Gut microbes contribute to variation in solid organ transplant outcomes in mice DOI Creative Commons
Christine McIntosh, Luqiu Chen, Alon Shaiber

et al.

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: May 25, 2018

Solid organ transplant recipients show heterogeneity in the occurrence and timing of acute rejection episodes. Understanding factors responsible for such variability patient outcomes may lead to improved diagnostic therapeutic approaches. Rejection kinetics transplanted organs mainly depends on extent genetic disparities between donor recipient, but a role environmental is emerging. We have recently shown that major alterations microbiota following broad-spectrum antibiotics, or use germ-free animals, promoted longer skin graft survival mice. Here, we tested whether spontaneous differences microbial colonization genetically similar individuals can contribute kinetics. compared minor mismatched grafts C57BL/6 mice from Jackson Laboratory (Jax) Taconic Farms (Tac), animals colonized by different commensal microbes. Female Tac rejected vendor-matched males more quickly than Jax observed prolonged when they were exposed microbiome through co-housing fecal transplantation (FMT) gastric gavage. In contrast, exposure did not change mice, suggesting dominant suppressive effect microbiota. High-throughput sequencing 16S rRNA gene amplicons samples confirmed convergence composition after cohousing transfer. Our analysis amplicon data associated members single bacterial genus, Alistipes, with survival. Consistent this finding, genus Alistipes absent separate cohort, which transfer failed prolong These results demonstrate resident healthy translate into distinct rejection, interpersonal outcomes. The association suggests might affect host physiology, including at sites distal gastrointestinal tract. Overall, these findings allude potential specific gut microbes promote administration probiotics, FMT.

Language: Английский

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis DOI Creative Commons
Benjamin J. Callahan, Paul J. McMurdie, Susan Holmes

et al.

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(12), P. 2639 - 2643

Published: July 21, 2017

Abstract Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting the customary construction of molecular operational taxonomic units (OTUs): clusters reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such amplicon sequence variants (ASVs) can be resolved exactly, down level single-nucleotide differences over sequenced gene region. The benefits finer resolution are immediately apparent, and arguments for ASV focused on their improved resolution. Less obvious, but we believe more important, broad derive from status ASVs as consistent labels with intrinsic biological meaning identified independently reference database. Here discuss how these features grant combined advantages closed-reference OTUs—including computational costs scale linearly study size, simple merging between processed sets, forward prediction—and de novo accurate measurement diversity applicability communities lacking deep coverage in databases. We argue improvements reusability, reproducibility comprehensiveness great should replace OTUs standard unit analysis reporting.

Language: Английский

Citations

2752
Phage puppet masters of the marine microbial realm DOI
Mya Breitbart,

Chelsea Bonnain,

Kema Malki

et al.

Nature Microbiology, Journal Year: 2018, Volume and Issue: 3(7), P. 754 - 766

Published: June 1, 2018

Language: Английский

Citations

580
Minimum Information about an Uncultivated Virus Genome (MIUViG) DOI Creative Commons
Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh

et al.

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 37(1), P. 29 - 37

Published: Dec. 17, 2018

This paper presents standards and best practices for reporting genome sequences of uncultivated viruses. We present an extension the Minimum Information about any (x) Sequence (MIxS) standard virus genomes. Uncultivated Virus Genome (MIUViG) were developed within Genomic Standards Consortium framework include origin, quality, annotation, taxonomic classification, biogeographic distribution in silico host prediction. Community-wide adoption MIUViG standards, which complement a Single Amplified (MISAG) Metagenome-Assembled (MIMAG) bacteria archaea, will improve genomes public databases. In turn, this should enable more robust comparative studies systematic exploration global virosphere.

Language: Английский

Citations

558
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units DOI Creative Commons
Sydney I. Glassman, Jennifer B. H. Martiny

mSphere, Journal Year: 2018, Volume and Issue: 3(4)

Published: July 26, 2018

Recent discussion focuses on the best method for delineating microbial taxa, based either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if binning approach (ESVs versus 97% OTUs) affected ecological conclusions a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences richness, we found that α β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, community composition dominant taxa did not vary Consequently, statistical inferences nearly indistinguishable. Furthermore, ESVs only moderately increased genetic resolution fungal bacterial (1.3 2.1 times OTU respectively). conclude broadscale (e.g., fungi) analyses, ESV methods will often reveal similar results. Thus, while there are good reasons employ ESVs, need question validity results OTUs.IMPORTANCE Microbial ecologists have made exceptional improvements our understanding microbiomes last decade due breakthroughs sequencing technologies. These advances wide-ranging implications fields ranging from agriculture human health. Due limitations databases, majority ecology studies use approximate taxonomy DNA similarity. There remains extensive debate way bin this taxonomy. Here examine two popular approaches using field-based examining major outcomes. it appears standard analyses overly sensitive particulars

Language: Английский

Citations

215
Alpha-, beta-, and gamma-diversity of bacteria varies across habitats DOI Creative Commons
Kendra E. Walters, Jennifer B. H. Martiny

PLoS ONE, Journal Year: 2020, Volume and Issue: 15(9), P. e0233872 - e0233872

Published: Sept. 23, 2020

Bacteria are essential parts of ecosystems and the most diverse organisms on planet. Yet, we still do not know which habitats support highest diversity bacteria across multiple scales. We analyzed alpha-, beta-, gamma-diversity bacterial assemblages using 11,680 samples compiled by Earth Microbiome Project. found that soils contained richness within a single sample (alpha-diversity), but sediment displayed gamma-diversity. Sediment, biofilms/mats, inland water exhibited variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, shrublands richness, while forests, cold tundra biomes consistently harbored fewer species. Surprisingly, encompassed similar levels beta-diversity as other soil biomes. These patterns were robust to alpha- beta- metrics used taxonomic binning approach. Overall, results idea spatial environmental heterogeneity is an important driver diversity.

Language: Английский

Citations

183
Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions DOI Open Access
Natalia García-García, Javier Tamames, Alexandra M. Linz

et al.

The ISME Journal, Journal Year: 2019, Volume and Issue: 13(12), P. 2969 - 2983

Published: Aug. 16, 2019

Language: Английский

Citations

177
Host-hijacking and planktonic piracy: how phages command the microbial high seas DOI Creative Commons
Joanna Warwick-Dugdale, Holger H. Buchholz, Michael J. Allen

et al.

Virology Journal, Journal Year: 2019, Volume and Issue: 16(1)

Published: Feb. 1, 2019

Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes ocean, marine microbes eke out a under constant assault from predatory viruses. Viral concentrations exceed those their bacterial prey by an order magnitude surface water, making these obligate parasites most abundant biological entities ocean. Like pirates 17th and 18th centuries that hounded ships plying trade exploration routes, viruses have evolved mechanisms to hijack microbial cells repurpose cargo indeed vessels themselves maximise viral propagation. Phenotypic reconfiguration host is often achieved through Auxiliary Metabolic Genes – genes originally derived genomes but maintained adapted redirect energy substrates towards synthesis. In this review, we critically evaluate literature describing used bacteriophages reconfigure metabolism plunder intracellular resources optimise production. We also highlight when, challenging environments, 'batten down hatches' strategy supersedes 'plunder pillage'. Here, infecting virus increases fitness phenotypic augmentation ride metaphorical storm, with concomitant impact on substrate uptake metabolism, ultimately, interactions wider community. Thus, traditional view virus-host relationship as predator does not fully characterise variety or significance observed. Recent advances metagenomics provided tantalising glimpse novel metabolic reprogramming oceans. Incorporation new findings into models requires experimental evidence model systems improvements our ability accurately predict protein function sequence data.

Language: Английский

Citations

146
Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data DOI Creative Commons
Jiwen Liu, Zhe Meng, Xiaoyue Liu

et al.

Marine Life Science & Technology, Journal Year: 2019, Volume and Issue: 1(1), P. 112 - 128

Published: Sept. 30, 2019

Abstract Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into ecology from a number perspectives. Both deterministic and stochastic processes contribute to assembly but their relative importance structuring subcommunities, that are categorized by traits such as abundance, functional type activity, differs. Through correlation-based network analysis, significant progress been made unraveling co-occurrence patterns dynamics response environmental changes. Prediction functioning, based data, is receiving increasing attention, closely related microbes often share similar ecological diversity exhibits correlations functioning. functioning likely executed not whole community, rather active fraction which can be inferred marker gene transcription level members. Furthermore, huge amount significantly expanded tree life illuminated phylogenetic divergence evolutionary history. This review summarizes important findings assembly, interaction, activity diversification, highlighting interacting different aspects, derived data.

Language: Английский

Citations

145
Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold DOI Creative Commons
Marlène Chiarello, Mark McCauley, Sébastien Villéger

et al.

PLoS ONE, Journal Year: 2022, Volume and Issue: 17(2), P. e0264443 - e0264443

Published: Feb. 24, 2022

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift how research teams investigate microbial biodiversity, away from identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods variants, ASVs). While several inherent properties that make them desirable compared clustering-based methods, questions remain as influence these pipelines on ecological patterns being assessed, especially when other choices made processing data (e.g. rarefaction) and computing diversity indices. We respective influences two widely used namely DADA2 (a method) vs. Mothur 16S rRNA gene (hypervariable region v4), such effects rarefaction community table OTU identity threshold (97% 99%) signals detected. dataset comprising freshwater invertebrate (three Unionidae species) gut environmental (sediment, seston) communities sampled six rivers southeastern USA. ranked each choice alpha beta diversity, taxonomic composition. The pipeline significantly influenced diversities changed signal detected, presence/absence indices richness index unweighted Unifrac. Interestingly, discrepancy between ASV-based metrics could be attenuated by use rarefaction. identification major classes genera also revealed significant discrepancies across pipelines. Compared pipeline's effect, had minimal impact all measurements.

Language: Английский

Citations

133
Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine DOI
Yue Yin,

Xiaojie Wang,

Yuanan Hu

et al.

Journal of Hazardous Materials, Journal Year: 2022, Volume and Issue: 442, P. 130063 - 130063

Published: Sept. 26, 2022

Language: Английский

Citations

77