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A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis

https://doi.org/10.1101/2020.09.24.311720

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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PHYLIP ( PHYLogeny Inference Package)

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The human microbiome

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

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Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

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Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

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A Clinician's Primer on the Role of the Microbiome in Human Health and Disease

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Unipept 4.0: Functional Analysis of Metaproteome Data

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Human gut microbes associated with obesity

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Shotgun metaproteomics of the human distal gut microbiota

inferredcites →https://doi.org/10.1038/nature06244openalex-snapshot

The Human Microbiome Project

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Alterations of the human gut microbiome in liver cirrhosis

inferredcites →https://doi.org/10.1038/nbt.2579openalex-snapshot

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

inferredcites →https://doi.org/10.1038/nbt.4229openalex-snapshot

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

inferredcites →https://doi.org/10.1038/nmeth.3103openalex-snapshot

Binning metagenomic contigs by coverage and composition

inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

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Next-generation sequencing transforms today's biology

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A new view of the tree of life

inferredcites →https://doi.org/10.1038/nrmicro2876openalex-snapshot

The interplay between the intestinal microbiota and the brain

inferredcites →https://doi.org/10.1038/s41564-017-0012-7openalex-snapshot

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

inferredcites →https://doi.org/10.1038/s41586-019-0965-1openalex-snapshot

A new genomic blueprint of the human gut microbiota

inferredcites →https://doi.org/10.1038/s41587-018-0009-7openalex-snapshot

A human gut bacterial genome and culture collection for improved metagenomic analyses

inferredcites →https://doi.org/10.1038/srep06504openalex-snapshot

Inferring phylogenies of evolving sequences without multiple sequence alignment

inferredcites →https://doi.org/10.1073/pnas.1319284111openalex-snapshot

Relating the metatranscriptome and metagenome of the human gut

inferredcites →https://doi.org/10.1073/pnas.87.12.4576openalex-snapshot

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

inferredcites →https://doi.org/10.1073/pnas.96.7.3801openalex-snapshot

Horizontal gene transfer among genomes: The complexity hypothesis

inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments

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APE: Analyses of Phylogenetics and Evolution in R language

inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

inferredcites →https://doi.org/10.1093/bioinformatics/btw290openalex-snapshot

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

inferredcites →https://doi.org/10.1093/molbev/msx302openalex-snapshot

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

inferredcites →https://doi.org/10.1093/nar/gkg128openalex-snapshot

The TIGRFAMs database of protein families

inferredcites →https://doi.org/10.1093/nar/gkq747openalex-snapshot

FragGeneScan: predicting genes in short and error-prone reads

inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot

Pfam: the protein families database

inferredcites →https://doi.org/10.1093/nar/gkv397openalex-snapshot

HMMER web server: 2015 update

inferredcites →https://doi.org/10.1093/nar/gkx351openalex-snapshot

CAFE: aCcelerated Alignment-FrEe sequence analysis

inferredcites →https://doi.org/10.1097/mog.0b013e3283573017openalex-snapshot

The impact of gut microbes in allergic diseases

inferredcites →https://doi.org/10.1098/rsbl.2018.0632openalex-snapshot

Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

inferredcites →https://doi.org/10.1099/acmi.ac2019.po0041openalex-snapshot

Redefining a new genomic blueprint of the human gut microbiota

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

inferredcites →https://doi.org/10.1101/gr.5969107openalex-snapshot

MEGAN analysis of metagenomic data

inferredcites →https://doi.org/10.1126/science.7542800openalex-snapshot

Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd

inferredcites →https://doi.org/10.1128/aem.66.4.1654-1661.2000openalex-snapshot

Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut

inferredcites →https://doi.org/10.1128/jb.01765-07openalex-snapshot

Bile Salts and Glycine as Cogerminants for Clostridium difficile Spores

inferredcites →https://doi.org/10.1177/1756283x13482996openalex-snapshot

Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ

inferredcites →https://doi.org/10.1186/2049-2618-2-26openalex-snapshot

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

inferredcites →https://doi.org/10.1186/gb-2009-10-8-r85openalex-snapshot

Community-wide analysis of microbial genome sequence signatures

inferredcites →https://doi.org/10.1186/s13059-017-1319-7openalex-snapshot

Alignment-free sequence comparison: benefits, applications, and tools

inferredcites →https://doi.org/10.1186/s13059-019-1891-0openalex-snapshot

Improved metagenomic analysis with Kraken 2

inferredcites →https://doi.org/10.12688/f1000research.10225.1openalex-snapshot

Recapitulating phylogenies using k-mers: from trees to networks

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0027731openalex-snapshot

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

inferredcites →https://doi.org/10.3389/fcimb.2012.00028openalex-snapshot

Toward a structural understanding of Clostridium difficile toxins A and B

inferredcites →https://doi.org/10.3390/proteomes6010002openalex-snapshot

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

inferredcites →https://doi.org/10.7717/peerj.603openalex-snapshot

GroopM: an automated tool for the recovery of population genomes from related metagenomes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-023-40023-wopenalex-snapshot

Diffusible signal factors (DSFs) bind and repress VirF, the leading virulence activator of Shigella flexneri

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