Publications

2021

Untargeted plasma metabolome and gut microbiome profiling provide novel insights in the regulation of platelet reactivity in healthy individuals Vadaq N, Schirmer M, Tunjungputri RN, Vlamakis H, Chiriac C, Ardiansyah E, Gasem MH, Joosten L, de Groot PG, Xavier RJ, Netea MG, van der Ven AJAM, de Mast Q.

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A.

pH and Proton Sensor GPR65 Determine Susceptibility to Atopic Dermatitis Xie L, McKenzie CI, Qu X, Mu Y, Wang Q, Bing N, Naidoo K, Alam MJ, Yu D, Gong F, Ang C, Robert R, Marques FZ, Furlotte N, Hinds D, Gasser O; 23andMe Research Team, Xavier RJ, Mackay CR.

Identification of the Active Principle Conferring Anti-Inflammatory and Antinociceptive Properties in Bamboo Plant Araujo Sousa B, Nascimento Silva O, Farias Porto W, Lima Rocha T, Paulino Silva L, Ferreira Leal AP, Buccini DF, Oluwagbamigbe Fajemiroye J, de Araujo Caldas R, Franco OL, Grossi-de-Sá MF, de la Fuente Nunez C, Moreno SE.

Structure-based protein function prediction using graph convolutional networks Gligorijević V, Renfrew PD, Kosciolek T, Leman JK, Berenberg D, Vatanen T, Chandler C, Taylor BC, Fisk IM, Vlamakis H, Xavier RJ, Knight R, Cho K, Bonneau R.

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties Blanquart S, Groussin M, Le Roy A, Szöllosi GJ, Girard E, Franzetti B, Gouy M, Madern D.

Translating the human microbiome: a path to improving health Xavier RJ.

Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1 Petersen AØ, Jokinen M, Plichta DR, Liebisch G, Gronwald W, Dettmer K, Oefner PJ, Vlamakis H, Chung DC, Ranki A, Xavier RJ.

Elevated rates of horizontal gene transfer in the industrialized human microbiome Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ.

Trained immunity, tolerance, priming and differentiation: distinct immunological processes Divangahi M, Aaby P, Khader SA, Barreiro LB, Bekkering S, Chavakis T, van Crevel R, Curtis N, DiNardo AR, Dominguez-Andres J, Duivenwoorden R, Fanucchi S, Fayad Z, Fuchs E, Hamon M, Jeffrey KL, Khan N, Joosten LAB, Kaufmann E, Latz E, Matarese G, van der Meer JWM, Mhlanga M, Moorlag SJCFM, Mulder WJM, Naik S, Novakovic B, O’Neill L, Ochando J, Ozato K, Riksen NP, Sauerwein R, Sherwood ER, Schlitzer A, Schultze JL, Sieweke MH, Benn CS, Stunnenberg H, Sun J, van de Veerdonk FL, Weis S, Williams DL, Xavier R, Netea MG.

Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort Diener C, Reyes-Escogido ML, Jimenez-Ceja LM, Matus M, Gomez-Navarro CM, Chu ND, Zhong V, Tejero ME, Alm E, Resendis-Antonio O, Guardado-Mendoza R.

2020

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D’Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.

The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study Perrotta AR, Borrelli GM, Martins CO, Kallas EG, Sanabani SS, Griffith LG, Alm EJ, Abrao MS.

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A, Gacesa R, Sinha T, Oosting M, Joosten LAB, Rutten JHW, Riksen NP, Xavier RJ, Kuipers F, Wijmenga C, Zhernakova A, Netea MG, Weersma RK, Fu J.

Epigenome-metabolome-microbiome axis in health and IBD Amatullah H, Jeffrey KL.

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level Kenny DJ, Plichta DR, Shungin D, Koppel N, Hall AB, Fu B, Vasan RS, Shaw SY, Vlamakis H, Balskus EP, Xavier RJ.

Synthetic Host Defense Peptides Inhibit Venezuelan Equine Encephalitis Virus Replication and the Associated Inflammatory Response Ahmed A, Bakovic A, Risner K, Kortchak S, Der Torossian Torres M, de la Fuente-Nunez C, Lu T, Bhalla N, Narayanan A.

Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn’s Disease Kong L, Lloyd-Price J, Vatanen T, Seksik P, Beaugerie L, Simon T, Vlamakis H, Sokol H, Xavier RJ.

Delivery Mode Affects Stability of Early Infant Gut Microbiota Mitchell CM, Mazzoni C, Hogstrom L, Bryant A, Bergerat A, Cher A, Pochan S, Herman P, Carrigan M, Sharp K, Huttenhower C, Lander ES, Vlamakis H, Xavier RJ, Yassour M.

Response of the human gut and saliva microbiome to urbanization in Cameroon Lokmer A, Aflalo S, Amougou N, Lafosse S, Froment A, Tabe FE, Poyet M, Groussin M, Said-Mohamed R, Ségurel L.

Pathway paradigms revealed from the genetics of inflammatory bowel disease Graham DB, Xavier RJ.

SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ.

Illuminating the human virome in health and disease Adiliaghdam F, Jeffrey KL.

Co-evolution and Co-speciation of Host-Gut Bacteria Systems Groussin M, Mazel F, Alm EJ.

SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Nagler J, Rhode SF, Santillana M, Tucker JA, Wuertz S, Zhao S, Thompson J, Alm EJ.

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ.

The human gut microbiota in people with amyotrophic lateral sclerosis Nicholson K, Bjornevik K, Abu-Ali G, Chan J, Cortese M, Dedi B, Jeon M, Xavier R, Huttenhower C, Ascherio A, Berry JD.

Making waves: Wastewater surveillance of SARS-CoV-2 for population-based health management Thompson JR, Nancharaiah YV, Gu X, Lee WL, Rajal VB, Haines MB, Girones R, Ng LC, Alm EJ, Wuertz S.

Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota Yu X, Gurry T, Nguyen LTT, Richardson HS, Alm EJ.

Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria Gomes ALC, Johns NI, Yang A, Velez-Cortes F, Smillie CS, Smith MB, Alm EJ, Wang HH.

16S rRNA sequencing analysis: the devil is in the details Tsou AM, Olesen SW, Alm EJ, Snapper SB.

2019

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shaek AK, Xavier RJ, Regev A.

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C.

Framework for rational donor selection in fecal microbiota transplant clinical trials. Duvallet C, Zellmer C, Panchal P, Budree S, Osman M, Alm EJ

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ.

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Poyet M, Groussin M, Gibbons SM, Avila-Pacheco J, Jiang X, Kearney SM, Perrotta AR, Berdy B, Zhao S, Lieberman TD, Swanson PK, Smith M, Roesemann S, Alexander JE, Rich SA, Livny J, Vlamakis H, Clish C, Bullock K, Deik A, Scott J, Pierce KA, Xavier RJ, Alm EJ

Computer-Aided Design of Mastoparan-like Peptides Enables the Generation of Nontoxic Variants with Extended Antibacterial Properties Oshiro KGN, Cândido ES, Chan LY, Torres MDT, Monges BED, Rodrigues SG, Porto WF, Ribeiro SM, Henriques ST, Lu TK, de la Fuente-Nunez C, Craik DJ, Franco OL, Cardoso MH.

Targeting innate immunity for tuberculosis vaccination Khader SA, Divangahi M, Hanekom W, Hill PC, Maeurer M, Makar KW, Mayer-Barber KD, Mhlanga MM, Nemes E, Schlesinger LS, van Crevel R, Vankayalapati R(, Xavier RJ, Netea MG; Bill and Melinda Gates Foundation Collaboration for TB Vaccine Discovery Innate Immunity Working Group18.

Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis Yehl K, Lemire S, Yang AC, Ando H, Mimee M, Torres MT, de la Fuente-Nunez C, Lu TK.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C6, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MG, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A1, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships. Plichta DR, Graham DB, Subramanian S, Xavier RJ

Microbial genes and pathways in inflammatory bowel disease. Schirmer M, Garner A, Vlamakis H, Xavier RJ

Mulit-omics of the gut microbial ecosystem in inflammatory bowel diseases Jason Lloyd-Price, Cesar Arze , Ashwin N. Ananthakrishnan, Melanie Schirmer, Julian Avila-Pacheco, Tiffany W. Poon , Elizabeth Andrews , Nadim J. Ajami , Kevin S. Bonham Colin J. Brislawn, David Casero , Holly Courtney , Antonio Gonzalez8, Thomas G. Graeber, A. Brantley Hall , Kathleen Lake, Carol J. Landers, Himel Mallick, Damian R. Plichta , Mahadev Prasad12, Gholamali Rahnavard, Jenny Sauk, Dmitry Shungin, Yoshiki Vázquez-Baeza, Richard A. White III, IBDMDB Investigators, Jonathan Braun , Lee A. Denson, Janet K. Jansson, Rob Knight, Subra Kugathasan, Dermot P. B. McGovern, Joseph F. Petrosino, Thaddeus S. Stappenbeck, Harland S. Winter, Clary B. Clish, Eric A. Franzosa, Hera Vlamakis , Ramnik J. Xavier & Curtis Huttenhower Nature 569, 655–662 (2019)

Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study. Hyams JS, Davis Thomas S, Gotman N, Haberman Y, Karns R, Schirmer M, Mo A, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Keljo DJ, Markowitz J, Baker SS, Rosh J, Baldassano RN, Patel A, Pfefferkorn M, Otley A, Heyman M, Noe J, Oliva-Hemker M, Rufo PA, Strople J, Ziring D, Guthery SL, Sudel B, Benkov K, Wali P, Moulton D, Evans J, Kappelman MD, Marquis MA, Sylvester FA, Collins MH, Venkateswaran S, Dubinsky M, Tangpricha V12, Spada KL, Saul B, Wang J, Serrano J, Hommel K, Marigorta UM, Gibson G, Xavier RJ, Kugathasan S, Walters T, Denson LA. Lancet. 2019 Apr 27;393(10182):1708-1720. doi: 10.1016/S0140-6736(18)32592-3. Epub 2019 Mar 29.

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K. Nature. 2019 Jan;565(7741):600-605. doi: 10.1038/s41586-019-0878-z. Epub 2019 Jan 23.

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function Claire Duvallet, Kara Larson, Scott Snapper, Sonia Iosim, Ann Lee, Katherine Freer, Kara May, Eric Alm, Rachel Rosen.

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J, Nakata T, Arthur TD, Fornelos N, Heim C, Franzosa EA, Watson N, Huttenhower C, Haiser HJ, Dillow G, Graham DB, Finlay BB, Kostic AD, Porter JA, Vlamakis H, Clish CB, Xavier RJ.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd; IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C.

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders Díaz-Sánchez S, Perrotta AR, Rockafellow I, Alm EJ, Okimoto R, Hawken R, Hanning I.

Massively parallel screening of synthetic microbial communities Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC8. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12804-12809

A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS) Wu MR, Nissim L, Stupp D, Pery E, Binder-Nissim A, Weisinger K, Enghuus C, Palacios SR, Humphrey M, Zhang Z, Maria Novoa E, Kellis M, Weiss R, Rabkin SD, Tabach Y, Lu TK.

A practical guide to methods controlling false discoveries in computational biology Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC.

Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis Ansaldo E, Slayden LC, Ching KL, Koch MA, Wolf NK, Plichta DR, Brown EM, Graham DB, Xavier RJ, Moon JJ, Barton GM.

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk Kurilshikov A, van den Munckhof ICL, Chen L, Bonder MJ, Schraa K, Rutten JHW, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LAB, van der Graaf M, Brand T, Koonen DPY, van Faassen M; LifeLines DEEP Cohort Study, BBMRI Metabolomics Consortium, Slagboom PE, Xavier RJ, Kuipers F, Hofker MH, Wijmenga C, Netea MG, Zhernakova A, Fu J.

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide. Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Xavier + Clardy R. gnavus Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12672-12677

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ

Transmission of human-associated microbiota along family and social networks. Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ. Nat Microbiol. 2019 Mar 25.

Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Science. 2019 Feb 8;363(6427)

Adaptive Evolution within Gut Microbiomes of Healthy People. Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ. Cell Host Microbe. 2019 May 8;25(5):656-667.e8

Metagenomic binning through low-density hashing. Luo Y, Yu YW, Zeng J, Berger B, Peng J. Bioinformatics. 2019 Jan 15;35(2):219-226.

Selective antibacterial activity of the cationic peptide PaDBS1R6 against Gram-negative bacteria. Fensterseifer ICM, Felício MR, Alves ESF, Cardoso MH, Torres MDT, Matos CO, Silva ON, Lu TK, Freire MV, Neves NC, Gonçalves S, Lião LM, Santos NC, Porto WF, de la Fuente-Nunez C, Franco OL. Biochim Biophys Acta Biomembr. 2019 Mar 26. pii: S0005-2736(19)30074-4.

Engineering advanced cancer therapies with synthetic biology. Wu MR, Jusiak B, Lu TK. Nat Rev Cancer. 2019 Apr;19(4):187-195

Interference With Quorum-Sensing Signal Biosynthesis as a Promising Therapeutic Strategy Against Multidrug-Resistant Pathogens. Fleitas Martínez O, Rigueiras PO, Pires ÁDS, Porto WF, Silva ON, de la Fuente-Nunez C, Franco OL. Front Cell Infect Microbiol. 2019 Feb 5;8:444.

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Jiang X, Hall AB, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ. Science. 2019 Jan 11;363(6423):181-187

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ. Nat Microbiol. 2019 Mar;4(3):470-479. doi: 10.1038/s41564-018-0321-

Gut microbiome structure and metabolic activity in inflammatory bowel disease. Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Nat Microbiol. 2019 Feb;4(2):293-305

Interactions in self-assembled microbial communities saturate with diversity. Yu X, Polz MF, Alm EJ. ISME J. 2019 Feb 26. doi: 10.1038/s41396-019-0356-5.

Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity. Brown EM, Kenny DJ, Xavier RJ. Annu Rev Immunol. 2019 Apr 26;37:599-624.

2018

A selective gut bacterial bile salt hydrolase alters host metabolism. Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI, Banks AS, Bry L, Devlin AS. Elife. 2018 Jul 17;7. pii: e37182

Streamlining standard bacteriophage methods for higher throughput. Kauffman KM, Polz MF. MethodsX. 2018 Jan 31;5:159-172

An ingestible bacterial-electronic system to monitor gastrointestinal health. Mimee M, Nadeau P, Hayward A, Carim S, Flanagan S, Jerger L, Collins J, McDonnell S, Swartwout R, Citorik RJ, Bulović V, Langer R, Traverso G, Chandrakasan AP, Lu TK. Science. 2018 May 25;360(6391):915-918.

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. Sci Transl Med. 2018 Dec 19;10(472)

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ. Nature. 2018 Oct;562(7728):589-594

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Graham DB, Luo C, O’Connell DJ, Lefkovith A, Brown EM, Yassour M, Varma M, Abelin JG, Conway KL, Jasso GJ, Matar CG, Carr SA, Xavier RJ. Nat Med. 2018 Nov;24(11):1762-1772

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort. Gurry T; HST Microbiome Consortium*, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ. Sci Rep. 2018 Aug 23;8(1):12699

Identification of Novel Cryptic Multifunctional Antimicrobial Peptides from the Human Stomach Enabled by a Computational-Experimental Platform. Pane K, Cafaro V, Avitabile A, Torres MT, Vollaro A, De Gregorio E, Catania MR, Di Maro A, Bosso A, Gallo G, Zanfardino A, Varcamonti M, Pizzo E, Di Donato A, Lu TK, de la Fuente-Nunez C, Notomista E. ACS Synth Biol. 2018 Sep 21;7(9):2105-2115

Multiomics Analyses to Deliver the Most Effective Treatment to Every Patient With Inflammatory Bowel Disease. Weersma RK, Xavier RJ; IBD Multi Omics Consortium, Vermeire S, Barrett JC. Gastroenterology. 2018 Nov;155(5):e1-e4.

Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH. Nat Methods. 2018 May;15(5):323-329

Defining the gut microbiota in individuals with periodontal diseases: an exploratory study. Lourenςo TGB, Spencer SJ, Alm EJ, Colombo APV. J Oral Microbiol. 2018 Jul 3;10(1):1487741

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota. Kearney SM, Gibbons SM, Poyet M, Gurry T, Bullock K, Allegretti JR, Clish CB, Alm EJ. ISME J. 2018 Oct;12(10):2403-2416.

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH 2nd, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM. BMC Biol. 2018 Jun 5;16(1):62

Searching for superstool: maximizing the therapeutic potential of FMT. Olesen SW, Leier MM, Alm EJ, Kahn SA. Nat Rev Gastroenterol Hepatol. 2018 Jul;15(7):387-388

Identification of Novel Cryptic Multifunctional Antimicrobial Peptides from the Human Stomach Enabled by a Computational-Experimental Platform. Pane K, Cafaro V, Avitabile A, Torres MT, Vollaro A, De Gregorio E, Catania MR, Di Maro A, Bosso A, Gallo G, Zanfardino A, Varcamonti M, Pizzo E, Di Donato A, Lu TK, de la Fuente-Nunez C, Notomista E. ACS Synth Biol. 2018 Aug 20.

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Takahashi MK, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, Donghia N, Ananthakrishnan A, Collins JJ. Nat Commun. 2018 Aug 21;9(1):3347

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy. Olesen SW, Gurry T, Alm EJ. Stat Methods Med Res. 2018 Oct;27(10):2906-2917

Correcting for batch effects in case-control microbiome studies. Gibbons SM, Duvallet C, Alm EJ PLoS Comput Biol. 2018 Apr 23;14(4):e1006102

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ. Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5.

C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions. Mohanan V, Nakata T, Desch AN, Lévesque C, Boroughs A, Guzman G, Cao Z, Creasey E, Yao J, Boucher G, Charron G, Bhan AK, Schenone M, Carr SA, Reinecker HC, Daly MJ, Rioux JD, Lassen KG, Xavier RJ. Science. 2018 Mar 9;359(6380):1161-1166.

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C. Nat Microbiol. 2018 Mar;3(3):337-346.

Neuromicrobiology: How Microbes Influence the Brain. de la Fuente-Nunez C, Meneguetti BT, Franco OL, Lu TK. ACS Chem Neurosci. 2018 Feb 21;9(2):141-150.

Designing synbiotics for improved human health. Kearney SM, Gibbons SM. Microb Biotechnol. 2018 Jan;11(1):141-144

2017

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Nat Commun. 2017 Dec 5;8(1):1784

Synbiotic approaches to human health and well-being. Gurry T Microb Biotechnol. 2017 Sep;10(5):1070-1073

Microbial Community Ecology: Function Over Phylogeny Gibbons SM Nat Ecol Evol. 2017 Jan 4;1(1):32.

The Human Cell Atlas. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe’er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants. Elife. 2017 Dec 5;6. pii: e27041

A single-cell survey of the small intestinal epithelium. Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A. Nature. 2017 Nov 16;551(7680):333-339.

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. Genome Med. 2017 Nov 28;9(1):103.

Salt-responsive gut commensal modulates TH17 axis and disease. Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN. Nature. 2017 Nov 30;551(7682):585-589

Chemical transformation of xenobiotics by the human gut microbiota. Koppel N, Maini Rekdal V, Balskus EP. Science. 2017 Jun 23;356(6344). pii: eaag2770.

A role for bacterial urease in gut dysbiosis and Crohn’s disease. Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD. Sci Transl Med. 2017 Nov 15;9(416).

Human genetic variation and the gut microbiome in disease. Hall AB, Tolonen AC, Xavier RJ. Nat Rev Genet. 2017 Nov;18(11):690-699.

Dissecting the human microbiome with single-cell genomics. Tolonen AC, Xavier RJ. Genome Med. 2017 Jun 14;9(1):56.

dbOTU3: A new implementation of distribution-based OTU calling. Olesen SW, Duvallet C, Alm EJ. PLoS One. 2017 May 4;12(5):e0176335.

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases. Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ. Cell Host Microbe. 2017 May 10;21(5):603-610.e3.

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ. Nat Commun. 2017 Feb 23;8:14319.

Two dynamic regimes in the human gut microbiome. Gibbons SM, Kearney SM, Smillie CS, Alm EJ. PLoS Comput Biol. 2017 Feb 21;13(2):e1005364.

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations. Chu ND, Smith MB, Perrotta AR, Kassam Z, Alm EJ. PLoS One. 2017 Jan 26;12(1):e0170922

Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicentre inception cohort study. Kugathasan S, Denson LA, Walters TD, Kim MO, Marigorta UM, Schirmer M, Mondal K, Liu C, Griffiths A, Noe JD, Crandall WV, Snapper S, Rabizadeh S, Rosh JR, Shapiro JM, Guthery S, Mack DR, Kellermayer R, Kappelman MD, Steiner S, Moulton DE, Keljo D, Cohen S, Oliva-Hemker M, Heyman MB, Otley AR, Baker SS, Evans JS, Kirschner BS, Patel AS, Ziring D, Trapnell BC, Sylvester FA, Stephens MC, Baldassano RN, Markowitz JF, Cho J, Xavier RJ, Huttenhower C, Aronow BJ, Gibson G, Hyams JS, Dubinsky MC. Lancet. 2017 Apr 29;389(10080):1710-1718

2016

Virtual microfluidics for digital quantification and single-cell sequencing. Xu L, Brito IL, Alm EJ, Blainey PC. Nat Methods. 2016 Sep;13(9):759-62.

Synthetic mixed-signal computation in living cells. Rubens JR, Selvaggio G, Lu TK. Nat Commun. 2016 Jun 3;7:11658.

Mechanisms of Pediatric Inflammatory Bowel Disease. Peloquin JM, Goel G, Villablanca EJ, Xavier RJ. Annu Rev Immunol. 2016 May 20;34:31-64.

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H. Nat Med. 2016 Jun;22(6):598-605.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. ISME J. 2016 Jul;10(7):1669-81

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C. Genome Med. 2016 Feb 17;8(1):17.

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Juhani Virta MP, Alm EJ. ISME J. 2016 Feb;10(2):427-36.

Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor. Bilate AM, Bousbaine D, Mesin L, Agudelo M, Leube J, Kratzert A, Dougan SK, Victora GD, PloeghHL. Sci Immunol. 2016 Aug 26;1(2):eaaf7471

Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Keith Pardee; Alexander A Green; Melissa K Takahashi; Dana Braff; Guillaume Lambert; Jeong W Lee; Tom Ferrante; Duo Ma; Nina Donghia; Melina Fan; Nichole M Daringer; Irene Bosch; Dawn M Dudley; David H O’Connor; Lee Gehrke; James J Collins DOI: 10.1016/j.cell.2016.04.059 , PMID: 27160350

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Cell. 2016 Dec 15;167(7):1897

TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation. Graham DB, Lefkovith A, Deelen P, de Klein N, Varma M, Boroughs A, Desch AN, Ng ACY, Guzman G, Schenone M, Petersen CP, Bhan AK, Rivas MA, Daly MJ, Carr SA, Wijmenga C, Xavier RJ. Cell Rep. 2016 Dec 13;17(11):2955-2965.

Microbiome therapeutics – Advances and challenges. Mimee M, Citorik RJ, Lu TK. Adv Drug Deliv Rev. 2016 Oct 1;105(Pt A):44-54.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Vatanen T, Kostic AD, d’Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M; DIABIMMUNE Study Group, Xavier RJ. Cell. 2016 Jun 2;165(6):1551.

Synthetic recombinase-based state machines in living cells. Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK. Science. 2016 Jul 22;353(6297):aad8559.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Science. 2016 Apr 29;352(6285):565-9.

2015

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ Nat Biotechnol. 2015 Oct;33(10):1053-60.

ConStrains identifies microbial strains in metagenomic datasets. Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D. Nat Biotechnol. 2015 Oct;33(10):1045-52

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst. Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng ACY, Doench JG, Root DE, Clish CB, Xavier RJ. Nat Commun. 2015 Jul 21;6:7838

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M; DIABIMMUNE Study Group, Xavier RJ. Cell Host Microbe. 2015 Feb 11;17(2):260-73.

2014

Complex host genetics influence the microbiome in inflammatory bowel disease. Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ. Genome Med. 2014 Dec 2;6(12):107.

The treatment-naive microbiome in new-onset Crohn’s disease. Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. Cell Host Microbe. 2014 Mar 12;15(3):382-392.