J. Sonnenburg

J. Sonnenburg, G. Farrugia, J. Szurszewski, 2016, Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society.

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

Kevin J. Thompson, Robin R. Shields-Cutler, J. Faith, 2019, Nature Communications.

Role for diet in normal gut barrier function: developing guidance within the framework of food-labeling regulations

M. Camilleri, J. Sonnenburg, G. Wu, 2019, American journal of physiology. Gastrointestinal and liver physiology.

A metabolomics pipeline enables mechanistic interrogation of the gut microbiome

M. Fischbach, J. Sonnenburg, Curt R. Fischer, 2021, bioRxiv.

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

William W. Van Treuren, M. Fischbach, J. Sonnenburg, 2021, Nature.

Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains

J. Sonnenburg, D. Bolam, E. Sonnenburg, 2018, mSphere.

Gut microbes promote colonic serotonin production through an effect of short‐chain fatty acids on enterochromaffin cells

J. Sonnenburg, G. Farrugia, J. Szurszewski, 2015, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome.

Hannah D. Holscher, C. Davis, J. Sonnenburg, 2018, American journal of physiology. Endocrinology and metabolism.

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

N. Neff, A. Jha, S. Holmes, 2022, bioRxiv.

Fermented foods restructure gut microbiota and promote immune regulation via microbial metabolites

J. Sonnenburg, Matthew M. Carter, S. Higginbottom, 2022, bioRxiv.

When Gut Microbiota Creep into Fat, the Fat Creeps Back

J. Sonnenburg, S. Spencer, 2020, Cell.

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model

William W. Van Treuren, J. Sonnenburg, D. Bouley, 2018, bioRxiv.

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation.

M. Fischbach, C. Tropini, J. Sonnenburg, 2020, Cell host & microbe.

Design, construction, and in vivo augmentation of a complex gut microbiome

N. Neff, M. Fischbach, A. Deutschbauer, 2022, Cell.

Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range predictions

William W. Van Treuren, J. Sonnenburg, E. Martens, 2020, bioRxiv.

Characterization of the Acid Stability of Glycosidically Linked Neuraminic Acid

A. Varki, J. Sonnenburg, H. van Halbeek, 2002, The Journal of Biological Chemistry.

Electron transfer proteins in gut bacteria yield metabolites that circulate in the host

William W. Van Treuren, J. Sonnenburg, S. Higginbottom, 2019, bioRxiv.

Gut Microbiota-Produced Tryptamine Activates an Epithelial G-Protein-Coupled Receptor to Increase Colonic Secretion.

Weston R. Whitaker, M. Fischbach, J. Sonnenburg, 2018, Cell host & microbe.

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

Yava L Jones-Hall, Robin Patel, T. Smyrk, 2018, Science Translational Medicine.

A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection.

William W. Van Treuren, K. C. Huang, J. Sonnenburg, 2018, Cell host & microbe.

Vulnerability of the industrialized microbiota

J. Sonnenburg, E. Sonnenburg, 2019, Science.

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs.

N. Neff, William W. Van Treuren, M. Fischbach, 2020, Cell host & microbe.

Electron transfer complexes in the gut dictate high abundance circulating metabolites

J. Sonnenburg, S. Higginbottom, Dylan Dodd, 2019 .

Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates.

J. Sonnenburg, E. Sonnenburg, 2014, Cell metabolism.

A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont

J. Sonnenburg, Curt R. Fischer, S. Higginbottom, 2020, Cell.

Commensal Microbes and Hair Follicle Morphogenesis Coordinately Drive Treg Migration into Neonatal Skin.

J. Sonnenburg, S. Millar, M. Rosenblum, 2017, Cell host & microbe.

Effects of sialic acid substitutions on recognition by Sambucus nigra agglutinin and Maackia amurensis hemagglutinin.

A. Varki, J. Sonnenburg, E. B. D. Brinkman-van der Linden, 2002, Analytical biochemistry.

Production of α-Galactosylceramide by a Prominent Member of the Human Gut Microbiota

M. Fischbach, J. Bluestone, J. Clardy, 2013, PLoS biology.

Gut Microbiota-Targeted Diets Modulate Human Immune Status

J. Sonnenburg, F. Yu, C. Gardner, 2020, bioRxiv.

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.

Taylor H. Nguyen, Joshua E. Elias, N. Neff, 2022, Cell host & microbe.

High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota

Joshua E. Elias, N. Neff, J. Elias, 2020, bioRxiv.

A refined palate: bacterial consumption of host glycans in the gut.

Justin L Sonnenburg, A. Southwick, J. Sonnenburg, 2013, Glycobiology.

Diet-induced extinction in the gut microbiota compounds over generations

Mikhail Tikhonov, Ned S. Wingreen, Justin L. Sonnenburg, 2015, Nature.

Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host

J. Gordon, J. Sonnenburg, Christina T. L. Chen, 2006, PLoS biology.

C. difficile exploits a host metabolite produced during toxin-mediated disease

J. Sonnenburg, K. Pruss, Kali M. Pruss, 2021, Nature.

Molecular hallmarks of heterochronic parabiosis at single cell resolution

James T. Webber, Martin Jinye Zhang, Robert C. Jones, 2020, bioRxiv.

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

G. Nolan, M. Fischbach, J. Sonnenburg, 2017, Nature.

Proximal colon–derived O-glycosylated mucus encapsulates and modulates the microbiota

T. Griffin, J. Sonnenburg, J. Braun, 2020, Science.

Quantitative Imaging of Gut Microbiota Spatial Organization.

Justin L Sonnenburg, Joshua E Elias, Joshua E. Elias, 2015, Cell host & microbe.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

N. Neff, A. Jha, J. Sonnenburg, 2022, bioRxiv.

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

Irving L. Weissman, Róbert Pálovics, Michael F. Clarke, 2020, Nature.

Pursuing Human-Relevant Gut Microbiota-Immune Interactions.

J. Sonnenburg, S. Spencer, G. Fragiadakis, 2019, Immunity.

A small-molecule antivirulence agent for treating Clostridium difficile infection

Megan C. Garland, M. Bogyo, J. Sonnenburg, 2015, Science Translational Medicine.

Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance.

B. Weimer, J. Sonnenburg, D. Bouley, 2014, Cell host & microbe.

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

B. Weimer, K. Ng, J. Sonnenburg, 2013, Nature.

Aging hallmarks exhibit organ-specific temporal signatures

James T. Webber, Martin Jinye Zhang, Robert C. Jones, 2020, Nature.

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

Ryan D. Crawford, E. Snitkin, J. Sonnenburg, 2020, Nature Microbiology.

Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

Ryan D. Crawford, E. Snitkin, J. Sonnenburg, 2019, bioRxiv.

An exclusive metabolic niche enables strain engraftment in the gut microbiota

Weston R. Whitaker, William C. Deloache, J. Sonnenburg, 2018, Nature.

A metabolic pathway for glucosinolate activation by the human gut symbiont Bacteroides thetaiotaomicron

J. Sonnenburg, Curt R. Fischer, S. Higginbottom, 2019, bioRxiv.

Eating for two: how metabolism establishes interspecies interactions in the gut.

Michael A Fischbach, Justin L Sonnenburg, M. Fischbach, 2011, Cell host & microbe.

Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet

J. Sonnenburg, C. Gardner, E. Sonnenburg, 2023, Gut microbes.

Depletion of microbiome-derived molecules in the host using Clostridium genetics

Kamir J. Hiam, William W. Van Treuren, M. Fischbach, 2018, Science.

Monitoring host responses to the gut microbiota

Justin L Sonnenburg, Joshua E Elias, Joshua E. Elias, 2015, The ISME Journal.

Reporting guidelines for human microbiome research: the STORMS checklist

Chris I. Hunter, Jennifer M. Fettweis, F. Bushman, 2021, Nature Medicine.

Links between environment, diet, and the hunter-gatherer microbiome

William W. Van Treuren, R. Knight, J. Sonnenburg, 2018, bioRxiv.

Gut microbiome transition across a lifestyle gradient in Himalaya

Emily R. Davenport, C. Bustamante, A. Jha, 2018, bioRxiv.

Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome

Weston R. Whitaker, Justin L. Sonnenburg, J. Sonnenburg, 2017, Cell.

Metabolome progression during early gut microbial colonization of gnotobiotic mice

Tahir Yusufaly, George I. Mias, Tahir I Yusufaly, 2015, Scientific Reports.

Quantifying rapid bacterial evolution and transmission within the mouse intestine.

Benjamin H. Good, Nate J. Cira, G. Sherlock, 2021, Cell host & microbe.

The Intestinal Microbiota and Viral Susceptibility

J. Sonnenburg, J. Pfeiffer, 2011, Front. Microbio..

Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials

Brad A. Krajina, Andrew J. Spakowitz, Sarah C. Heilshorn, 2017, ACS central science.

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

E. Segal, K. Kalari, Tal Korem, 2020, Cell.

Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?

L. T. Angenent, J. Gordon, J. Sonnenburg, 2004, Nature Immunology.

Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade

Mark M. Davis, M. Fischbach, A. M. Rush, 2020, Proceedings of the National Academy of Sciences.

Functional Genomic Studies of the Intestinal Response to a Foodborne Enteropathogen in a Humanized Gnotobiotic Mouse Model*

J. Gordon, P. Cossart, J. Sonnenburg, 2007, Journal of Biological Chemistry.

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

Paul M. Ruegger, S. Horvath, C. Huttenhower, 2013, Microbiome.

Ancient human faeces reveal gut microbes of the past

J. Sonnenburg, Matthew R. Olm, 2021, Nature.

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition

K. Ng, K. C. Huang, J. Sonnenburg, 2020, Nature Microbiology.

Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans.

T. McLaughlin, Daniel Hornburg, J. Sonnenburg, 2022, Cell host & microbe.

Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice.

J. Sonnenburg, S. Smits, A. Marcobal, 2013, mSystems.

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs.

N. Neff, William W. Van Treuren, M. Fischbach, 2019, Cell host & microbe.

The ancestral and industrialized gut microbiota and implications for human health

J. Sonnenburg, E. Sonnenburg, 2019, Nature Reviews Microbiology.

Ageing hallmarks exhibit organ-specific temporal signatures

James T. Webber, Martin Jinye Zhang, Robert C. Jones, 2020, Nature.

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes

William W. Van Treuren, M. Fischbach, T. Meyer, 2021, bioRxiv.

A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism.

Justin L Sonnenburg, J. Gordon, J. Sonnenburg, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Western diet regulates immune status and the response to LPS-driven sepsis independent of diet-associated microbiome

J. Sonnenburg, B. Napier, D. Monack, 2019, Proceedings of the National Academy of Sciences.

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs

N. Neff, William W. Van Treuren, M. Fischbach, 2019, bioRxiv.

Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization

William W. Van Treuren, J. Sonnenburg, Curt R. Fischer, 2022, Nature metabolism.

Ageing hallmarks exhibit organ-specific temporal signatures

James T. Webber, Martin Jinye Zhang, Robert C. Jones, 2021, Yearbook of Paediatric Endocrinology.

In vivo augmentation of a complex gut bacterial community

N. Neff, M. Fischbach, K. C. Huang, 2021, bioRxiv.

Your gut microbiome, deconstructed

C. Tropini, J. Sonnenburg, Dylan Dodd, 2015, Nature Biotechnology.

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight

J. Sonnenburg, C. Gardner, E. Sonnenburg, 2019, bioRxiv.

Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid

William W. Van Treuren, M. Fischbach, J. Sonnenburg, 2023, Nature Communications.

De-N-acetyl-gangliosides in humans: unusual subcellular distribution of a novel tumor antigen.

A. Varki, J. Sonnenburg, M. Farquhar, 1999, Cancer research.

Editorial overview: insights into molecular mechanisms of microbiota.

D. Relman, J. Sonnenburg, E. Martens, 2014, Journal of molecular biology.

A uniquely human consequence of domain-specific functional adaptation in a sialic acid-binding receptor.

T. K. Altheide, A. Varki, J. Sonnenburg, 2004, Glycobiology.

Community Health Care: Therapeutic Opportunities in the Human Microbiome

M. Fischbach, J. Sonnenburg, 2011, Science Translational Medicine.

The clinical drug candidate ebselen attenuates inflammation and promotes microbiome recovery after antibiotic treatment for Clostridium difficile infection

Megan C. Garland, William W. Van Treuren, M. Bogyo, 2019 .

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model

William W. Van Treuren, J. Sonnenburg, D. Bouley, 2018, bioRxiv.

The Clinical Drug Ebselen Attenuates Inflammation and Promotes Microbiome Recovery in Mice after Antibiotic Treatment for CDI

Megan C. Garland, William W. Van Treuren, M. Bogyo, 2020, Cell reports medicine.

In Vivo Wireless Sensors for Gut Microbiome Redox Monitoring

Marcus Weber, Amin Arbabian, Spyridon Baltsavias, 2019, IEEE Transactions on Biomedical Engineering.

The effect of microbial colonization on the host proteome varies by gastrointestinal location

Joshua E. Elias, J. Elias, K. C. Huang, 2015, The ISME Journal.

The human intestinal microbiota and its relationship to energy balance

F. Bäckhed, R. Ley, J. Gordon, 2006 .

Intestinal IgA Regulates Expression of a Fructan Polysaccharide Utilization Locus in Colonizing Gut Commensal Bacteroides thetaiotaomicron

P. Pasricha, J. Sonnenburg, D. Peterson, 2019, mBio.

Nutrition: A personal forecast

J. Sonnenburg, E. Sonnenburg, 2015, Nature.

Resolution of Subunit Interactions and Cytoplasmic Subcomplexes of the Yeast Vacuolar Proton-translocating ATPase (*)

D. Klionsky, J. Sonnenburg, J. Tomashek, 1996, The Journal of Biological Chemistry.

Lifestyle of Lactobacillus plantarum in the mouse caecum.

M. Kleerebezem, J. Gordon, J. Sonnenburg, 2009, Environmental microbiology.

Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system

J. Sonnenburg, J. Lynch, 2012, Molecular microbiology.

Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice

J. Sonnenburg, E. Sonnenburg, S. Higginbottom, 2023, bioRxiv.

The emerging metabolic view of Clostridium difficile pathogenesis.

J. Sonnenburg, K. Pruss, A. J. Hryckowian, 2017, Current opinion in microbiology.

Operon prediction without a training set

Jeremy Buhler, Benjamin P. Westover, Justin L. Sonnenburg, 2005, Bioinform..

Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice

J. Sonnenburg, S. Smits, A. Marcobal, 2016, mSystems.

Host-centric Proteomics of Stool: A Novel Strategy Focused on intestinal Responses to the Gut Microbiota*

Joshua E. Elias, J. Elias, J. Sonnenburg, 2013, Molecular & Cellular Proteomics.

Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates

William W. Van Treuren, E. Robilotti, C. Bertozzi, 2022, bioRxiv.

Microbiome Engineering

J. Sonnenburg, 2015, Nature.

Microbiota Accessible Carbohydrates Suppress Clostridium difficile Infection in a Murine Model

William W. Van Treuren, J. Sonnenburg, D. Bouley, 2018, Nature Microbiology.

Rapid evolution of binding specificities and expression patterns of inhibitory CD33‐related Siglecs in primates

X. Chen, V. Nizet, A. Varki, 2014, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Quantifying dynamic host‐microbiota signatures of antibiotic‐associated GI infection: What can the host proteome tell us?

J. Elias, J. Sonnenburg, Joshua S Lichtman, 2015 .

Competitively Selected Donor Fecal Microbiota Transplantation: Butyrate Concentration and Diversity as Measures of Donor Quality

K. Ng, J. Sonnenburg, S. Smits, 2018, Journal of pediatric gastroenterology and nutrition.

A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

M. Fischbach, A. Spormann, J. Sonnenburg, 2013, The ISME Journal.

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

N. Neff, A. Jha, J. Sonnenburg, 2023, Cell.

Microbiology: Genetic pot luck

J. Sonnenburg, 2010, Nature.

Microbiota Accessible Carbohydrates Suppress Clostridium difficile Infection in a Murine Model

William W. Van Treuren, J. Sonnenburg, D. Bouley, 2018, Nature Microbiology.

Gut microbes take their vitamins.

J. Sonnenburg, E. Sonnenburg, 2014, Cell host & microbe.

Human milk oligosaccharide consumption by intestinal microbiota.

J. Sonnenburg, A. Marcobal, J. Sonnenburg, 2012, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

In Vivo Wireless Sensors for Gut Microbiome Redox Monitoring

Sam W. Baker, William W. Van Treuren, J. Sonnenburg, 2019, IEEE Transactions on Biomedical Engineering.

Gut-microbiota-targeted diets modulate human immune status

J. Sonnenburg, F. Yu, E. Sonnenburg, 2021, Cell.

Functional Adaptation in a Sialic Acid-binding Receptor sialic acid/Siglec/human evolution/domain-specific adaptation/comparative biology

T. K. Altheide, A. Varki, J. Sonnenburg, 2003 .

Functional Genomic Studies of the Intestinal Response to a Foodborne Enteropathogen in a Humanized Gnotobiotic Mouse Model*

J. Gordon, P. Cossart, J. Sonnenburg, 2007, Journal of Biological Chemistry.

The ancestral and industrialized gut microbiota and implications for human health

J. Sonnenburg, E. Sonnenburg, J. Sonnenburg, 2019, Nature Reviews Microbiology.

A Microbiota Assimilation.

J. Sonnenburg, E. Sonnenburg, 2018, Cell metabolism.