Reconstruction of ancient microbial genomes from the human gut DOI Creative Commons
Marsha C. Wibowo, Zhen Yang, Maxime Borry

et al.

Nature, Journal Year: 2021, Volume and Issue: 594(7862), P. 234 - 239

Published: May 12, 2021

Abstract Loss of gut microbial diversity 1–6 in industrial populations is associated with chronic diseases 7 , underscoring the importance studying our ancestral microbiome. However, relatively little known about composition pre-industrial microbiomes. Here we performed a large-scale de novo assembly genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) well-preserved DNA southwestern USA and Mexico, reconstructed 498 medium- high-quality genomes. Among 181 strongest evidence being ancient origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for key symbiont Methanobrevibacter smithii . In comparison to 789 present-day microbiome countries, are more similar non-industrialized than industrialized Functional profiling reveals markedly lower abundance antibiotic-resistance mucin-degrading genes, as well enrichment mobile genetic elements relative This study facilitates discovery characterization microorganisms microbiomes investigation evolutionary history microbiota through reconstruction

Language: Английский

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale DOI Creative Commons
Carlos P. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunić

et al.

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5825 - 5829

Published: Sept. 30, 2021

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe major upgrade to eggNOG-mapper, tool for based on precomputed orthology assignments, now optimized vast (meta)genomic data sets. Improvements version 2 include full update both the genomes databases those from eggNOG v5, as well several efficiency enhancements new features. Most notably, eggNOG-mapper v2 allows for: 1) de novo gene prediction raw contigs, 2) built-in pairwise prediction, 3) fast protein domain discovery, 4) GFF decoration. is available standalone or an online service http://eggnog-mapper.embl.de.

Language: Английский

Citations

2320
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 DOI Creative Commons
Francesco Beghini, Lauren J. McIver, Aitor Blanco‐Míguez

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: May 4, 2021

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest sequences now available. Compared current alternatives, MetaPhlAn 3 increases accuracy taxonomic profiling, HUMAnN improves that functional potential activity. These detected novel disease-microbiome links applications CRC (1262 metagenomes) IBD (1635 817 metatranscriptomes). Strain-level an additional 4077 StrainPhlAn PanPhlAn unraveled structure common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations cloud-deployable reproducible workflows, platform can help researchers deepen resolution, scale, multi-omic community studies.

Language: Английский

Citations

1397
GTDB-Tk v2: memory friendly classification with the genome taxonomy database DOI Creative Commons
Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz

et al.

Bioinformatics, Journal Year: 2022, Volume and Issue: 38(23), P. 5315 - 5316

Published: Oct. 11, 2022

Abstract Summary The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, growing size of GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts memory (∼320 GB) which limits its adoption ease use. Here, we present an update to that uses a divide-and-conquer approach where user genomes are initially placed into with family-level representatives followed placement appropriate class-level subtree comprising species representatives. This substantially reduces requirements while having minimal impact on classification. Availability implementation is implemented Python licenced under GNU General Public Licence v3.0. Source code documentation available at: https://github.com/ecogenomics/gtdbtk. Supplementary information data at Bioinformatics online.

Language: Английский

Citations

778
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 DOI Creative Commons
Aitor Blanco‐Míguez, Francesco Beghini, Fabio Cumbo

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(11), P. 1633 - 1644

Published: Feb. 23, 2023

Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. 4 explains ~20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome proves accurate than available alternatives on synthetic evaluations while also reliably quantifying with no cultured isolates. Application method to >24,500 metagenomes highlights previously undetected be strong biomarkers host conditions lifestyles mouse shows that even uncharacterized genetically profiled resolution single strains.

Language: Английский

Citations

545
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank DOI Creative Commons
Chang Liu, Meng-Xuan Du,

Rexiding Abuduaini

et al.

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: May 21, 2021

Abstract Background In gut microbiome studies, the cultured microbial resource plays essential roles, such as helping to unravel functions and host-microbe interactions. Although several major studies have been performed elucidate human microbiota, up 70% of Unified Human Gastrointestinal Genome species not date. Large-scale isolation identification well availability public are imperative for further characterizing functions. Results this study, we constructed a Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn ) through cultivation 10,558 isolates from 31 sample mixtures 239 fresh fecal samples healthy Chinese volunteers, deposited 1170 strains representing 400 different in culture collections International Depository Authority long-term preservation access worldwide. Following rules Code Nomenclature Prokaryotes, 102 new were characterized denominated, while 28 genera 3 families proposed. hGMB represented over 80% common dominant global 16S rRNA gene amplicon data ( n = 11,647) 24 “most-wanted” “medium priority” taxa proposed by Microbiome Project. We total sequenced 115 genomes novel 13 previously known species. Further silico analysis revealed that newly 22 uncultured (UHGG) contributed representatives potentially “dark taxa” had discovered UHGG. The nonredundant catalogs generated covered 50% functionally genes (KEGG orthologs) largest approximately 10% “most wanted” unknown proteins FUnkFams database. Conclusions A publicly accessible (hGMB) was established contained represents expands resources genomic repository adding species, genera, families, microbes.

Language: Английский

Citations

526
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut DOI Creative Commons
Ann Gregory, Olivier Zablocki, Ahmed A. Zayed

et al.

Cell Host & Microbe, Journal Year: 2020, Volume and Issue: 28(5), P. 724 - 740.e8

Published: Aug. 24, 2020

Language: Английский

Citations

523
Assessment of global health risk of antibiotic resistance genes DOI Creative Commons
Zhenyan Zhang, Qi Zhang, Tingzhang Wang

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 23, 2022

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many can confer resistance, but evaluating relative risks of ARGs is complex. Factors such as abundance, propensity for lateral transmission and ability be expressed pathogens are all important. Here, an analysis at metagenomic level from various habitats (6 types habitats, 4572 samples) detects 2561 that collectively conferred 24 classes antibiotics. We quantitatively evaluate risk humans, defined will confound clinical treatment pathogens, these by integrating accessibility, mobility, pathogenicity availability. Our results demonstrate 23.78% pose a risk, especially those which multidrug resistance. also calculate antibiotic samples four main with machine learning, successfully map global marine over 75% accuracy. novel method surveilling help manage one most important animal health.

Language: Английский

Citations

506
Massive expansion of human gut bacteriophage diversity DOI Creative Commons

Luis F. Camarillo-Guerrero,

Alexandre Almeida, Guillermo Rangel-Piñeros

et al.

Cell, Journal Year: 2021, Volume and Issue: 184(4), P. 1098 - 1109.e9

Published: Feb. 1, 2021

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database, a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters (VCs) are not restricted to single species, across phylogenetically distinct species. Epidemiological analysis uncovered 280 VCs found at least 5 continents highly prevalent phage clade with features reminiscent p-crAssphage. This high-quality, large-scale catalog will improve future virome studies enable bacteriophages.

Language: Английский

Citations

471
Prevotella diversity, niches and interactions with the human host DOI
Adrian Tett, Edoardo Pasolli, Giulia Masetti

et al.

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 19(9), P. 585 - 599

Published: May 28, 2021

Language: Английский

Citations

452
Role and Mechanism of Gut Microbiota in Human Disease DOI Creative Commons
Yinwei Chen,

Jinghua Zhou,

Li Wang

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2021, Volume and Issue: 11

Published: March 17, 2021

The human gut microbiome is a huge microbial community that plays an irreplaceable role in life. With the further development of research, influence intestinal flora on diseases has been gradually excavated. Gut microbiota (GM) dysbiosis adverse health effects body will lead to variety chronic diseases. underlying mechanisms GM are incredibly complicated. This review focuses regulation and mechanism neurodegenerative diseases, cardiovascular metabolic gastrointestinal thus providing potential target for prevention treatment disease.

Language: Английский

Citations

443