Selected Publications

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Xu J, Kong L, Oliver BA, et al. Constitutively active autophagy in macrophages dampens inflammation through metabolic and post-transcriptional regulation of cytokine production. Cell Rep. 2023 Jun 30;42(7):112708. doi: 10.1016/j.celrep.2023.112708. Epub ahead of print. PMID: 37392388.
 
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Stražar M, Park J, Abelin JG, et al. HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery. Immunity. 2023 Jun 8:S1074-7613(23)00226-1. doi: 10.1016/j.immuni.2023.05.009. Epub ahead of print. PMID: 37301199.
 
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Kalam H, Chou CH, Kadoki M, et al. Identification of host regulators of Mycobacterium tuberculosis phenotypes uncovers a role for the MMGT1-GPR156 lipid droplet axis in persistence. Cell Host Microbe. 2023 Jun 14;31(6):978-992.e5. doi: 10.1016/j.chom.2023.05.009. Epub 2023 Jun 2. PMID: 37269834.
 
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Johansen J, Atarashi K, Arai Y, et al. Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan. Nat Microbiol. 2023 Jun;8(6):1064-1078. doi: 10.1038/s41564-023-01370-6. Epub 2023 May 15. PMID: 37188814.
 
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Lee JWJ, Plichta DR, Asher S, et al. Association of distinct microbial signatures with premalignant colorectal adenomas. Cell Host Microbe. 2023 May 10;31(5):827-838.e3. doi: 10.1016/j.chom.2023.04.007. PMID: 37130517.
 
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Brown EM, Clardy J, Xavier RJ. Gut microbiome lipid metabolism and its impact on host physiology. Cell Host Microbe. 2023 Feb 8;31(2):173-186. doi: 10.1016/j.chom.2023.01.009. PMID: 36758518.
 
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Scheid JF, Eraslan B, Hudak A, et al. Remodeling of colon plasma cell repertoire within ulcerative colitis patients. J Exp Med. 2023 Apr 3;220(4):e20220538. doi: 10.1084/jem.20220538. Epub 2023 Feb 8. PMID: 36752797.
 
Graphical abstract from Kong et al.
Kong L, Pokatayev V, Lefkovith A, et al. The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon. Immunity. 2023 Feb 14;56(2):444-458.e5. doi: 10.1016/j.immuni.2023.01.002. PMID: 36720220.
 
Graphical abstract from Vatanen et al.
Vatanen T, Jabbar KS, Ruohtula T, et al. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell. 2022 Dec 22;185(26):4921-4936.e15. doi: 10.1016/j.cell.2022.11.023. PMID: 36563663.
 
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Vatanen T, Ang QY, Siegwald L, et al. A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning. Cell. 2022 Nov 10;185(23):4280-4297.e12. doi: 10.1016/j.cell.2022.10.011. Epub 2022 Nov 1. PMID: 36323316.
 
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Rojas-Tapias DF, Brown EM, Temple ER, et al. Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine. Nat Microbiol. 2022 Oct;7(10):1673-1685. doi: 10.1038/s41564-022-01224-7. Epub 2022 Sep 22. PMID: 36138166.
 
Graphical abstract from Pedersen et al.

The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease
Pedersen TK, Brown EM, Plichta DR, et al. The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease. Immunity. 2022 Sep 10:S1074-7613(22)00410-1. doi: 10.1016/j.immuni.2022.08.016. Epub ahead of print. PMID: 36115338.

 

Identification of trypsin-degrading commensals in the large intestine
Li Y, Watanabe E, Kawashima Y, et al. Identification of trypsin-degrading commensals in the large intestine. Nature. 2022 Sep;609(7927):582-589. doi: 10.1038/s41586-022-05181-3. Epub 2022 Sep 7. PMID: 36071157.

 
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Pawlak M, DeTomaso D, Schnell A, et al. Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling. Immunity. 2022 Sep 13;55(9):1663-1679.e6. doi: 10.1016/j.immuni.2022.08.007. Epub 2022 Sep 6. PMID: 36070768.
 
Sazonovs A, Stevens CR, Venkataraman GR, et al. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet. 2022 Sep;54(9):1275-1283. doi: 10.1038/s41588-022-01156-2. Epub 2022 Aug 29. PMID: 36038634.

 

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Akkermansia muciniphila phospholipid induces homeostatic immune responses
Bae M, Cassilly CD, Liu X, et al. Akkermansia muciniphila phospholipid induces homeostatic immune responses. Nature. 2022 Aug;608(7921):168-173. doi: 10.1038/s41586-022-04985-7. Epub 2022 Jul 27. PMID: 35896748.

 

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pH sensing controls tissue inflammation by modulating cellular metabolism and endo-lysosomal function of immune cells
Chen X, Jaiswal A, Costliow Z, et al. pH sensing controls tissue inflammation by modulating cellular metabolism and endo-lysosomal function of immune cells. Nat Immunol. 2022 Jul;23(7):1063-1075. doi: 10.1038/s41590-022-01231-0. Epub 2022 Jun 6. PMID: 35668320.

 

Sequence-structure-function relationships in the microbial protein universe
Leman JK, Szczerbiak P, Renfrew PD, et al. Sequence-structure-function relationships in the microbial protein universe. bioRxiv 2022.03.18.484903; doi: 10.1101/2022.03.18.484903.

 

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Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens
Szamosvári D, Bae M, Bang S, et al. Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens. J Am Chem Soc. 2022 Feb 16;144(6):2474-2478. doi: 10.1021/jacs.1c12202. Epub 2022 Feb 7. PMID: 35129341.

 

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Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing
Jasso GJ, Jaiswal A, Varma M, et al. Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing. PLoS Biol. 2022 Jan 27;20(1):e3001532. doi: 10.1371/journal.pbio.3001532. PMID: 35085231.

 

Graphical abstract from Brown et al.

Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors
Brown EM, Arellano-Santoyo H, Temple ER, et al. Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe. 2021 Sep 8;29(9):1351-1365.e11. doi: 10.1016/j.chom.2021.07.011. Epub 2021 Aug 16. PMID: 34403684.

 

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations
Stražar M, Temba GS, Vlamakis H, et al. Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nat Commun. 2021 Aug 11;12(1):4845. doi: 10.1038/s41467-021-25213-2. PMID: 34381036.

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians
Sato Y, Atarashi K, Plichta DR, et al. Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021 Nov;599(7885):458-464. doi: 10.1038/s41586-021-03832-5. Epub 2021 Jul 29. PMID: 34325466.

 

Graphical abstract from Liu et al.

SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance
Liu K, Kong L, Graham DB, et al. SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance. Cell Rep. 2021 Jul 27;36(4):109434. doi: 10.1016/j.celrep.2021.109434. PMID: 34320354.

 

Graphical abstract from Lee et al.

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease
Lee JWJ, Plichta D, Hogstrom L, et al. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe. 2021 Aug 11;29(8):1294-1304.e4. doi: 10.1016/j.chom.2021.06.019. Epub 2021 Jul 22. PMID: 34297922.

 

Graphical abstract from Scheid et al.

B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV
Scheid JF, Barnes CO, Eraslan B, et al. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell. 2021 Jun 10;184(12):3205-3221.e24. doi: 10.1016/j.cell.2021.04.032. Epub 2021 Apr 24. PMID: 34015271.

 

Graphical abstract from Groussin et al.

Elevated rates of horizontal gene transfer in the industrialized human microbiome
Groussin M, Poyet M, Sistiaga A, et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. 2021 Apr 15;184(8):2053-2067.e18. doi: 10.1016/j.cell.2021.02.052. Epub 2021 Mar 31. PMID: 33794144.

 

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QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis
You K, Wang L, Chou CH, et al. QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis. Science. 2021 Jan 1;371(6524):eabb6896. doi: 10.1126/science.abb6896. PMID: 33384352.

 

Sorting nexin 5 mediates virus-induced autophagy and immunity
Dong X, Yang Y, Zou Z, et al. Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature. 2021 Jan;589(7842):456-461. doi: 10.1038/s41586-020-03056-z. Epub 2020 Dec 16. PMID: 33328639.

 

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TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41
Carey KL, Paulus GLC, Wang L, et al. TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Rep. 2020 Nov 10;33(6):108371. doi: 10.1016/j.celrep.2020.108371. PMID: 33176151.

 

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A missense variant in SLC39A8 confers risk for Crohn's disease by disrupting manganese homeostasis and intestinal barrier integrity
Nakata T, Creasey EA, Kadoki M, et al. A missense variant in SLC39A8 confers risk for Crohn's disease by disrupting manganese homeostasis and intestinal barrier integrity. Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28930-28938. doi: 10.1073/pnas.2014742117. Epub 2020 Nov 2. PMID: 33139556.

 

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The Human and Mouse Enteric Nervous System at Single-Cell Resolution
Drokhlyansky E, Smillie CS, Van Wittenberghe N, et al. The Human and Mouse Enteric Nervous System at Single-Cell Resolution. Cell. 2020 Sep 17;182(6):1606-1622.e23. doi: 10.1016/j.cell.2020.08.003. Epub 2020 Sep 3. PMID: 32888429.

 

Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease
Kong L, Lloyd-Price J, Vatanen T, et al. Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease. Gastroenterology. 2020 Dec;159(6):2193-2202.e5. doi: 10.1053/j.gastro.2020.08.045. Epub 2020 Aug 26. PMID: 32860788.

 

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Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level
Kenny DJ, Plichta DR, Shungin D, et al. Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. Cell Host Microbe. 2020 Aug 12;28(2):245-257.e6. doi: 10.1016/j.chom.2020.05.013. Epub 2020 Jun 15. PMID: 32544460.

 

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease
Fornelos N, Franzosa EA, Bishai J, et al. Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nat Microbiol. 2020 Mar;5(3):486-497. doi: 10.1038/s41564-019-0655-7. Epub 2020 Jan 20. PMID: 31959971.

 

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Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses
Xu H, Ding J, Porter CBM, et al. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity. 2019 Oct 15;51(4):696-708.e9. doi: 10.1016/j.immuni.2019.09.004. PMID: 31618654.

 

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
Poyet M, Groussin M, Gibbons SM, et al. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nat Med. 2019 Sep;25(9):1442-1452. doi: 10.1038/s41591-019-0559-3. Epub 2019 Sep 2. PMID: 31477907.

 

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Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Smillie CS, Biton M, Ordovas-Montanes J, et al. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell. 2019 Jul 25;178(3):714-730.e22. doi: 10.1016/j.cell.2019.06.029. PMID: 31348891.

 

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide
Henke MT, Kenny DJ, Cassilly CD, et al. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12672-12677. doi: 10.1073/pnas.1904099116. Epub 2019 Jun 10. PMID: 31182571.

 

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 May;569(7758):655-662. doi: 10.1038/s41586-019-1237-9. Epub 2019 May 29. PMID: 31142855.

 

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Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis
Brown EM, Ke X, Hitchcock D, et al. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe. 2019 May 8;25(5):668-680.e7. doi: 10.1016/j.chom.2019.04.002. PMID: 31071294.

 

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut
Jiang X, Hall AB, Arthur TD, et al. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science. 2019 Jan 11;363(6423):181-187. doi: 10.1126/science.aau5238. PMID: 30630933.

 

Gut microbiome structure and metabolic activity in inflammatory bowel disease
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 Feb;4(2):293-305. doi: 10.1038/s41564-018-0306-4. Epub 2018 Dec 10. PMID: 30531976.

 

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T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
Biton M, Haber AL, Rogel N, et al. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. 2018 Nov 15;175(5):1307-1320.e22. doi: 10.1016/j.cell.2018.10.008. Epub 2018 Nov 1. PMID: 30392957.

 

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes
Graham DB, Luo C, O'Connell DJ, et al. Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med. 2018 Nov;24(11):1762-1772. doi: 10.1038/s41591-018-0203-7. Epub 2018 Oct 22. PMID: 30349087.

 

C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions
Mohanan V, Nakata T, Desch AN, et al. C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions. Science. 2018 Mar 9;359(6380):1161-1166. doi: 10.1126/science.aan0814. Epub 2018 Feb 1. PMID: 29420262.