@article {pmid35051998,
year = {2022},
author = {Hiraoka, S and Sumida, T and Hirai, M and Toyoda, A and Kawagucci, S and Yokokawa, T and Nunoura, T},
title = {Diverse DNA modification in marine prokaryotic and viral communities.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkab1292},
pmid = {35051998},
issn = {1362-4962},
support = {JP16H06429//Ministry of Education, Culture, Sports, Science and Technology/ ; JP18K11636//Japan Society for the Promotion of Science/ ; //Institute for Fermentation, Osaka/ ; },
abstract = {DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.},
}

@article {pmid35051682,
year = {2022},
author = {Kieft, K and Anantharaman, K},
title = {Virus genomics: what is being overlooked?.},
journal = {Current opinion in virology},
volume = {53},
number = {},
pages = {101200},
doi = {10.1016/j.coviro.2022.101200},
pmid = {35051682},
issn = {1879-6265},
abstract = {Viruses are diverse biological entities that influence all life. Even with limited genome sizes, viruses can manipulate, drive, steal from, and kill their hosts. The field of virus genomics, using sequencing data to understand viral capabilities, has seen significant innovations in recent years. However, with advancements in metagenomic sequencing and related technologies, the bottleneck to discovering and employing the virosphere has become the analysis of genomes rather than generation. With metagenomics rapidly expanding available data, vital components of virus genomes and features are being overlooked, with the issue compounded by lagging databases and bioinformatics methods. Despite the field moving in a positive direction, there are noteworthy points to keep in mind, from how software-based virus genome predictions are interpreted to what information is overlooked by current standards. In this review, we discuss conventions and ideologies that likely need to be revised while continuing forward in the study of virus genomics.},
}

@article {pmid35051652,
year = {2022},
author = {Wang, J and Li, L and Xu, Y and Mao, T and Ma, Y and Sun, X and Liu, X and Wang, Y and Duan, ZJ},
title = {fIdentification of a novel norovirus species in fox.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105214},
doi = {10.1016/j.meegid.2022.105214},
pmid = {35051652},
issn = {1567-7257},
abstract = {A novel Norovirus (NoV) was identified by viral metagenomic analysis in fox fecal samples from the Xinjiang Uygur Autonomous Region of China. The virus exhibited typical genomic characteristics of NoVs. It was closely related to the canine NoV GVII strains with 86.0-86.2% and 91.9% amino acid identities in the capsid protein VP1 and RNA-dependent RNA polymerase (RdRp), respectively. The fox NoV clustered phylogenetically with the two canine NoV GVII strains, and it was distant from other NoVs. According to the new classification criteria of NoVs, the new fox NoV belongs to the same genotype as GVII, similar to canine GVII NoVs. Moreover, key amino acid residues in the Histo-blood group antigen (HBGA) binding sites and the HBGA binding pattern of the fox NoV differed significantly from those of human and canine GVII NoVs. This study identified a new GVII norovirus from wild foxes in China. These findings enrich our understanding of the diversity of NoVs and provide further evidence regarding the genetic heterogeneity of NoVs in carnivores.},
}

@article {pmid35051422,
year = {2022},
author = {Volodina, DE and Gureev, AP and Shaforostova, EA and Gryaznova, MV and Ignatyeva, DA and Popov, VN},
title = {Effect of l-carnitine and mildronate on the mitochondrial metabolism of heart and bacterial composition of the gut microbiome in ageing mice.},
journal = {Life sciences},
volume = {},
number = {},
pages = {120333},
doi = {10.1016/j.lfs.2022.120333},
pmid = {35051422},
issn = {1879-0631},
abstract = {Ageing is the most significant risk factor for cardiovascular diseases. l-Carnitine has a potent cardioprotective effect and its synthesis decreases during ageing. At the same time, there are pharmaceuticals, such as mildronate which, on the contrary, are aimed at reducing the concentration of l-carnitine in the heart and lead to slows down the oxidation of fatty acids in mitochondria. Despite this, both l-carnitine and mildronate are positioned as cardio protectors. We showed that l-carnitine supplementation to the diet of 15-month-old mice increased expression of the PGC-1α gene, which is responsible for the regulation of fatty acid oxidation, and the Nrf2 gene, which is responsible for protecting mitochondria by regulating the expression of antioxidants and mitophagy, in the heart. Mildronate activated the expression of genes that regulate glucose metabolism. Probably, this metabolic shift may protect the mitochondria of the heart from the accumulation of acyl-carnitine, which occurs during the oxidation of fatty acids under oxygen deficiency. Both pharmaceuticals impacted the gut microbiome bacterial composition. l-Carnitine increased the level of Lachnoanaerobaculum and [Eubacterium] hallii group, mildronate increased the level of Bifidobacterium, Rikinella, Christensenellaceae. Considered, that these bacteria for protection the organism from various pathogens and chronic inflammation. Thus, we suggested that the positive effects of both drugs on the mitochondria metabolism and gut microbiome bacterial composition may contribute to the protection of the heart during ageing.},
}

@article {pmid35051309,
year = {2022},
author = {Fan, C and Zhang, L and Jia, S and Tang, X and Fu, H and Li, W and Liu, C and Zhang, H and Cheng, Q and Zhang, Y},
title = {Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12630},
pmid = {35051309},
issn = {1749-4877},
abstract = {Seasonal variations in gut microbiota of small mammals and how it is influenced by environmental variables is relatively poorly understood. We sampled 162 wild plateau pikas (Ochotona curzoniae) in four seasons over two and a half years and recorded the air temperature, precipitation, and nutrient content in edible vegetation at the sampling site. After conducting 16S rRNA and shotgun metagenomic sequencing, we found that the highest alpha diversity, the relative abundance of Firmicutes, and the simplest co-occurrence network occurred in winter, whereas that the highest relative abundance of Proteobacteria and the most complex network structure was observed in spring. The highest relative abundance of Verrucomicrobiota and Spirochaetota were seen in summer and autumn, respectively. Air temperature, precipitation, and the contents of crude protein, crude fiber, and polysaccharide in vegetation had significant effects on the seasonal changes in gut microbiota. Diet contributed more to microbial variation than climatic factors. Metagenomic analysis revealed that the amino acid metabolism pathway and axillary activity enzymes were most abundant in summer, while abundance of carbohydrate-binding modules and carbohydrate esterases were highest in spring. These microbial variations were related to the changes in dietary nutrition, indicating that gut microbiota of plateau pika contribute to the efficient use of food resources. This study provides new evidence of how external environmental factors affect the intestinal environment of small mammals. This article is protected by copyright. All rights reserved.},
}

@article {pmid35050030,
year = {2022},
author = {Liu, D and Cai, J and He, H and Yang, S and Chater, CCC and Yu, F},
title = {Anemochore Seeds Harbor Distinct Fungal and Bacterial Abundance, Composition, and Functional Profiles.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/jof8010089},
pmid = {35050030},
issn = {2309-608X},
support = {202103AC100003//Key R & D program of Yunnan Province, China/ ; },
abstract = {Many plants adapted to harsh environments have evolved low seed mass ('light seeds') with specific dispersal strategies, primarily either by wind (anemochory) or water (hydrochory). However, the role of their seed microbiota in their survival, and their seed microbial abundance and structure, remain insufficiently studied. Herein, we studied the light seed microbiome of eight anemochores and two hydrochores (as controls) collected from four provinces in China, using qPCR and metagenomic sequencing targeting both bacteria and fungi. Substantial variations were found for seed endophytic fungi (9.9 × 1010~7.3 × 102 gene copy numbers per seed) and bacteria (1.7 × 1010~8.0 × 106). Seed microbial diversity and structure were mainly driven by the plant genotype (species), with weak influences from their host plant classification level or dispersal mode. Seed microbial composition differences were clear at the microbial phylum level, with dominant proportions (~75%) for Proteobacteria and Ascomycota. The light seeds studied harbored unique microbial signatures, sharing only two Halomonas amplicon sequence variants (ASVs) and two fungal ASVs affiliated to Alternaria and Cladosporium. A genome-level functional profile analysis revealed that seed bacterial microbiota were enriched in amino acid, nucleoside, and nucleotide biosynthesis, while in fungal communities the generation of precursor metabolites and respiration were more highly represented. Together, these novel insights provide a deeper understanding of highly diversified plant-specific light seed microbiota and ecological strategies for plants in harsh environments.},
}

@article {pmid35049773,
year = {2022},
author = {Fu, H and Li, W},
title = {Metagenomic Comparisons between Soft and Hard Feces of Plateau Pikas (Ochotona curzoniae).},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/ani12020149},
pmid = {35049773},
issn = {2076-2615},
support = {no. 2017-ZJ-714//Applied Basic Research Programs of Qinghai Province/ ; },
abstract = {The division of hard and soft feces is an effective digestion strategy in the order Lagomorpha. Although previous studies have reported that hard and soft feces differ in morphology and component, the discrepancy in the microbiome remains unclear. This study explored the microbiomes of hard and soft feces in plateau pikas by sequencing the V3 and V4 regions of 16S rDNA. We found that hard feces harbored higher Firmicutes, while soft feces harbored higher Akkermansia. Increased rare bacterial taxa were observed in hard feces compared with soft feces. Moreover, hard and soft feces displayed a greater difference in terms of core operational taxonomy units (OTUs) compared to the total OTUs. The soft feces showed enhancements in all predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functions, indicating an advancing microbial metabolism compared to hard feces. The significantly upregulated pathways in soft feces were mainly enriched in metabolism of energy and carbohydrate, glycan biosynthesis, cofactors and vitamins, and amino acids-all of which are associated with increased contents of microbial proteins, vitamins, and short-chain fatty acids. Our study reports, for the first time, the differential microbiomes between hard and soft feces of pikas and provides direction for the future studies on cecotrophy.},
}

@article {pmid35049348,
year = {2022},
author = {Crossfield, M and Gilroy, R and Ravi, A and Baker, D and La Ragione, RM and Pallen, MJ},
title = {Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces.},
journal = {Microbiology resource announcements},
volume = {11},
number = {1},
pages = {e0114221},
doi = {10.1128/mra.01142-21},
pmid = {35049348},
issn = {2576-098X},
support = {BBS/E/F/000PR10351//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MR/L015080/1//UKRI | Medical Research Council (MRC)/ ; 773830//Horizon 2020/ ; },
abstract = {We report the recovery of metagenome-assembled genomes (MAGs) from fecal samples collected in 2018 from five healthy adult female pigs in southeast England. The resulting nonredundant catalog of 192 MAGs encompasses 102 metagenomic species, 41 of them novel, spanning 10 bacterial and 2 archaeal phyla.},
}

@article {pmid35049196,
year = {2021},
author = {Wang, G and Cong, D and Ju, H and Sun, J and Li, C and Zhang, Z and Chu, Y and Wu, X},
title = {Community intervention study of viscera massage in overweight/obese type 2 diabetes high-risk population.},
journal = {Medicine},
volume = {100},
number = {48},
pages = {e27932},
doi = {10.1097/MD.0000000000027932},
pmid = {35049196},
issn = {1536-5964},
support = {[2020]498//Department of Finance of Jilin Province/ ; 2019YFC1709904//National Basic Research Program of China (973 Program)/ ; JJKH20210959KJ//Education Department of Jilin Province/ ; 20200403124SF//Jilin Scientific and Technological Development Program/ ; 2020J065//Jilin Provincial Health and Family Planning Commission/ ; },
abstract = {BACKGROUND: Prediabetes is an intermediate metabolic state between normoglycemia and diabetes. Without intervention, prediabetes often progresses to diabetes and prediabetes is associated with increased risk of cardiovascular disease, cancer, renal disease, and dementia. Lifestyle modification play a major role in controlling prediabetes. But lifestyle interventions are often with poor compliance and side effects of drugs are often be dislike by people. As a non-invasive therapy with no side effects, abdominal massage (AM), also called viscera massage in China, has been used to treat prediabetes and obesity-associated diseases. The gut microbiota has been recognized as an important factor in the development of metabolic diseases. Individuals with prediabetes have aberrant intestinal microbiota character. Colonic transport time and stool consistency are strongly associated with gut microbiota. Viscera massage can ease constipation by reducing colonic transport time and promoting intestinal motility. We can infer that viscera massage can modulate composition of gut microbiota affects human metabolism. So, in this trial, we will explore the mechanism of viscera massage on prediabetes from the perspective of intestinal microbiota.

METHODS AND DESIGN: Eighty prediabetes individuals will be recruited for this study. Eighty prediabetes individuals will be divided into lifestyle intervention group and viscera massage + lifestyle intervention group by a simple random method. Each group will have 40 individuals. The manipulation of the viscera massage + lifestyle intervention group will be mainly carried out through rubbing the abdomen, kneading abdomen, vibrating abdomen, and pressing the abdomen, 30 minutes per time, once a day, with 2 days off every 5 days. Lifestyle interventions will be performed by combining pushing healthy lifestyle guidance information through Wechat application and giving face-to-face advice together daily. The lifestyle intervention group will receive healthy lifestyle intervention only. All the intervention will be conducted for 4 weeks. Weight, body mass index (BMI), waist circumference, waist-to-hip ratio, and waist-to-height ratio will be measured at the last day of every week. Triglycerides, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, fasting blood-glucose, 2-hour post-meal blood glucose (2hPG) and glycosylated hemoglobin, fasting insulin and insulin resistance index will be tested at the first day and last day of the intervention course. The fecal samples of subjects will be gathered at the first day and last day of the intervention course and will be performed 16S rRNA gene sequencing and metagenomic detection. Finally, the effect and potential mechanism of viscera massage on prediabetes will be discussed in combination with all the results.

DISCUSSION: The results of this study will be used to verify the effect of AM on prediabetes and explore the mechanism of AM on prediabetes from the perspective of gut microbiota.},
}

@article {pmid35049120,
year = {2022},
author = {Youngblut, ND and de la Cuesta-Zuluaga, J and Ley, RE},
title = {Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15910},
pmid = {35049120},
issn = {1462-2920},
abstract = {Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). Utilizing the Genome Taxonomy Database (GTDB) for species-level metagenome profiling allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 30 studies and 2943 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or equivalent to tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity, which is a fundamental component of microbiome science. This article is protected by copyright. All rights reserved.},
}

@article {pmid35049092,
year = {2022},
author = {Furuhashi, H and Takayasu, L and Isshi, K and Hara, Y and Ono, S and Kato, M and Sumiyama, K and Suda, W},
title = {Effect of storage temperature and flash-freezing on salivary microbiota profiles based on 16S rRNA-targeted sequencing.},
journal = {European journal of oral sciences},
volume = {},
number = {},
pages = {e12852},
doi = {10.1111/eos.12852},
pmid = {35049092},
issn = {1600-0722},
support = {//RIKEN Integrated Symbiology/ ; },
abstract = {The sample storage environment affects gut microbial profiles as assessed using 16S rRNA sequencing. However, the influence of storage condition on human salivary microbial profiles has not been well characterized. Here, we performed an observational study to assess the robustness of microbiota profiles in three different storage environments (-80°C after flash-freezing, -80°C, and -15°C; all for 14 days) compared to immediate DNA extraction using the MiSeq Illumina platform. Notably, the 16S rRNA V1-V2 region amplicon sequencing revealed no difference in microbiota profiles between the immediate extraction and each of three storage conditions. An almost perfect correlation was shown between the immediate extraction and the -15°C storage group for relative abundance at the genus and operational taxonomic unit levels. The intraindividual UniFrac distances among storage methods were significantly shorter than those of interindividual distances. None of the amount of extracted DNA, the α-diversity indices, or the relative abundance at the phylum/genus/operational taxonomic unit level differed among storage methods. These findings indicate that a storage temperature of -15°C without flash-freezing may be optimal in terms of cost advantage and simplicity in 16S rRNA sequencing-based salivary microbial research.},
}

@article {pmid35048500,
year = {2022},
author = {Zhou, H and Zhao, D and Zhang, S and Xue, Q and Zhang, M and Yu, H and Zhou, J and Li, M and Kumar, S and Xiang, H},
title = {Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15899},
pmid = {35048500},
issn = {1462-2920},
abstract = {The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation, and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes (MAGs) demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising of four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favorable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials, and evolutional significance of Ca. Haloplasmatales. This article is protected by copyright. All rights reserved.},
}

@article {pmid35048279,
year = {2022},
author = {Serag, AM and Abdel-Sabour, MS and El-Hadidi, M and Maged, M and Magdy, M and Ramadan, MF and Refaat, MH},
title = {Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {35048279},
issn = {1559-0291},
abstract = {Nile tilapia, Oreochromis niloticus, is the principal fish bred in Egypt. A pilot study was designed to analyze the bacterial composition of the Nile tilapia fish guts from two saltwater lakes in Northern Egypt. Fish samples were obtained from two Delta lakes: Manzala (ML) and Borollus (BL). DNA was extracted, and the bacterial communities in the stomach content were classified (down to the species level) using the 16S rRNA-based analysis. From the two metagenomics libraries in this study, 1,426,740 reads of the amplicon sequence corresponding to 508 total taxonomic operational units were recorded. The most prevalent bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes in all samples. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. A notable difference was observed between gut bacteria of Nile tilapia fish obtained from BL and ML. There is a remarkable indication that Nile tilapia fish living in BL is heavily burdened with pathogenic microbes most remarkably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This result was also consistent with the metagenomic data's functional prediction that indicated that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The findings show that the host environment has a significant impact on the composition of its microbiota. The first step towards exploring the better management of this profit-making fish is recognizing the structure of the microbiome.},
}

@article {pmid35048071,
year = {2021},
author = {Dame-Teixeira, N and de Lima, AKA and Do, T and Stefani, CM},
title = {Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {770917},
doi = {10.3389/froh.2021.770917},
pmid = {35048071},
issn = {2673-4842},
abstract = {Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data. Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54-3.90); p = 0.01]. Conclusions: Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.},
}

@article {pmid35047625,
year = {2021},
author = {Chen, L and Su, Y and Xiong, XZ},
title = {Rhizopus microsporus lung infection in an immunocompetent patient successfully treated with amphotericin B: A case report.},
journal = {World journal of clinical cases},
volume = {9},
number = {35},
pages = {11108-11114},
doi = {10.12998/wjcc.v9.i35.11108},
pmid = {35047625},
issn = {2307-8960},
abstract = {BACKGROUND: Rhizopus microsporus (R. microsporus) lung infection is an invasive fungal disease with high mortality that is increasingly common in immunocompromised patients. However, it is very rare in immunocompetent patients. Here, we present the case of a 19-year-old girl who developed R. microsporus lung infection without any known immunodeficiency.

CASE SUMMARY: The patient presented to our hospital because of hemoptysis and irritative cough without expectoration. She was first treated for community-acquired pneumonia until the detection of R. microsporus in bronchoalveolar lavage fluid by metagenomics next-generation sequencing (mNGS). After a combination therapy of intravenous inhalation and local airway perfusion of amphotericin B, she eventually recovered, with significant absorption of lung infections.

CONCLUSION: Early diagnosis and treatment are very important for pulmonary mucormycosis. Compared to fungal culture, mNGS is a relatively precise and convenient method to obtain pathogenic results. A combination therapy of intravenous inhalation and local airway perfusion of amphotericin B may be a promising strategy for the treatment of pulmonary mucormycosis in the future.},
}

@article {pmid35047117,
year = {2021},
author = {Passaro, AP and Marzuillo, P and Guarino, S and Scaglione, F and Miraglia Del Giudice, E and Di Sessa, A},
title = {Omics era in type 2 diabetes: From childhood to adulthood.},
journal = {World journal of diabetes},
volume = {12},
number = {12},
pages = {2027-2035},
doi = {10.4239/wjd.v12.i12.2027},
pmid = {35047117},
issn = {1948-9358},
abstract = {Parallel to the dramatic rise of pediatric obesity, estimates reported an increased prevalence of type 2 diabetes (T2D) already in childhood. The close relationship between obesity and T2D in children is mainly sustained by insulin resistance (IR). In addition, the cardiometabolic burden of T2D including nonalcoholic fatty liver disease, cardiovascular disease and metabolic syndrome is also strictly related to IR. Although T2D pathophysiology has been largely studied in an attempt to improve therapeutic options, molecular mechanisms are still not fully elucidated. In this perspective, omics approaches (including lipidomics, metabolomics, proteomics and metagenomics) are providing the most attractive therapeutic options for T2D. In particular, distinct both lipids and metabolites are emerging as potential therapeutic tools. Of note, among lipid classes, the pathogenic role of ceramides in T2D context has been supported by several data. Thus, selective changes of ceramides expression might represent innovative therapeutic strategies for T2D treatment. More, distinct metabolomics pathways have been also found to be associated with higher T2D risk, by providing novel potential T2D biomarkers. Taken together, omics data are responsible for the expanding knowledge of T2D pathophysiology, by providing novel insights to improve therapeutic strategies for this tangled disease. We aimed to summarize the most recent evidence in the intriguing field of the omics approaches in T2D both in adults and children.},
}

@article {pmid35047015,
year = {2021},
author = {Mukai, T and Amikura, K and Fu, X and Söll, D and Crnković, A},
title = {Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {794509},
doi = {10.3389/fgene.2021.794509},
pmid = {35047015},
issn = {1664-8021},
abstract = {Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.},
}

@article {pmid35046673,
year = {2022},
author = {Zhan, L and Huang, K and Xia, W and Chen, J and Wang, L and Lu, J and Wang, J and Lin, J and Wu, W},
title = {The Diagnosis of Severe Fever with Thrombocytopenia Syndrome Using Metagenomic Next-Generation Sequencing: Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {15},
number = {},
pages = {83-89},
doi = {10.2147/IDR.S345991},
pmid = {35046673},
issn = {1178-6973},
abstract = {Background: Severe fever with thrombocytopenia syndrome (SFTS) is an infectious disease caused by a bunyaviridae virus. Its main clinical manifestation is fever with thrombocytopenia, which may be accompanied by other clinical symptoms. Here, we report a patient diagnosed with SFTS using metagenomic next‑generation sequencing (mNGS).

Case Presentation: A 56-year-old female patient was hospitalized with intermittent diarrhea and fever. She visited a local clinic for treatment, but instead of improving, the symptoms progressed to unconsciousness.

Diagnosis: Using mNGS, we isolated the bunyaviridae virus and several other pathogens from the patient's blood samples to confirm the diagnosis.

Interventions: The patient was treated with symptomatic and supportive therapy, including intravenous human γ-globulin (20 g/d), platelet transfusion, platelet elevation (subcutaneous injection of recombinant human thrombopoietin, 15,000 IU), white blood cell elevation (subcutaneous injection of recombinant human granulocyte colony-stimulating factor, 200 ug, qd); and antibiotic (cefoperazone sodium and tazobactam sodium, 2 g, q8h), antiviral (ganciclovir, 250 mg, q12h), and antifungal therapy (voriconazole for injection, 0.2 g, q12h). After ten days of treatment, the patient's condition gradually improved.

Conclusion: Compared to traditional detection methods, mNGS has many advantages. It can quickly identify the pathogen when the patient's clinical manifestations are complex and difficult to diagnose, resulting in the formulation of an effective treatment.},
}

@article {pmid35045876,
year = {2022},
author = {Pan, J and Xu, W and Zhou, Z and Shao, Z and Dong, C and Liu, L and Luo, Z and Li, M},
title = {Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {8},
pmid = {35045876},
issn = {2049-2618},
support = {91851105//National Natural Science Foundation of China/ ; 32070108//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 41506163//National Natural Science Foundation of China/ ; 41776170//National Natural Science Foundation of China/ ; 41606145//National Natural Science Foundation of China/ ; DY135-B-09//China Ocean Mineral Resources Research and Development Association/ ; DY135-B-01//China Ocean Mineral Resources Research and Development Association/ ; 2016M602506//Postdoctoral Research Foundation of China/ ; 2020KCXTD023//Innovation Team Project of Universities in Guangdong Province/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; },
abstract = {BACKGROUND: Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field.

RESULTS: In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields.

CONCLUSIONS: This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.},
}

@article {pmid35045853,
year = {2022},
author = {Sun, Z and Song, ZG and Liu, C and Tan, S and Lin, S and Zhu, J and Dai, FH and Gao, J and She, JL and Mei, Z and Lou, T and Zheng, JJ and Liu, Y and He, J and Zheng, Y and Ding, C and Qian, F and Zheng, Y and Chen, YM},
title = {Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients.},
journal = {BMC medicine},
volume = {20},
number = {1},
pages = {24},
pmid = {35045853},
issn = {1741-7015},
support = {2017SHZDZX01//Science and Technology Commission of Shanghai Municipality/ ; 20490780100//Science and Technology Commission of Shanghai Municipality for International Partnership Project/ ; 31741072//National Natural Science Foundation of China/ ; 81973032//National Natural Science Foundation of China/ ; 32041004//National Natural Science Foundation of China/ ; 31930001//National Natural Science Foundation of China/ ; 3213000167//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology.

METHODS: To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients.

RESULTS: Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients.

CONCLUSIONS: Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.},
}

@article {pmid35045830,
year = {2022},
author = {Jiang, Z and Li, X and Guo, L},
title = {MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset's complexity.},
journal = {BMC bioinformatics},
volume = {22},
number = {Suppl 12},
pages = {315},
pmid = {35045830},
issn = {1471-2105},
support = {no. 61373057//Innovative Research Group Project of the National Natural Science Foundation of China/ ; No. LGF21F020008//Zhejiang Province Public Welfare Technology Application Research Project/ ; no. 2019RC05//the Science and Technology Planning Project of Lishui City/ ; no. 2018A610057//Natural Science Foundation of Ningbo Municipality/ ; },
abstract = {BACKGROUND: Metagenomics technology can directly extract microbial genetic material from the environmental samples to obtain their sequencing reads, which can be further assembled into contigs through assembly tools. Clustering methods of contigs are subsequently applied to recover complete genomes from environmental samples. The main problems with current clustering methods are that they cannot recover more high-quality genes from complex environments. Firstly, there are multiple strains under the same species, resulting in assembly of chimeras. Secondly, different strains under the same species are difficult to be classified. Thirdly, it is difficult to determine the number of strains during the clustering process.

RESULTS: In view of the shortcomings of current clustering methods, we propose an unsupervised clustering method which can improve the ability to recover genes from complex environments and a new method for selecting the number of sample's strains in clustering process. The sequence composition characteristics (tetranucleotide frequency) and co-abundance are combined to train the probability model for clustering. A new recursive method that can continuously reduce the complexity of the samples is proposed to improve the ability to recover genes from complex environments. The new clustering method was tested on both simulated and real metagenomic datasets, and compared with five state-of-the-art methods including CONCOCT, Maxbin2.0, MetaBAT, MyCC and COCACOLA. In terms of the number and quality of recovered genes from metagenomic datasets, the results show that our proposed method is more effective.

CONCLUSIONS: A new contigs clustering method is proposed, which can recover more high-quality genes from complex environmental samples.},
}

@article {pmid34525937,
year = {2021},
author = {Moran-Ramos, S and Macias-Kauffer, L and López-Contreras, BE and Villamil-Ramírez, H and Ocampo-Medina, E and León-Mimila, P and Del Rio-Navarro, BE and Granados-Portillo, O and Ibarra-Gonzalez, I and Vela-Amieva, M and Tovar, AR and Torres, N and Gomez-Perez, FJ and Aguilar-Salinas, C and Canizales-Quinteros, S},
title = {A higher bacterial inward BCAA transport driven by Faecalibacterium prausnitzii is associated with lower serum levels of BCAA in early adolescents.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {27},
number = {1},
pages = {108},
pmid = {34525937},
issn = {1528-3658},
support = {248765//consejo nacional de ciencia y tecnología/ ; },
mesh = {Adolescent ; Age Factors ; Amino Acids, Branched-Chain/*blood/metabolism ; Biomarkers ; Body Weights and Measures ; Child ; Faecalibacterium prausnitzii/*physiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Insulin Resistance ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Obesity/metabolism ; Public Health Surveillance ; },
abstract = {BACKGROUND: Elevations of circulating branched-chain amino acids (BCAA) are observed in humans with obesity and metabolic comorbidities, such as insulin resistance. Although it has been described that microbial metabolism contributes to the circulating pool of these amino acids, studies are still scarce, particularly in pediatric populations. Thus, we aimed to explore whether in early adolescents, gut microbiome was associated to circulating BCAA and in this way to insulin resistance.

METHODS: Shotgun sequencing was performed in DNA from fecal samples of 23 early adolescents (10-12 years old) and amino acid targeted metabolomics analysis was performed by LC-MS/MS in serum samples. By using the HUMAnN2 algorithm we explored microbiome functional profiles to identify whether bacterial metabolism contributed to serum BCAA levels and insulin resistance markers.

RESULTS: We identified that abundance of genes encoding bacterial BCAA inward transporters were negatively correlated with circulating BCAA and HOMA-IR (P < 0.01). Interestingly, Faecalibacterium prausnitzii contributed to approximately ~ 70% of bacterial BCAA transporters gene count. Moreover, Faecalibacterium prausnitzii abundance was also negatively correlated with circulating BCAA (P = 0.001) and with HOMA-IR (P = 0.018), after adjusting for age, sex and body adiposity. Finally, the association between Faecalibacterium genus and BCAA levels was replicated over an extended data set (N = 124).

CONCLUSIONS: We provide evidence that gut bacterial BCAA transport genes, mainly encoded by Faecalibacterium prausnitzii, are associated with lower circulating BCAA and lower insulin resistance. Based on the later, we propose that the relationship between Faecalibacterium prausnitzii and insulin resistance, could be through modulation of BCAA.},
}

Adolescent
Age Factors
Amino Acids, Branched-Chain/*blood/metabolism
Biomarkers
Body Weights and Measures
Child
Faecalibacterium prausnitzii/*physiology
Female
*Gastrointestinal Microbiome
Humans
Insulin Resistance
Male
Metabolomics/methods
Metagenome
Metagenomics/methods
Obesity/metabolism
Public Health Surveillance

@article {pmid34424154,
year = {2021},
author = {Pereira, D and Oggenfuss, U and McDonald, BA and Croll, D},
title = {Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen.},
journal = {Microbial genomics},
volume = {7},
number = {8},
pages = {},
pmid = {34424154},
issn = {2057-5858},
mesh = {Ascomycota/genetics/isolation & purification ; *DNA Transposable Elements ; Evolution, Molecular ; Genetic Variation ; Genome ; Genome, Fungal ; Genomics ; *Metagenomics ; Plant Diseases/microbiology ; Retroelements ; },
abstract = {The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.},
}

Ascomycota/genetics/isolation & purification
*DNA Transposable Elements
Evolution, Molecular
Genetic Variation
Genome
Genome, Fungal
Genomics
*Metagenomics
Plant Diseases/microbiology
Retroelements

@article {pmid34356001,
year = {2021},
author = {Zeng, Q and Yang, Z and Wang, F and Li, D and Liu, Y and Wang, D and Zhao, X and Li, Y and Wang, Y and Feng, X and Chen, J and Li, Y and Zheng, Y and Kenney, T and Gu, H and Feng, S and Li, S and He, Y and Xu, X and Dai, W},
title = {Association between metabolic status and gut microbiome in obese populations.},
journal = {Microbial genomics},
volume = {7},
number = {8},
pages = {},
pmid = {34356001},
issn = {2057-5858},
mesh = {Bacteria/*classification/genetics ; Biomarkers ; China ; Cohort Studies ; Diet ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Diseases ; Metagenome ; *Obesity ; },
abstract = {Despite that obesity is associated with many metabolic diseases, a significant proportion (10-30 %) of obese individuals is recognized as 'metabolically healthy obeses' (MHOs). The aim of the current study is to characterize the gut microbiome for MHOs as compared to 'metabolically unhealthy obeses' (MUOs). We compared the gut microbiome of 172 MHO and 138 MUO individuals from Chongqing (China) (inclined to eat red meat and food with a spicy taste), and performed validation with selected biomarkers in 40 MHOs and 33 MUOs from Quanzhou (China) (inclined to eat seafood and food with a light/bland taste). The genera Alistipes, Faecalibacterium and Odoribacter had increased abundance in both Chongqing and Quanzhou MHOs. We also observed different microbial functions in MUOs compared to MHOs, including an increased abundance of genes associated with glycan biosynthesis and metabolism. In addition, the microbial gene markers identified from the Chongqing cohort bear a moderate accuracy [AUC (area under the operating characteristic curve)=0.69] for classifying MHOs distinct from MUOs in the Quanzhou cohort. These findings indicate that gut microbiome is significantly distinct between MHOs and MUOs, implicating the potential of the gut microbiome in stratification and refined management of obesity.},
}

Bacteria/*classification/genetics
Biomarkers
China
Cohort Studies
Diet
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Humans
Metabolic Diseases
Metagenome
*Obesity

@article {pmid34183041,
year = {2021},
author = {Jiang, R and Li, WV and Li, JJ},
title = {mbImpute: an accurate and robust imputation method for microbiome data.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {192},
pmid = {34183041},
issn = {1474-760X},
support = {R01 GM120507/GM/NIGMS NIH HHS/United States ; },
mesh = {Actinobacteria/classification/genetics/isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Case-Control Studies ; Colorectal Neoplasms/diagnosis/*microbiology/pathology ; DNA, Bacterial/*genetics ; Diabetes Mellitus, Type 2/diagnosis/*microbiology/pathology ; Firmicutes/classification/genetics/isolation & purification ; Fusobacteria/classification/genetics/isolation & purification ; Humans ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Software ; Whole Genome Sequencing ; },
abstract = {A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.},
}

Actinobacteria/classification/genetics/isolation & purification
Bacteroidetes/classification/genetics/isolation & purification
Case-Control Studies
Colorectal Neoplasms/diagnosis/*microbiology/pathology
DNA, Bacterial/*genetics
Diabetes Mellitus, Type 2/diagnosis/*microbiology/pathology
Firmicutes/classification/genetics/isolation & purification
Fusobacteria/classification/genetics/isolation & purification
Humans
*Metagenome
Microbiota/*genetics
Phylogeny
Polymerase Chain Reaction/methods
Proteobacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Software
Whole Genome Sequencing

@article {pmid35045174,
year = {2022},
author = {Shilo, S and Godneva, A and Rachmiel, M and Korem, T and Bussi, Y and Kolobkov, D and Karady, T and Bar, N and Wolf, BC and Glantz-Gashai, Y and Cohen, M and Levin, NZ and Shehadeh, N and Gruber, N and Levran, N and Koren, S and Weinberger, A and Pinhas-Hamiel, O and Segal, E},
title = {The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dc21-1656},
pmid = {35045174},
issn = {1935-5548},
abstract = {OBJECTIVE: Previous studies have demonstrated an association between gut microbiota composition and type 1 diabetes (T1D) pathogenesis. However, little is known about the composition and function of the gut microbiome in adults with longstanding T1D or its association with host glycemic control.

RESEARCH DESIGN AND METHODS: We performed a metagenomic analysis of the gut microbiome obtained from fecal samples of 74 adults with T1D, 14.6 ± 9.6 years following diagnosis, and compared their microbial composition and function to 296 age-matched healthy control subjects (1:4 ratio). We further analyzed the association between microbial taxa and indices of glycemic control derived from continuous glucose monitoring measurements and blood tests and constructed a prediction model that solely takes microbiome features as input to evaluate the discriminative power of microbial composition for distinguishing individuals with T1D from control subjects.

RESULTS: Adults with T1D had a distinct microbial signature that separated them from control subjects when using prediction algorithms on held-out subjects (area under the receiver operating characteristic curve = 0.89 ± 0.03). Linear discriminant analysis showed several bacterial species with significantly higher scores in T1D, including Prevotella copri and Eubacterium siraeum, and species with higher scores in control subjects, including Firmicutes bacterium and Faecalibacterium prausnitzii (P < 0.05, false discovery rate corrected for all). On the functional level, several metabolic pathways were significantly lower in adults with T1D. Several bacterial taxa and metabolic pathways were associated with the host's glycemic control.

CONCLUSIONS: We identified a distinct gut microbial signature in adults with longstanding T1D and associations between microbial taxa, metabolic pathways, and glycemic control indices. Additional mechanistic studies are needed to identify the role of these bacteria for potential therapeutic strategies.},
}

@article {pmid35044669,
year = {2022},
author = {Kumar, RS and Mishra, N and Kumar, A},
title = {Characterization of Tobacco Microbiome by Metagenomics Approach.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2413},
number = {},
pages = {229-244},
pmid = {35044669},
issn = {1940-6029},
abstract = {Chronic consumption of tobacco in all forms, either smoked/smokeless forms, causes major health hazards to humans that include cancer, cardiovascular, lung diseases, diabetes, fertility issues, etc. Among tobacco-mediated cancers, the prominent one being the oral cancers are caused due to chronic tobacco chewing. The biochemicals present in tobacco are involved in carcinogenesis, and their presence is partly mediated by the existence of microbes in tobacco products. The microbial characterization has been evolved from classical microscopical observation to the recent development of 16S rRNA sequencing by next-generation sequencing methods. The metagenomics approach using 16S rRNA-based next-generation sequencing methods enables the detection and characterization of the complete microbial community of tobacco, including both cultivable and non-cultivable microorganisms. Identification of microbes will help in devising strategies to limit the carcinogenic compounds present in tobacco.},
}

@article {pmid33563315,
year = {2021},
author = {Wu, G and Zhao, N and Zhang, C and Lam, YY and Zhao, L},
title = {Guild-based analysis for understanding gut microbiome in human health and diseases.},
journal = {Genome medicine},
volume = {13},
number = {1},
pages = {22},
pmid = {33563315},
issn = {1756-994X},
mesh = {Databases, Genetic ; *Disease ; Female ; *Gastrointestinal Microbiome/genetics ; *Health ; Humans ; Metagenomics ; Obesity/genetics ; Phylogeny ; Polycystic Ovary Syndrome/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same "guild" if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of "guild" to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.},
}

Databases, Genetic
*Disease
Female
*Gastrointestinal Microbiome/genetics
*Health
Humans
Metagenomics
Obesity/genetics
Phylogeny
Polycystic Ovary Syndrome/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid35041771,
year = {2022},
author = {Ahearn-Ford, S and Berrington, JE and Stewart, CJ},
title = {Development of the gut microbiome in early life.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP089919},
pmid = {35041771},
issn = {1469-445X},
abstract = {NEW FINDINGS: What is the topic of this review? This symposium report discusses the importance of the early life gut microbiome, with a focus on preterm infants and microbially-related diseases. Current techniques to study the preterm gut microbiome are appraised, and the potential of recent methodological advancements is discussed. What advances does it highlight? Recent findings in the field achieved by the application of advanced technologies are acknowledged. The review also highlights the applicability of intestinal-derived organoid models to study host-microbiome interactions in the preterm gut, and recent developments in enhancing the physiological relevance of such models. Preterm intestinal-derived organoids may provide novel insights into the mechanisms underlying preterm disease, as well as diagnosis and treatment opportunities. These models have huge translational potential, offering a step towards precision medicine.

ABSTRACT: Accumulating evidence affirms the importance of the gut microbiome in both health and disease. In early life, there exists a critical period in which the composition of gut microbes is particularly malleable and subject to a wide range of influencing factors. Disturbances to microbial communities during this time may be beneficial or detrimental to short and long-term health outcomes. For infants born prematurely, naïve immune systems, immature gastrointestinal tracts and additional clinical needs put this population at high risk of abnormal microbial colonisation, resulting in an increased susceptibility to diseases including necrotising enterocolitis (NEC) and late-onset sepsis (LOS). Traditional cell culture methods, gnotobiotic animals, molecular sequencing techniques (16S rRNA gene sequencing and metagenomics) and advanced "omics" technologies (transcriptomics, proteomics and metabolomics) have been fundamental in exploring the associations between diet, gut microbes, microbial functions, and disease. Despite significant investment and ongoing research efforts, prevention and treatment strategies in NEC and LOS remain limited. Recent endeavours have focused on searching for new, more physiologically relevant models to simulate the preterm intestine. Preterm intestinal-derived organoids represent a promising in vitro approach in the study of host-microbial interactions in the preterm infant gut, offering new and exciting possibilities in this field. This article is protected by copyright. All rights reserved.},
}

@article {pmid35040752,
year = {2022},
author = {Chen, Y and Wang, H and Lu, W and Wu, T and Yuan, W and Zhu, J and Lee, YK and Zhao, J and Zhang, H and Chen, W},
title = {Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2025016},
doi = {10.1080/19490976.2021.2025016},
pmid = {35040752},
issn = {1949-0984},
abstract = {The human gut microbiome is a complex ecosystem that is closely related to the aging process. However, there is currently no reliable method to make full use of the metagenomics data of the gut microbiome to determine the age of the host. In this study, we considered the influence of geographical factors on the gut microbiome, and a total of 2604 filtered metagenomics data from the gut microbiome were used to construct an age prediction model. Then, we developed an ensemble model with multiple heterogeneous algorithms and combined species and pathway profiles for multi-view learning. By integrating gut microbiome metagenomics data and adjusting host confounding factors, the model showed high accuracy (R2 = 0.599, mean absolute error = 8.33 years). Besides, we further interpreted the model and identify potential biomarkers for the aging process. Among these identified biomarkers, we found that Finegoldia magna, Bifidobacterium dentium, and Clostridium clostridioforme had increased abundance in the elderly. Moreover, the utilization of amino acids by the gut microbiome undergoes substantial changes with increasing age which have been reported as the risk factors for age-associated malnutrition and inflammation. This model will be helpful for the comprehensive utilization of multiple omics data, and will allow greater understanding of the interaction between microorganisms and age to realize the targeted intervention of aging.},
}

@article {pmid35040702,
year = {2022},
author = {Dragone, NB and Henley, JB and Holland-Moritz, H and Diaz, M and Hogg, ID and Lyons, WB and Wall, DH and Adams, BJ and Fierer, N},
title = {Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0133021},
doi = {10.1128/msystems.01330-21},
pmid = {35040702},
issn = {2379-5077},
abstract = {The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.},
}

@article {pmid35039619,
year = {2022},
author = {Mousavi, SH and Sadeghian Motahar, SF and Salami, M and Kavousi, K and Sheykh Abdollahzadeh Mamaghani, A and Ariaeenejad, S and Salekdeh, GH},
title = {Author Correction: In vitro bioprocessing of corn as poultry feed additive by the influence of carbohydrate hydrolyzing metagenome derived enzyme cocktail.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {1176},
doi = {10.1038/s41598-022-05555-7},
pmid = {35039619},
issn = {2045-2322},
}

@article {pmid35039616,
year = {2022},
author = {Zheng, X and Jahn, MT and Sun, M and Friman, VP and Balcazar, JL and Wang, J and Shi, Y and Gong, X and Hu, F and Zhu, YG},
title = {Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35039616},
issn = {1751-7370},
support = {RSG\R1\180213//Royal Society/ ; },
abstract = {Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.},
}

@article {pmid35039534,
year = {2022},
author = {Lee, SJ and Rho, M},
title = {Multimodal deep learning applied to classify healthy and disease states of human microbiome.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {824},
pmid = {35039534},
issn = {2045-2322},
support = {2017M3A9F3041232//National Research Foundation of Korea/ ; 2020-0-01373//Institute of Information & Communications Technology Planning & Evaluation (IITP)/ ; },
abstract = {Metagenomic sequencing methods provide considerable genomic information regarding human microbiomes, enabling us to discover and understand microbial diseases. Compositional differences have been reported between patients and healthy people, which could be used in the diagnosis of patients. Despite significant progress in this regard, the accuracy of these tools needs to be improved for applications in diagnostics and therapeutics. MDL4Microbiome, the method developed herein, demonstrated high accuracy in predicting disease status by using various features from metagenome sequences and a multimodal deep learning model. We propose combining three different features, i.e., conventional taxonomic profiles, genome-level relative abundance, and metabolic functional characteristics, to enhance classification accuracy. This deep learning model enabled the construction of a classifier that combines these various modalities encoded in the human microbiome. We achieved accuracies of 0.98, 0.76, 0.84, and 0.97 for predicting patients with inflammatory bowel disease, type 2 diabetes, liver cirrhosis, and colorectal cancer, respectively; these are comparable or higher than classical machine learning methods. A deeper analysis was also performed on the resulting sets of selected features to understand the contribution of their different characteristics. MDL4Microbiome is a classifier with higher or comparable accuracy compared with other machine learning methods, which offers perspectives on feature generation with metagenome sequences in deep learning models and their advantages in the classification of host disease status.},
}

@article {pmid35039079,
year = {2022},
author = {Adu-Oppong, B and Thänert, R and Wallace, MA and Burnham, CD and Dantas, G},
title = {Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {6},
pmid = {35039079},
issn = {2049-2618},
abstract = {BACKGROUND: The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota.

RESULTS: The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as 'insignificant', 'contaminated', or 'no-growth' by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae.

CONCLUSION: Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract.},
}

@article {pmid35038864,
year = {2022},
author = {Xie, J and Jin, L and Wu, D and Pruden, A and Li, X},
title = {Inhalable Antibiotic Resistome from Wastewater Treatment Plants to Urban Areas: Bacterial Hosts, Dissemination Risks, and Source Contributions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.1c07023},
pmid = {35038864},
issn = {1520-5851},
abstract = {Antibiotic resistance genes (ARGs) are commonly detected in the atmosphere, but questions remain regarding their sources and relative contributions, bacterial hosts, and corresponding human health risks. Here, we conducted a qPCR- and metagenomics-based investigation of inhalable fine particulate matter (PM2.5) at a large wastewater treatment plant (WWTP) and in the ambient air of Hong Kong, together with an in-depth analysis of published data of other potential sources in the area. PM2.5 was observed with increasing enrichment of total ARGs along the coastal-urban-WWTP gradient and clinically relevant ARGs commonly identified in urban and WWTP sites, illustrating anthropogenic impacts on the atmospheric accumulation of ARGs. With certain kinds of putative antibiotic-resistant pathogens detected in urban and WWTP PM2.5, a comparable proportion of ARGs that co-occurred with MGEs was found between the atmosphere and WWTP matrices. Despite similar emission rates of bacteria and ARGs within each WWTP matrix, about 11-13% of the bacteria and >57% of the relevant ARGs in urban and WWTP PM2.5 were attributable to WWTPs. Our study highlights the importance of WWTPs in disseminating bacteria and ARGs to the ambient air from a quantitative perspective and, thus, the need to control potential sources of inhalation exposure to protect the health of urban populations.},
}

@article {pmid35038509,
year = {2022},
author = {Wen, L and Huang, L and Wang, Y and Yuan, Y and Zhou, L},
title = {Facet-engineered hematite boosts microbial electrogenesis by synergy of promoting electroactive biofilm formation and extracellular electron transfer.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {153154},
doi = {10.1016/j.scitotenv.2022.153154},
pmid = {35038509},
issn = {1879-1026},
abstract = {Hematite has been proven to be an excellent material for enhancing extracellular electron transfer (EET) in microbial bioelectrochemical systems (BESs). However, the effect of hematite with different exposed facets on microbial EET remains unclear. Here, we synthesized two types of hematite nanoparticles with high {100}
and {001}
facet exposure (Hem_{100}
and Hem_{001})
, respectively, which were coated on ITO electrode to stimulate the microbial EET in the BESs. The results showed that the maximum biocurrent density of commercial hematite nanoparticles (Hem_NPs), Hem_{100}
and Hem_{001}
electrodes reached 73.33 ± 5.68, 129.33 ± 9.12 and 287.00 ± 19.89 μA cm-2 from three replicates of each treatment, respectively. The current generation achieved from the Hem_{001}
electrode was nearly 199-times higher than that of the blank ITO electrode (1.44 ± 0.10 μA cm-2). The electrochemical measurements showed that the lowest charge transfer resistance (Rct) was observed for the Hem_{001},
and the promoted biofilm formation and EPS secretion on the Hem_{001}
electrode were also revealed, which could contribute the high performance of this electrode. Moreover, metagenomic analysis revealed that Hem_{001}
might facilitate the microbial EET by stimulating the expression of genes related to cytochrome c and conductive nanowires. This study not only provides a new strategy to enhance microbial electrogenesis but also expands the knowledge of the effect of facet on microbial EET, helping to develop more efficient electrode materials in the future.},
}

@article {pmid35038012,
year = {2022},
author = {Zhou, SP and Zhou, HY and Sun, JC and Liu, C and Ke, X and Zou, SP and Xue, YP and Zheng, YG},
title = {Bacterial dynamics and functions driven by bulking agents to enhance organic degradation in food waste in-situ rapid biological reduction (IRBR).},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {35038012},
issn = {1615-7605},
abstract = {This study investigated the effects of different bulking agents (i.e., sawdust, wheat straw, rice straw, and corncob) on bacterial structure and functions for organic degradation during food waste in-situ rapid biological reduction (IRBR) inoculated with microbial agent. Results showed that the highest organic degradation (409.5 g/kg total solid) and volatile solids removal efficiency (41.0%) were achieved when wheat straw was used, largely because the degradation of readily degradable substrates and cellulose was promoted by this bulking agent. Compared with other three bulking agents, the utilization of wheat straw was conducive to construct a more suitable environmental condition (moisture content of 18.0-28.2%, pH of 4.91-5.87) for organic degradation during IRBR process, by virtue of its excellent structural and physiochemical properties. Microbial community analysis suggested that the high-moisture environment in rice straw treatment promoted the growth of Staphylococcus and inhibited the activity of the inoculum. By contrast, lowest bacterial richness was observed in corncob treatment due to the faster water loss. Compared with these two bulking agents, sawdust and wheat straw treatment led to a more stable bacterial community structure, and the inoculated Bacillus gradually became the dominant genus (36.6-57.8%) in wheat straw treatment. Predicted metagenomics analysis showed that wheat straw treatment exhibited the highest carbohydrate metabolism activity which improved the pyruvate, amino sugar and nucleotide sugar metabolism, and thereby promoted the organic degradation and humic substrate production. These results indicated that wheat straw was a more desirable bulking agent, and revealed the potential microbial organics degradation mechanism in IRBR process.},
}

@article {pmid35037933,
year = {2022},
author = {Costa, SS and Lago, LAB and Silva, A and Graças, DAD and Lameira, J and Baraúna, RA},
title = {Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin.},
journal = {Genetics and molecular biology},
volume = {45},
number = {1},
pages = {e20210204},
doi = {10.1590/1678-4685-GMB-2021-0204},
pmid = {35037933},
issn = {1415-4757},
abstract = {Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.},
}

@article {pmid35037767,
year = {2022},
author = {Shen, Y and Laue, HE and Shrubsole, MJ and Wu, H and Bloomquist, TR and Larouche, A and Zhao, K and Gao, F and Boivin, A and Prada, D and Hunting, DJ and Gillet, V and Takser, L and Baccarelli, AA},
title = {Associations of Childhood and Perinatal Blood Metals with Children's Gut Microbiomes in a Canadian Gestation Cohort.},
journal = {Environmental health perspectives},
volume = {130},
number = {1},
pages = {17007},
doi = {10.1289/EHP9674},
pmid = {35037767},
issn = {1552-9924},
abstract = {BACKGROUND: The gut microbiome is important in modulating health in childhood. Metal exposures affect multiple health outcomes, but their ability to modify bacterial communities in children is poorly understood.

OBJECTIVES: We assessed the associations of childhood and perinatal blood metal levels with childhood gut microbiome diversity, structure, species, gene family-inferred species, and potential pathway alterations.

METHODS: We assessed the gut microbiome using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing in stools collected from 6- to 7-year-old children participating in the GESTation and Environment (GESTE) cohort study. We assessed blood metal concentrations [cadmium (Cd), manganese (Mn), mercury (Hg), lead (Pb), selenium (Se)] at two time points, namely, perinatal exposures at delivery (N=70) and childhood exposures at the 6- to 7-y follow-up (N=68). We used multiple covariate-adjusted statistical models to determine microbiome associations with continuous blood metal levels, including linear regression (Shannon and Pielou alpha diversity indexes), permutational multivariate analysis of variance (adonis; beta diversity distance matrices), and multivariable association model (MaAsLin2; phylum, family, species, gene family-inferred species, and pathways).

RESULTS: Children's blood Mn and Se significantly associated with microbiome phylum [e.g., Verrucomicrobiota (coef=-0.305, q=0.031; coef=0.262, q=0.084, respectively)] and children's blood Mn significantly associated with family [e.g., Eggerthellaceae (coef=-0.228, q=0.052)]-level differences. Higher relative abundance of potential pathogens (e.g., Flavonifractor plautii), beneficial species (e.g., Bifidobacterium longum, Faecalibacterium prausnitzii), and both potentially pathogenic and beneficial species (e.g., Bacteriodes vulgatus, Eubacterium rectale) inferred from gene families were associated with higher childhood or perinatal blood Cd, Hg, and Pb (q<0.1). We found significant negative associations between childhood blood Pb and acetylene degradation pathway abundance (q<0.1). Finally, neither perinatal nor childhood metal concentrations were associated with children's gut microbial inter- and intrasubject diversity.

DISCUSSION: Our findings suggest both long- and short-term associations between metal exposure and the childhood gut microbiome, with stronger associations observed with more recent exposure. Future epidemiologic analyses may elucidate whether the observed changes in the microbiome relate to children's health. https://doi.org/10.1289/EHP9674.},
}

@article {pmid35037474,
year = {2022},
author = {Rayo, E and Ferrari, G and Neukamm, J and Akgül, G and Breidenstein, AM and Cooke, M and Phillips, C and Bouwman, AS and Rühli, FJ and Schuenemann, VJ},
title = {Non-destructive extraction of DNA from preserved tissues in medical collections.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2021-0014},
pmid = {35037474},
issn = {1940-9818},
support = {URPP Evolution in Action pilot project grant//Universität Zürich/ ; },
abstract = {Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections.},
}

@article {pmid35036827,
year = {2021},
author = {Goller, CC and Srougi, MC and Chen, SH and Schenkman, LR and Kelly, RM},
title = {Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules.},
journal = {Frontiers in education},
volume = {6},
number = {},
pages = {},
doi = {10.3389/feduc.2021.711403},
pmid = {35036827},
issn = {2504-284X},
abstract = {The accelerating expansion of online bioinformatics tools has profoundly impacted molecular biology, with such tools becoming integral to the modern life sciences. As a result, molecular biology laboratory education must train students to leverage bioinformatics in meaningful ways to be prepared for a spectrum of careers. Institutions of higher learning can benefit from a flexible and dynamic instructional paradigm that blends up-to-date bioinformatics training with best practices in molecular biology laboratory pedagogy. At North Carolina State University, the campus-wide interdisciplinary Biotechnology (BIT) Program has developed cutting-edge, flexible, inquiry-based Molecular Biology Laboratory Education Modules (MBLEMs). MBLEMs incorporate relevant online bioinformatics tools using evidenced-based pedagogical practices and in alignment with national learning frameworks. Students in MBLEMs engage in the most recent experimental developments in modern biology (e.g., CRISPR, metagenomics) through the strategic use of bioinformatics, in combination with wet-lab experiments, to address research questions. MBLEMs are flexible educational units that provide a menu of inquiry-based laboratory exercises that can be used as complete courses or as parts of existing courses. As such, MBLEMs are designed to serve as resources for institutions ranging from community colleges to research-intensive universities, involving a diverse range of learners. Herein, we describe this new paradigm for biology laboratory education that embraces bioinformatics as a critical component of inquiry-based learning for undergraduate and graduate students representing the life sciences, the physical sciences, and engineering.},
}

@article {pmid35036659,
year = {2021},
author = {Borroni, D and Rachwani-Anil, R and González, JMS and Rodríguez-Calvo-de-Mora, M and Rocha de Lossada, C},
title = {Metagenome techniques to reduce diagnostic delay in Acanthamoeba keratitis.},
journal = {Romanian journal of ophthalmology},
volume = {65},
number = {3},
pages = {307-308},
doi = {10.22336/rjo.2021.63},
pmid = {35036659},
issn = {2501-2533},
}

@article {pmid35036494,
year = {2022},
author = {Tran, DM and Huynh, TU and Nguyen, TH and Do, TO and Tran, TPH and Nguyen, QV and Nguyen, AD},
title = {Soil microbiome dataset from Yok Don national park in the Central Highlands region of Vietnam.},
journal = {Data in brief},
volume = {40},
number = {},
pages = {107798},
doi = {10.1016/j.dib.2022.107798},
pmid = {35036494},
issn = {2352-3409},
abstract = {The Central Highlands region contains most of the national parks in Vietnam with different ecosystems, including the national parks of Kon Ka Kinh, Chu Mon Ray, Chu Yang Sin, Yok Don, Bidoup-Nui Ba, and Ta Dung. Thus, this region is considered a center with the highest biodiversity in Vietnam [1]. Among the national parks, Yok Don is unique in its conservation of the dry deciduous dipterocarp forest. Furthermore, Yok Don is the second-largest park in Vietnam; it has the most different ecosystem compared with other national parks in this region [2]. Although some studies have investigated biodiversity preservation in the region, some other studies have only dealt with medicinal plants, lichens, and the rhizospheric bacteria of cultivated black pepper [1,[3], [4], [5]. To the best of our knowledge, no research on the microbial communities in Yok Don national park and in the Central Highlands has been reported. At present, global warming and a decrease in the forest area in the Central Highlands have led to the ongoing reduction in biodiversity and microbial resources. The current study reports the microbiome dataset from the soil sample collected in Yok Don national park. Metagenomic next-generation sequencing was used to characterize the microbial communities in the sample. The metagenome dataset generated provides information on microbial diversity and its functionality and can be useful for further studies on the conservation and use of microbial genetic resources in this region.},
}

@article {pmid35035791,
year = {2022},
author = {Piquer-Esteban, S and Ruiz-Ruiz, S and Arnau, V and Diaz, W and Moya, A},
title = {Exploring the universal healthy human gut microbiota around the World.},
journal = {Computational and structural biotechnology journal},
volume = {20},
number = {},
pages = {421-433},
pmid = {35035791},
issn = {2001-0370},
abstract = {The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.},
}

@article {pmid35035382,
year = {2021},
author = {Díaz-García, L and Chaparro, D and Jiménez, H and Gómez-Ramírez, LF and Bernal, AJ and Burbano-Erazo, E and Jiménez, DJ},
title = {Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {744075},
pmid = {35035382},
issn = {1664-302X},
abstract = {Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1-T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4-5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.},
}

@article {pmid35035239,
year = {2022},
author = {Chu, LL and Bae, H},
title = {Bacterial endophytes from ginseng and their biotechnological application.},
journal = {Journal of ginseng research},
volume = {46},
number = {1},
pages = {1-10},
pmid = {35035239},
issn = {1226-8453},
abstract = {Ginseng has been well-known as a medicinal plant for thousands of years. Bacterial endophytes ubiquitously colonize the inside tissues of ginseng without any disease symptoms. The identification of bacterial endophytes is conducted through either the internal transcribed spacer region combined with ribosomal sequences or metagenomics. Bacterial endophyte communities differ in their diversity and composition profile, depending on the geographical location, cultivation condition, and tissue, age, and species of ginseng. Bacterial endophytes have a significant effect on the growth of ginseng through indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and nitrogen fixation. Moreover, bacterial endophytes can protect ginseng by acting as biocontrol agents. Interestingly, bacterial endophytes isolated from Panax species have the potential to produce ginsenosides and bioactive metabolites, which can be used in the production of food and medicine. The ability of bacterial endophytes to transform major ginsenosides into minor ginsenosides using β-glucosidase is gaining increasing attention as a promising biotechnology. Recently, metabolic engineering has accelerated the possibilities for potential applications of bacterial endophytes in producing beneficial secondary metabolites.},
}

@article {pmid35034639,
year = {2022},
author = {Amundson, KK and Borton, MA and Daly, RA and Hoyt, DW and Wong, A and Eder, E and Moore, J and Wunch, K and Wrighton, KC and Wilkins, MJ},
title = {Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {5},
pmid = {35034639},
issn = {2049-2618},
support = {EAR-1847684//National Science Foundation/ ; },
abstract = {BACKGROUND: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.

RESULTS: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.

CONCLUSIONS: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.},
}

@article {pmid35034083,
year = {2022},
author = {Liaskou, E and Quraishi, MN and Trivedi, PJ},
title = {Mucosal immunity in primary sclerosing cholangitis: from the bowel to bile ducts and back again.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000000809},
pmid = {35034083},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: In this article, we provide a contemporary overview on PSC pathogenesis, with a specific focus on the role of mucosal immunity.

RECENT FINDINGS: The extent of enteric dysbiosis in PSC has been extensively quantified, with evidence of reduced bacterial diversity and enrichment of species capable of driving lymphocyte recruitment from the gut to the liver. Integrative pathway-based analysis and metagenomic sequencing indicate a reduction in butyrate-producing species, near absence of bacteria that activate the nuclear bile acid receptor FXR, and depletion of species that regulate the synthesis of vitamin B6 and branched-chain amino acids. Immunotyping of the cellular inflammatory infiltrate has identified a population of intrahepatic naive T cells, with tendency to acquire a Th17 polarisation state, paralleled by heightened responses to pathogen stimulation. Moreover, the search for antigen specificity has revealed the presence of overlapping nucleotide clonotypes across the gut and liver, highlighting the ability to recognize a common pool of epitopes bearing structural similarities across afflicted sites.

SUMMARY: Understanding the complex mechanisms that underpin mucosal immune responses between the liver and gut will help identify new druggable targets in PSC, centring on gut microbial manipulation, bile acid therapies, and restoration of immune homeostasis.},
}

@article {pmid35033645,
year = {2022},
author = {Pang, L and Xu, K and Qi, L and Chatzisymeon, E and Liu, X and Yang, P},
title = {Response behavior of antibiotic resistance genes to zinc oxide nanoparticles in cattle manure thermophilic digestion process: A metagenomic analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {126709},
doi = {10.1016/j.biortech.2022.126709},
pmid = {35033645},
issn = {1873-2976},
abstract = {This work investigated the metagenomics-based behavior of antibiotic resistance genes (ARGs) during cattle manure anaerobic digestion with zinc oxide nanoparticles (ZnO NPs) that are commonly used as animal feed additives. The 6.6% decrease in total ARGs abundance while remained unchanged ARGs diversity with ZnO NPs (5 mg/g total solid), suggested ZnO NPs may mitigate ARGs risk by abundance. Also, ZnO NPs affected ARGs with mechanisms specifically of antibiotic inactivation and antibiotic target change, and declined potential hosts' abundance (bacterial genus Ruminiclostridium, Riminococcus, and Paenibacillus) which mainly contributed to the decreased ARGs' abundance. Besides, microbial chemotaxis decreased by 17% with ZnO NPs compared to that without nanoparticles indicated a depression on potential hosts, who could develop the mechanism to adapt to altered digestion conditions, which probably inhibited the ARGs' propagation. These findings are important to promote understanding of the potential ARGs risks in treatments of livestock wastes containing animal feed additives.},
}

@article {pmid35034142,
year = {2022},
author = {Tran, HT and Nguyen, HM and Nguyen, TM and Chang, C and Huang, WL and Huang, CL and Chiang, TY},
title = {Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35034142},
issn = {1432-184X},
support = {105-2622-B-006 -008 -CC2//Ministry of Science and Technology, Taiwan/ ; },
abstract = {The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.},
}

@article {pmid35033744,
year = {2021},
author = {Pérez-Cataluña, A and Chiner-Oms, Á and Cuevas-Ferrando, E and Díaz-Reolid, A and Falcó, I and Randazzo, W and Girón-Guzmán, I and Allende, A and Bracho, MA and Comas, I and Sánchez, G},
title = {Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater.},
journal = {Water research},
volume = {211},
number = {},
pages = {118007},
doi = {10.1016/j.watres.2021.118007},
pmid = {35033744},
issn = {1879-2448},
abstract = {Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.7 lineage and the ability of the technique to anticipate the detection of certain mutations before they are detected in clinical samples. The study proves the usefulness of sewage sequencing to track Variants of Concern that can complement clinical testing to help in decision-making and in the analysis of the evolution of the pandemic.},
}

@article {pmid35033203,
year = {2022},
author = {Jankowski, P and Gan, J and Le, T and McKennitt, M and Garcia, A and Yanaç, K and Yuan, Q and Uyaguari-Diaz, M},
title = {Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {3},
pmid = {35033203},
issn = {2524-6372},
support = {322388//Research Start-up Funds, University of Manitoba/ ; 322930//Research Grants Program, University of Manitoba/ ; 322788//The Faculty of Science Collaborative grant, University of Manitoba/ ; },
abstract = {BACKGROUND: Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period.

RESULTS: Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL).

CONCLUSIONS: Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.},
}

@article {pmid34446078,
year = {2021},
author = {Alser, M and Rotman, J and Deshpande, D and Taraszka, K and Shi, H and Baykal, PI and Yang, HT and Xue, V and Knyazev, S and Singer, BD and Balliu, B and Koslicki, D and Skums, P and Zelikovsky, A and Alkan, C and Mutlu, O and Mangul, S},
title = {Technology dictates algorithms: recent developments in read alignment.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {249},
pmid = {34446078},
issn = {1474-760X},
support = {R01 HL153122/HL/NHLBI NIH HHS/United States ; K08 HL128867/HL/NHLBI NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; R01 EB025022/EB/NIBIB NIH HHS/United States ; R01 HL149883/HL/NHLBI NIH HHS/United States ; },
mesh = {*Algorithms ; Computational Biology/*methods ; Genome, Human ; HIV/physiology ; Humans ; Metagenomics ; *Sequence Alignment ; Sulfites ; },
abstract = {Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.},
}

*Algorithms
Computational Biology/*methods
Genome, Human
HIV/physiology
Humans
Metagenomics
*Sequence Alignment
Sulfites

@article {pmid34309504,
year = {2021},
author = {Wang, Q and Ye, J and Xu, T and Zhou, N and Lu, Z and Ying, J},
title = {Prediction of prokaryotic transposases from protein features with machine learning approaches.},
journal = {Microbial genomics},
volume = {7},
number = {7},
pages = {},
pmid = {34309504},
issn = {2057-5858},
mesh = {Amino Acid Sequence/genetics ; Bacteria/*genetics ; Computational Biology/methods ; DNA Transposable Elements/*genetics ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/genetics ; *Machine Learning ; Metagenome/genetics ; Transposases/*genetics ; Virulence Factors/genetics ; },
abstract = {Identification of prokaryotic transposases (Tnps) not only gives insight into the spread of antibiotic resistance and virulence but the process of DNA movement. This study aimed to develop a classifier for predicting Tnps in bacteria and archaea using machine learning (ML) approaches. We extracted a total of 2751 protein features from the training dataset including 14852 Tnps and 14852 controls, and selected 75 features as predictive signatures using the combined mutual information and least absolute shrinkage and selection operator algorithms. By aggregating these signatures, an ensemble classifier that integrated a collection of individual ML-based classifiers, was developed to identify Tnps. Further validation revealed that this classifier achieved good performance with an average AUC of 0.955, and met or exceeded other common methods. Based on this ensemble classifier, a stand-alone command-line tool designated TnpDiscovery was established to maximize the convenience for bioinformaticians and experimental researchers toward Tnp prediction. This study demonstrates the effectiveness of ML approaches in identifying Tnps, facilitating the discovery of novel Tnps in the future.},
}

Amino Acid Sequence/genetics
Bacteria/*genetics
Computational Biology/methods
DNA Transposable Elements/*genetics
DNA, Bacterial/*genetics
Drug Resistance, Bacterial/genetics
*Machine Learning
Metagenome/genetics
Transposases/*genetics
Virulence Factors/genetics

@article {pmid34126062,
year = {2021},
author = {Nooij, S and Ducarmon, QR and Laros, JFJ and Zwittink, RD and Norman, JM and Smits, WK and Verspaget, HW and Keller, JJ and Terveer, EM and Kuijper, EJ and , },
title = {Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients.},
journal = {Gastroenterology},
volume = {161},
number = {4},
pages = {1218-1228.e5},
doi = {10.1053/j.gastro.2021.06.009},
pmid = {34126062},
issn = {1528-0012},
mesh = {Adult ; Aged ; Aged, 80 and over ; Clostridioides difficile/*pathogenicity ; Clostridium Infections/diagnosis/microbiology/*therapy ; Dysbiosis ; Escherichia coli/enzymology/genetics/*growth & development ; Escherichia coli Proteins/genetics/metabolism ; *Fecal Microbiota Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Polyketide Synthases/genetics/metabolism ; Reinfection ; Retrospective Studies ; Time Factors ; Treatment Outcome ; },
abstract = {BACKGROUND & AIMS: Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks+) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks+E coli is influenced by pks status of the donor feces.

METHODS: In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks+E coli and compared the presence of pks in patients before and after treatment and to their respective donors.

RESULTS: The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks+E coli in pks+ patients was correlated to pks in the donor (P = .004).

CONCLUSIONS: We conclude that FMT contributes to pks+E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks+E coli is unlikely.},
}

Adult
Aged
Aged, 80 and over
Clostridioides difficile/*pathogenicity
Clostridium Infections/diagnosis/microbiology/*therapy
Dysbiosis
Escherichia coli/enzymology/genetics/*growth & development
Escherichia coli Proteins/genetics/metabolism
*Fecal Microbiota Transplantation/adverse effects
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenome
Metagenomics
Middle Aged
Polyketide Synthases/genetics/metabolism
Reinfection
Retrospective Studies
Time Factors
Treatment Outcome

@article {pmid33878301,
year = {2021},
author = {Pedersen, MW and De Sanctis, B and Saremi, NF and Sikora, M and Puckett, EE and Gu, Z and Moon, KL and Kapp, JD and Vinner, L and Vardanyan, Z and Ardelean, CF and Arroyo-Cabrales, J and Cahill, JA and Heintzman, PD and Zazula, G and MacPhee, RDE and Shapiro, B and Durbin, R and Willerslev, E},
title = {Environmental genomics of Late Pleistocene black bears and giant short-faced bears.},
journal = {Current biology : CB},
volume = {31},
number = {12},
pages = {2728-2736.e8},
doi = {10.1016/j.cub.2021.04.027},
pmid = {33878301},
issn = {1879-0445},
support = {WT220023/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Metagenomics ; Phylogeny ; *Ursidae/genetics ; },
abstract = {Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.},
}

Animals
DNA, Ancient
DNA, Mitochondrial
Fossils
Humans
Metagenomics
Phylogeny
*Ursidae/genetics

@article {pmid35032616,
year = {2022},
author = {Matsushima, N and Kretsinger, RH},
title = {Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses.},
journal = {Gene},
volume = {},
number = {},
pages = {146156},
doi = {10.1016/j.gene.2021.146156},
pmid = {35032616},
issn = {1879-0038},
abstract = {Leucine rich repeats (LRRs) occurring in tandem are 20 - 29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Directly before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs 547 LRR proteins were identified and 502 were used for analysis. A comprehensive analysis of TpLRR and FNIP that belong to an LRR type was first performed. The repeating unit lengths (RULs) in five types are 19 residues which is the shortest among all LRRs. The RULs of eight LRR types including FNIP are one to five residues shorter than those of the known, corresponding LRR types. The conserved hydrophobic residues such as Leu, Val or Ile in the consensus sequences are frequently substituted by cysteine at one or two positions. Four unique LRR motifs that are different from those identified previously are observed. The present study enhances the previous result that the sequence novelty is a general feature of viral LRR proteins. An evolutionary scenario of short or unique LRR was discussed.},
}

@article {pmid35032364,
year = {2022},
author = {Nie, J and Yang, L and Huang, L and Gao, L and Young, KH and Le Grange, JM and Yang, X and Wei, J and Xiao, M and Zhou, J},
title = {Infection complications in febrile chimeric antigen receptor (CAR)-T recipients during the peri-CAR-T cell treatment period examined using metagenomic next-generation sequencing (mNGS).},
journal = {Cancer communications (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/cac2.12260},
pmid = {35032364},
issn = {2523-3548},
support = {82070217//National Natural Science Foundation of China/ ; 81873427//National Natural Science Foundation of China/ ; 81770211//National Natural Science Foundation of China/ ; 81670152//National Natural Science Foundation of China/ ; 81700145//National Natural Science Foundation of China/ ; 81830008//Key Program of the National Natural Science Foundation of China/ ; 81630006//Key Program of the National Natural Science Foundation of China/ ; CXPJJH12000009-113//CHEN XIAO-PING Foundation for the Development of Science and Technology of Hubei Province/ ; },
}

@article {pmid35032344,
year = {2022},
author = {Rasmussen, JA and Villumsen, KR and von Gersdorff Jørgensen, L and Forberg, T and Zuo, S and Kania, PW and Buchmann, K and Kristiansen, K and Bojesen, AM and Limborg, MT},
title = {Integrative analyses of probiotics, pathogenic infections, and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss).},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.15433},
pmid = {35032344},
issn = {1365-2672},
abstract = {AIMS: Given the pivotal role played by the gut microbiota in regulating the host immune system, interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, the need for a better understanding of the host-microbiota interactions after disease responses to optimise the use of probiotics to strengthen disease resilience and recovery.

METHODS AND RESULTS: We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric redmouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and on the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.

CONCLUSIONS: We discuss the relevance of these results emphasising the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.

Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota and the resulting host immune response.},
}

@article {pmid35030982,
year = {2022},
author = {Tan, R and Jin, M and Shao, Y and Yin, J and Li, H and Chen, T and Shi, D and Zhou, S and Li, J and Yang, D},
title = {High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2022442},
doi = {10.1080/19490976.2021.2022442},
pmid = {35030982},
issn = {1949-0984},
abstract = {Diet can not only provide nutrition for intestinal microbiota, it can also remodel them. However, is unclear whether and how diet affects the spread of antibiotic resistance genes (ARGs) in the intestinal microbiota. Therefore, we employed selected high-sugar, high-fat, high-protein, and normal diets to explore the effect. The results showed that high-sugar, high-fat, and high-protein diets promoted the amplification and transfer of exogenous ARGs among intestinal microbiota, and up-regulated the expression of trfAp and trbBp while significantly altered the intestinal microbiota and its metabolites. Inflammation-related products were strongly correlated with the spread of ARGs, suggesting the intestinal microenvironment after diet remodeling might be conducive to the spreading of ARGs. This may be attributed to changes in bacterial membrane permeability, the SOS response, and bacterial composition and diversity caused by diet-induced inflammation. In addition, acceptor bacteria (zygotes) screened by flow cytometry were mostly Proteobacteria, Firmicutes and Actinobacteria, and most were derived from dominant intestinal bacteria remodeled by diet, indicating that the transfer of ARGs was closely linked to diet, and had some selectivity. Metagenomic results showed that the gut resistance genome could be affected not only by diet, but by exogenous antibiotic resistant bacteria (ARB). Many ARG markers coincided with bacterial markers in diet groups. Therefore, dominant bacteria in different diets are important hosts of ARGs in specific dietary environments, but the many pathogenic bacteria present may cause serious harm to human health.},
}

@article {pmid35030359,
year = {2022},
author = {Xu, X and Chen, H and Hu, J and Zheng, T and Zhang, R and Zhong, H and Gao, Q and Sun, W and Chen, Q and Ni, J},
title = {Unveil the role of dissolved and sedimentary metal(loid)s on bacterial communities and metal resistance genes (MRGs) in an urban river of the Qinghai-Tibet Plateau.},
journal = {Water research},
volume = {211},
number = {},
pages = {118050},
doi = {10.1016/j.watres.2022.118050},
pmid = {35030359},
issn = {1879-2448},
abstract = {Though metal resistance genes (MRGs) are of global concern in aquatic ecosystems, the underlying factors responsible for MRGs dissemination, especially in urban rivers on the vulnerable Qinghai-Tibet Plateau, are rarely known. Here, we collected 64 samples including water and sediments during the wet and dry seasons and effluents from six wastewater treatment plants (WWTPs) during the dry season and measured 50 metal(loid)s, 60 bacterial phyla, and 259 MRGs. We observed the distinct difference of metal(loid)s, bacterial communities, and MRGs between water and sediments and the great seasonal changes in metal(loid)s and bacterial communities instead of MRGs. Thirty-one metal(loid)s were detectable in the water, with relatively low concentrations and no significant effects on the planktonic bacterial communities and MRGs. Interestingly, the WWTPs effluent partially promoted the prevalence of dissolved metal(loid)s, bacterial communities, and MRGs along the river. In the sediments, the average concentrations of 17 metal(loid)s exceeded their corresponding background levels in this region and strongly influenced the bacterial communities and the MRGs. Sedimentary Hg and Cd, mainly sourced from the intensive animal husbandry, were the major pollutants causing ecological risks and largely shaped their corresponding resistomes. Moreover, we found that bacterial communities predominantly determined the variation of MRGs in both water and sediments. Metagenome-assembled genomes further reveals the widespread co-occurrence of MRGs and antibiotic resistance genes (ARGs) in MRG hosts. Our study highlighted the concern of effluents discharged from WWTPs and emphasized the importance of controlling the anthropogenic inputs of sedimentary metal(loid)s in the plateau river ecosystems.},
}

@article {pmid35030192,
year = {2022},
author = {El Mouzan, M and Assiri, A and Al Sarkhy, A and Alasmi, M and Saeed, A and Al-Hussaini, A and AlSaleem, B and Al Mofarreh, M},
title = {Viral dysbiosis in children with new-onset celiac disease.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0262108},
doi = {10.1371/journal.pone.0262108},
pmid = {35030192},
issn = {1932-6203},
abstract = {Viruses are common components of the intestinal microbiome, modulating host bacterial metabolism and interacting with the immune system, with a possible role in the pathogenesis of immune-mediated diseases such as celiac disease (CeD). The objective of this study was to characterize the virome profile in children with new-onset CeD. We used metagenomic analysis of viral DNA in mucosal and fecal samples from children with CeD and controls and performed sequencing using the Nextera XT library preparation kit. Abundance log2 fold changes were calculated using differential expression and linear discriminant effect size. Shannon alpha and Bray-Curtis beta diversity were determined. A total of 40 children with CeD and 39 controls were included. We found viral dysbiosis in both fecal and mucosal samples. Examples of significantly more abundant species in fecal samples of children with CeD included Human polyomavirus 2, Enterobacteria phage mEpX1, and Enterobacteria phage mEpX2; whereas less abundant species included Lactococcus phages ul36 and Streptococcus phage Abc2. In mucosal samples however, no species were significantly associated with CeD. Shannon alpha diversity was not significantly different between CeD and non-CeD groups and Bray-Curtis beta diversity showed no significant separation between CeD and non-CeD samples in either mucosal or stool samples, whereas separation was clear in all samples. We identified significant viral dysbiosis in children with CeD, suggesting a potential role in the pathogenesis of CeD indicating the need for further studies.},
}

@article {pmid35029658,
year = {2022},
author = {Takada, N and Takasugi, M and Nonaka, Y and Kamiya, T and Takemura, K and Satoh, J and Ito, S and Fujimoto, K and Uematsu, S and Yoshida, K and Morita, T and Nakamura, H and Uezumi, A and Ohtani, N},
title = {Galectin-3 promotes the adipogenic differentiation of PDGFRα+ cells and ectopic fat formation in regenerating muscle.},
journal = {Development (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1242/dev.199443},
pmid = {35029658},
issn = {1477-9129},
support = {19H04002//Japan Society for the Promotion of Science (JSPS)/ ; //Takeda Science Foundation/ ; },
abstract = {Worldwide prevalence of obesity is associated with the increase of lifestyle-related diseases. The accumulation of intermuscular adipose tissue (IMAT) is considered a major problem whereby obesity leads to sarcopenia and metabolic disorders and thus is a promising target for treating these pathological conditions. However, whereas obesity-associated IMAT is suggested to originate from PDGFRα+ mesenchymal progenitors, processes underlying their adipogenesis remain largely unexplored. Here, we comprehensively investigated intra- and extracellular changes associated with these processes using single-cell RNA sequencing (scRNA-Seq) and mass spectrometry. Our scRNA-Seq analysis identified a small PDGFRα+ cell population in obese mice directed strongly toward adipogenesis. Proteomic analysis showed that the appearance of this cell population is accompanied by an increase in galectin-3 in interstitial environments, which was found to activate adipogenic PPARγ signals in PDGFRα+ cells. Moreover, IMAT formation during muscle regeneration was significantly suppressed in galectin-3 KO mice. Our findings, together with these multi-omics datasets, could unravel microenvironmental networks during muscle regeneration highlighting possible therapeutic targets against IMAT formation in obesity.},
}

@article {pmid35028627,
year = {2021},
author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F},
title = {Fungal allergic sensitisation in young rural Zimbabwean children: Gut mycobiome and seroreactivity characteristics.},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100082},
doi = {10.1016/j.crmicr.2021.100082},
pmid = {35028627},
issn = {2666-5174},
abstract = {Background: The prevalence of allergic diseases has increased over the last few decades, with sensitisation to fungal allergens and gut microbiome dysbiosis implicated in this trend. The fungal community in the gut (mycobiome) has yet to be characterised and related to fungal allergic sensitisation. Thus, we characterised the gut mycobiome and related it to fungal sensitisation and seroreactivity among Zimbabwean children. We further determined the effect of host age, sex, Schistosoma haematobium infection and mycobiome composition on fungal sensitisation and seroreactivity.

Methods: Using shotgun metagenomic sequencing, we characterised the gut microbiome of stool samples of 116 preschool aged children (PSAC) (≤5 years old, 57(49.1%) male and 59 (50.9%) female). Sensitisation to common fungi in Zimbabwe was assessed using skin prick tests (SPTs). Allergen-specific IgM, IgA, IgG, IgE and IgG4 antibodies were quantified by ELISA. We analysed the relationship between fungal genera and SPT reactivity by ANOVA; fungal genera and IgE antibody reactivity by linear regression; variation in mycobiome abundance with host and environmental factors by PERMANOVA; SPT reactivity and host and environmental factors by logistic regression; seroreactivity and host and environmental factors by ANOVA.

Results: The mycobiome formed <1% of the sequenced gut microbiome and 228 fungal genera were identified. The most abundant genera detected were Protomyces, Taphrina, and Aspergillus. S.haematobium infection had a significant effect on fungal genera. Prevalence of SPT sensitisation to ≥1 fungal species was 96%, and individuals were frequently sensitised to Saccharomyces cerevisiae. Antibodies were detected in 100% of the population. There was no relationship between mycobiome abundance and IgE titres or IgE/IgG4 ratios for each fungal species; no significant differences between SPT reactivity and abundance of fungal species except for S. cerevisiae; and fungal seroreactivity did not significantly differ with age. There were some sex (m>f for, Epicoccum nigrum and Penicillium chrysogenum) and SPT reactivity -related differences in seroreactivity.

Conclusion: This is the first comprehensive characterisation of gut mycobiome and fungal allergic sensitisation of rural children in Zimbabwe. Although reported allergic disease is low there is a high percentage of sensitisation. Further studies with larger populations are required to understand the role of the mycobiome in allergic diseases.},
}

@article {pmid35028498,
year = {2022},
author = {Li, J and Li, J and Yu, Y and Wang, R and Zhou, M and Lu, L},
title = {Pneumocystis pneumonia and rheumatic disease: diagnostic potential of circulating microbial cell-free DNA sequencing.},
journal = {Rheumatology advances in practice},
volume = {6},
number = {1},
pages = {rkab105},
doi = {10.1093/rap/rkab105},
pmid = {35028498},
issn = {2514-1775},
abstract = {Objectives: The aim of this study was to explore the clinical utility of circulating microbial cell-free DNA (cfDNA) sequencing as a non-invasive approach for diagnosis of Pneumocystis jirovecii pneumonia (PJP) in immunocompromised patients with rheumatic disease (RD).

Methods: The study included 72 RD patients with suspected lung infections admitted to Renji hospital. Eighteen individuals were diagnosed with PJP, and 54 patients without PJP were enrolled as the control group. All patients had undergone pulmonary CT scans, and blood and respiratory tract specimens had been subjected to metagenomic next-generation sequencing (mNGS) and conventional microbiological tests. The clinical and laboratory parameters were collected, and the efficacy of circulating microbial cfDNA of P. jirovecii was evaluated.

Results: Of the 18 patients with PJP, the average age was 53.0 years, and the median time between RD diagnosis and PJP presentation was 126.0 days (interquartile range 84.0-176.3 days). Low circulating CD4+ cell counts and a lack of PJP prophylaxis were observed in the patients. Metagenomic NGS of circulating microbial cfDNA was performed in 69 patients, including 15 cases with PJP and 54 controls. Twelve (80%) of 15 analysed blood samples contained P. jirovecii sequences in the PJP group, with P. jirovecii not detected among controls. There was a significant difference between PJP and non-PJP groups (P < 0.001), with a sensitivity of 83.3% and specificity of 100% when using plasma cfDNA sequencing. Higher β-D-glucan levels were found in patients with positive results for P. jirovecii in plasma cfDNA sequencing.

Conclusion: Metagenomic NGS of circulating microbial cfDNA is a potential tool for diagnosis of PJP in RD patients.},
}

@article {pmid35027725,
year = {2022},
author = {Muñoz-Gómez, SA and Susko, E and Williamson, K and Eme, L and Slamovits, CH and Moreira, D and López-García, P and Roger, AJ},
title = {Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {35027725},
issn = {2397-334X},
support = {735923LPI//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; ALTF 21-2020//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.},
}

@article {pmid35027090,
year = {2022},
author = {Rajala, P and Cheng, DQ and Rice, SA and Lauro, FM},
title = {Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {4},
pmid = {35027090},
issn = {2049-2618},
abstract = {BACKGROUND: Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.

METHODS: We used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa.

RESULTS: The surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic corrosion. Based on this metabolic model, we propose that sulfate reduction and sulfur disproportionation might play key roles in deep-sea corrosion.

CONCLUSIONS: The corrosion rate observed was higher than what could be expected from abiotic corrosion mechanisms under these environmental conditions. High corrosion rate and the form of corrosion (deep pitting) suggest that the corrosion of the chain links was driven by both abiotic and biotic processes. We posit that the corrosion is driven by deep-sea sulfur-cycling microorganisms which may gain energy by accelerating the reaction between metallic iron and elemental sulfur. The results of this field study provide important new insights on the ecophysiology of the corrosion process in the deep sea.},
}

@article {pmid34772759,
year = {2021},
author = {Kardos, M and Armstrong, EE and Fitzpatrick, SW and Hauser, S and Hedrick, PW and Miller, JM and Tallmon, DA and Funk, WC},
title = {The crucial role of genome-wide genetic variation in conservation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {48},
pages = {},
pmid = {34772759},
issn = {1091-6490},
support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Genetic Fitness/genetics ; Genetic Variation/*genetics ; Genetics ; Genetics, Population/methods ; Genome/*genetics ; Genomics ; Inbreeding ; Metagenomics/methods ; Population Dynamics/*trends ; },
abstract = {The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.},
}

Animals
Biodiversity
Conservation of Natural Resources
Ecosystem
Genetic Fitness/genetics
Genetic Variation/*genetics
Genetics
Genetics, Population/methods
Genome/*genetics
Genomics
Inbreeding
Metagenomics/methods
Population Dynamics/*trends

@article {pmid33926534,
year = {2021},
author = {Kobras, CM and Fenton, AK and Sheppard, SK},
title = {Next-generation microbiology: from comparative genomics to gene function.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {123},
pmid = {33926534},
issn = {1474-760X},
support = {MR/S009280/1/MRC_/Medical Research Council/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Bacteria/genetics ; DNA Transposable Elements ; *Gene Expression Regulation ; Genetic Association Studies ; Genetic Fitness ; Genetic Variation ; Genome-Wide Association Study/methods ; *Genomics/methods ; Metagenome ; Metagenomics/methods ; Microbiological Techniques/*trends ; Microbiology/*trends ; Mutagenesis, Insertional ; },
abstract = {Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.},
}

Bacteria/genetics
DNA Transposable Elements
*Gene Expression Regulation
Genetic Association Studies
Genetic Fitness
Genetic Variation
Genome-Wide Association Study/methods
*Genomics/methods
Metagenome
Metagenomics/methods
Microbiological Techniques/*trends
Microbiology/*trends
Mutagenesis, Insertional

@article {pmid35026256,
year = {2022},
author = {Wang, J and Zhang, Y and Ding, Y and Song, H and Liu, T},
title = {Analysis of microbial community resistance mechanisms in groundwater contaminated with SAs and high NH4+-Fe-Mn.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {153036},
doi = {10.1016/j.scitotenv.2022.153036},
pmid = {35026256},
issn = {1879-1026},
abstract = {The resistance mechanism of microbial communities in contaminated groundwater under the combined stress of sulfonamide antibiotics (SAs), NH4+, and Fe-Mn exceeding the standard levels was studied in an agricultural area along the Songhua River in Northeast China with developed livestock and poultry breeding. Representative points were selected in the study area to explore the response of environmental parameters and microbial communities, and microscopic experiments with different SA concentrations were conducted with background groundwater. The results showed a complex relationship between microbial communities and environmental factors. The environmental factors SM, SM2, SMX, DOC, NO3-, Fe, Mn, and HCO3- significantly affected the microbial community, with SMX, DOC, and Mn having the greatest effect. Three types of antibiotics with similar properties had different effects on the microbial community, and these effects were not simply additive or superimposed. After adding SAs, Proteobacteria with multi-resistance (99.85%) became the dominant phylum, and Acinetobacter (98.68%) became the dominant genus with SA resistance. SAs have a significant influence on bacterial chemotaxis, transporters, substance transport, and metabolism. Microorganisms resist the influence of SAs via a series of resistance mechanisms, such as enhancing the synthesis of relevant enzymes, generating new biochemical reactions, and reducing the transport of harmful substances through cell membranes. We also found that the proportion of exogenous compound degradation and metabolism-related functional genes in the presence of high SA concentrations increased significantly, which may be related to the degradation of SAs by microorganisms.},
}

@article {pmid35026253,
year = {2022},
author = {Shi, L and Zhang, J and Lu, T and Zhang, K},
title = {Metagenomics revealed the mobility and hosts of antibiotic resistance genes in typical pesticide wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {153033},
doi = {10.1016/j.scitotenv.2022.153033},
pmid = {35026253},
issn = {1879-1026},
abstract = {Pesticide showed a crucial selective pressure of antibiotic resistance genes (ARGs) in the environmental dimension, especially in the pesticide wastewater treatment process, where the information on the mobility and hosts of ARGs was very important but limited. This study tried to clarify the mobile antibiotic resistome and ARG hosts in three typical pesticide wastewater treatment plants (PWWTPs) through metagenomics. Results showed that ARGs associated with antibiotic efflux and multi-drug resistance generally dominated in the PWWTPs, and the relative abundance of ARGs was generally higher in the water phase than that in sludge phase. The mobile antibiotic resistome accounted for 43.6% ± 16.2% and 44.8% ± 18.0% of the total relative abundance of ARGs in the water phase and sludge phase, respectively. The tnpA, IS91 and intI1 were the dominant mobile genetic elements (MGEs) closely associated with ARGs. MCR-5 and MCR-9 were first identified in the PWWTPs and located together with the tnpA, tnpA2 and int2. The potential human pathogens belonging to Citrobacter, Pseudomonas, Enterobacter, Acinetobacter, and Kluyvern were the major ARG hosts in the PWWTPs. Statistical analysis indicated that microbial community contributed the most to the occurrence of antibiotic resistome, and the reduction of the major ARG hosts was crucial from the perspective of ARGs control.},
}

@article {pmid35024477,
year = {2022},
author = {Ahlinder, J and Svedberg, AL and Nystedt, A and Dryselius, R and Jacobsson, K and Hägglund, M and Brindefalk, B and Forsman, M and Ottoson, J and Troell, K},
title = {Use of metagenomic microbial source tracking to investigate the source of a foodborne outbreak of cryptosporidiosis.},
journal = {Food and waterborne parasitology},
volume = {26},
number = {},
pages = {e00142},
doi = {10.1016/j.fawpar.2021.e00142},
pmid = {35024477},
issn = {2405-6766},
abstract = {Cryptosporidium is a protozoan parasite of global public health importance that causes gastroenteritis in a variety of vertebrate hosts, with many human outbreaks reported yearly, often from ingestion of contaminated water or food. Despite the major public health implications, little is typically known about sources of contamination of disease outbreaks caused by Cryptosporidium. Here, we study a national foodborne outbreak resulted from infection with Cryptosporidium parvum via romaine lettuce, with the main goal to trace the source of the parasite. To do so, we combined traditional outbreak investigation methods with molecular detection and characterization methods (i.e. PCR based typing, amplicon and shotgun sequencing) of romaine lettuce samples collected at the same farm from which the contaminated food was produced. Using 18S rRNA typing, we detected C. parvum in two out of three lettuce samples, which was supported by detections in the metagenome analysis. Microbial source tracking analysis of the lettuce samples suggested sewage water as a likely source of the contamination, albeit with some uncertainty. In addition, the high degree of overlap in bacterial species content with a public human gut microbial database corroborated the source tracking results. The combination of traditional and molecular based methods applied here is a promising tool for future source tracking investigations of food- and waterborne outbreaks of Cryptosporidium spp. and can help to control and mitigate contamination risks.},
}

@article {pmid35024099,
year = {2022},
author = {Pettersen, VK and Antunes, LCM and Dufour, A and Arrieta, MC},
title = {Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics.},
journal = {Computational and structural biotechnology journal},
volume = {20},
number = {},
pages = {274-286},
doi = {10.1016/j.csbj.2021.12.012},
pmid = {35024099},
issn = {2001-0370},
abstract = {Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.},
}

@article {pmid35024091,
year = {2022},
author = {Pust, MM and Tümmler, B},
title = {Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life.},
journal = {Computational and structural biotechnology journal},
volume = {20},
number = {},
pages = {175-186},
doi = {10.1016/j.csbj.2021.12.008},
pmid = {35024091},
issn = {2001-0370},
abstract = {The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) were reanalysed to study the development of the rare species biosphere, which was here defined by either the 15th, 25th or 35th species abundance percentile. We found that healthy children contained an age-independent network of abundant (core) and rare species with both entities being essential in maintaining the network structure. The protein sequence usage for more than 100 bacterial metabolic pathways differed between the core and rare species biosphere. In CF children, the background structure was underdeveloped and random forest bootstrapping based on all constituents of the early airway metagenome and host-associated factors indicated that rare taxa were the most important variables in deciding whether a child was healthy or suffered from the life-limiting CF disease. Attempts failed to make the age-independent CF network as robust as the healthy structure when an increasing number of bacterial taxa from the healthy network was incorporated into the CF structure by computer-based model simulations. However, the transfer of a key combination of taxa from the healthy to the CF network structure with high species diversity and low species dominance, correlated with a more robust CF network and a topological approximation of CF and healthy graph structures. Rothia mucilaginosa, Streptococci and rare species were essential in improving the underdeveloped CF network.},
}

@article {pmid35023810,
year = {2022},
author = {Udayan, S and Stamou, P and Crispie, F and Hickey, A and Floyd, AN and Hsieh, CS and Cotter, PD and O'Sullivan, O and Melgar, S and O'Toole, PW and Newberry, RD and Rossini, V and Nally, K},
title = {Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88-/- Mice.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2007743},
doi = {10.1080/19490976.2021.2007743},
pmid = {35023810},
issn = {1949-0984},
abstract = {In healthy hosts the gut microbiota is restricted to gut tissues by several barriers some of which require MyD88-dependent innate immune sensor pathways. Nevertheless, some gut taxa have been reported to disseminate to systemic tissues. However, the extent to which this normally occurs during homeostasis in healthy organisms is still unknown. In this study, we recovered viable gut bacteria from systemic tissues of healthy wild type (WT) and MyD88-/- mice. Shotgun metagenomic-sequencing revealed a marked increase in the relative abundance of L. johnsonii in intestinal tissues of MyD88-/- mice compared to WT mice. Lactobacillus johnsonii was detected most frequently from multiple systemic tissues and at higher levels in MyD88-/- mice compared to WT mice. Viable L. johnsonii strains were recovered from different cell types sorted from intestinal and systemic tissues of WT and MyD88-/- mice. L. johnsonii could persist in dendritic cells and may represent murine immunomodulatory endosymbionts.},
}

@article {pmid35022515,
year = {2022},
author = {Qin, F and Du, S and Zhang, Z and Ying, H and Wu, Y and Zhao, G and Yang, M and Zhao, Y},
title = {Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35022515},
issn = {1751-7370},
support = {41706173//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Viruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.},
}

@article {pmid35022403,
year = {2022},
author = {Bornemann, TLV and Adam, PS and Turzynski, V and Schreiber, U and Figueroa-Gonzalez, PA and Rahlff, J and Köster, D and Schmidt, TC and Schunk, R and Krauthausen, B and Probst, AJ},
title = {Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {284},
pmid = {35022403},
issn = {2041-1723},
abstract = {Earth's mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.},
}

@article {pmid35021874,
year = {2022},
author = {Wang, Y and Tian, S and Wu, N and Liu, W and Li, L and Wang, X},
title = {Differential microbial communities in paddy soils between Guiyang plateaus and Chengdu basins drive the incidence of rice bacterial diseases.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-09-21-1974-RE},
pmid = {35021874},
issn = {0191-2917},
abstract = {Southwest China has the most complex rice-growing regions in China. With great differences in topography, mainly consisting of basins and plateaus, ecological factors in above region differ greatly. In this study, bulk paddy soils collected from a long-term rice field in Chengdu (basins) and in Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared more than 70% of the dominant genera (abundance > 1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively related with the higher incidence of rice bacterial foot rot in Guiyang, while temperature had a greater effect on soil microbial functions and positively related with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.},
}

@article {pmid35021085,
year = {2022},
author = {Gulyaeva, A and Garmaeva, S and Ruigrok, RAAA and Wang, D and Riksen, NP and Netea, MG and Wijmenga, C and Weersma, RK and Fu, J and Vila, AV and Kurilshikov, A and Zhernakova, A},
title = {Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts.},
journal = {Cell reports},
volume = {38},
number = {2},
pages = {110204},
doi = {10.1016/j.celrep.2021.110204},
pmid = {35021085},
issn = {2211-1247},
abstract = {The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.},
}

@article {pmid35021078,
year = {2022},
author = {Hu, D and Fuller, NR and Caterson, ID and Holmes, AJ and Reeves, PR},
title = {Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome.},
journal = {Cell reports},
volume = {38},
number = {2},
pages = {110239},
doi = {10.1016/j.celrep.2021.110239},
pmid = {35021078},
issn = {2211-1247},
abstract = {Gut microbiome is of major interest due to its close relationship to health and disease. Bacteria usually vary in gene content, leading to functional variations within species, so resolution higher than species-level methods is needed for ecological and clinical relevance. We design a protocol to identify strains in selected species with high discrimination and in high numbers by amplicon sequencing of the flagellin gene. We apply the protocol to fecal samples from a human diet trial, targeting Escherichia coli. Across the 119 samples from 16 individuals, there are 1,532 amplicon sequence variants (ASVs), but only 32 ASVs are dominant in one or more fecal samples, despite frequent dominant strain turnover. Major strains in an intestine are found to be commonly accompanied by a large number of satellite cells, and many are identified as potential extraintestinal pathogens. The protocol could be used to track epidemics or investigate the intra- or inter-host diversity of pathogens.},
}

@article {pmid35020455,
year = {2022},
author = {Cao, Y and Zhang, B and Greer, CW and Lee, K and Cai, Q and Song, X and Tremblay, J and Zhu, Z and Dong, G and Chen, B},
title = {Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {aem0215121},
doi = {10.1128/aem.02151-21},
pmid = {35020455},
issn = {1098-5336},
abstract = {The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.},
}

@article {pmid35020412,
year = {2022},
author = {Du, Y and Laperriere, SM and Fuhrman, J and Sun, F},
title = {Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2021.0439},
pmid = {35020412},
issn = {1557-8666},
abstract = {High-throughput chromosome conformation capture (Hi-C) has recently been applied to natural microbial communities and revealed great potential to study multiple genomes simultaneously. Several extraneous factors may influence chromosomal contacts rendering the normalization of Hi-C contact maps essential for downstream analyses. However, the current paucity of metagenomic Hi-C normalization methods and the ignorance for spurious interspecies contacts weaken the interpretability of the data. Here, we report on two types of biases in metagenomic Hi-C experiments: explicit biases and implicit biases, and introduce HiCzin, a parametric model to correct both types of biases and remove spurious interspecies contacts. We demonstrate that the normalized metagenomic Hi-C contact maps by HiCzin result in lower biases, higher capability to detect spurious contacts, and better performance in metagenomic contig clustering.},
}

@article {pmid35019890,
year = {2022},
author = {Zhu, J and Xia, H and Tang, R and Ng, TK and Yao, F and Liao, X and Zhang, Q and Ke, X and Shi, T and Chen, H},
title = {Metagenomic Next-generation Sequencing Detects Pathogens in Endophthalmitis Patients.},
journal = {Retina (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/IAE.0000000000003406},
pmid = {35019890},
issn = {1539-2864},
abstract = {PURPOSE: To investigate the utility of metagenomic next-generation sequencing (mNGS) in identifying the pathogens in endophthalmitis.

METHODS: In this prospective study, 36 cases of endophthalmitis were recruited. All patients received surgical treatment and intraocular drug lavage. The samples of vitreous or aqueous humor were extracted for mNGS and microbiological culture. The diagnostic performance of pathogens was compared between mNGS and culture.

RESULTS: The positive rates of mNGS and culture were 88.89% (32/36) and 27.78% (10/36), respectively. There was a statistically significant difference between mNGS and culture (χ2=27.657, P <0.01). Staphylococcus epidermidis, Streptococcus pneumoniae and Klebsiella pneumoniae were the most pathogenic bacteria in traumatic, postoperative, and endogenous endophthalmitis respectively. The concordance of pathogen identified by mNGS and culture was 70% for culture-positive cases. Antibiotic resistance genes were identified in 9 cases. There was a marginal correlation between the final visual acuity and the microbial sequence read (rs=0.498, P=0.05).

CONCLUSIONS: mNGS has a higher positive rate of identifying pathogens in endophthalmitis than culture. It can also provide information on antibiotic resistance and visual prognosis. However, caution must be taken when interpreting the results of mNGS because they may be not concordant with culture.},
}

@article {pmid35019699,
year = {2022},
author = {Jeon, S and Kim, H and Kim, J and Seol, D and Jo, J and Choi, Y and Cho, S and Kim, H},
title = {Positive Effect of Lactobacillus acidophilus EG004 on Cognitive Ability of Healthy Mice by Fecal Microbiome Analysis Using Full-Length 16S-23S rRNA Metagenome Sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0181521},
doi = {10.1128/spectrum.01815-21},
pmid = {35019699},
issn = {2165-0497},
abstract = {Evidence for the concept of the "gut-brain axis" (GBA) has risen. Many types of research demonstrated the mechanism of the GBA and the effect of probiotic intake. Although many studies have been reported, most were focused on neurodegenerative disease and, it is still not clear what type of bacterial strains have positive effects. We designed an experiment to discover a strain that positively affects brain function, which can be recognized through changes in cognitive processes using healthy mice. The experimental group consisted of a control group and three probiotic consumption groups, namely, Lactobacillus acidophilus, Lacticaseibacillus paracasei, and Lacticaseibacillus rhamnosus. Three experimental groups fed probiotics showed an improved cognitive ability by cognitive-behavioral tests, and the group fed on L. acidophilus showed the highest score. To provide an understanding of the altered microbial composition effect on the brain, we performed full 16S-23S rRNA sequencing using Nanopore, and operational taxonomic units (OTUs) were identified at species level. In the group fed on L. acidophilus, the intestinal bacterial ratio of Firmicutes and Proteobacteria phyla increased, and the bacterial proportions of 16 species were significantly different from those of the control group. We estimated that the positive results on the cognitive behavioral tests were due to the increased proportion of the L. acidophilus EG004 strain in the subjects' intestines since the strain can produce butyrate and therefore modulate neurotransmitters and neurotrophic factors. We expect that this strain expands the industrial field of L. acidophilus and helps understand the mechanism of the gut-brain axis. IMPORTANCE Recently, the concept of the "gut-brain axis" has risen and suggested that microbes in the GI tract affect the brain by modulating signal molecules. Although many pieces of research were reported in a short period, a signaling mechanism and the effects of a specific bacterial strain are still unclear. Besides, since most of the research was focused on neurodegenerative disease, the study with a healthy animal model is still insufficient. In this study, we show using a healthy animal model that a bacterial strain (Lactobacillus acidophilus EG004) has a positive effect on mouse cognitive ability. We experimentally verified an improved cognitive ability by cognitive behavioral tests. We performed full 16S-23S rRNA sequencing using a Nanopore MinION instrument and provided the gut microbiome composition at the species level. This microbiome composition consisted of candidate microbial groups as a biomarker that shows positive effects on cognitive ability. Therefore, our study suggests a new perspective for probiotic strain use applicable for various industrialization processes.},
}

@article {pmid35019688,
year = {2022},
author = {Lin, B and Wang, M and Gao, R and Ye, Z and Yu, Y and He, W and Qiao, N and Ma, Z and Ji, C and Shi, C and Zhou, X and Wang, Y and Zeng, F and Zhang, L and Gong, W and Cao, Z and Zhou, P and Melnikov, V and Ye, H and Li, Y and Zhang, Z and He, M and Qin, H and Zhang, Y},
title = {Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0042521},
doi = {10.1128/spectrum.00425-21},
pmid = {35019688},
issn = {2165-0497},
abstract = {Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, n = 28) and healthy controls (n = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of Oscillibacter and Enterobacter was remarkably increased in patients and Blautia and Romboutsia genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND, derived from Enterobacter, were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between Enterobacter and baseline insulin-like growth factor 1 (IGF-1), indicating that Enterobacter may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. IMPORTANCE Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND were enriched in patients. Also, we were pleasantly surprised to find that the Enterobacter genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.},
}

@article {pmid35019675,
year = {2022},
author = {Lombardino, J and Bijlani, S and Singh, NK and Wood, JM and Barker, R and Gilroy, S and Wang, CCC and Venkateswaran, K},
title = {Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0199421},
doi = {10.1128/spectrum.01994-21},
pmid = {35019675},
issn = {2165-0497},
abstract = {In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis (n = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCE Sphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.},
}

@article {pmid35019672,
year = {2022},
author = {Sun, Z and Zhang, M and Li, M and Bhaskar, Y and Zhao, J and Ji, Y and Cui, H and Zhang, H and Sun, Z},
title = {Interactions between Human Gut Microbiome Dynamics and Sub-Optimal Health Symptoms during Seafaring Expeditions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0092521},
doi = {10.1128/spectrum.00925-21},
pmid = {35019672},
issn = {2165-0497},
abstract = {During long ocean voyages, crew members are subject to complex pressures from their living and working environment, which lead to chronic diseases-like sub-optimal health status. Although the association between dysbiotic gut microbiome and chronic diseases has been broadly reported, the correlation between the sub-optimal health status and gut microbiome remains elusive. Here, the health status of 77 crew members (20-35 years old Chinese, male) during a 135-day sea expedition was evaluated using the shotgun metagenomics of stool samples and health questionnaires taken before and after the voyage. We found five core symptoms (e.g., abnormal defecation frequency, insomnia, poor sleep quality, nausea, and overeating) in 55 out of 77 crew members suffering from sub-optimal health status, and this was termed "seafaring syndrome" (SS) in this study. Significant correlation was found between the gut microbiome and SS rather than any single symptom. For example, SS was proven to be associated with individual perturbation in the gut microbiome, and the microbial dynamics between SS and non-SS samples were different during the voyage. Moreover, the microbial signature for SS was identified using the variation of 19 bacterial species and 26 gene families. Furthermore, using a Random Forest model, SS was predicted with high accuracy (84.4%, area under the concentration-time curve = 0.91) based on 28 biomarkers from pre-voyage samples, and the prediction model was further validated by another 30-day voyage cohort (accuracy = 83.3%). The findings in this study provide insights to help us discover potential predictors or even therapeutic targets for dysbiosis-related diseases. IMPORTANCE Systemic and chronic diseases are important health problems today and have been proven to be strongly associated with dysbiotic gut microbiome. Studying the association between the gut microbiome and sub-optimal health status of humans in extreme environments (such as ocean voyages) will give us a better understanding of the interactions between observable health signs and a stable versus dysbiotic gut microbiome states. In this paper, we illustrated that ocean voyages could trigger different symptoms for different crew member cohorts due to individual differences; however, the co-occurrence of high prevalence symptoms indicated widespread perturbation of the gut microbiome. By investigating the microbial signature and gut microbiome dynamics, we demonstrated that such sub-optimal health status can be predicted even before the voyage. We termed this phenomenon as "seafaring syndrome." This study not only provides the potential strategy for health management in extreme environments but also can assist the prediction of other dysbiosis-related diseases.},
}

@article {pmid35019069,
year = {2022},
author = {Herlinger, AL and Monteiro, FLL and D'arc, M and Moreira, FRR and Westgarth, HJ and Galliez, RM and Mariani, D and da Costa, LJ and de Almeida, LGP and Voloch, CM and , and Melo, ASO and Aguiar, RS and Dos Santos, AFA and Castiñeiras, TMPP and de Vasconcelos, ATR and João Filho, EC and Escosteguy, CC and Ferreira Junior, ODC and Tanuri, A and Higa, LM},
title = {Identification and characterisation of SARS-CoV-2 and Human alphaherpesvirus 1 from a productive coinfection in a fatal COVID-19 case.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {116},
number = {},
pages = {e210176},
doi = {10.1590/0074-02760210176},
pmid = {35019069},
issn = {1678-8060},
abstract = {BACKGROUND: During routine Coronavirus disease 2019 (COVID-19) diagnosis, an unusually high viral load was detected by reverse transcription real-time polymerase chain reaction (RT-qPCR) in a nasopharyngeal swab sample collected from a patient with respiratory and neurological symptoms who rapidly succumbed to the disease. Therefore we sought to characterise the infection.

OBJECTIVES: We aimed to determine and characterise the etiological agent responsible for the poor outcome.

METHODS: Classical virological methods, such as plaque assay and plaque reduction neutralisation test combined with amplicon-based sequencing, as well as a viral metagenomic approach, were performed to characterise the etiological agents of the infection.

FINDINGS: Plaque assay revealed two distinct plaque phenotypes, suggesting either the presence of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains or a productive coinfection of two different species of virus. Amplicon-based sequencing did not support the presence of any SARS-CoV-2 genetic variants that would explain the high viral load and suggested the presence of a single SARS-CoV-2 strain. Nonetheless, the viral metagenomic analysis revealed that Coronaviridae and Herpesviridae were the predominant virus families within the sample. This finding was confirmed by a plaque reduction neutralisation test and PCR.

MAIN CONCLUSIONS: We characterised a productive coinfection of SARS-CoV-2 and Herpes simplex virus 1 (HSV-1) in a patient with severe symptoms that succumbed to the disease. Although we cannot establish the causal relationship between the coinfection and the severity of the clinical case, this work serves as a warning for future studies focused on the interplay between SARS-CoV-2 and HSV-1 coinfection and COVID-19 severity.},
}

@article {pmid35017197,
year = {2022},
author = {Belda, E and Voland, L and Tremaroli, V and Falony, G and Adriouch, S and Assmann, KE and Prifiti, E and Aron-Wisnewsky, J and Debédat, J and Le Roy, T and Nielsen, T and Amouyal, C and André, S and Andreelli, F and Blüher, M and Chakaroun, R and Chilloux, J and Coelho, LP and Dao, MC and Das, P and Fellahi, S and Forslund, S and Galleron, N and Hansen, TH and Holmes, B and Ji, B and Krogh Pedersen, H and Le, P and Le Chatelier, E and Lewinter, C and Mannerås-Holm, L and Marquet, F and Myridakis, A and Pelloux, V and Pons, N and Quinquis, B and Rouault, C and Roume, H and Salem, JE and Sokolovska, N and Søndertoft, NB and Touch, S and Vieira-Silva, S and , and Galan, P and Holst, J and Gøtze, JP and Køber, L and Vestergaard, H and Hansen, T and Hercberg, S and Oppert, JM and Nielsen, J and Letunic, I and Dumas, ME and Stumvoll, M and Pedersen, OB and Bork, P and Ehrlich, SD and Zucker, JD and Bäckhed, F and Raes, J and Clément, K},
title = {Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2021-325753},
pmid = {35017197},
issn = {1468-3288},
abstract = {OBJECTIVES: Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome's functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.

DESIGN: We performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.

RESULTS: Severe obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration.

CONCLUSION: Strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.

TRIAL REGISTRATION NUMBER: NCT02059538.},
}

@article {pmid35017031,
year = {2022},
author = {Boeri, L and Donnaloja, F and Campanile, M and Sardelli, L and Tunesi, M and Fusco, F and Giordano, C and Albani, D},
title = {Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {105614},
doi = {10.1016/j.nbd.2022.105614},
pmid = {35017031},
issn = {1095-953X},
abstract = {The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.},
}

@article {pmid35016998,
year = {2022},
author = {Franck, M and de Toro-Martín, J and Varin, TV and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC},
title = {Raspberry consumption: identification of distinct immune-metabolic response profiles by whole blood transcriptome profiling.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {108946},
doi = {10.1016/j.jnutbio.2022.108946},
pmid = {35016998},
issn = {1873-4847},
abstract = {Numerous studies have reported that diets rich in phenolic compounds are beneficial to immune-metabolic health, yet these effects are heterogeneous and the underlying mechanisms are poorly understood. To investigate the inter-individual variability of the immune-metabolic response to raspberry consumption, whole-blood RNAseq data from 24 participants receiving 280g/day of raspberries for 8 weeks were used for the identification of responsiveness subgroups by using partial least squares-discriminant analysis (PLSDA) and hierarchical clustering. Transcriptomic-based clustering regrouped participants into two distinct subgroups of 13 and 11 participants, so-called responders and non-responders, respectively. Following raspberry consumption, a significant decrease in triglycerides, cholesterol and C-reactive protein levels were found in responders, as compared to non-responders. Two major gene expression components of 100 and 220 genes were identified by sparse PLSDA as those better discriminating responders from non-responders, and functional analysis identified pathways related to cytokine production, leukocyte activation and immune response as significantly enriched with most discriminant genes. As compared to non-responders, the plasma lipidomic profile of responders was characterized by a significant decrease in triglycerides and an increase in phosphatidylcholines following raspberry consumption. Prior to the intervention, a distinct metagenomic profile was identified by PLSDA between responsiveness subgroups, and the Firmicutes-to-Bacteroidota ratio was found significantly lower in responders, as compared to non-responders. Findings point to this transcriptomic-based clustering approach as a suitable tool to identify distinct responsiveness subgroups to raspberry consumption. This approach represents a promising framework to tackle the issue of inter-individual variability in the understanding of the impact of foods on immune-metabolic health.},
}

@article {pmid35016706,
year = {2022},
author = {Bolte, EE and Moorshead, D and Aagaard, KM},
title = {Maternal and early life exposures and their potential to influence development of the microbiome.},
journal = {Genome medicine},
volume = {14},
number = {1},
pages = {4},
pmid = {35016706},
issn = {1756-994X},
support = {HD091731//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; DK089201//National Institutes of Health (US)/ ; },
abstract = {At the dawn of the twentieth century, the medical care of mothers and children was largely relegated to family members and informally trained birth attendants. As the industrial era progressed, early and key public health observations among women and children linked the persistence of adverse health outcomes to poverty and poor nutrition. In the time hence, numerous studies connecting genetics ("nature") to public health and epidemiologic data on the role of the environment ("nurture") have yielded insights into the importance of early life exposures in relation to the occurrence of common diseases, such as diabetes, allergic and atopic disease, cardiovascular disease, and obesity. As a result of these parallel efforts in science, medicine, and public health, the developing brain, immune system, and metabolic physiology are now recognized as being particularly vulnerable to poor nutrition and stressful environments from the start of pregnancy to 3 years of age. In particular, compelling evidence arising from a diverse array of studies across mammalian lineages suggest that modifications to our metagenome and/or microbiome occur following certain environmental exposures during pregnancy and lactation, which in turn render risk of childhood and adult diseases. In this review, we will consider the evidence suggesting that development of the offspring microbiome may be vulnerable to maternal exposures, including an analysis of the data regarding the presence or absence of a low-biomass intrauterine microbiome.},
}

@article {pmid34838108,
year = {2021},
author = {Lin, D and Zheng, X and Sanogo, B and Ding, T and Sun, X and Wu, Z},
title = {Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China.},
journal = {Parasites & vectors},
volume = {14},
number = {1},
pages = {586},
pmid = {34838108},
issn = {1756-3305},
support = {2020YFC1200100//the National Key R&D Program of China/ ; 2016YFC1200500//the National Key R&D Program of China/ ; 2019A1515012068//Natural Science Foundation of Guangdong Province/ ; 2020A1515010896//Natural Science Foundation of Guangdong Province/ ; 2021A1515010976//Natural Science Foundation of Guangdong Province/ ; 82072308//the National Natural Science Foundation of China/ ; 82002168//the National Natural Science Foundation of China/ ; 20201192//the 6th Nuclear Energy R&D Project/ ; B12003//The 111 Project/ ; },
mesh = {Aedes/*microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification ; China ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Laboratories ; Metagenomics ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male Aedes mosquitoes. The relationship between the midgut and entire body microbiota of Aedes is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.

METHODS: In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.

RESULTS: A total of 341 OTUs were identified, showing that Proteobacteria was the dominant phylum and Methylobacterium the dominant genus in both Aedes aegypti and Aedes albopictus. The bacterial diversity and community structures of the entire bodies were similar between males and females in both Aedes aegypti and Aedes albopictus. Conversely, the bacterial compositions of male and female Aedes aegypti and Aedes albopictus were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of Aedes aegypti and Aedes albopictus. Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female Aedes albopictus and Aedes Aegypti.

CONCLUSIONS: Our findings that Aedes aegypti and Aedes albopictus reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of Aedes mosquitoes.},
}

Aedes/*microbiology
Animals
*Bacteria/classification/genetics/isolation & purification
China
Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing
Laboratories
Metagenomics
Mosquito Vectors/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid34030623,
year = {2021},
author = {Méndez-Salazar, EO and Vázquez-Mellado, J and Casimiro-Soriguer, CS and Dopazo, J and Çubuk, C and Zamudio-Cuevas, Y and Francisco-Balderas, A and Martínez-Flores, K and Fernández-Torres, J and Lozada-Pérez, C and Pineda, C and Sánchez-González, A and Silveira, LH and Burguete-García, AI and Orbe-Orihuela, C and Lagunas-Martínez, A and Vazquez-Gomez, A and López-Reyes, A and Palacios-González, B and Martínez-Nava, GA},
title = {Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {27},
number = {1},
pages = {50},
pmid = {34030623},
issn = {1528-3658},
mesh = {Biodiversity ; Computational Biology/methods ; *Dysbiosis ; *Gastrointestinal Microbiome ; Gout/etiology/*metabolism/pathology ; Humans ; *Metagenome ; *Metagenomics/methods ; Protein Interaction Mapping ; Protein Interaction Maps ; Uric Acid/*metabolism ; },
abstract = {OBJECTIVE: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.

METHODS: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.

RESULTS: We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.

CONCLUSION: Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.},
}

Biodiversity
Computational Biology/methods
*Dysbiosis
*Gastrointestinal Microbiome
Gout/etiology/*metabolism/pathology
Humans
*Metagenome
*Metagenomics/methods
Protein Interaction Mapping
Protein Interaction Maps
Uric Acid/*metabolism

@article {pmid35016010,
year = {2022},
author = {Murchie, TJ and Karpinski, E and Eaton, K and Duggan, AT and Baleka, S and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN},
title = {Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2021.12.023},
pmid = {35016010},
issn = {1879-0445},
abstract = {Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.},
}

@article {pmid35015746,
year = {2022},
author = {Ghare, S and Singhal, R and Bryant, V and Gautam, S and Tirumala, CC and Srisailam, PK and Reyes-Vega, A and Ghooray, D and McClain, CJ and Hoffman, K and Petrosino, J and Bryant, K and Govind, V and Cohen, R and Cook, RL and Barve, S},
title = {Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV.},
journal = {Journal of acquired immune deficiency syndromes (1999)},
volume = {89},
number = {Suppl 1},
pages = {S56-S64},
doi = {10.1097/QAI.0000000000002866},
pmid = {35015746},
issn = {1944-7884},
abstract = {BACKGROUND: Imbalance in tryptophan (TRP) metabolism and its neuroactive metabolites, serotonin and kynurenine (KYN), is a known pathogenic mechanism underlying neurocognitive impairment. Gut microbiota plays an important role in TRP metabolism, and the production of these neuroactive molecules affects neurocognitive function. Although both HIV infection and normal aging independently induce gut dysbiosis and influence TRP metabolism, their interactive effects on compositional/functional changes in gut microbiota and consequent alterations in TRP metabolites remain largely undetermined.

METHODS: Older people living with HIV infection (PLWH, aged 50-70 years, n = 22) were enrolled in this cross-sectional pilot study. Metagenomic analysis of fecal microbiome using 16S Ribosomal ribonucleic acid gene sequencing and metabolomics analysis of plasma using mass spectrometry with a reverse-phase iquid chromatography tandem mass spectrometry were performed. Statistical analyses included the univariate linear regression and Spearman correlation analyses.

RESULTS: Age-associated changes in plasma levels of key neuroactive TRP metabolites, serotonin and KYN, were seen in PLWH. Specifically, we observed age-dependent decreases in serotonin and increases in KYN and KYN-to-TRP ratio, indicative of dysfunctional TRP metabolism. Furthermore, the gut dysbiosis seen in older PLWH is characterized by a reduction of Firmicutes/Bacteroidetes ratio and butyrate-producing microbial families Lachnospiraceae and Lactobacillaceae. Of importance, correspondent with gut dysbiosis, increasing age was significantly associated with decreased plasma butyrate levels, which in turn correlated positively with serotonin and negatively with KYN/TRP ratio.

CONCLUSIONS: Age-dependent gut microbial dysbiosis distinguished by a decrease in butyrogenic potential is a key pathogenic feature associated with the shift in TRP metabolism from serotonin to KYN in older PLWH.},
}

@article {pmid35015311,
year = {2022},
author = {Negrey, JD and Mitani, JC and Wrangham, RW and Otali, E and Reddy, RB and Pappas, TE and Grindle, KA and Gern, JE and Machanda, ZP and Muller, MN and Langergraber, KE and Emery Thompson, M and Goldberg, TL},
title = {Viruses associated with ill health in wild chimpanzees.},
journal = {American journal of primatology},
volume = {},
number = {},
pages = {e23358},
doi = {10.1002/ajp.23358},
pmid = {35015311},
issn = {1098-2345},
support = {BCS-1355014//National Science Foundation/ ; BCS-1613392//National Science Foundation/ ; BCS-1613393//National Science Foundation/ ; DGE-1256260//National Science Foundation/ ; NCS-FO 1926653//National Science Foundation/ ; R01AG049395/NH/NIH HHS/United States ; //Nacey-Maggioncalda Foundation/ ; //Wenner-Gren Foundation/ ; 9742-15//National Geographic Society/ ; 9824-15//National Geographic Society/ ; //Leakey Foundation/ ; //University of New Mexico/ ; //University of Wisconsin-Madison/ ; //Boston University/ ; //University of Michigan/ ; },
abstract = {Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.},
}

@article {pmid35014949,
year = {2022},
author = {Gaio, D and Anantanawat, K and To, J and Liu, M and Monahan, L and Darling, AE},
title = {Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.},
journal = {Microbial genomics},
volume = {8},
number = {1},
pages = {},
doi = {10.1099/mgen.0.000744},
pmid = {35014949},
issn = {2057-5858},
abstract = {We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.},
}

@article {pmid35014874,
year = {2022},
author = {Palomo, A and Dechesne, A and Cordero, OX and Smets, BF},
title = {Evolutionary Ecology of Natural Comammox Nitrospira Populations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113921},
doi = {10.1128/msystems.01139-21},
pmid = {35014874},
issn = {2379-5077},
abstract = {Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. Nitrospira species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. IMPORTANCE Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent Nitrospira populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from Nitrospira species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.},
}