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Systems biology illuminates alternative metabolic niches in the human gut microbiome

https://doi.org/10.1101/2022.09.19.508335

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What this work says

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

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Metabolism of hydrogen gases and bile acids in the gut microbiome

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Intestinal tumor and agmatine (decarboxylated arginine)

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Basic Laboratory Culture Methods for Anaerobic Bacteria

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ggplot2

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Diversity in enoyl-acyl carrier protein reductases

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Mathematical modelling supports the existence of a threshold hydrogen concentration and media-dependent yields in the growth of a reductive acetogen

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The metabolomics standards initiative (MSI)

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Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

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Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

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CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog

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A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria

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In vivo commensal control of Clostridioides difficile virulence

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Human Gut Bacterial Metabolism Drives Th17 Activation and Colitis

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Advances in constraint-based modelling of microbial communities

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Agmatine: clinical applications after 100 years in translation

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Wall Teichoic Acid in Staphylococcus aureus Host Interaction

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Microbial Regulation of Host Physiology by Short-chain Fatty Acids

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clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

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Variation and evolution of the citric-acid cycle: a genomic perspective

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Mass Spectral Feature List Optimizer (MS-FLO): A Tool To Minimize False Positive Peak Reports in Untargeted Liquid Chromatography–Mass Spectroscopy (LC-MS) Data Processing

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Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

inferredcites →https://doi.org/10.1038/nbt.1672openalex-snapshot

High-throughput generation, optimization and analysis of genome-scale metabolic models

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

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iML1515, a knowledgebase that computes Escherichia coli traits

inferredcites →https://doi.org/10.1038/nbt.4163openalex-snapshot

KBase: The United States Department of Energy Systems Biology Knowledgebase

inferredcites →https://doi.org/10.1038/nchembio.1864openalex-snapshot

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

inferredcites →https://doi.org/10.1038/nprot.2009.203openalex-snapshot

A protocol for generating a high-quality genome-scale metabolic reconstruction

inferredcites →https://doi.org/10.1038/nrmicro1861openalex-snapshot

Teichoic acids and related cell-wall glycopolymers in Gram-positive physiology and host interactions

inferredcites →https://doi.org/10.1038/nrmicro2746openalex-snapshot

How glycan metabolism shapes the human gut microbiota

inferredcites →https://doi.org/10.1038/s41467-018-05470-4openalex-snapshot

Microbial tryptophan catabolites in health and disease

inferredcites →https://doi.org/10.1038/s41467-018-07946-9openalex-snapshot

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

inferredcites →https://doi.org/10.1038/s41564-018-0123-9openalex-snapshot

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

inferredcites →https://doi.org/10.1038/s41564-018-0306-4openalex-snapshot

Gut microbiome structure and metabolic activity in inflammatory bowel disease

inferredcites →https://doi.org/10.1038/s41564-019-0596-1openalex-snapshot

Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria

inferredcites →https://doi.org/10.1038/s41564-022-01109-9openalex-snapshot

Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites

inferredcites →https://doi.org/10.1038/s41586-021-03707-9openalex-snapshot

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

inferredcites →https://doi.org/10.1038/s41586-022-04480-zopenalex-snapshot

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

inferredcites →https://doi.org/10.1038/s41587-019-0201-4openalex-snapshot

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

inferredcites →https://doi.org/10.1038/s41592-020-0933-6openalex-snapshot

Feature-based molecular networking in the GNPS analysis environment

inferredcites →https://doi.org/10.1038/s41596-018-0098-2openalex-snapshot

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

inferredcites →https://doi.org/10.1038/s42255-021-00506-4openalex-snapshot

Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization

inferredcites →https://doi.org/10.1073/pnas.1307797110openalex-snapshot

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

inferredcites →https://doi.org/10.1073/pnas.1711235114openalex-snapshot

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models

inferredcites →https://doi.org/10.1080/19490976.2017.1320468openalex-snapshot

Cultured microbes represent a substantial fraction of the human and mouse gut microbiota

inferredcites →https://doi.org/10.1080/19490976.2018.1458180openalex-snapshot

Bile acid oxidation byEggerthella lentastrains C592 and DSM 2243T

inferredcites →https://doi.org/10.1093/bioinformatics/btab622openalex-snapshot

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

inferredcites →https://doi.org/10.1093/bioinformatics/btq476openalex-snapshot

The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btw313openalex-snapshot

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot

fastp: an ultra-fast all-in-one FASTQ preprocessor

inferredcites →https://doi.org/10.1093/nar/gkab353openalex-snapshot

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota

inferredcites →https://doi.org/10.1093/nar/gkt1226openalex-snapshot

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

inferredcites →https://doi.org/10.1093/nar/gkv1049openalex-snapshot

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

inferredcites →https://doi.org/10.1093/nar/gky992openalex-snapshot

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

inferredcites →https://doi.org/10.1093/nar/gkz114openalex-snapshot

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

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

Redefining a new genomic blueprint of the human gut microbiota

inferredcites →https://doi.org/10.1101/2020.11.09.375451openalex-snapshot

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities

inferredcites →https://doi.org/10.1111/j.1365-2958.2004.04339.xopenalex-snapshot

An alternative pathway for reduced folate biosynthesis in bacteria and halophilic archaea

inferredcites →https://doi.org/10.1111/j.1574-6941.2011.01085.xopenalex-snapshot

Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species

inferredcites →https://doi.org/10.1126/science.1235872openalex-snapshot

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

inferredcites →https://doi.org/10.1126/science.aau6323openalex-snapshot

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

inferredcites →https://doi.org/10.1126/science.abc3421openalex-snapshot

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy

inferredcites →https://doi.org/10.1128/aem.01416-08openalex-snapshot

Development of Chemically Defined Media Supporting High-Cell-Density Growth of Lactococci, Enterococci, and Streptococci

inferredcites →https://doi.org/10.1128/aem.68.10.5186-5190.2002openalex-snapshot

Acetate Utilization and Butyryl Coenzyme A (CoA):Acetate-CoA Transferase in Butyrate-Producing Bacteria from the Human Large Intestine

inferredcites →https://doi.org/10.1128/jb.00490-10openalex-snapshot

Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

inferredcites →https://doi.org/10.1128/jb.01216-06openalex-snapshot

The Gene Cluster for Agmatine Catabolism ofEnterococcus faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing Its Reaction

inferredcites →https://doi.org/10.1128/jb.127.2.780-784.1976openalex-snapshot

Arginine, a growth-limiting factor for Eubacterium lentum

inferredcites →https://doi.org/10.1128/jcm.02926-14openalex-snapshot

Clinical and Microbiological Characteristics of Eggerthella lenta Bacteremia

inferredcites →https://doi.org/10.1128/msystems.00480-21openalex-snapshot

Untargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus

inferredcites →https://doi.org/10.1128/msystems.00493-20openalex-snapshot

Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

inferredcites →https://doi.org/10.1128/msystems.00606-19openalex-snapshot

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

inferredcites →https://doi.org/10.1134/s0006297909120086openalex-snapshot

Microbial origin of phenylcarboxylic acids in the human body

inferredcites →https://doi.org/10.1146/annurev-micro-091213-112949openalex-snapshot

Lipoteichoic Acid Synthesis and Function in Gram-Positive Bacteria

inferredcites →https://doi.org/10.1146/annurev-micro-092412-155620openalex-snapshot

Wall Teichoic Acids of Gram-Positive Bacteria

inferredcites →https://doi.org/10.1152/ajpgi.90374.2008openalex-snapshot

Regulatory mechanisms underlying agmatine homeostasis in humans

inferredcites →https://doi.org/10.1186/1471-2105-12-124openalex-snapshot

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

inferredcites →https://doi.org/10.1186/1471-2164-8-245openalex-snapshot

Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations

inferredcites →https://doi.org/10.1186/s12859-016-1016-7openalex-snapshot

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-019-1730-3openalex-snapshot

Current status and applications of genome-scale metabolic models

inferredcites →https://doi.org/10.1186/s13068-017-0856-3openalex-snapshot

A new genome-scale metabolic model of Corynebacterium glutamicum and its application

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An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis

inferredcites →https://doi.org/10.1186/s13321-016-0174-yopenalex-snapshot

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

inferredcites →https://doi.org/10.1186/s40168-021-01028-7openalex-snapshot

Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation

inferredcites →https://doi.org/10.1371/journal.pcbi.1003695openalex-snapshot

Emergent Biosynthetic Capacity in Simple Microbial Communities

inferredcites →https://doi.org/10.1371/journal.pgen.1010156openalex-snapshot

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

inferredcites →https://doi.org/10.15252/msb.20178157openalex-snapshot

Deciphering microbial interactions in synthetic human gut microbiome communities

inferredcites →https://doi.org/10.18637/jss.v082.i13openalex-snapshot

lmerTest Package: Tests in Linear Mixed Effects Models

inferredcites →https://doi.org/10.18637/jss.v093.i13openalex-snapshot

webchem : An R Package to Retrieve Chemical Information from the Web

inferredcites →https://doi.org/10.21203/rs.3.rs-113330/v1openalex-snapshot

Ecological and Evolutionary Alterations in Graves’ Disease Gut Microbiome Reveal Specific Diagnostic Biomarkers

inferredcites →https://doi.org/10.21203/rs.3.rs-1195626/v1openalex-snapshot

Reproducible and Opposing Microbiome Signatures Distinguish Autoimmune Diseases and Cancers: A Systematic Review and Meta-Analysis

inferredcites →https://doi.org/10.3389/fmicb.2012.00199openalex-snapshot

Focused Review: Agmatine in Fermented Foods

inferredcites →https://doi.org/10.3389/fmicb.2014.00674openalex-snapshot

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota

inferredcites →https://doi.org/10.3389/fmicb.2019.01316openalex-snapshot

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

inferredcites →https://doi.org/10.3390/metabo9070144openalex-snapshot

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

inferredcites →https://doi.org/10.3390/microorganisms10010195openalex-snapshot

Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity

inferredcites →https://doi.org/10.7554/elife.33953openalex-snapshot

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins

inferredcites →https://doi.org/10.7554/elife.50845openalex-snapshot

A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols

What points at this work

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

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