Cross-feeding in the gut microbiome: Ecology and mechanisms

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

(2022) Jun Feng et al.   Cell Host & Microbe

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network

(2022) Marcus C. de Goffau et al.   Nature Microbiology

A functional Wood–Ljungdahl pathway devoid of a formate dehydrogenase in the gut acetogens Blautia wexlerae , Blautia luti and beyond

(2022) Raphael Trischler et al.   ENVIRONMENTAL MICROBIOLOGY

Regulation of auxotrophic lactobacilli growth by amino acid cross-feeding interaction

(2022) Lin Lin et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Ecological dynamics of the gut microbiome in response to dietary fiber

(2022) Hongbin Liu et al.   ISME Journal

Exchange of Vitamin B 1 and Its Biosynthesis Intermediates Shapes the Composition of Synthetic Microbial Cocultures and Reveals Complexities of Nutrient Sharing

(2022) Rupali R. M. Sathe et al.   JOURNAL OF BACTERIOLOGY

Noisy metabolism can promote microbial cross-feeding

(2022) Jaime G Lopez et al.   eLife

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance

(2022) Jason S. L. Yu et al.   Nature Microbiology

Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota

(2022) Matthew P. Ostrowski et al.   Nature Microbiology

Distinct N and C Cross-Feeding Networks in a Synthetic Mouse Gut Consortium

(2022) Pau Pérez Escriva et al.   mSystems

A Salvaging Strategy Enables Stable Metabolite Provisioning among Free-Living Bacteria

(2022) Sebastian Gude et al.   mSystems

High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure

(2022) Juan P. Molina Ortiz et al.   Gut Microbes

A microbial transporter of the dietary antioxidant ergothioneine

(2022) Daniel G. Dumitrescu et al.   CELL

The Role of Intestinal Bacteria and Gut–Brain Axis in Hepatic Encephalopathy

(2021) Zefeng Chen et al.   Frontiers in Cellular and Infection Microbiology

Ergothioneine, recent developments

(2021) Irwin K. CHEAH et al.   Redox Biology

Polarization of microbial communities between competitive and cooperative metabolism

(2021) Daniel Machado et al.   Nature Ecology & Evolution

Kin selection explains the evolution of cooperation in the gut microbiota

(2021) Camille Simonet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome

(2021) Akshit Goyal et al.   Nature Communications

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

(2021) Hualan Liu et al.   Cell Reports

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life

(2021) Naoki Tsukuda et al.   ISME Journal

Design of synthetic human gut microbiome assembly and butyrate production

(2021) Ryan L. Clark et al.   Nature Communications

Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods

(2021) Mariana Noto Guillen et al.   Cell Systems

Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition

(2021) K. E. Huus et al.   Nature Communications

Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut

(2021) Judith Behnsen et al.   Nature Communications

Overlapping Roles of Yeast Transporters Aqr1, Qdr2, and Qdr3 in Amino Acid Excretion and Cross-Feeding of Lactic Acid Bacteria

(2021) George C. Kapetanakis et al.   Frontiers in Microbiology

Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis

(2020) Wenhan Zhu et al.   Cell Host & Microbe

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

(2020) Stéphane L. Benoit et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut

(2020) Albane Ruaud et al.   mBio

B vitamin acquisition by gut commensal bacteria

(2020) Emily E. Putnam et al.   PLoS Pathogens

Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts

(2020) Christopher C. Cheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Competitors versus Collaborators: Micronutrient Processing by Pathogenic and Commensal Human-Associated Gut Bacteria

(2020) Arianna I. Celis et al.   MOLECULAR CELL

Competition for Hydrogen Prevents Coexistence of Human Gastrointestinal Hydrogenotrophs in Continuous Culture

(2020) Nick W. Smith et al.   Frontiers in Microbiology

Several ways one goal—methanogenesis from unconventional substrates

(2020) Julia M. Kurth et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community

(2020) Ryan K. Fritts et al.   ISME Journal

Functional Roles of B‐Vitamins in the Gut and Gut Microbiome

(2020) Takashi Uebanso et al.   MOLECULAR NUTRITION & FOOD RESEARCH

The host-associated archaeome

(2020) Guillaume Borrel et al.   NATURE REVIEWS MICROBIOLOGY

Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities

(2020) Eva C. Soto-Martin et al.   mBio

Vitamin B12 Deficiency Alters the Gut Microbiota in a Murine Model of Colitis

(2020) Eberhard Lurz et al.   Frontiers in Nutrition

Trophic Interactions and the Drivers of Microbial Community Assembly

(2020) Matti Gralka et al.   CURRENT BIOLOGY

Gut microbial metabolites as multi-kingdom intermediates

(2020) Kimberly A. Krautkramer et al.   NATURE REVIEWS MICROBIOLOGY

Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour

(2020) Sílvia F. Henriques et al.   Nature Communications

Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron

(2020) Jennie L. Catlett et al.   mSystems

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

Public goods and cheating in microbes

(2019) Parker Smith et al.   CURRENT BIOLOGY

Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

(2019) Mattia Zampieri et al.   Nature Communications

B-Vitamin Sharing Promotes Stability of Gut Microbial Communities

(2019) Vandana Sharma et al.   Frontiers in Microbiology

Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium

(2019) Marika Ziesack et al.   mSystems

The Role of Glutamine in the Complex Interaction between Gut Microbiota and Health: A Narrative Review

(2019) Simone Perna et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community

(2019) Lisa Fazzino et al.   ISME Journal

Evidence for a multi-level trophic organization of the human gut microbiome

(2019) Tong Wang et al.   PLoS Computational Biology

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut

(2018) Whitman B. Schofield et al.   Cell Host & Microbe

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

(2018) Morgan N. Price et al.   PLoS Genetics

Signatures of ecological processes in microbial community time series

(2018) Karoline Faust et al.   Microbiome

Towards predicting the environmental metabolome from metagenomics with a mechanistic model

(2018) Daniel R. Garza et al.   Nature Microbiology

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Identification and quantitation of cobalamin and cobalamin analogues in human feces

(2018) Robert H Allen et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

(2018) Gregory L. Medlock et al.   Cell Systems

A shared limiting resource leads to competitive exclusion in a cross-feeding system

(2018) Sarah P. Hammarlund et al.   ENVIRONMENTAL MICROBIOLOGY

Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria

(2018) Jenny A. Laverde Gomez et al.   ENVIRONMENTAL MICROBIOLOGY

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation

(2018) Alan Cartmell et al.   Nature Microbiology

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing

(2018) Rebecca A. Daly et al.   Nature Microbiology

Surface Exposure and Packing of Lipoproteins into Outer Membrane Vesicles Are Coupled Processes in Bacteroides

(2018) Ezequiel Valguarnera et al.   mSphere

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities

(2017) Margaret F Romine et al.   ISME Journal

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

A role for bacterial urease in gut dysbiosis and Crohn’s disease

(2017) Josephine Ni et al.   Science Translational Medicine

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B 12 Production by Intestinal Symbionts

(2017) Clara Belzer et al.   mBio

Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation

(2017) Noreen Lanigan et al.   Frontiers in Microbiology

Anaerobic utilization of Fe(III)-xenosiderophores among Bacteroides species and the distinct assimilation of Fe(III)-ferrichrome by Bacteroides fragilis within the genus

(2017) Edson R. Rocha et al.   MicrobiologyOpen

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

(2017) Olga Ponomarova et al.   Cell Systems

Vitamin B12 deficiency

(2017) Ralph Green et al.   Nature Reviews Disease Primers

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides

(2017) Ana S. Luis et al.   Nature Microbiology

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron

(2017) Zachary A. Costliow et al.   mSystems

Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii

(2016) Frédéric Moens et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism

(2016) Tim A. Hoek et al.   PLOS BIOLOGY

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

(2016) Sebastian Germerodt et al.   PLoS Computational Biology

A sensitive bacterial-growth-based test reveals how intestinal Bacteroides meet their porphyrin requirement

(2015) David Halpern et al.   BMC MICROBIOLOGY

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Glycan complexity dictates microbial resource allocation in the large intestine

(2015) Artur Rogowski et al.   Nature Communications

Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice

(2015) Yen-Lin Huang et al.   Nature Communications

Milk kefir: composition, microbial cultures, biological activities, and related products

(2015) Maria R. Prado et al.   Frontiers in Microbiology

Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut

(2014) Patrick H. Degnan et al.   Cell Host & Microbe

A novel mode of lactate metabolism in strictly anaerobic bacteria

(2014) Marie Charlotte Weghoff et al.   ENVIRONMENTAL MICROBIOLOGY

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

New Iron Acquisition System in Bacteroidetes

(2014) Pablo Manfredi et al.   INFECTION AND IMMUNITY

Autoinducer-2 Plays a Crucial Role in Gut Colonization and Probiotic Functionality of Bifidobacterium breve UCC2003

(2014) Steven E. A. Christiaen et al.   PLoS One

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

(2014) Morgan N. Price et al.   Frontiers in Microbiology

Microbiota-Derived Hydrogen Fuels Salmonella Typhimurium Invasion of the Gut Ecosystem

(2013) Lisa Maier et al.   Cell Host & Microbe

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

(2013) Samay Pande et al.   ISME Journal

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) H. J. Haiser et al.   SCIENCE

The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases

(2012) M Tanweer Khan et al.   ISME Journal

Engineering ecosystems and synthetic ecologies

(2012) Michael T. Mee et al.   Molecular BioSystems

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Intestinal luminal nitrogen metabolism: Role of the gut microbiota and consequences for the host

(2012) Anne-Marie Davila et al.   PHARMACOLOGICAL RESEARCH

An Ancient Pathway Combining Carbon Dioxide Fixation with the Generation and Utilization of a Sodium Ion Gradient for ATP Synthesis

(2012) Anja Poehlein et al.   PLoS One

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Rates of production and utilization of lactate by microbial communities from the human colon

(2011) Alvaro Belenguer et al.   FEMS MICROBIOLOGY ECOLOGY

RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture

(2011) Adam Z Rosenthal et al.   ISME Journal

Prebiotic Effects of Wheat Arabinoxylan Related to the Increase in Bifidobacteria, Roseburia and Bacteroides/Prevotella in Diet-Induced Obese Mice

(2011) Audrey M. Neyrinck et al.   PLoS One

Potential beneficial effects of butyrate in intestinal and extraintestinal diseases

(2011) Roberto Berni Canani   WORLD JOURNAL OF GASTROENTEROLOGY

Dissecting thein VivoMetabolic Potential of Two Human Gut Acetogens

(2010) Federico E. Rey et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structural and Biochemical Foundations of Thiamin Biosynthesis

(2009) Christopher T. Jurgenson et al.   Annual Review of Biochemistry

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

(2009) Yan Zhang et al.   BMC GENOMICS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

(2008) T. Kosaka et al.   GENOME RESEARCH