annotation by MEGAN showed that the termitarium microbial community was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Functional annotation using the CAZY database revealed a huge diversity of glycosyl hydrolase genes from 104 families, some of which appeared to be part of polysaccharide utilization systems (PUL). Strikingly, Actinobacteria was the main contributor of the cellulolytic and hemicellulolytic GHs. Genes involving in lignin degradation were also abundantly identified in this metagenome. Comparative analysis of COG profiles of termitarium with those of other lignocellulolytic microbial communities showed a distant clustering pattern resulting from the dietary differences in carbohydrate compositions. Altogether, this study revealed that termitarium hosts a unique microbial community, which can efficiently degrade lignocelluloses.}, }
@article {pmid33672887, year = {2021}, author = {Gao, B and Zhang, X and Schnabl, B}, title = {Fungi-Bacteria Correlation in Alcoholic Hepatitis Patients.}, journal = {Toxins}, volume = {13}, number = {2}, pages = {}, pmid = {33672887}, issn = {2072-6651}, support = {R01 AA24726, R01AA020703, U01 AA026939/NH/NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/*genetics/growth &amp; development/metabolism ; Case-Control Studies ; Dysbiosis ; Feces/microbiology ; Female ; Fungi/*genetics/growth &amp; development/metabolism ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Hepatitis, Alcoholic/diagnosis/*microbiology ; Humans ; Intestines/*microbiology ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Ribotyping ; }, abstract = {Alcohol-related liver disease is one of the most prevalent types of chronic liver diseases globally. Alcohol-related liver disease begins with fatty liver, which further develops into hepatic inflammation, hepatocyte injury, and progresses to fibrosis and cirrhosis. Compositional changes of gut bacteria and fungi were found in patients with alcohol-related liver disease. However, the functional changes of fungi and correlations between fungi and bacteria have not been investigated. In this study, we first examined the functional capacity of fungi in patients with alcohol-related liver disease using shotgun metagenomics. Among 24 MetaCyc pathways contributed by fungi, superpathway of allantoin degradation in yeast was enriched in patients with alcoholic hepatitis. Furthermore, we compared the predictive power of bacteria versus fungi and found that bacteria performed better than fungi to separate patients with alcoholic hepatitis from non-alcoholic controls and patients with alcohol use disorder. Finally, we investigated the associations between the intestinal fungi and bacteria in alcoholic hepatitis patients. Positive association between fungi and bacteria was found between Cladosporium and Gemmiger, meanwhile negative association was found between Cryptococcus and Pseudomonas in alcoholic hepatitis patients.}, }
@article {pmid33669932, year = {2021}, author = {Pane, S and Sacco, A and Iorio, A and Romani, L and Putignani, L}, title = {Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, pmid = {33669932}, issn = {1422-0067}, support = {Ricerca Corrente 201905_ Genetica_Putignani and 202005_ Genetica_Putignani//Italian Ministry of Health/ ; }, mesh = {Animals ; Biodiversity ; Child ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; Principal Component Analysis ; Strongyloides stercoralis/genetics/isolation &amp; purification/*physiology ; Strongyloidiasis/metabolism/*microbiology/*parasitology ; }, abstract = {Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples' ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.}, }
@article {pmid33663163, year = {2021}, author = {Zhao, CZ and Chen, Z and Li, MY}, title = {[Research progress of polymicrobial synergy and dysbiosis in periodontitis].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {56}, number = {3}, pages = {301-305}, doi = {10.3760/cma.j.cn112144-20200429-00239}, pmid = {33663163}, issn = {1002-0098}, support = {81400501//National Natural Science Foundation of China/ ; 2021YFH0188//Science and Technology Planning Project of Sichuan Province of China/ ; }, mesh = {Dysbiosis ; Humans ; *Microbiota ; *Periodontitis ; }, abstract = {Human oral cavity is colonized by various microbial communities which play an important role in the initiation and progression of periodontitis. However, it is still not clear how these microbial communities mediate the disease. With the rise of metagenomics research, polymicrobial synergy and dysbiosis (PSD) model, a new periodontitis pathogenesis mechanism, was proposed. The importance of the microbial communities acting as a whole system in the development of periodontitis is gradually recognized. Host susceptibility, as another key factor in the initiation of the disease, is vital in PSD model. This article reviews the mechanisms of the PSD model and its research progress in periodontitis as well as some other diseases and briefly highlights the positive significance in terms of prevention and treatment of periodontitis in order to provide insights and perspectives for the future periodontal researches.}, }
@article {pmid33661648, year = {2021}, author = {Verschaffelt, P and Van Den Bossche, T and Gabriel, W and Burdukiewicz, M and Soggiu, A and Martens, L and Renard, BY and Schiebenhoefer, H and Mesuere, B}, title = {MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets.}, journal = {Journal of proteome research}, volume = {20}, number = {4}, pages = {2083-2088}, doi = {10.1021/acs.jproteome.0c00926}, pmid = {33661648}, issn = {1535-3907}, mesh = {Computational Biology ; Gene Ontology ; Metagenomics ; *Microbiota ; Semantics ; *Software ; }, abstract = {The study of microbiomes has gained in importance over the past few years and has led to the emergence of the fields of metagenomics, metatranscriptomics, and metaproteomics. While initially focused on the study of biodiversity within these communities, the emphasis has increasingly shifted to the study of (changes in) the complete set of functions available in these communities. A key tool to study this functional complement of a microbiome is Gene Ontology (GO) term analysis. However, comparing large sets of GO terms is not an easy task due to the deeply branched nature of GO, which limits the utility of exact term matching. To solve this problem, we here present MegaGO, a user-friendly tool that relies on semantic similarity between GO terms to compute the functional similarity between multiple data sets. MegaGO is high performing: Each set can contain thousands of GO terms, and results are calculated in a matter of seconds. MegaGO is available as a web application at https://megago.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the MIT license and is available at https://github.com/MEGA-GO/.}, }
@article {pmid33653887, year = {2021}, author = {Yanuka-Golub, K and Dubinsky, V and Korenblum, E and Reshef, L and Ofek-Lalzar, M and Rishpon, J and Gophna, U}, title = {Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33653887}, issn = {2150-7511}, abstract = {Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs' efficiency, especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for shortening startup times and improving MFC performance, making this technology cost-effective and sustainable. Here, we use metagenomics to show that bioaugmentation of the anode surface with a taxonomically defined electroactive consortium, dominated by Desulfuromonas, resulted in an extremely rapid current density generation. Conversely, the untreated anode surface resulted in a highly stochastic and slower biofilm assembly. Remarkably, an efficient anode colonization process was obtained only if wastewater was added, leading to a nearly complete replacement of the bioaugmented community by Geobacter lovleyi Although different approaches to improve MFC startup have been investigated, we propose that only the combination of anode bioaugmentation with wastewater inoculation can reduce stochasticity. Such an approach provides the conditions that support the growth of specific newly arriving species that positively support the fast establishment of a highly functional anode biofilm.IMPORTANCE Mixed microbial communities play important roles in treating wastewater, in producing renewable energy, and in the bioremediation of pollutants in contaminated environments. While these processes are well known, especially the community structure and biodiversity, how to efficiently and robustly manage microbial community assembly remains unknown. Moreover, it has been shown that a high degree of temporal variation in microbial community composition and structure often occurs even under identical environmental conditions. This heterogeneity is directly related to stochastic processes involved in microbial community organization, similarly during the initial stages of biofilm formation on surfaces. In this study, we show that anode surface pretreatment alone is not sufficient for a substantial improvement in startup times in microbial fuel cells (MFCs), as previously thought. Rather, we have discovered that the combination of applying a well-known consortium directly on the anode surface together with wastewater (including the bacteria that they contain) is the optimized management scheme. This allowed a selected colonization process by the wastewater species, which improved the functionality relative to that of untreated systems.}, }
@article {pmid33653268, year = {2021}, author = {Casanova, A and Maroso, F and Blanco, A and Hermida, M and Ríos, N and García, G and Manuzzi, A and Zane, L and Verissimo, A and García-Marín, JL and Bouza, C and Vera, M and Martínez, P}, title = {Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {150}, pmid = {33653268}, issn = {1471-2164}, support = {GRC2014/010//Xunta de Galicia/ ; EAPA_458/2016//Interreg/ ; MPCUdG2016/060//Universitat de Girona/ ; }, mesh = {Animals ; Benchmarking ; Genome ; *Metagenomics ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer's 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control.<br><br>RESULTS: Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons.<br><br>CONCLUSIONS: Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study.}, }
@article {pmid33649957, year = {2021}, author = {Milani, C}, title = {Metagenomic Analyses of Bifidobacterial Communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2278}, number = {}, pages = {183-193}, pmid = {33649957}, issn = {1940-6029}, mesh = {Animals ; Bifidobacterium/classification/*genetics ; Gastrointestinal Microbiome ; Gene Expression Profiling/methods ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.}, }
@article {pmid33649565, year = {2021}, author = {Meyer, F and Lesker, TR and Koslicki, D and Fritz, A and Gurevich, A and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC}, title = {Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.}, journal = {Nature protocols}, volume = {16}, number = {4}, pages = {1785-1801}, pmid = {33649565}, issn = {1750-2799}, mesh = {Animals ; *Benchmarking ; Computer Simulation ; Databases, Genetic ; Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/*methods ; Mice ; Phylogeny ; Reference Standards ; Reproducibility of Results ; *Software ; }, abstract = {Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.}, }
@article {pmid33648263, year = {2021}, author = {Yang, Y and Wang, ST and Lu, ZM and Zhang, XJ and Chai, LJ and Shen, CH and Shi, JS and Xu, ZH}, title = {Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter.}, journal = {Food research international (Ottawa, Ont.)}, volume = {140}, number = {}, pages = {110037}, doi = {10.1016/j.foodres.2020.110037}, pmid = {33648263}, issn = {1873-7145}, mesh = {Alcoholic Beverages/analysis ; Metabolic Networks and Pathways ; *Metagenomics ; *Microbiota/genetics ; Temperature ; }, abstract = {As a widely used Asian starter culture, the quality of daqu can significantly affect the organoleptic characteristics of the final products, yet the microbial metabolic network involved in flavor development remains unclear. This study aims to investigate that network based on the dynamics of physicochemical properties, microbial community, and volatile compounds in medium-temperature daqu (MT-daqu) during spontaneous fermentation. Analyses using the metagenomic data set facilitated the gene repertoire overview of this ecosystem, indicating that Lactobacillales (mainly Weissella, Lactobacillus, and Pediococcus), Mucorales (mainly Lichtheimia), and Eurotiales (mainly Aspergillus, Rasamsonia and Byssochlamys) were the potential predominant populations successively responsible for the production of lytic enzymes and flavor precursors/compounds in MT-daqu. Flavor-relevant pathways were found to exist in multiple species, but only bacteria showed the potential to participate in butane-2,3-diol (e.g. Weissella, Lactobacillus, and Staphylococcus) and butanoate (Thermoactinomyces) metabolism, and only fungi were potentially involved in biosynthesis of guaiacol (Byssochlamys) and 4-vinylguaiacol (Aspergillus). Furthermore, a combined analysis revealed that the acidic thermal environment present in early phases was mainly due to the catabolic activities of Lactobacillales and Lichtheimia, which could contribute to the effective self-domestication of microbiota. The study helps elucidate the different metabolic roles of microorganisms and disclose the formation mechanism of daqu's partial functions, namely providing various aromatic substances/precursors and enzymes.}, }
@article {pmid33639022, year = {2021}, author = {Říhová, J and Batani, G and Rodríguez-Ruano, SM and Martinů, J and Vácha, F and Nováková, E and Hypša, V}, title = {A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice.}, journal = {Molecular ecology}, volume = {30}, number = {9}, pages = {2178-2196}, doi = {10.1111/mec.15866}, pmid = {33639022}, issn = {1365-294X}, mesh = {Animals ; *Anoplura ; *Microbiota/genetics ; Neisseria ; *Neisseriaceae ; Phylogeny ; Symbiosis ; }, abstract = {The phylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have a complex history of symbiont acquisition, loss, and replacement throughout their evolution. These processes have resulted in the establishment of different, phylogenetically distant bacteria as obligate mutualists in different louse groups. By combining metagenomics and amplicon screening across several populations of three louse species (members of the genera Polyplax and Hoplopleura) we describe a novel louse symbiont lineage related to Neisseria and Snodgrassella, and show its independent origin in the two louse genera. While the genomes of these symbionts are highly similar, their respective distributions and status within lice microbiomes indicate that they have different functions and history. In Hoplopleura acanthopus, the Neisseriaceae-related bacterium is a dominant obligate symbiont present across several host populations. In contrast, the Polyplax microbiomes are dominated by the obligate symbiont Legionella polyplacis, with the Neisseriaceae-related bacterium co-occurring only in some samples and with much lower abundance. The results thus support the view that compared to other exclusively blood feeding insects, Anoplura possess a unique capacity to acquire symbionts from diverse groups of bacteria.}, }
@article {pmid33637740, year = {2021}, author = {Goyal, A and Wang, T and Dubinkina, V and Maslov, S}, title = {Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1335}, pmid = {33637740}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology/methods ; *Ecology ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Intestines/*microbiology ; Machine Learning ; Metabolome ; Metabolomics ; Metagenomics ; Models, Biological ; }, abstract = {Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. These metabolites are exchanged via a large network of cross-feeding interactions, and are crucial for predicting the functional state of the microbiome. However, till date, we only have information for a part of this network, limited by experimental throughput. Here, we propose an ecology-based computational method, GutCP, using which we predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. GutCP utilizes a mechanistic model of the gut microbiome with the explicit exchange of metabolites and their effects on the growth of microbial species. To build GutCP, we combine metagenomic and metabolomic measurements from the gut microbiome with optimization techniques from machine learning. Close to 65% of the cross-feeding interactions predicted by GutCP are supported by evidence from genome annotations, which we provide for experimental testing. Our method has the potential to greatly improve existing models of the human gut microbiome, as well as our ability to predict the metabolic profile of the gut.}, }
@article {pmid33623780, year = {2021}, author = {Alzahrani, FM and Al-Amri, A and Shaikh, SS and Muzaheed,  and Alomar, AI and Acharya, S and Aldossary, MA and Hassan, FM}, title = {Direct DNA Sequencing-Based Analysis of Microbiota Associated with Hematological Malignancies in the Eastern Province of Saudi Arabia.}, journal = {BioMed research international}, volume = {2021}, number = {}, pages = {4202019}, pmid = {33623780}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Aged ; *Bacteremia/complications/diagnosis/epidemiology/microbiology ; Bacteria/classification/genetics ; Coinfection/complications/diagnosis/epidemiology/microbiology ; DNA, Bacterial/analysis/genetics ; Female ; Hematologic Neoplasms/*complications ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; Molecular Diagnostic Techniques/*methods ; Saudi Arabia ; Sequence Analysis, DNA/*methods ; Young Adult ; }, abstract = {Introduction: Bloodstream infections (BSI) among patients with hematological malignancies (HM) could predispose them to higher morbidity and mortality for various underlying conditions. Several microorganisms, either pathogenic or opportunistic normal human flora, could cause severe bacteremia and septicemia. While conventional methods have their own limitations, molecular methods such as next-generation sequencing (NGS) can detect these blood infections with more reliability, specificity, and sensitivity, in addition to information on microbial population landscape. Methodology. Blood samples from HM patients (n = 50) and volunteer blood donor control individuals with no HM (n = 50) were subjected to 16S rRNA gene amplification using standard PCR protocols. A metagenomic library was prepared, and NGS was run on a MiSeq (Illumina) sequencer. Sequence reads were analyzed using MiSeq Reporter, and microbial taxa were aligned using the Green Genes library.<br><br>Results: 82% of the patients showed BSI with Gram-negative bacteria as the most predominant group. E. coli comprised a major chunk of the bacterial population (19.51%), followed by K. pneumoniae (17.07%). The CoNS and Viridans Streptococci groups are 17.07% and 14.63%, respectively. Other major species were S. aureus (9.75%), P. aeruginosa (7.31%), A. baumannii (4.87%), E. cloacae (4.87%), and P. mirabilis (4.87%). 34.14% of the cases among patients showed a Gram-positive infection, while 14.63% showed polymicrobial infections.<br><br>Conclusion: Most of the BSI in patients were characterized by polymicrobial infections, unlike the control samples. Molecular methods like NGS showed robust, fast, and specific identification of infectious agents in BSI in HM, indicating the possibility of its application in routine follow-up of such patients for infections.}, }
@article {pmid33618119, year = {2021}, author = {Pu, Y and Pan, J and Yao, Y and Ngan, WY and Yang, Y and Li, M and Habimana, O}, title = {Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {276}, number = {}, pages = {116737}, doi = {10.1016/j.envpol.2021.116737}, pmid = {33618119}, issn = {1873-6424}, mesh = {Biofilms ; *Erythromycin/toxicity ; Metabolomics ; Metagenome ; *Microbiota ; }, abstract = {The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Here, we used a lab-cultured multispecies biofilm model to elucidate the holistic response of a microbial community to erythromycin exposure using metagenomic and metabolomic approaches. Metagenomic analyses revealed that biofilm microbial diversity did not alter following erythromycin exposure. Notably, certain predicted metabolic pathways such as cell-cell communication pathways, amino acid metabolism, and peptidoglycan biosynthesis, mainly by the phyla Actinobacteria, Alpha/Beta-proteobacteria, Bacteroidetes, and Verrucomicrobia, were found to be involved in the maintenance of homeostasis-like balance in the freshwater biofilm. Further untargeted metabolomics data highlighted changes in lipid metabolism and linoleic acid metabolism and their related molecules as a direct consequence of erythromycin exposure. Overall, the study presented a unique picture of how multispecies biofilms respond to single environmental stress exposures. Moreover, the study demonstrated the feasibility of using lab simulated multispecies biofilms for investigating their interaction and reactivity of specific bioactive compounds or pollutants at a fundamental level.}, }
@article {pmid33609137, year = {2021}, author = {L Neal, A and McLaren, T and Lourenço Campolino, M and Hughes, D and Marcos Coelho, A and Gomes de Paula Lana, U and Aparecida Gomes, E and Morais de Sousa, S}, title = {Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab033}, pmid = {33609137}, issn = {1574-6941}, support = {BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Brazil ; Fertilization ; Phosphoric Monoester Hydrolases ; *Phosphorus ; Phylogeny ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.}, }
@article {pmid33608294, year = {2021}, author = {Fortunato, CS and Butterfield, DA and Larson, B and Lawrence-Slavas, N and Algar, CK and Zeigler Allen, L and Holden, JF and Proskurowski, G and Reddington, E and Stewart, LC and Topçuoğlu, BD and Vallino, JJ and Huber, JA}, title = {Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {9}, pages = {}, pmid = {33608294}, issn = {1098-5336}, mesh = {Autotrophic Processes ; Bacteria/genetics ; Bacteriological Techniques/*methods ; Base Sequence ; Hydrothermal Vents/*microbiology ; Metagenome ; Microbiota/*genetics ; Pressure ; RNA, Ribosomal, 16S/genetics ; Seawater ; Ships ; Time Factors ; }, abstract = {Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth's ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.}, }
@article {pmid33606255, year = {2021}, author = {Joseph, TA and Pe'er, I}, title = {An Introduction to Whole-Metagenome Shotgun Sequencing Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2243}, number = {}, pages = {107-122}, pmid = {33606255}, issn = {1940-6029}, mesh = {Archaea/genetics ; Bacteria/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Viruses/genetics ; }, abstract = {Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome-a collection of bacteria, fungi, archaea, and viruses inhabiting an environment--is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.}, }
@article {pmid33604305, year = {2020}, author = {Song, H and Kim, J and Guk, JH and Kim, WH and Nam, H and Suh, JG and Seong, JK and Cho, S}, title = {Metagenomic Analysis of the Gut Microbiota of Wild Mice, a Newly Identified Reservoir of Campylobacter.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {596149}, pmid = {33604305}, issn = {2235-2988}, mesh = {Animals ; Animals, Wild ; *Campylobacter/genetics ; *Campylobacter Infections/veterinary ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics ; Mice ; Multilocus Sequence Typing ; }, abstract = {Campylobacter, the most common etiologic agent of zoonotic gastroenteritis in humans, is present in many reservoirs including livestock animals, wildlife, soil, and water. Previously, we reported a novel Campylobacter jejuni strain SCJK02 (MLST ST-8388) from the gut of wild mice (Micromys minutus) using culture-dependent methods. However, due to fastidious growth conditions and the presence of viable but non-culturable Campylobacter spp., it is unclear whether M. minutus is a Campylobacter reservoir. This study aimed to: 1) determine the distribution and proportion of Campylobacter spp. in the gut microbiota of wild mice using culture-independent methods and 2) investigate the gut microbiota of wild mice and the relationship of Campylobacter spp. with other gut microbes. The gut microbiota of 38 wild mice captured from perilla fields in Korea and without any clinical symptoms (18 M. minutus and 20 Mus musculus) were analyzed. Metagenomic analysis showed that 77.8% (14 of 18) of the captured M. minutus harbored Campylobacter spp. (0.24-32.92%) in the gut metagenome, whereas none of the captured M. musculus carried Campylobacter spp. in their guts. Notably, 75% (6 of 8) of M. minutus determined to be Campylobacter-negative using culture-dependent methods showed a high proportion of Campylobacter through metagenome analysis. The results of metagenome analysis and the absence of clinical symptoms suggest that Campylobacter may be a component of the normal gut flora of wild M. minutus. Furthermore, linear discriminant analysis (LDA) showed that Campylobacter was the most enriched genus in the gut microbiota of M. minutus (LDA score, 5.37), whereas Lactobacillus was the most enriched genus in M. musculus (LDA score, -5.96). The differences in the presence of Campylobacter between the two species of wild mice may be attributed to the differential abundance of Campylobacter and Lactobacillus in their respective gut microbiota. In conclusion, the results indicate that wild M. minutus may serve as a potential Campylobacter reservoir. This study presents the first metagenomics analysis of the M. minutus gut microbiota to explore its possible role as an environmental Campylobacter reservoir and provides a basis for future studies using culture-independent methods to determine the role of environmental reservoirs in Campylobacter transmission.}, }
@article {pmid33602895, year = {2021}, author = {Zhang, W and Qu, W and Wang, H and Yan, H}, title = {Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress.}, journal = {Translational psychiatry}, volume = {11}, number = {1}, pages = {131}, pmid = {33602895}, issn = {2158-3188}, mesh = {Amitriptyline ; Animals ; Antidepressive Agents ; Fluoxetine ; *Gastrointestinal Microbiome ; Rats ; Stress, Psychological ; }, abstract = {Antidepressant medications are known to modulate the central nervous system, and gut microbiota can play a role in depression via microbiota-gut-brain axis. But the impact of antidepressants on gut microbiota function and composition remains poorly understood. Thus this study assessed the effect of serotonin reuptake inhibitor antidepressant fluoxetine (Flu) and tricyclic antidepressant amitriptyline (Ami) administration on gut microbiota composition, diversity, and species abundance, along with microbial function in a chronic unpredictable mild stress (CUMS)-induced depression rat model. Oral administration of Ami and Flu significantly altered the overall gut microbiota profile of CUMS-induced rats, as assessed using the permutational multivariate analysis of variance test. At the phylum level, 6-week of antidepressant treatment led to a decreased Firmicutes/Bacteroidetes ratio due to an enhanced Bacteroidetes and reduced Firmicutes relative abundance. Flu was more potent than Ami at altering the Firmicutes and Bacteroidetes levels in the CUMS rats. At the family level, both antidepressants significantly increased the abundance of Porphyromonadaceae. However, an increased Bacteroidaceae level was significantly associated with Ami, not Flu treatment. Furthermore, at the genus level, an increase in the relative abundance of Parabacteroides, Butyricimonas, and Alistipes was observed following Ami and Flu treatment. Subsequent metagenomics and bioinformatics analysis further indicated that Ami and Flu likely also modulated metabolic pathways, such as those involved in carbohydrate metabolism, membrane transport, and signal transduction. Additionally, both antidepressants affected antibiotic resistome, such as for aminoglycoside (aph3iiiA), multidrug (mdtK, mdtP, mdtH, mdtG, acrA), and tetracycline (tetM) resistance in CUMS rats. These data clearly illustrated the direct impact of oral administration of Flu and Ami on the gut microbiome, thus set up the foundation to reveal more insights on the therapeutic function of the antidepressants and their overall contribution to host health.}, }
@article {pmid33602336, year = {2021}, author = {Bashir, AK and Wink, L and Duller, S and Schwendner, P and Cockell, C and Rettberg, P and Mahnert, A and Beblo-Vranesevic, K and Bohmeier, M and Rabbow, E and Gaboyer, F and Westall, F and Walter, N and Cabezas, P and Garcia-Descalzo, L and Gomez, F and Malki, M and Amils, R and Ehrenfreund, P and Monaghan, E and Vannier, P and Marteinsson, V and Erlacher, A and Tanski, G and Strauss, J and Bashir, M and Riedo, A and Moissl-Eichinger, C}, title = {Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {50}, pmid = {33602336}, issn = {2049-2618}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification ; *Exobiology ; *Extreme Environments ; Metagenome ; Microbiota/genetics/*physiology ; }, abstract = {BACKGROUND: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth's ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen.<br><br>METHODS: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort.<br><br>RESULTS: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites.<br><br>CONCLUSIONS: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders. Video abstract.}, }
@article {pmid33600956, year = {2021}, author = {Zhang, S and Zeng, B and Chen, Y and Yang, M and Kong, F and Wei, L and Li, F and Zhao, J and Li, Y}, title = {Gut microbiota in healthy and unhealthy long-living people.}, journal = {Gene}, volume = {779}, number = {}, pages = {145510}, doi = {10.1016/j.gene.2021.145510}, pmid = {33600956}, issn = {1879-0038}, mesh = {Aged, 80 and over ; Amino Acids/metabolism ; Asian Continental Ancestry Group ; Carbohydrate Metabolism ; Drug Resistance, Microbial/genetics ; Dysbiosis/*microbiology ; Enzymes/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metagenome ; Streptococcus/pathogenicity ; Virulence Factors/genetics ; }, abstract = {The human gut microbiota in long-living people has been characterized, however, its metabolic potential is still largely unknown in this group. In this study, the gut microbiota was assessed in 37 Chinese long-living participants (aged 90 + years) by metagenomic sequencing of stool samples. Participants were categorized into two groups, healthy long-living (n = 28) and unhealthy long-living (n = 9). Gut microbiota composition and function were compared among these two groups. We found that the gut microbiota in the healthy long-living group was significantly separated from the unhealthy group. The healthy long-living group contained a higher abundance of Bacteroidetes and more functional pathways in energy metabolism, glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The unhealthy group contained a higher abundance of Streptococcus and other pathogenic bacteria, and also contained more functional pathways for xenobiotics biodegradation and metabolism than the healthy group. Additionally, the unhealthy group had decreased levels of carbohydrate-active enzymes, including host-glycan and fiber degrading enzymes, and an increase in starch-degrading enzymes. In conclusion, the gut microbiota of unhealthy long-living people contains more pathogenic bacteria, and the overall gut microbiota may be in an unhealthy state, "dysbiosis", which leads to a decrease in carbohydrate digestion, glycan and thiamine (B1) metabolites, and fatty acid biosynthesis.}, }
@article {pmid33597537, year = {2021}, author = {Jensen, BAH and Holm, JB and Larsen, IS and von Burg, N and Derer, S and Sonne, SB and Pærregaard, SI and Damgaard, MV and Indrelid, SA and Rivollier, A and Agrinier, AL and Sulek, K and Arnoldussen, YJ and Fjære, E and Marette, A and Angell, IL and Rudi, K and Treebak, JT and Madsen, L and Åkesson, CP and Agace, W and Sina, C and Kleiveland, CR and Kristiansen, K and Lea, TE}, title = {Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1093}, pmid = {33597537}, issn = {2041-1723}, support = {//CIHR/Canada ; }, mesh = {Animals ; Diet ; Forkhead Transcription Factors/immunology/metabolism ; Homeostasis/immunology ; Interleukin-17/immunology/metabolism ; Intestine, Large/*immunology/metabolism/microbiology ; Intestine, Small/*immunology/metabolism/microbiology ; Male ; Methylococcus capsulatus/chemistry/*immunology ; Mice, Inbred C57BL ; Microbiota/*immunology ; Nuclear Receptor Subfamily 1, Group F, Member 3/immunology/metabolism ; Obesity/immunology ; Proteins/*immunology/metabolism ; T-Lymphocytes, Regulatory/*immunology/metabolism ; }, abstract = {Interactions between host and gut microbial communities are modulated by diets and play pivotal roles in immunological homeostasis and health. We show that exchanging the protein source in a high fat, high sugar, westernized diet from casein to whole-cell lysates of the non-commensal bacterium Methylococcus capsulatus Bath is sufficient to reverse western diet-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22 °C) and at thermoneutrality (T30 °C). Concomitant with microbiota changes, mice fed the Methylococcus-based western diet exhibit improved glucose regulation, reduced body and liver fat, and diminished hepatic immune infiltration. Intake of the Methylococcu-based diet markedly boosts Parabacteroides abundances in a manner depending on adaptive immunity, and upregulates triple positive (Foxp3+RORγt+IL-17+) regulatory T cells in the small and large intestine. Collectively, these data point to the potential for leveraging the use of McB lysates to improve immunometabolic homeostasis.}, }
@article {pmid33597514, year = {2021}, author = {Chen, C and Zhou, Y and Fu, H and Xiong, X and Fang, S and Jiang, H and Wu, J and Yang, H and Gao, J and Huang, L}, title = {Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1106}, pmid = {33597514}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Microbial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Phylogeny ; Species Specificity ; Swine ; }, abstract = {Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.}, }
@article {pmid33597039, year = {2021}, author = {Li, Z and Xia, J and Jiang, L and Tan, Y and An, Y and Zhu, X and Ruan, J and Chen, Z and Zhen, H and Ma, Y and Jie, Z and Xiao, L and Yang, H and Wang, J and Kristiansen, K and Xu, X and Jin, L and Nie, C and Krutmann, J and Liu, X and Wang, J}, title = {Characterization of the human skin resistome and identification of two microbiota cutotypes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {47}, pmid = {33597039}, issn = {2049-2618}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; China/ethnology ; Drug Resistance, Microbial/drug effects/genetics ; Ethnic Groups ; Female ; Genes, Bacterial/drug effects ; Humans ; Male ; Metagenomics ; *Microbiota/drug effects/genetics ; Middle Aged ; Moraxella/drug effects/*genetics/*isolation &amp; purification ; North America/ethnology ; Propionibacteriaceae/drug effects/*genetics/*isolation &amp; purification ; Skin/*microbiology ; Staphylococcus/drug effects/genetics/isolation &amp; purification ; Symbiosis ; Young Adult ; }, abstract = {BACKGROUND: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity.<br><br>RESULTS: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development.<br><br>CONCLUSIONS: The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.}, }
@article {pmid33597026, year = {2021}, author = {de Nies, L and Lopes, S and Busi, SB and Galata, V and Heintz-Buschart, A and Laczny, CC and May, P and Wilmes, P}, title = {PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {49}, pmid = {33597026}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/*pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; *Metagenomics ; *Software ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.<br><br>RESULTS: Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases.<br><br>CONCLUSION: PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.}, }
@article {pmid33596519, year = {2021}, author = {Kleerebezem, R and Stouten, G and Koehorst, J and Langenhoff, A and Schaap, P and Smidt, H}, title = {Experimental infrastructure requirements for quantitative research on microbial communities.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {158-165}, doi = {10.1016/j.copbio.2021.01.017}, pmid = {33596519}, issn = {1879-0429}, mesh = {Bacteria/genetics ; *Ecosystem ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.}, }
@article {pmid33593778, year = {2021}, author = {Williams, AJ and Paramsothy, R and Wu, N and Ghaly, S and Leach, S and Paramsothy, S and Corte, C and O'Brien, C and Burke, C and Wark, G and Samocha-Bonet, D and Lambert, K and Ahlenstiel, G and Wasinger, V and Dutt, S and Pavli, P and Grimm, M and Lemberg, D and Connor, S and Leong, R and Hold, G}, title = {Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study.}, journal = {BMJ open}, volume = {11}, number = {2}, pages = {e042493}, pmid = {33593778}, issn = {2044-6055}, mesh = {Australia/epidemiology ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; *Microbiota ; Multicenter Studies as Topic ; Prospective Studies ; Proteomics ; }, abstract = {INTRODUCTION: Crohn's disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia's first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota.<br><br>METHODS: The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD.<br><br>ETHICS AND DISSEMINATION: Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBER: ACTRN12619000911190.}, }
@article {pmid33593429, year = {2021}, author = {Moshkelgosha, S and Verhasselt, HL and Masetti, G and Covelli, D and Biscarini, F and Horstmann, M and Daser, A and Westendorf, AM and Jesenek, C and Philipp, S and Diaz-Cano, S and Banga, JP and Michael, D and Plummer, S and Marchesi, JR and Eckstein, A and Ludgate, M and Berchner-Pfannschmidt, U and , }, title = {Modulating gut microbiota in a mouse model of Graves' orbitopathy and its impact on induced disease.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {45}, pmid = {33593429}, issn = {2049-2618}, mesh = {Animals ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Graves Ophthalmopathy/immunology/metabolism/*microbiology/pathology ; Humans ; Mice ; Mice, Inbred BALB C ; }, abstract = {BACKGROUND: Graves' disease (GD) is an autoimmune condition in which autoantibodies to the thyrotropin receptor (TSHR) cause hyperthyroidism. About 50% of GD patients also have Graves' orbitopathy (GO), an intractable disease in which expansion of the orbital contents causes diplopia, proptosis and even blindness. Murine models of GD/GO, developed in different centres, demonstrated significant variation in gut microbiota composition which correlated with TSHR-induced disease heterogeneity. To investigate whether correlation indicates causation, we modified the gut microbiota to determine whether it has a role in thyroid autoimmunity. Female BALB/c mice were treated with either vancomycin, probiotic bacteria, human fecal material transfer (hFMT) from patients with severe GO or ddH2O from birth to immunization with TSHR-A subunit or beta-galactosidase (βgal; age ~ 6 weeks). Incidence and severity of GD (TSHR autoantibodies, thyroid histology, thyroxine level) and GO (orbital fat and muscle histology), lymphocyte phenotype, cytokine profile and gut microbiota were analysed at sacrifice (~ 22 weeks).<br><br>RESULTS: In ddH2O-TSHR mice, 84% had pathological autoantibodies, 67% elevated thyroxine, 77% hyperplastic thyroids and 70% orbital pathology. Firmicutes were increased, and Bacteroidetes reduced relative to ddH2O-βgal; CCL5 was increased. The random forest algorithm at the genus level predicted vancomycin treatment with 100% accuracy but 74% and 70% for hFMT and probiotic, respectively. Vancomycin significantly reduced gut microbiota richness and diversity compared with all other groups; the incidence and severity of both GD and GO also decreased; reduced orbital pathology correlated positively with Akkermansia spp. whilst IL-4 levels increased. Mice receiving hFMT initially inherited their GO donors' microbiota, and the severity of induced GD increased, as did the orbital brown adipose tissue volume in TSHR mice. Furthermore, genus Bacteroides, which is reduced in GD patients, was significantly increased by vancomycin but reduced in hFMT-treated mice. Probiotic treatment significantly increased CD25+ Treg cells in orbital draining lymph nodes but exacerbated induced autoimmune hyperthyroidism and GO.<br><br>CONCLUSIONS: These results strongly support a role for the gut microbiota in TSHR-induced disease. Whilst changes to the gut microbiota have a profound effect on quantifiable GD endocrine and immune factors, the impact on GO cellular changes is more nuanced. The findings have translational potential for novel, improved treatments. Video abstract.}, }
@article {pmid33592536, year = {2021}, author = {Taş, N and de Jong, AE and Li, Y and Trubl, G and Xue, Y and Dove, NC}, title = {Metagenomic tools in microbial ecology research.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {184-191}, doi = {10.1016/j.copbio.2021.01.019}, pmid = {33592536}, issn = {1879-0429}, mesh = {Ecology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.}, }
@article {pmid33587158, year = {2021}, author = {Ma, Z and Lee, S and Fan, P and Zhai, Y and Lim, J and Galvão, KN and Nelson, C and Jeong, KC}, title = {Diverse β-lactam antibiotic-resistant bacteria and microbial community in milk from mastitic cows.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {5}, pages = {2109-2121}, pmid = {33587158}, issn = {1432-0614}, support = {2015-68003-22971//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Cattle ; Female ; Humans ; *Mastitis/drug therapy ; *Mastitis, Bovine/drug therapy ; *Microbiota ; Milk ; }, abstract = {Intramammary bacterial infection, the most common cause of mastitis, is the most costly disease in dairy cattle in the US and reason for antibiotic usage. Ceftiofur, a third-generation cephalosporin, is generally used to treat such disease, but it has a high treatment failure rate. Though the reason is not known clearly, it is hypothesized that multiple factors are associated with the treatment failure. In this study, we analyzed 169 milk samples from cows with mastitis in two independent dairy farms (Farm A and B) in which 19.4% (Farm A) and 14.3% (Farm B) of the antibiotic treated cows were not cured. The prevalence of cephalosporin-resistant bacteria (CRB) in milk was 72.0% and 42.1% in Farm A and B, respectively. Nineteen and nine bacterial genera were identified in Farm A and B respectively, with the most abundant genus being Staphylococcus (27.1%; Farm A) and Bacillus (63.5%; Farm B). However, no strong relationship between the treatment failure rate and the CRB prevalence was observed. Furthermore, the metagenomic analysis showed no significant differences in the α- and β-diversities of microbiota in milk samples from cured and uncured cows, suggesting that antibiotic-resistant bacteria were not the sole reason for the antibiotic treatment failure. KEY POINTS: • The mastitic milk samples had high prevalence of cephalosporin-resistant bacteria (CRB). • The CRB identified belong to diversified species. • Antibiotic treatment failure was not solely caused by the abundance of CRB.}, }
@article {pmid33583433, year = {2021}, author = {Raimundo, I and Silva, R and Meunier, L and Valente, SM and Lago-Lestón, A and Keller-Costa, T and Costa, R}, title = {Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {43}, pmid = {33583433}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/microbiology ; Aquatic Organisms/*microbiology ; Bacteria/enzymology/genetics/*metabolism ; Chitin/*metabolism ; Chitinases/genetics/metabolism ; Geologic Sediments/*microbiology ; *Metagenomics ; *Microbiota/genetics ; Oceans and Seas ; Phylogeny ; Porifera/microbiology ; Seawater/*microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.<br><br>RESULTS: We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.<br><br>CONCLUSIONS: Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.}, }
@article {pmid33578068, year = {2021}, author = {Núñez, A and García, AM and Moreno, DA and Guantes, R}, title = {Seasonal changes dominate long-term variability of the urban air microbiome across space and time.}, journal = {Environment international}, volume = {150}, number = {}, pages = {106423}, doi = {10.1016/j.envint.2021.106423}, pmid = {33578068}, issn = {1873-6750}, mesh = {*Air Microbiology ; Cities ; Fungi ; Humans ; *Microbiota ; Seasons ; Spain ; }, abstract = {Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km2 around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both groups characteristic of seasonal periods, but not of specific sampling sites or plant coverage. The present study suggests that the near surface atmosphere of urban environments contains an ecosystem stable across relatively large spatial and temporal scales, with a rather homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.}, }
@article {pmid33564113, year = {2021}, author = {Tran, PQ and Bachand, SC and McIntyre, PB and Kraemer, BM and Vadeboncoeur, Y and Kimirei, IA and Tamatamah, R and McMahon, KD and Anantharaman, K}, title = {Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {1971-1986}, pmid = {33564113}, issn = {1751-7370}, support = {CGSD3 - 532474 - 2019//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; DEB-1030242//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-0842253//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1344254//NSF | BIO | Division of Environmental Biology (DEB)/ ; }, abstract = {Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.}, }
@article {pmid33562073, year = {2021}, author = {Bergner, LM and Mollentze, N and Orton, RJ and Tello, C and Broos, A and Biek, R and Streicker, DG}, title = {Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats.}, journal = {Viruses}, volume = {13}, number = {2}, pages = {}, pmid = {33562073}, issn = {1999-4915}, support = {MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; 217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 102507/Z/13/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Chiroptera/*virology ; Disease Reservoirs/veterinary/virology ; Feces/virology ; Genome, Viral/genetics ; Humans ; Machine Learning ; Metagenomics ; Phylogeny ; Rabies virus/classification/genetics/isolation &amp; purification ; Saliva/virology ; Viruses/classification/genetics/*isolation &amp; purification ; Zoonoses/*virology ; }, abstract = {The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.}, }
@article {pmid33559707, year = {2021}, author = {Fromentin, M and Ricard, JD and Roux, D}, title = {Respiratory microbiome in mechanically ventilated patients: a narrative review.}, journal = {Intensive care medicine}, volume = {47}, number = {3}, pages = {292-306}, pmid = {33559707}, issn = {1432-1238}, support = {Established Investigator award//European Society of Intensive Care Medicine/ ; Basic Science Award//European Society of Intensive Care Medicine/ ; MSD/SRLF//Société de Réanimation de Langue Française/ ; Young investigator award//Société de Pathologie Infectieuse de Langue Française/ ; }, mesh = {Dysbiosis ; Humans ; *Microbiota ; *Pneumonia, Ventilator-Associated ; Respiration, Artificial/adverse effects ; *Respiratory Distress Syndrome/therapy ; }, abstract = {The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.}, }
@article {pmid33541264, year = {2021}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {Hierarchical non-negative matrix factorization using clinical information for microbial communities.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {104}, pmid = {33541264}, issn = {1471-2164}, support = {19H05210//Japan Society for the Promotion of Science (JP)/ ; 20H04281//Japan Society for the Promotion of Science/ ; 20H04841//Japan Society for the Promotion of Science/ ; 20K21832//Japan Society for the Promotion of Science/ ; 20K19921//Japan Society for the Promotion of Science/ ; JP20dm0107087h0005//Japan Agency for Medical Research and Development/ ; JP20ek0109488h0001//Japan Agency for Medical Research and Development/ ; JP20km0405207h9905//Japan Agency for Medical Research and Development/ ; JP20gm1010002h0005//Japan Agency for Medical Research and Development/ ; }, mesh = {*Algorithms ; Bayes Theorem ; Computer Simulation ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: The human microbiome forms very complex communities that consist of hundreds to thousands of different microorganisms that not only affect the host, but also participate in disease processes. Several state-of-the-art methods have been proposed for learning the structure of microbial communities and to investigate the relationship between microorganisms and host environmental factors. However, these methods were mainly designed to model and analyze single microbial communities that do not interact with or depend on other communities. Such methods therefore cannot comprehend the properties between interdependent systems in communities that affect host behavior and disease processes.<br><br>RESULTS: We introduce a novel hierarchical Bayesian framework, called BALSAMICO (BAyesian Latent Semantic Analysis of MIcrobial COmmunities), which uses microbial metagenome data to discover the underlying microbial community structures and the associations between microbiota and their environmental factors. BALSAMICO models mixtures of communities in the framework of nonnegative matrix factorization, taking into account environmental factors. We proposes an efficient procedure for estimating parameters. A simulation then evaluates the accuracy of the estimated parameters. Finally, the method is used to analyze clinical data. In this analysis, we successfully detected bacteria related to colorectal cancer.<br><br>CONCLUSIONS: These results show that the method not only accurately estimates the parameters needed to analyze the connections between communities of microbiota and their environments, but also allows for the effective detection of these communities in real-world circumstances.}, }
@article {pmid33540579, year = {2021}, author = {Conti, A and Corte, L and Casagrande Pierantoni, D and Robert, V and Cardinali, G}, title = {What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33540579}, issn = {2076-2607}, abstract = {Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.}, }
@article {pmid33537122, year = {2021}, author = {Theil, S and Rifa, E}, title = {rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {7}, pmid = {33537122}, issn = {2046-1402}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota/genetics ; Reproducibility of Results ; Software ; Workflow ; }, abstract = {Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques and tools is challenging. We present an R package for data analysis of 16S and ITS amplicons based sequencing. This workflow is based on several R functions and performs automatic treatments from fastq sequence files to diversity and differential analysis with statistical validation. The main purpose of this package is to automate bioinformatic analysis, ensure reproducibility between projects, and to be flexible enough to quickly integrate new bioinformatic tools or statistical methods. rANOMALY is an easy to install and customizable R package, that uses amplicon sequence variants (ASV) level for microbial community characterization. It integrates all assets of the latest bioinformatics methods, such as better sequence tracking, decontamination from control samples, use of multiple reference databases for taxonomic annotation, all main ecological analysis for which we propose advanced statistical tests, and a cross-validated differential analysis by four different methods. Our package produces ready to publish figures, and all of its outputs are made to be integrated in Rmarkdown code to produce automated reports.}, }
@article {pmid33537012, year = {2020}, author = {Zhu, XY and Liu, J and Xue, CX and Tian, J and Zhang, XH}, title = {Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {603692}, pmid = {33537012}, issn = {1664-302X}, abstract = {Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.}, }
@article {pmid33535685, year = {2021}, author = {Izco, M and Vettorazzi, A and de Toro, M and Sáenz, Y and Alvarez-Erviti, L}, title = {Oral Sub-chronic Ochratoxin A Exposure Induces Gut Microbiota Alterations in Mice.}, journal = {Toxins}, volume = {13}, number = {2}, pages = {}, pmid = {33535685}, issn = {2072-6651}, support = {6FRSSABC008//European Regional Development Fund/ ; }, mesh = {Administration, Oral ; Animals ; Bacteria/*drug effects/growth &amp; development/metabolism ; Dysbiosis ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Intestines/*microbiology ; Male ; Mice, Inbred BALB C ; Ochratoxins/administration &amp; dosage/*toxicity ; Ribotyping ; Time Factors ; Toxicity Tests, Subchronic ; }, abstract = {Gut microbiota plays crucial roles in maintaining host health. External factors, such as diet, medicines, and environmental toxins, influence the composition of gut microbiota. Ochratoxin A (OTA) is one of the most prevalent and relevant mycotoxins and is a highly abundant food and animal feed contaminant. In the present study, we aimed to investigate OTA gut microbiome toxicity in mice sub-chronically exposed to low doses of OTA (0.21, 0.5, and 1.5 mg/kg body weight) by daily oral gavage for 28 days. Fecal microbiota from control and OTA-treated mice was analyzed using 16S ribosomal RNA (rRNA) gene sequencing followed by metagenomics. OTA exposure caused marked changes in gut microbial community structure, including the decrease in the diversity of fecal microbiota and the relative abundance of Firmicutes, as well as the increase in the relative abundance of Bacteroidetes at the phylum level. At the family level, six bacterial families (unclassified Bacteroidales, Porphyromonadaceae, unclassified Cyanobacteria, Streptococcaceae, Enterobacteriaceae, Ruminococcaceae) were significantly altered by OTA exposure. Interestingly, OTA-induced changes were observed in the lower-dose OTA groups, while high-dose OTA group microbiota was similar to control group. Our results demonstrated that sub-chronic exposure at low doses of OTA alters the structure and diversity of the gut microbial community.}, }
@article {pmid33531031, year = {2021}, author = {Liem, M and Regensburg-Tuïnk, T and Henkel, C and Jansen, H and Spaink, H}, title = {Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing.}, journal = {BMC research notes}, volume = {14}, number = {1}, pages = {42}, pmid = {33531031}, issn = {1756-0500}, mesh = {*High-Throughput Nucleotide Sequencing ; *Nanopores ; Pilot Projects ; Seawater ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVE: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.<br><br>RESULTS: With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in > 1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.}, }
@article {pmid33528260, year = {2021}, author = {Bassignani, A and Plancade, S and Berland, M and Blein-Nicolas, M and Guillot, A and Chevret, D and Moritz, C and Huet, S and Rizkalla, S and Clément, K and Doré, J and Langella, O and Juste, C}, title = {Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets.}, journal = {Journal of proteome research}, volume = {20}, number = {3}, pages = {1522-1534}, doi = {10.1021/acs.jproteome.0c00669}, pmid = {33528260}, issn = {1535-3907}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota ; Proteomics ; Tandem Mass Spectrometry ; }, abstract = {The gut microbiota are increasingly considered as a main partner of human health. Metaproteomics enables us to move from the functional potential revealed by metagenomics to the functions actually operating in the microbiome. However, metaproteome deciphering remains challenging. In particular, confident interpretation of a myriad of MS/MS spectra can only be pursued with smart database searches. Here, we compare the interpretation of MS/MS data sets from 48 individual human gut microbiomes using three interrogation strategies of the dedicated Integrated nonredundant Gene Catalog (IGC 9.9 million genes from 1267 individual fecal samples) together with the Homo sapiens database: the classical single-step interrogation strategy and two iterative strategies (in either two or three steps) aimed at preselecting a reduced-sized, more targeted search space for the final peptide spectrum matching. Both iterative searches outperformed the single-step classical search in terms of the number of peptides and protein clusters identified and the depth of taxonomic and functional knowledge, and this was the most convincing with the three-step approach. However, iterative searches do not help in reducing variability of repeated analyses, which is inherent to the traditional data-dependent acquisition mode, but this variability did not affect the hierarchical relationship between replicates and all other samples.}, }
@article {pmid33522965, year = {2021}, author = {Dada, N and Jupatanakul, N and Minard, G and Short, SM and Akorli, J and Villegas, LM}, title = {Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {36}, pmid = {33522965}, issn = {2049-2618}, mesh = {Animals ; Culicidae/*microbiology ; *Metagenomics ; *Microbiota ; Reproducibility of Results ; Research/*organization &amp; administration/*trends ; }, abstract = {In the past decade, there has been increasing interest in mosquito microbiome research, leading to large amounts of data on different mosquito species, with various underlying physiological characteristics, and from diverse geographical locations. However, guidelines and standardized methods for conducting mosquito microbiome research are lacking. To streamline methods in mosquito microbiome research and optimize data quality, reproducibility, and comparability, as well as facilitate data curation in a centralized location, we are establishing the Mosquito Microbiome Consortium, a collaborative initiative for the advancement of mosquito microbiome research. Our overall goal is to collectively work on unraveling the role of the mosquito microbiome in mosquito biology, while critically evaluating its potential for mosquito-borne disease control. This perspective serves to introduce the consortium and invite broader participation. It highlights the issues we view as most pressing to the community and proposes guidelines for conducting mosquito microbiome research. We focus on four broad areas in this piece: (1) sampling/experimental design for field, semi-field, or laboratory studies; (2) metadata collection; (3) sample processing, sequencing, and use of appropriate controls; and (4) data handling and analysis. We finally summarize current challenges and highlight future directions in mosquito microbiome research. We hope that this piece will spark discussions around this area of disease vector biology, as well as encourage careful considerations in the design and implementation of mosquito microbiome research. Video Abstract.}, }
@article {pmid33517907, year = {2021}, author = {Blaustein, RA and Michelitsch, LM and Glawe, AJ and Lee, H and Huttelmaier, S and Hellgeth, N and Ben Maamar, S and Hartmann, EM}, title = {Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {32}, pmid = {33517907}, issn = {2049-2618}, support = {TL1 TR001423/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; *Built Environment ; Drug Resistance, Microbial/drug effects/genetics ; Humans ; Metagenome/drug effects/genetics ; *Microbiota/drug effects/genetics ; Middle Aged ; Mouth/drug effects/*microbiology ; *Toothbrushing ; Triclosan/pharmacology ; Young Adult ; }, abstract = {BACKGROUND: While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors.<br><br>RESULTS: Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features.<br><br>CONCLUSIONS: Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.}, }
@article {pmid33517034, year = {2021}, author = {Dou, R and Sun, J and Lu, J and Deng, F and Yang, C and Lu, G and Dang, Z}, title = {Bacterial communities and functional genes stimulated during phenanthrene degradation in soil by bio-microcapsules.}, journal = {Ecotoxicology and environmental safety}, volume = {212}, number = {}, pages = {111970}, doi = {10.1016/j.ecoenv.2021.111970}, pmid = {33517034}, issn = {1090-2414}, mesh = {Bacteria/metabolism ; *Biodegradation, Environmental ; Capsules/metabolism ; Environmental Pollutants/metabolism ; Metagenomics ; Microbiota ; Phenanthrenes/*metabolism ; Polycyclic Aromatic Hydrocarbons/analysis ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {In this study, a taxonomic and functional metagenomic method was used to investigate the difference produced between degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules or not during the bioremediation of a soil polluted with phenanthrene (PHE). Bioaugmentation with LBL microcapsule immobilized degrading bacteria could result in different changes of native microbial communities, shifting the functional gene constructions of polluted soils. The LBL treatment enhanced PHE degradation (initial concentration of 100 mg kg-1 dry soil) by 60% after 25 d compared to the free bacteria (FB). The enhancing effect of PHE degradation produced by the LBL treatment was found to be significantly associated with some crucial phyla (e.g., Bacteroides, Gemmatimonadetes and Acidobacteria) and genera including Streptomyces, Ramlibacter, Mycobacterium, Phycicoccus, Gemmatirosa, Flavisolibacter, Micromonospora, Acid_Candidatus_Koribacter and Gemmatimonas. The main differences of functional metagenomics between LBL and FB treatments were observed in higher levels in metabolism of aromatic hydrocarbons and its related functions or enzymes in the former, e.g., membrane transport systems, binding, substrate transporter, cleavage enzymes, dehydrogenation, oxidase, esterase and glycosidase, greatly favoring PHE mineralization. Therefore, our results provide useful findings on understanding of how immobilization strategies can influence the taxonomic and functional gene composition in soils, as well as polycyclic aromatic hydrocarbons (PAH) degradation.}, }
@article {pmid33517011, year = {2021}, author = {Jin, L and Huang, Y and Yang, S and Wu, D and Li, C and Deng, W and Zhao, K and He, Y and Li, B and Zhang, G and Xiong, Y and Wei, R and Li, G and Wu, H and Zhang, H and Zou, L}, title = {Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas.}, journal = {The Science of the total environment}, volume = {770}, number = {}, pages = {145316}, doi = {10.1016/j.scitotenv.2021.145316}, pmid = {33517011}, issn = {1879-1026}, mesh = {Animals ; Diet ; Ecosystem ; *Gastrointestinal Microbiome ; Life Style ; *Ursidae ; }, abstract = {Gut microbiota (GM) are important for the health of giant pandas (GPs), in addition to the utilization of bamboo in their diets. However, it is not fully understood how diet, habitat environment and lifestyle contribute to the composition of GM in GP. Consequently, we evaluated how dietary changes, habitat environment conversions and lifestyle shifts influence the GM of GPs using high-throughput sequencing and genome-resolved metagenomics. The GM of GPs were more similar when their hosts exhibited the same diet. High fiber diets significantly increased the diversity and decreased the richness of gut bacterial communities alone or interacted with the age factor (p < 0.05). The abundances of Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium significantly increased during diet conversion process (Non-parametric factorial Kruskal-Wallis sum-rank test, LDA > 4). Reconstruction of 60 metagenome-assembled-genomes (MAGs) indicated that these bacteria were likely responsible for bamboo digestion via gene complements involved in cellulose, hemicellulose, and lignin degradation. While habitat environment may play a more important role in shaping the GM of GP, lifestyle can also greatly affect bacterial communities. The GM structure in reintroduced GPs notably converged to that of wild pandas. Importantly, the main bacterial genera of wild GPs could aid in lignin degradation, while those of reintroduced GPs were related to cellulose and hemicellulose digestion. Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium may contribute to lignocellulose digestion in GP. The results revealed that diet conversion, habitat environment and lifestyle could remarkably influence the GM of GP. In addition, results suggested that increasing the ability of lignin degradation with GM may aid to change the GM of reintroduced pandas to resemble those of wild pandas.}, }
@article {pmid33512248, year = {2021}, author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R}, title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.}, journal = {BioTechniques}, volume = {70}, number = {3}, pages = {149-159}, doi = {10.2144/btn-2020-0153}, pmid = {33512248}, issn = {1940-9818}, support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; W81XWH-17-1-0589//DOD/ ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; 2019-67013-29137//USDA-NIFA/ ; GI18518//Defense Advanced Research Projects Agency/ ; R01 HL134887/HL/NHLBI NIH HHS/United States ; 5K12GM068524-17//NIH-SD-IRACDA/ ; 675191//Crohn's and Colitis Foundation of America/ ; RF1 AG058942/AG/NIA NIH HHS/United States ; R01 DK102932/DK/NIDDK NIH HHS/United States ; //NSF/CAICE/ ; 1RF1-AG058942-01,R01DK102932,R01HL134887,R01HL140976,U01AI124316,U19AG063744/GF/NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Cats ; Chemical Fractionation/methods ; DNA, Viral/*isolation &amp; purification ; Feces/microbiology/virology ; Female ; Fermented Foods and Beverages/microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Limit of Detection ; Male ; Metagenomics/methods ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*isolation &amp; purification ; SARS-CoV-2/*genetics ; Saliva/microbiology/virology ; Skin/microbiology/virology ; }, abstract = {One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.}, }
@article {pmid33509277, year = {2021}, author = {Arnold, JW and Roach, J and Fabela, S and Moorfield, E and Ding, S and Blue, E and Dagher, S and Magness, S and Tamayo, R and Bruno-Barcena, JM and Azcarate-Peril, MA}, title = {The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {31}, pmid = {33509277}, issn = {2049-2618}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; }, mesh = {Aging/drug effects/genetics/*physiology ; Animals ; Female ; Gastrointestinal Microbiome/*drug effects ; Intestines/drug effects/microbiology/physiology ; Mice ; Mice, Inbred C57BL ; Oligosaccharides/*pharmacology ; Phosphatidylinositol 3-Kinases/metabolism ; *Prebiotics ; Proto-Oncogene Proteins c-akt/metabolism ; }, abstract = {BACKGROUND: Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects ("leaky gut"). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder-non-responder phenotypes observed in vivo.<br><br>RESULTS: Old animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia, Clostridium, Coprococcus, Bacillus, Bacteroides, and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1, a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype.<br><br>CONCLUSIONS: Dietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice. Video abstract.}, }
@article {pmid33508686, year = {2021}, author = {Dionizio, A and Uyghurturk, DA and Melo, CGS and Sabino-Arias, IT and Araujo, TT and Ventura, TMS and Perles, JVCM and Zanoni, JN and Den Besten, P and Buzalaf, MAR}, title = {Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses.}, journal = {Chemosphere}, volume = {273}, number = {}, pages = {129607}, pmid = {33508686}, issn = {1879-1298}, support = {R01 DE013508/DE/NIDCR NIH HHS/United States ; T32 DE007306/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Firmicutes ; *Fluorides/toxicity ; *Gastrointestinal Microbiome ; Male ; Mice ; Proteome ; Proteomics ; Rats ; }, abstract = {Gastrointestinal signs and symptoms are the first signs of toxicity due to exposure to fluoride (F). This suggests the possibility that lower levels of subchronic F exposure may affect the gut. The aim of this study was to evaluate changes in the morphology, proteome and microbiome of the ileum of rats, after subchronic exposure to F. Male rats ingested water with 0, 10, or 50 mgF/L for thirty days. Treatment with F, regardless of the dose, significantly decreased the density of HuC/D-IR neurons, whereas CGRP-IR and SP-IR varicosities were significantly increased compared to the control group. Increased VIP-IR varicosities were significantly increased only in the group treated with 50 mgF/L. A significant increase in thickness of the tunica muscularis, as well as in the total thickness of the ileum wall was observed at both F doses when compared to controls. In proteomics analysis, myosin isoforms were increased, and Gastrotopin was decreased in F-exposed mice. In the microbiome metagenomics analysis, Class Clostridia was significantly reduced upon exposure to 10 mgF/L. At the higher F dose of 50 mg/L, genus Ureaplasma was significantly reduced in comparison with controls. Morphological and proteomics alterations induced by F were marked by changes associated with inflammation, and alterations in the gut microbiome. Further studies are needed to determine whether F exposure increases inflammation with secondary effects of the gut microbiome, and/or whether primary effects of F on the gut microbiome enhance changes associated with inflammation.}, }
@article {pmid33503844, year = {2021}, author = {Raja, G and Gupta, H and Gebru, YA and Youn, GS and Choi, YR and Kim, HS and Yoon, SJ and Kim, DJ and Kim, TJ and Suk, KT}, title = {Recent Advances of Microbiome-Associated Metabolomics Profiling in Liver Disease: Principles, Mechanisms, and Applications.}, journal = {International journal of molecular sciences}, volume = {22}, number = {3}, pages = {}, pmid = {33503844}, issn = {1422-0067}, support = {Hallym University Research Fund//Hallym University Research Fund/ ; NRF-2018M3A9F3020956, NRF-2019R1I1A3A01060447, NRF-2020R1I1A3073530 and NRF-2020R1A6A1A03043026//Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology/ ; }, mesh = {Animals ; Biomarkers ; Computational Biology/methods ; *Disease Susceptibility ; Energy Metabolism ; Gene Expression Profiling ; Genomics/methods ; Humans ; Liver Diseases/diagnosis/*etiology/*metabolism/therapy ; *Metabolome ; *Metabolomics/methods ; *Microbiota ; Phenomics ; }, abstract = {Advances in high-throughput screening of metabolic stability in liver and gut microbiota are able to identify and quantify small-molecule metabolites (metabolome) in different cellular microenvironments that are closest to their phenotypes. Metagenomics and metabolomics are largely recognized to be the "-omics" disciplines for clinical therapeutic screening. Here, metabolomics activity screening in liver disease (LD) and gut microbiomes has significantly delivered the integration of metabolomics data (i.e., a set of endogenous metabolites) with metabolic pathways in cellular environments that can be tested for biological functions (i.e., phenotypes). A growing literature in LD and gut microbiomes reports the use of metabolites as therapeutic targets or biomarkers. Although growing evidence connects liver fibrosis, cirrhosis, and hepatocellular carcinoma, the genetic and metabolic factors are still mainly unknown. Herein, we reviewed proof-of-concept mechanisms for metabolomics-based LD and gut microbiotas' role from several studies (nuclear magnetic resonance, gas/lipid chromatography, spectroscopy coupled with mass spectrometry, and capillary electrophoresis). A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to improve liver health.}, }
@article {pmid33499981, year = {2020}, author = {Wei, J and Gao, H and Yang, Y and Liu, H and Yu, H and Chen, Z and Dong, B}, title = {Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi.}, journal = {Animal microbiome}, volume = {2}, number = {1}, pages = {30}, pmid = {33499981}, issn = {2524-4671}, support = {2018YFD0900705//National Key Research and Development Program of China/ ; 31970487//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Gut microbiota plays important roles in host animal metabolism, homeostasis and environmental adaptation. However, the interplay between the gut microbiome and urochordate ascidian, the most closet relative of vertebrate, remains less explored. In this study, we characterized the gut microbial communities of urochordate ascidian (Halocynthia roretzi) across the changes of season and starvation stress using a comprehensive set of omic approaches including 16S rRNA gene amplicon sequencing, shotgun metagenomics, metabolomic profiling, and transcriptome sequencing.<br><br>RESULTS: The 16S rRNA gene amplicon profiling revealed that ascidians harbor indigenous gut microbiota distinctly different to the marine microbial community and significant variations in composition and abundance of gut bacteria, with predominant bacterial orders representing each season. Depressed alpha-diversities of gut microbiota were observed across starvation stress when compared to the communities in aquafarm condition. Synechococcales involving photosynthesis and its related biosynthesis was reduced in abundance while the enrichments of Xanthomonadales and Legionellales may facilitate bile acid biosynthesis during starvation. Metabolomics analysis found that long chain fatty acids, linolenic acid, cyanoamino acid, and pigments derived from gut bacteria were upregulated, suggesting a beneficial contribution of the gut microbiome to the ascidian under starvation stress.<br><br>CONCLUSIONS: Our findings revealed seasonal variation of ascidian gut microbiota. Defense and energy-associated metabolites derived from gut microbiome may provide an adaptive interplay between gut microbiome and ascidian host that maintains a beneficial metabolic system across season and starvation stress. The diversity-generating metabolisms from both microbiota and host might lead to the co-evolution and environmental adaptation.}, }
@article {pmid33498458, year = {2021}, author = {Aylward, FO and Moniruzzaman, M}, title = {ViralRecall-A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in 'Omic Data.}, journal = {Viruses}, volume = {13}, number = {2}, pages = {}, pmid = {33498458}, issn = {1999-4915}, mesh = {Amino Acid Sequence ; Biodiversity ; Computational Biology/*methods ; Cytoplasm/*virology ; Eukaryotic Cells/*virology ; Gene Library ; Genome, Viral ; Giant Viruses/*classification/genetics ; *Metagenomics ; Phylogeny ; }, abstract = {Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in 'omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.}, }
@article {pmid33496989, year = {2021}, author = {Nelson, JW and Phillips, SC and Ganesh, BP and Petrosino, JF and Durgan, DJ and Bryan, RM}, title = {The gut microbiome contributes to blood-brain barrier disruption in spontaneously hypertensive stroke prone rats.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {2}, pages = {e21201}, pmid = {33496989}, issn = {1530-6860}, support = {R21 NS094806/NS/NINDS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R56 NS102594/NS/NINDS NIH HHS/United States ; T32 GM008231/GM/NIGMS NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS102594/NS/NINDS NIH HHS/United States ; DK56338 to the Texas Medical Center Digestive Disease Center//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Animals ; *Blood Pressure ; Blood-Brain Barrier/metabolism/*pathology ; Environment ; *Gastrointestinal Microbiome ; Ileum/microbiology/pathology ; Rats, Inbred SHR ; Rats, Inbred WKY ; }, abstract = {In recent years, it has become apparent that the gut microbiome can influence the functioning and pathological states of organs and systems throughout the body. In this study, we tested the hypothesis that the gut microbiome has a major role in the disruption of the blood-brain barrier (BBB) in the spontaneously hypertensive stroke prone rats (SHRSP), an animal model for hypertensive cerebral small vessel disease (CSVD). Loss of BBB is thought to be an early and initiating component to the full expression of CSVD in animal models and humans. To test this hypothesis, newly born SHRSP pups were placed with foster dams of the SHRSP strain or dams of the WKY strain, the control strain that does not demonstrate BBB dysfunction or develop hypertensive CSVD. Similarly, WKY pups were placed with foster dams of the same or opposite strain. The rationale for cross fostering is that the gut microbiomes are shaped by environmental bacteria of the foster dam and the nesting surroundings. Analysis of the bacterial genera in feces, using 16S rRNA analysis, demonstrated that the gut microbiome in the rat pups was influenced by the foster dam. SHRSP offspring fostered on WKY dams had systolic blood pressures (SBPs) that were significantly decreased by 26 mmHg (P < .001) from 16-20 weeks, compared to SHRSP offspring fostered on SHRSP dams. Similarly WKY offspring fostered on SHRSP dams had significantly increased SBP compared to WKY offspring fostered on WKY dams, although the magnitude of SBP change was not as robust. At ~20 weeks of age, rats fostered on SHRSP dams showed enhanced inflammation in distal ileum regardless of the strain of the offspring. Disruption of BBB integrity, an early marker of CSVD onset, was improved in SHRSPs that were fostered on WKY dams when compared to the SHRSP rats fostered on SHRSP dams. Although SHRSP is a genetic model for CSVD, environmental factors such as the gut microbiota of the foster dam have a major influence in the loss of BBB integrity.}, }
@article {pmid33495623, year = {2021}, author = {He, C and Keren, R and Whittaker, ML and Farag, IF and Doudna, JA and Cate, JHD and Banfield, JF}, title = {Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.}, journal = {Nature microbiology}, volume = {6}, number = {3}, pages = {354-365}, pmid = {33495623}, issn = {2058-5276}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture ; Archaea/classification/*physiology/ultrastructure ; Bacteria/classification/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Adhesion ; Cell Proliferation ; *Ecosystem ; Groundwater/chemistry/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.}, }
@article {pmid33494335, year = {2021}, author = {Baragetti, A and Severgnini, M and Olmastroni, E and Dioguardi, CC and Mattavelli, E and Angius, A and Rotta, L and Cibella, J and Caredda, G and Consolandi, C and Grigore, L and Pellegatta, F and Giavarini, F and Caruso, D and Norata, GD and Catapano, AL and Peano, C}, title = {Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, pmid = {33494335}, issn = {2072-6643}, support = {AL_RIC19ABARA_01//Vini di Batasiolo S.p.A/ ; 2020-3318//Fondazione Umberto Veronesi/ ; 2016-0852//Fondazione Cariplo/ ; GGP19146//Fondazione Telethon/ ; PRIN 2017K55HLC//Italian Ministry of Health/ ; H2020 REPROGRAM PHC-03-2015/667837-2//European Union Commission/ ; 2015-0524//Fondazione Cariplo/ ; 2015-0564//Fondazione Cariplo/ ; ERANET ER-2017-2364981//European Union Commission/ ; PRIN 2017 - LS 4 2017HTKLRF_003//Italian Ministry of Health/ ; PRIN 2017H5F943//Italian Ministry of Health/ ; GR-2011-02346974//Italian Ministry of Health-IRCCS MultiMedica/ ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/drug effects ; Carnitine/therapeutic use ; Carotid Artery Diseases/*complications/microbiology ; Choline/therapeutic use ; *Diet ; Dysbiosis/*complications/drug therapy/microbiology ; Escherichia coli ; Faecalibacterium prausnitzii ; Feces/microbiology ; Feeding Behavior ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Life Style ; Male ; Metagenomics ; Methylamines ; Middle Aged ; Palmitates/therapeutic use ; }, abstract = {Gut Microbiota (GM) dysbiosis associates with Atherosclerotic Cardiovascular Diseases (ACVD), but whether this also holds true in subjects without clinically manifest ACVD represents a challenge of personalized prevention. We connected exposure to diet (self-reported by food diaries) and markers of Subclinical Carotid Atherosclerosis (SCA) with individual taxonomic and functional GM profiles (from fecal metagenomic DNA) of 345 subjects without previous clinically manifest ACVD. Subjects without SCA reported consuming higher amounts of cereals, starchy vegetables, milky products, yoghurts and bakery products versus those with SCA (who reported to consume more mechanically separated meats). The variety of dietary sources significantly overlapped with the separations in GM composition between subjects without SCA and those with SCA (RV coefficient between nutrients quantities and microbial relative abundances at genus level = 0.65, p-value = 0.047). Additionally, specific bacterial species (Faecalibacterium prausnitzii in the absence of SCA and Escherichia coli in the presence of SCA) are directly related to over-representation of metagenomic pathways linked to different dietary sources (sulfur oxidation and starch degradation in absence of SCA, and metabolism of amino acids, syntheses of palmitate, choline, carnitines and Trimethylamine n-oxide in presence of SCA). These findings might contribute to hypothesize future strategies of personalized dietary intervention for primary CVD prevention setting.}, }
@article {pmid33493841, year = {2021}, author = {Das, J and Yadav, SK and Ghosh, S and Tyagi, K and Magotra, A and Krishnan, A and Jha, G}, title = {Enzymatic and non-enzymatic functional attributes of plant microbiome.}, journal = {Current opinion in biotechnology}, volume = {69}, number = {}, pages = {162-171}, doi = {10.1016/j.copbio.2020.12.021}, pmid = {33493841}, issn = {1879-0429}, mesh = {Agriculture ; Metagenomics ; Microbial Interactions ; *Microbiota/genetics ; Plants ; }, abstract = {Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.}, }
@article {pmid33486296, year = {2021}, author = {Zhou, Z and Xu, L and Zhu, L and Liu, Y and Shuai, X and Lin, Z and Chen, H}, title = {Metagenomic analysis of microbiota and antibiotic resistome in household activated carbon drinking water purifiers.}, journal = {Environment international}, volume = {148}, number = {}, pages = {106394}, doi = {10.1016/j.envint.2021.106394}, pmid = {33486296}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/pharmacology ; Charcoal ; *Drinking Water/analysis ; Genes, Bacterial ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Existing drinking water treatment systems have limited ability to control emerging contaminants such as antibiotic resistance genes (ARGs). Household activated carbon water purifiers (HWPs) are convenient measures to assure drinking water quality. However, ARGs distribution in HWPs has not been reported. Here, ARGs, mobile genetic elements (MGEs) and bacteria communities were profiled in tap water (TW), filter water (FW) and activated carbon (AC) biofilm from six kinds of HWPs after 80 days operation, using metagenomics. Results showed that the bacteria community diversities in FW and AC were higher than those in TW. A total of 88, 116 and 80 ARG subtypes were detected in TW, AC and FW, respectively. The AC structure was an important factor influencing the bacterial communities and ARG profiles in FW. The network analysis revealed the co-occurrence patterns between ARGs and bacteria. SourceTracker analyses showed AC biofilms were important contributors of microbes (29-79%) and ARGs (17-53%) in FW. Moreover, MGEs e.g. pBBta01, pMKMS02 and pMFLV01 plasmids, and ISMysp3 had significant co-occurrence patterns with ARGs in the AC biofilms. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.}, }
@article {pmid33484236, year = {2021}, author = {Bergner, LM and Becker, DJ and Tello, C and Carrera, JE and Streicker, DG}, title = {Detection of Trypanosoma cruzi in the saliva of diverse neotropical bats.}, journal = {Zoonoses and public health}, volume = {68}, number = {3}, pages = {271-276}, doi = {10.1111/zph.12808}, pmid = {33484236}, issn = {1863-2378}, support = {MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; RGP0013/2018//Human Frontier Science Program/ ; //University of Glasgow/ ; 102507/Z/13/Z//Wellcome Senior Research Fellowship/ ; 102507/Z/13/A/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Trypanosoma cruzi is widely reported in bats, yet transmission routes remain unclear. We present evidence from metagenomic sequence data that T. cruzi occurs in the saliva of diverse Neotropical bats. Phylogenetic analyses demonstrated that the bat-associated T. cruzi sequences described here formed part of a bat-specific clade, suggesting an independent transmission cycle. Our results highlight the value in repurposing metagenomic data generated for viral discovery to reveal insights into the biology of other parasites. Evaluating whether the presence of T. cruzi in the saliva of two hematophagous bat species represents an ecological route for zoonotic transmission of Chagas disease is an interesting avenue for future research.}, }
@article {pmid33484150, year = {2021}, author = {Raffner Basson, A and Gomez-Nguyen, A and LaSalla, A and Buttó, L and Kulpins, D and Warner, A and Di Martino, L and Ponzani, G and Osme, A and Rodriguez-Palacios, A and Cominelli, F}, title = {Replacing Animal Protein with Soy-Pea Protein in an "American Diet" Controls Murine Crohn Disease-Like Ileitis Regardless of Firmicutes: Bacteroidetes Ratio.}, journal = {The Journal of nutrition}, volume = {151}, number = {3}, pages = {579-590}, pmid = {33484150}, issn = {1541-6100}, support = {P01 DK091222/DK/NIDDK NIH HHS/United States ; P30 DK097948/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; F32 DK117585/DK/NIDDK NIH HHS/United States ; R21 DK118373/DK/NIDDK NIH HHS/United States ; T32 DK083251/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acids/chemistry/metabolism ; Animal Feed ; Animals ; Bacteroidetes ; Colitis/chemically induced/prevention &amp; control ; Dextran Sulfate ; Diet/veterinary ; Dietary Carbohydrates ; Dietary Fats ; Dietary Proteins/*administration &amp; dosage ; Feces/chemistry ; Female ; Firmicutes ; Gastrointestinal Microbiome/*physiology ; Humans ; Ileitis/*prevention &amp; control ; Male ; Mice ; Mice, Inbred C57BL ; *Peas ; *Soybeans ; Specific Pathogen-Free Organisms ; }, abstract = {BACKGROUND: The current nutritional composition of the "American diet" (AD; also known as Western diet) has been linked to the increasing incidence of chronic diseases, including inflammatory bowel disease (IBD), namely Crohn disease (CD).<br><br>OBJECTIVES: This study investigated which of the 3 major macronutrients (protein, fat, carbohydrates) in the AD has the greatest impact on preventing chronic inflammation in experimental IBD mouse models.<br><br>METHODS: We compared 5 rodent diets designed to mirror the 2011-2012 "What We Eat in America" NHANES. Each diet had 1 macronutrient dietary source replaced. The formulated diets were AD, AD-soy-pea (animal protein replaced by soy + pea protein), AD-CHO ("refined carbohydrate" by polysaccharides), AD-fat [redistribution of the ω-6:ω-3 (n-6:n-3) PUFA ratio; ∼10:1 to 1:1], and AD-mix (all 3 "healthier" macronutrients combined). In 3 separate experiments, 8-wk-old germ-free SAMP1/YitFC mice (SAMP) colonized with human gut microbiota ("hGF-SAMP") from CD or healthy donors were fed an AD, an AD-"modified," or laboratory rodent diet for 24 wk. Two subsequent dextran sodium sulfate-colitis experiments in hGF-SAMP (12-wk-old) and specific-pathogen-free (SPF) C57BL/6 (20-wk-old) mice, and a 6-wk feeding trial in 24-wk-old SPF SAMP were performed. Intestinal inflammation, gut metagenomics, and MS profiles were assessed.<br><br>RESULTS: The AD-soy-pea diet resulted in lower histology scores [mean ± SD (56.1% ± 20.7% reduction)] in all feeding trials and IBD mouse models than did other diets (P < 0.05). Compared with the AD, the AD-soy-pea correlated with increased abundance in Lactobacillaceae and Leuconostraceae (1.5-4.7 log2 and 3.0-5.1 log2 difference, respectively), glutamine (6.5 ± 0.8 compared with 3.9 ± 0.3 ng/μg stool, P = 0.0005) and butyric acid (4:0; 3.3 ± 0.5 compared with 2.54 ± 0.4 ng/μg stool, P = 0.006) concentrations, and decreased linoleic acid (18:2n-6; 5.4 ± 0.4 compared with 8.6 ± 0.3 ng/μL plasma, P = 0.01).<br><br>CONCLUSIONS: Replacement of animal protein in an AD by plant-based sources reduced the severity of experimental IBD in all mouse models studied, suggesting that similar, feasible adjustments to the daily human diet could help control/prevent IBD in humans.}, }
@article {pmid33482928, year = {2021}, author = {Klassen, L and Reintjes, G and Tingley, JP and Jones, DR and Hehemann, JH and Smith, AD and Schwinghamer, TD and Arnosti, C and Jin, L and Alexander, TW and Amundsen, C and Thomas, D and Amann, R and McAllister, TA and Abbott, DW}, title = {Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {23}, pmid = {33482928}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Cattle ; *Fluorescence ; Fluorescent Dyes/analysis ; *Gastrointestinal Microbiome ; Metagenomics ; Polysaccharides/*analysis/*metabolism ; Rumen/*microbiology ; }, abstract = {Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as "medium grower" and "high grower." Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and "omics" approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. Video abstract.}, }
@article {pmid33482026, year = {2021}, author = {Canivet, CM and David, N and Pailhoriès, H and Briand, M and Guy, CD and Bouchez, O and Hunault, G and Fizanne, L and Lannes, A and Oberti, F and Fouchard, I and Calès, P and Diehl, AM and Barret, M and Boursier, J}, title = {Cross-linkage between bacterial taxonomy and gene functions: a study of metagenome-assembled genomes of gut microbiota in adult non-alcoholic fatty liver disease.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {53}, number = {6}, pages = {722-732}, doi = {10.1111/apt.16262}, pmid = {33482026}, issn = {1365-2036}, mesh = {Adult ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; *Non-alcoholic Fatty Liver Disease/genetics ; }, abstract = {BACKGROUND: The reconstruction of metagenome-assembled genomes (MAGs) has emerged as a powerful approach for combining the taxonomic and functional content of microbial populations.<br><br>AIM: To use this new approach to highlight mechanisms linking gut microbiota to NAFLD severity METHODS: Stool samples were collected from 96 NAFLD patients on the day of liver biopsy. Shotgun DNA sequencing of the gut microbiota was performed on an Illumina HiSeq3000 system. Contigs were binned into MAGs according to their co-abundances and tetranucleotide frequencies using Metabat v.0.32.4. Predicted protein-coding genes were clustered in orthologous groups (OGs) with DIAMOND against the EggNOG v4.5 database. Liver biopsies were read in accordance with the NASH CRN classification.<br><br>RESULTS: Fifty-four patients had NASH and 44 had significant fibrosis (F ≥ 2). Sequencing of DNA extracted from stools resulted in 13.8 + 3.2 million paired-end reads per sample. Of the 4,000 reconstructed MAGs, 220 in NASH patients, 192 in non-NASH patients, 203 in F ≥ 2 patients and 230 in F0-1 patients had > 70% completeness and < 5% contamination. Within these MAGs, 28 OGs were associated with NASH, 33 with significant fibrosis, and seven with both NASH and significant fibrosis. The study of MAGs showed associations between NAFLD severity and some gut bacteria with microbiota functions related to hydrogen sulfide production, citrate transport, hemicellulose degradation, aldehyde production and vitamin B12 synthesis.<br><br>CONCLUSION: Using new metagenomics methods, our study unveils potential mechanisms by which certain bacteria from the gut microbiota could protect or contribute to the development of NASH and liver fibrosis in NAFLD.}, }
@article {pmid33463854, year = {2020}, author = {Furey, PC and Lee, SS and Clemans, DL}, title = {Substratum-associated microbiota.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {92}, number = {10}, pages = {1629-1648}, doi = {10.1002/wer.1410}, pmid = {33463854}, issn = {1554-7531}, mesh = {*Cyanobacteria ; Ecology ; Fresh Water ; Metagenomics ; *Microbiota ; }, abstract = {Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.}, }
@article {pmid33461660, year = {2021}, author = {Urban, L and Holzer, A and Baronas, JJ and Hall, MB and Braeuninger-Weimer, P and Scherm, MJ and Kunz, DJ and Perera, SN and Martin-Herranz, DE and Tipper, ET and Salter, SJ and Stammnitz, MR}, title = {Freshwater monitoring by nanopore sequencing.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33461660}, issn = {2050-084X}, support = {Graduate Student Fellowship//Gates Cambridge Trust/International ; OPP1144//Bill and Melinda Gates Foundation/International ; OpenPlant Fund (BBSRC BB/L014130/1)/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Public Engagement Starter Grant (RCUK Catalyst Seed Fund)//University of Cambridge/International ; Graduate Student Fellowship//European Bioinformatics Institute/International ; Graduate Student Fellowship (203828/Z/16/A, 203828/Z/16/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship (102453/Z/13/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship//Oliver Gatty Studentship/International ; Standard Grant (NE/P011659/1)//Natural Environment Research Council/International ; }, mesh = {Bacteria/classification/genetics ; Base Sequence ; Cluster Analysis ; Computational Biology/methods ; Environmental Monitoring/methods ; Fresh Water/*microbiology ; Geography ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Nanopore Sequencing/*methods ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sequence Homology, Nucleic Acid ; Species Specificity ; United Kingdom ; *Water Microbiology ; }, abstract = {While t