J. J. Faith

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment

The paper determines strain richness of common gut species and finds it is species-specific and limited in the gut, with temporary increases from therapeutic administration.

The protozoan commensal Tritrichomonas musculis is a natural adjuvant for mucosal IgA.

This study shows that the protozoan commensal Tritrichomonas musculis promotes T-cell dependent IgA class-switch recombination and enhances IgA-secreting plasma cell accumulation and dissemination.

Species-specific CD4+ T cells Enable Prediction of Mucosal Immune Phenotypes from Microbiota Composition

The paper identifies bacterial strains that drive specific mucosal T cell phenotypes using gnotobiotic mice and ex vivo assays, showing strain-specific T cell responses.

Defining Innate Immune Responses to the Human Gut Microbiota from Phylum to Strain

This study screens 277 gut bacterial strains to define innate immune responses, showing strain-specific and phylum-level variations in immune activation.

Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis

This study identifies gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis, finding that vancomycin treatment promotes bacteria that induce regulatory T cells and ameliorate disease.

Gut IgA Enhances Systemic IgG Responses to Pneumococcal Vaccines Through the Commensal Microbiota

This study shows gut IgA enhances systemic IgG responses to pneumococcal vaccines by regulating antigen translocation and immune activation via the microbiota.

Immunoglobulin A Antibody Composition Is Sculpted to Bind the Self Gut Microbiome

The paper investigates IgA antibody reactivity towards gut commensal bacteria in germ-free mice, finding species-level specificity and some strain-level recognition.

Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals

The study quantifies strain population sizes across bacterial species and finds prevalent strains in common gut microbiota are more likely to be shared among unrelated individuals.

Quantification of discrete gut bacterial strains following fecal transplantation for recurrent Clostridioides difficile infection demonstrates long-term stable engraftment in non-relapsing recipients

The paper quantifies bacterial strain engraftment after FMT for rCDI and shows long-term stability in non-relapsing recipients, linking strain presence to clinical outcomes.

Human Microbial Transplant Restores T Cell Cytotoxicity and Anti-Tumor Response to PD-L1 Blockade in Gnotobiotic Mice

The paper shows that human microbial transplants can restore T cell cytotoxicity and anti-tumor response to PD-L1 blockade in gnotobiotic mice by altering immune cell infiltration and gene expression.

Defined microbiota transplant restores Th17/RORtγ+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

The paper shows that transplanting healthy microbiota into mice with IBD microbiotas restores Th17/RORγt+ regulatory T cell balance by reducing pathogenic strains.

Strain-level differences in gut microbiome composition determine fecal IgA levels and are modifiable by gut microbiota manipulation

The paper identifies Bacteroides ovatus strains that induce IgA production and shows that manipulating these strains can modify gut IgA levels in mice.

Diet Modifies Colonic Microbiota and CD4+ T Cell Repertoire to Trigger Flares in a Novel Model of Colitis Induced by IL-23

This study shows that diet modifies the microbiota and CD4+ T cell repertoire in a mouse model of IL-23-induced colitis, leading to disease flares.

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD

This study evaluates FMT efficacy in CDI patients with and without IBD, finding no difference in recurrence rates and showing engraftment depends on IBD treatment, not disease severity.

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis

This study investigates how diet and microbiota interact to influence colitis severity in mice, finding that protein and psyllium fiber have significant effects through microbiota-dependent and independent mechanisms.