News from Xavier lab

Congratulations to Johannes Scheid, Basak Eraslan, and colleagues on their JEM paper that describes remodeling of the colon plasma cell repertoire in patients with ulcerative colitis.


The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon was published in Immunity – congratulations to Lingjia Kong and colleagues!


Tiny genetic sequences in a mother's bacteria seem to hop into the infant's bacteria, perhaps ensuring a healthy microbiome later in life. Quanta Magazine featured our recent Cell paper, co-authored by Tommi Vatanen and Karolina Jabbar, that describes horizontal gene transfer between infant gut bacteria and maternal gut bacteria that fail to engraft. Read the full Quanta article here.


Xavier Lab Cell Journal cover

Read our latest cover paper, published in Cell
By characterizing the fecal microbiomes and metabolomes of 222 Bangladeshi children during the first two years of life, we uncovered three highly prevalent clades of Bifidobacterium longum and associated metabolites, including a transitional clade that expanded during weaning and was associated with growth and diarrhea. The comparatively high abundance of this clade may reflect feeding practices that differ across human populations, highlighting the importance of increasing diversity in microbiome studies. Congratulations to Tommi Vatanen, Qi Yan Ang, and colleagues on this great study!


Congratulations to Daniel Rojas-Tapias, now an Investigator in the Department of Microbiology at Agrosavia in Colombia, and Eric Brown on their latest paper in Nature Microbiology! Daniel, Eric, and colleagues describe how the oral microbe Veillonella parvula ectopically colonizes the gut of patients with inflammatory bowel diseases by switching its metabolism to utilize inflammatory nitrate.


The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease – read the Immunity Preview.


Our collaboration with Kenya Honda’s lab identifying trypsin-degrading Paraprevotella strains in the gut that protect IgA from degradation and prevent pathogen infection was published in Nature!


pH sensing controls tissue inflammation by modulating cellular metabolism and endo-lysosomal function of immune cells – read Nature Immunology’s News & Views.


Using single-cell RNA sequencing and other methods to study blood samples from 14 people who recovered from COVID-19, Johannes Scheid, Basak Eraslan, and collaborators identified distinct patterns of gene expression in B cells producing antibodies that bind tightly to and neutralize SARS-CoV-2. They also discovered a new antibody that neutralizes SARS-CoV-2 and the coronavirus that caused the 2003 SARS outbreak. Their findings, published in Cell, suggest some B cells are especially effective at producing antibodies and offer insight on how to design antibodies against several coronaviruses.


Congratulations to Kwontae You for publishing the study describing how QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis in Science!


TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41 – read the Cell Reports study here.


In collaboration with Aviv Regev’s lab, we generated a transcriptional atlas of intestinal immune cells and revealed that the neuropeptide α-CGRP modulates group 2 innate lymphoid cell responses. Read the full study in Immunity


Congratulations to Moshe Biton, now at the Weizmann Institute, Adam Haber, Noga Rogel, and colleagues on their Cell paper describing how Th cell cytokines modulate intestinal stem cell renewal and differentiation!


In a Nature Medicine study, we profiled the peptidome of potential antigens bound to MHC class II molecules and used the data to build and train BOTA, a machine learning algorithm that predicts antigenic peptides based on bacterial whole genome data.


Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes – read the full study in Cell Reports.


Guided by human disease genetics, we demonstrated that an IBD risk allele of C1orf106 destabilizes epithelial cell junctions. Read the full study in Science.