CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Nature Methods, Journal Year: 2023, Volume and Issue: 20(8), P. 1203 - 1212

Published: July 27, 2023

Language: Английский

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A rooted phylogeny resolves early bacterial evolution

Science, Journal Year: 2021, Volume and Issue: 372(6542)

Published: May 6, 2021

A rooted bacterial tree is necessary to understand early evolution, but the position of root contested. Here, we model evolution 11,272 gene families identify root, extent horizontal transfer (HGT), and nature last common ancestor (LBCA). Our analyses between major clades Terrabacteria Gracilicutes suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary recent proposals, our reject basal placement Candidate Phyla Radiation, which instead branches sister Chloroflexota within Terrabacteria. While most (92%) have evidence HGT, overall, two-thirds transmissions been vertical, suggesting provides meaningful frame reference for interpreting evolution.

Language: Английский

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Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Dec. 1, 2020

Abstract Introduction Microbial residents of the human oral cavity have long been a major focus microbiology due to their influence on host health and intriguing patterns site specificity amidst lack dispersal limitation. However, determinants niche partitioning in this habitat are yet be fully understood, especially among taxa that belong recently discovered branches microbial life. Results Here, we assemble metagenomes from tongue dental plaque samples multiple individuals reconstruct 790 non-redundant genomes, 43 which resolve TM7, member Candidate Phyla Radiation, forming six monophyletic clades distinctly associate with either or tongue. Both pangenomic phylogenomic analyses group tongue-specific other host-associated TM7 genomes. In contrast, plaque-specific environmental Besides offering deeper insights into ecology, evolution, mobilome cryptic members microbiome, our study reveals an resemblance between non-host environments indicated by suggesting may served as stepping stone for microbes adapt some microbes. Additionally, report prophages widespread oral-associated while absent played role adaptation environment. Conclusions Our data illuminate enigmatic cavity, including SR1, GN02, provide genomes poorly characterized prevalent biome, such uncultivated Flavobacteriaceae.

Language: Английский

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Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

mBio, Journal Year: 2020, Volume and Issue: 11(3)

Published: June 15, 2020

Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated grown the lab. Though vast majority cannot isolated, we extract genetic information search it for genes compounds. These understudied offer a wealth potential discovery new important microbial products. Here, identified ability diverse novel range environments. This will other researchers who wish isolate certain Beyond use humans, understanding distribution function products is key communities effects on biogeochemical cycles.

Language: Английский

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Machine learning for microbiologists

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(4), P. 191 - 205

Published: Nov. 15, 2023

Language: Английский

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Unifying the known and unknown microbial coding sequence space

eLife, Journal Year: 2022, Volume and Issue: 11

Published: March 31, 2022

Genes of unknown function are among the biggest challenges in molecular biology, especially microbial systems, where 40-60% predicted genes unknown. Despite previous attempts, systematic approaches to include fraction into analytical workflows still lacking. Here, we present a conceptual framework, its translation computational workflow AGNOSTOS and demonstration on how can bridge known-unknown gap genomes metagenomes. By analyzing 415,971,742 from 1749 metagenomes 28,941 bacterial archaeal genomes, quantify extent fraction, diversity, relevance across multiple organisms environments. The sequence space is exceptionally diverse, phylogenetically more conserved than known predominantly taxonomically restricted at species level. From 71 M identified be function, compiled collection 283,874 lineage-specific for

Language: Английский

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Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

Cell, Journal Year: 2023, Volume and Issue: 186(22), P. 4803 - 4817.e13

Published: Sept. 7, 2023

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute disproportionately large fraction microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow epibionts on host Actinobacteria. Due lack suitable tools, genetic basis this lifestyle and other unique features Patescibacteira remain unexplored. Here, we show Saccharibacteria exhibit natural competence, exploit property for their manipulation. Imaging fluorescent protein-labeled provides high spatiotemporal resolution phenomena accompanying epibiotic growth, transposon-insertion sequencing (Tn-seq) genome-wide screen reveals contribution enigmatic Saccharibacterial genes growth hosts. Finally, leverage metagenomic data provide cutting-edge protein structure-based bioinformatic resources support strain Southlakia epibionticum its corresponding host, Actinomyces israelii, model system unlocking molecular underpinnings lifestyle.

Language: Английский

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SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 31, 2024

Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem microbial ecology. To address limitations existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities known species, only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency, applied it to 248,559 publicly available metagenomes show vast majority samples from marine, freshwater, sediment soil environments are dominated by lacking representation (median 75.0%). also provides way identify for recovery metagenome-assembled genomes lineages interest, can incorporate user-recovered into its reference database improve profiling resolution. Quantifying full diversity Bacteria Archaea shows genome databases far saturated.

Language: Английский

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Large freshwater phages with the potential to augment aerobic methane oxidation

Nature Microbiology, Journal Year: 2020, Volume and Issue: 5(12), P. 1504 - 1515

Published: Aug. 24, 2020

Abstract There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed phage from freshwater lakes to contain bacteria oxidize methane. Of manually curated genomes, 22 (18 complete), ranging 159 kilobase (kb) 527 kb in length, were found encode pmoC gene, an enzymatically critical subunit of particulate methane monooxygenase, predominant oxidation catalyst nature. The phage-associated PmoC sequences show high similarity (>90%), and affiliate phylogenetically with, those coexisting bacterial methanotrophs, including members Methyloparacoccus , Methylocystis Methylobacter spp. addition, pmoC-phage abundance patterns correlate supporting host–phage relationships. Future work needed determine whether has similar functions additional copies encoded thus contributing growth on Transcriptomics data Lake Rotsee (Switzerland) showed some genes highly expressed situ and, interest, most rapidly methanotroph was infected by three pmoC-phages. Thus, augmentation pmoC-phages during infection could modulate efflux this potent greenhouse gas into environment.

Language: Английский

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Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: April 28, 2021

The Candidate Phyla Radiation (CPR) constitutes a large group of mostly uncultured bacterial lineages with small cell sizes and limited biosynthetic capabilities. They are thought to be symbionts other organisms, but the nature this symbiosis has been ascertained only for cultured Saccharibacteria, which epibiotic parasites bacteria. Here, we study biology genome Vampirococcus lugosii, becomes first described species Vampirococcus, genus bacteria morphologically identified decades ago. belongs CPR phylum Absconditabacteria. It feeds on anoxygenic photosynthetic gammaproteobacteria, fully absorbing their cytoplasmic content. cells divide epibiotically, forming multicellular stalks whose apical can reach new hosts. is (1.3 Mbp) highly reduced in metabolism genes, enriched genes possibly related fibrous surface likely involved interactions host. Gene loss continuous during evolution Absconditabacteria, generally most bacteria, compensated by gene acquisition horizontal transfer de novo evolution. Our findings support parasitism as widespread lifestyle probably contribute control populations diverse ecosystems. Moreira et al. an parasite supporting common

Language: Английский

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