Metagenomic microbial community profiling using unique clade-specific marker genes

Nature Methods
Nicola SegataCurtis Huttenhower

Abstract

Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large data sets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/metaphlan/.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 12, 2005·Nature Reviews. Microbiology·Edward F DeLong
Jun 3, 2005·Nature Reviews. Microbiology·Rolf Daniel
Nov 4, 2005·The New England Journal of Medicine·David N FredricksJeanne M Marrazzo
Mar 4, 2006·Science·Francesca D CiccarelliPeer Bork
Dec 21, 2006·Nature Methods·Alice C McHardyIsidore Rigoutsos
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
May 1, 2007·Nature Methods·Konstantinos MavromatisNikos C Kyrpides
Oct 15, 2008·Genome Biology·Martin Wu, Jonathan A Eisen
Oct 18, 2008·Nucleic Acids Research·Kim D PruittDonna R Maglott
Nov 14, 2008·Nucleic Acids Research·J R ColeJames M Tiedje
Dec 2, 2008·Nature·Peter J TurnbaughJeffrey I Gordon
Aug 4, 2009·Nature Methods·Arthur Brady, Steven L Salzberg
Oct 30, 2009·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides
Nov 3, 2009·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Jan 1, 2008·Advances in Bioinformatics·Gail L RosenBahrad Sokhansanj
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jacques RavelLarry J Forney
Aug 17, 2010·Bioinformatics·Robert C Edgar
Oct 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Patrick VeigaWendy S Garrett
Jan 8, 2011·Environmental Microbiology·Frank J StewartEdward F DeLong
Mar 2, 2011·Nature Methods·Kaustubh R PatilAlice C McHardy
Apr 22, 2011·Nature·Manimozhiyan ArumugamPeer Bork
Apr 30, 2011·Nature Methods·Arthur Brady, Steven L Salzberg
May 19, 2011·Nucleic Acids Research·Wolfgang Gerlach, Jens Stoye
Jun 4, 2011·Bioinformatics·Simon A Berger, Alexandros Stamatakis
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Aug 11, 2011·BMC Bioinformatics·Donovan H ParksRobert G Beiko
Jun 16, 2012·Nature·Human Microbiome Project Consortium

Citations

Aug 21, 2013·The ISME Journal·Timothy L TickleCurtis Huttenhower
Aug 15, 2013·Nature Communications·Nicola SegataCurtis Huttenhower
Sep 17, 2013·Nature Communications·A V TyakhtVadim M Govorun
Oct 22, 2013·Nature Methods·Shinichi SunagawaPeer Bork
Jul 10, 2013·Proceedings of the National Academy of Sciences of the United States of America·Samuel MinotFrederic D Bushman
Jul 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Roie Levy, Elhanan Borenstein
Feb 26, 2014·BMC Genomics·Satish M Srinivasan, Chittibabu Guda
Dec 25, 2012·Genome Biology·Sébastien BoisvertJacques Corbeil
Jan 16, 2013·Genome Biology·Yanjiao ZhouGeorge M Weinstock
Aug 21, 2012·PLoS Biology·Dirk GeversCurtis Huttenhower
Dec 5, 2012·PLoS Computational Biology·Dirk GeversCurtis Huttenhower
Oct 23, 2013·PLoS Computational Biology·Rogan CarrElhanan Borenstein
Jan 15, 2014·PloS One·Mariel M FinucaneKatherine S Pollard
Mar 7, 2014·PloS One·Philippe M HauserGaudenz M Hafen
Mar 15, 2014·PloS One·David KoslickiGail L Rosen
Oct 1, 2014·Nature Reviews. Genetics·D S GuttmanPaul Schulze-Lefert
Feb 1, 2014·PeerJ·Aaron E DarlingJonathan A Eisen
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Jan 24, 2014·Japanese Journal of Infectious Diseases·Fumihiko TakeuchiMakoto Kuroda
Mar 13, 2014·Bioinformatics·Gianmauro CuccuruGiorgio Fotia
May 23, 2014·Science Translational Medicine·Kjersti AagaardJ Versalovic
Nov 2, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Lucas R HoffmanSamuel I Miller
Apr 9, 2014·BMC Genomics·Jun Hong XiaGen Hua Yue
Jul 6, 2013·Bioinformatics·Sasha K AmesJonathan E Allen
Feb 14, 2014·Nucleic Acids Research·Qichao TuJizhong Zhou
Jun 7, 2014·Nature Communications·Francesco BaldiniFlaminia Catteruccia
May 23, 2014·Bioinformatics·Sohan SethAntti Honkela
Nov 2, 2014·Bioinformatics·Nam-Phuong NguyenTandy Warnow
Dec 10, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Christina WarinnerMatthew J Collins
Dec 10, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mikkel Winther PedersenEske Willerslev
Aug 12, 2014·Systematic Biology·Frederick A Matsen
Oct 23, 2014·BMC Genomics·Amirhossein ShamsaddiniRaja Mazumder
Nov 25, 2015·Cell Systems·Ebrahim AfshinnekooChristopher E Mason
Jun 20, 2015·Journal of Immunology Research·Caroline VincentAmee R Manges
Jul 16, 2014·International Journal of Molecular Sciences·Kathrin P AßhauerPeter Meinicke
Jan 6, 2016·Nature Reviews. Endocrinology·Mikael Knip, Heli Siljander
Feb 18, 2016·Genome Medicine·Moran YassourCurtis Huttenhower
Jan 13, 2015·Proceedings of the National Academy of Sciences of the United States of America·Jeremiah J FaithJeffrey I Gordon
Feb 13, 2016·Frontiers in Immunology·Heidi Mulcahy-O'Grady, Matthew L Workentine
Jan 24, 2016·Journal of Crohn's & Colitis·Mireia Valles-ColomerJeroen Raes
Oct 11, 2015·Bioinformatics·Genivaldo Gueiros Z SilvaRobert A Edwards
Nov 10, 2013·Nucleic Acids Research·Katherine HuangNicola Segata
Oct 16, 2015·Proceedings of the National Academy of Sciences of the United States of America·Iwijn De VlaminckStephen R Quake
Jan 19, 2016·Scientific Reports·Stinus LindgreenPaul P Gardner
Feb 27, 2015·The Australasian Journal of Dermatology·Laura S WeyrichAlan J Cooper
May 9, 2015·Environmental Microbiology Reports·Naseer SangwanRup Lal
Jan 18, 2016·BMC Bioinformatics·V B DubinkinaD G Alexeev
Nov 13, 2012·Trends in Genetics : TIG·Xochitl C MorganCurtis Huttenhower
Aug 21, 2015·The Journal of Urology·Clea BarnettMartin J Blaser
Feb 7, 2016·FEMS Microbiology Ecology·Ke-Qing XiaoYong-Guan Zhu
Dec 31, 2015·Biomedit︠s︡inskai︠a︡ khimii︠a︡·V B DubinkinaVadim M Govorun
Jan 25, 2014·Environmental Science & Technology·Chen CaoTing F Zhu
Dec 19, 2015·BMC Genomics·Anne H RowleyTodd N Wylie
Nov 4, 2015·The American Journal of Gastroenterology·Christopher QuinceKonstantinos Gerasimidis
Feb 3, 2016·Bioinformatics·Magali JaillardJean-Baptiste Veyrieras
Dec 15, 2015·BioData Mining·Emanuel WeitschekGiovanni Felici
Aug 31, 2016·Nature Microbiology·Molly K GibsonGautam Dantas
Dec 5, 2015·Frontiers in Genetics·Matteo RamazzottiDuccio Cavalieri
May 15, 2015·Computational and Structural Biotechnology Journal·Sevasti FilippidouPilar Junier
Feb 2, 2016·The Journal of Investigative Dermatology·Jacquelyn S MeiselElizabeth A Grice
Jul 3, 2015·Scientific Reports·Andaine Seguin-OrlandoLudovic Orlando
Mar 19, 2014·The American Journal of Pathology·Xingshen SunJohn F Engelhardt
May 15, 2013·Molecular Systems Biology·Nicola SegataCurtis Huttenhower
Mar 21, 2016·Journal of Microbiological Methods·Antony T VincentSteve J Charette
Mar 13, 2014·Molecular Ecology·Clio Der SarkissianLudovic Orlando
Mar 22, 2016·Nature Methods·Matthias ScholzNicola Segata
Sep 8, 2015·Nature Biotechnology·Chengwei LuoDirk Gevers
Oct 9, 2015·Nature Biotechnology·C Titus Brown
Nov 14, 2015·Scientific Reports·Kirsten A ZiesemerChristina Warinner
Sep 30, 2015·Nature Methods·Duy Tin TruongNicola Segata
Feb 13, 2015·Briefings in Bioinformatics·Marie Lisandra Zepeda MendozaM Thomas P Gilbert
Oct 10, 2015·International Journal of Genomics·Graham RoseSaheer Gharbia
Jul 18, 2015·Genomics, Proteomics & Bioinformatics·Rahul Shubhra MandalSantasabuj Das
May 6, 2016·Frontiers in Microbiology·Ankit GuptaVineet K Sharma
Oct 6, 2015·Cell Systems·Y William YuBonnie Berger
Aug 27, 2015·Microbiome·Emily B HollisterJ Versalovic
Apr 14, 2016·Journal of Internal Medicine·T Arora, Fredrik Bäckhed
Apr 18, 2016·Environmental Pollution·Huange GouXiaowu Zheng
May 28, 2015·Blood·Veronica E Manzo, Ami S Bhatt
Jun 10, 2015·Nature Reviews. Genetics·Ludovic OrlandoEske Willerslev
Jul 11, 2015·PeerJ·Katelyn McNair, Robert A Edwards
Jun 18, 2015·Briefings in Bioinformatics·Wynand AlkemaSacha A F T van Hijum
May 30, 2015·The ISME Journal·Corinne F MauricePeter J Turnbaugh
Mar 15, 2015·Nucleic Acids Research·Tracey Allen K FreitasPatrick S G Chain
Jan 6, 2015·American Journal of Obstetrics and Gynecology·Kathleen M AntonyKjersti Aagaard
May 21, 2015·BMC Genomics·Ankit Gupta, Vineet K Sharma
Apr 29, 2015·Nature Reviews. Microbiology·Eric A FranzosaCurtis Huttenhower
Apr 3, 2014·Gut Microbes·A V TyakhtVadim M Govorun
May 6, 2016·Frontiers in Microbiology·Juan JovelGane K-S Wong
Jan 13, 2015·Annual Review of Immunology·Silvia Caballero, Eric G Pamer
Mar 17, 2015·ELife·Jenny TungElizabeth A Archie
May 7, 2016·Bioinformatics·Vitor C PiroBernhard Y Renard
Mar 31, 2015·BioData Mining·D G AlexeevVadim M Govorun
Dec 3, 2014·The Journal of Allergy and Clinical Immunology·Michelle Huffaker, Wanda Phipatanakul
Nov 29, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes· AfiahayatiYasubumi Sakakibara
Jun 27, 2014·Frontiers in Plant Science·Ulrich MelcherWilliam L Schneider
Jul 2, 2014·Frontiers in Plant Science·Thomas J Sharpton
Dec 17, 2014·Proceedings of the National Academy of Sciences of the United States of America·Mikkel SchubertLudovic Orlando
Sep 26, 2013·Diabetes·Fredrik H KarlssonFredrik Bäckhed
Feb 3, 2015·PloS One·Martin S Lindner, Bernhard Y Renard
Aug 31, 2016·Nature Microbiology·Claudio DonatiNicola Segata
May 31, 2016·Journal of Biotechnology·Yu Jung KimSeung-Goo Lee
Jun 10, 2016·Nature·Thaddeus S Stappenbeck, Herbert W Virgin
Jun 18, 2016·Health Security·Norman A DoggettSegaran Pillai
Jul 26, 2016·Frontiers in Microbiology·Mario López-PérezFrancisco Rodriguez-Valera
Jul 10, 2016·Translational Research : the Journal of Laboratory and Clinical Medicine·Yvonne J HuangMeiLan K Han
Jul 11, 2014·PLoS Computational Biology·Fredrik H KarlssonJens Nielsen
Jun 15, 2016·Bioinformatics·Panu SomervuoOtso Ovaskainen
Jul 12, 2016·PLoS Computational Biology·Edoardo PasolliNicola Segata
Jul 20, 2016·Trends in Microbiology·Jason W ArnoldM Andrea Azcarate-Peril
Jul 30, 2016·Gut Microbes·Andrew J GasparriniGautam Dantas
Aug 2, 2016·Nature Methods·Liyi XuPaul C Blainey
Jul 15, 2016·Evolution, Medicine, and Public Health·Thomas Arn HansenAnders Johannes Hansen
May 6, 2015·Annual Review of Genomics and Human Genetics·Knut ReinertDirk J Evers
Aug 28, 2016·Cell·Stephen Nayfach, Katherine S Pollard
Sep 8, 2016·Environmental Science & Technology·Erica M HartmannJessica L Green
Aug 16, 2016·Bioinformatics·Niels W HansonSteven J Hallam
Sep 22, 2016·Nucleic Acids Research·Moreno ZolfoNicola Segata
Oct 7, 2016·Frontiers in Microbiology·Kirsten M Ellegaard, Philipp Engel
Aug 9, 2016·Molecular Nutrition & Food Research·Borja SanchezAbelardo Margolles
Jul 30, 2016·Microbial Biotechnology·Kate M O'BrienMatthew W Nonnenmann
Oct 22, 2016·Annals of the New York Academy of Sciences·Boahemaa Adu-OppongGautam Dantas
Nov 12, 2016·Frontiers in Pharmacology·Angeliki BalasopoulouTheodora Katsila
Oct 26, 2016·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Hai-Jing YuQi Wang
Jul 28, 2016·Neurogastroenterology and Motility : the Official Journal of the European Gastrointestinal Motility Society·K PokusaevaJ Versalovic
Oct 30, 2016·Molecular Ecology Resources·Sanne BoessenkoolBastiaan Star
Sep 30, 2016·PloS One·Ahmed A MetwallyDavid L Perkins
Jan 5, 2017·Scientific Reports·Carlus DenekeBernhard Y Renard
Oct 21, 2016·PloS One·Philippe ChouvarineBurkhard Tümmler
Jul 14, 2016·JPEN. Journal of Parenteral and Enteral Nutrition·Hannah G PiperAndrew Y Koh
Dec 20, 2015·PLoS Computational Biology·James KaminskiCurtis Huttenhower
Jan 21, 2017·Microbiome·Jeremy W CoxAleksey Porollo
Feb 22, 2017·PLoS Computational Biology·Zachary S L FosterNiklaus J Grünwald
Mar 28, 2017·Journal of Bioinformatics and Computational Biology·Diem-Trang PhamVinhthuy Phan
Apr 4, 2017·The New Phytologist·Laura ParducciMikkel Winther Pedersen
Oct 29, 2015·Scientific Reports·Christian MilaniMarco Ventura
Feb 9, 2017·Genome Research·Duy Tin TruongNicola Segata
Dec 23, 2016·Médecine sciences : M/S·Patrick VeigaMuriel Derrien
Apr 2, 2016·Therapeutic Advances in Infectious Disease·Robyn S Lee, Marcel A Behr
Sep 21, 2017·International Journal of Molecular Sciences·Stefano LeoJacques Schrenzel
Jan 5, 2018·Genes·Sandra Christine Andersen, Jeffrey Hoorfar
Dec 2, 2017·Bioinformatics·Lauren J McIverCurtis Huttenhower
Mar 13, 2018·Nucleic Acids Research·Justin WagnerHéctor Corrada Bravo
Nov 27, 2014·Nature Communications·Emilie E L MullerPaul Wilmes
Dec 1, 2017·Briefings in Bioinformatics·Aitor Blanco-MíguezAnália Lourenço
Dec 1, 2017·Briefings in Bioinformatics·Nikolas DovrolisIoanna Maroulakou
Dec 1, 2017·PloS One·Kevin J ThompsonKrishna R Kalari
May 20, 2015·Bioinformatics and Biology Insights·Anastasis OulasIoannis Iliopoulos
Dec 24, 2017·Nature Communications·Davide Albanese, Claudio Donati
Feb 13, 2018·Evidence-based Complementary and Alternative Medicine : ECAM·Cui LiuShining Guo
Jan 4, 2018·BMC Bioinformatics·Quang TranVinhthuy Phan
Oct 3, 2017·Environmental Microbiology·Marc Garcia-GarceraEduardo P C Rocha
Jun 26, 2018·PLoS Computational Biology·Jennifer Lu, Steven L Salzberg
Oct 11, 2017·Biometrics·Michael B Sohn, Hongzhe Li
Dec 3, 2017·Applied and Environmental Microbiology·Ilario FerrocinoLuca Cocolin
Jul 7, 2018·Journal of Clinical Microbiology·John P Dekker
Dec 23, 2016·Applied and Environmental Microbiology·Matthew J HarkeChristopher J Gobler
Apr 17, 2015·Clinical Microbiology Reviews·Carol A GilchristErik L Hewlett
Feb 11, 2015·Applied and Environmental Microbiology·Morgan M SteffenSteven W Wilhelm
Sep 20, 2015·Applied and Environmental Microbiology·Susan R LeonardChristopher A Elkins
Nov 25, 2016·Applied and Environmental Microbiology·Andrew D HuangKonstantinos T Konstantinidis
Oct 29, 2014·Intestinal research·Dong Soo Han
Nov 1, 2018·Nature Methods·Eric A FranzosaCurtis Huttenhower
Nov 10, 2018·Biological Research for Nursing·Katherine A MakiPaule V Joseph
Jun 25, 2017·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Lian Yee YipEric Chun Yong Chan
Sep 30, 2018·Applied and Environmental Microbiology·Marius VitalJames M Tiedje
Dec 1, 2017·F1000Research·Amy L LongmuirMark F Richardson
Oct 31, 2018·Nature Medicine·Aimee M Baumann-DudenhoefferGautam Dantas
Jan 18, 2018·Nature Ecology & Evolution·Åshild J VågeneJohannes Krause
Jan 24, 2019·PLoS Biology·Nandita R GarudKatherine S Pollard
Feb 28, 2018·Biotechnology for Biofuels·Noriko A CassmanEiko E Kuramae
Mar 21, 2018·Genes & Nutrition·Bastian HornungPeter J Schaap
Nov 17, 2017·Nature·Nicola WilckDominik N Müller
Mar 1, 2018·Nature·Daphna RothschildEran Segal
Oct 3, 2017·Nature Methods·Alexander SczyrbaAlice C McHardy
May 2, 2017·Annual Review of Genomics and Human Genetics·Christina WarinnerJohannes Krause
Apr 4, 2019·GigaScience·Stuart M BrownKonstantinos Krampis
Apr 11, 2019·BMC Genomics·Kui Hua, Xuegong Zhang
Jun 13, 2012·Nature Methods·Daniel H Haft, Andrey Tovchigrechko
Jan 1, 2014·Scientific Data·Tree of Sex Consortium
Sep 13, 2017·Nature Biotechnology·Christopher QuinceNicola Segata
Aug 22, 2017·Nature Reviews. Genetics·A Brantley HallRamnik J Xavier
Jun 13, 2019·Omics : a Journal of Integrative Biology·Ilaria LaudadioClaudia Carissimi
Oct 15, 2013·Genomics & Informatics·Mincheol KimHana Yi
Aug 12, 2018·Nature Communications·Nadim J AjamiJoseph F Petrosino
Aug 12, 2017·Scientific Reports·Etienne RuppéJacques Schrenzel
Apr 25, 2018·Mediators of Inflammation·Anna PiccaEmanuele Marzetti
Jul 19, 2018·Bioinformatics·Ben LangmeadRone Charles
Nov 6, 2018·BMC Bioinformatics·Jaesik Kwak, Joonhong Park
Dec 24, 2019·IUBMB Life·Giovanna De SimonePaolo Ascenzi
Sep 11, 2019·Nucleic Acids Research·Sicheng WuWei-Hua Chen
Dec 29, 2016·Journal of Clinical Gastroenterology·David L SuskindSamuel I Miller
Dec 19, 2019·Briefings in Bioinformatics·Richa Bharti, Dominik G Grimm
Jan 17, 2020·Molecular Ecology Resources·Eleonora RachtmanSiavash Mirarab
Jan 26, 2020·FEMS Microbiology Reviews·Dan I AnderssonTone Tønjum
Apr 8, 2016·Water Science and Technology : a Journal of the International Association on Water Pollution Research·Will P M RoweGareth P Pearce
Nov 10, 2017·Microbiology and Molecular Biology Reviews : MMBR·Christian MilaniMarco Ventura
Sep 24, 2017·Microbiome·Niamh B O'HaraChristopher E Mason
Oct 5, 2017·Genome Biology·Xin XingWenxuan Zhong
Sep 14, 2016·Experimental Dermatology·Pamela FerrettiNicola Segata
Apr 8, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Barbara H McGovernMichele Trucksis
Jul 13, 2019·Nature Communications·Alexander T DiltheyAdam M Phillippy
Jul 14, 2020·Bioinformatics·Anuradha WickramarachchiYu Lin
Aug 14, 2020·Applied Microbiology and Biotechnology·Cecília de Souza ValenteDaniel Lee Merrifield
Aug 29, 2020·Water Science and Technology : a Journal of the International Association on Water Pollution Research·Jing Wang, Jiti Zhou
Jul 8, 2016·Microbes and Environments·Satoshi HiraokaWataru Iwasaki
Aug 28, 2020·Journal of Periodontology·Georgios A KotsakisDiane Daubert
Dec 14, 2016·Annual Review of Pathology·Susan BullmanAleksandar D Kostic
Mar 14, 2017·Frontiers in Cellular and Infection Microbiology·Shaocun ZhangHe Huang
Jun 16, 2012·Nature·David A Relman
Aug 9, 2016·Annual Review of Virology·Shirlee WohlPardis C Sabeti
Feb 12, 2017·BMC Genomics·Nam-Phuong NguyenTandy Warnow
Apr 6, 2017·Frontiers in Microbiology·Jing LiHeping Zhang
Sep 9, 2017·Bioinformatics·Martina FischerBernhard Y Renard
Dec 16, 2017·BMC Genomics·Samuele GirottoCinzia Pizzi
Sep 26, 2018·Proceedings of the National Academy of Sciences of the United States of America·Meriam GuellilBarbara Bramanti
Aug 23, 2018·Nature Communications·Melissa K TakahashiJames J Collins
Nov 30, 2018·Forensic Sciences Research·Wei Zhou, Yingnan Bian
Nov 30, 2018·Frontiers in Microbiology·Bing MaRose M Viscardi
Jan 29, 2019·Frontiers in Microbiology·Jessica D ForbesNatalie C Knox
Apr 7, 2019·Nature Reviews. Genetics·Maria A SpyrouJohannes Krause
Jul 19, 2019·Nature Communications·Himel MallickCurtis Huttenhower
Nov 30, 2019·Genome Biology·Derrick E WoodBen Langmead
Nov 24, 2019·Scientific Reports·Andrew T OzgaAnne C Stone
Dec 12, 2019·Frontiers in Genetics·Kai SongFengzhu Sun
Apr 21, 2020·Parasites & Vectors·Rojelio MejiaBarton Slatko
Jul 14, 2020·Bioinformatics·Metin Balaban, Siavash Mirarab
Jul 24, 2020·International Journal of Environmental Research and Public Health·Ariana SaraivaAntónio Raposo
Jun 16, 2012·Nature·Human Microbiome Project Consortium
May 21, 2014·Proceedings of the National Academy of Sciences of the United States of America·Eric A FranzosaCurtis Huttenhower
Apr 6, 2013·Expert Review of Clinical Immunology·Petter BrodinMarkus J Maeurer
Feb 6, 2016·Inflammatory Bowel Diseases·Jessica M Moore-ConnorsJohan Van Limbergen
May 13, 2015·Proceedings of the National Academy of Sciences of the United States of America·Eric A FranzosaCurtis Huttenhower
Jan 1, 2015·Terapevticheskiĭ arkhiv·N V ShalikianiVadim M Govorun
Feb 12, 2017·BMC Genomics·Michael Nute, Tandy Warnow
Mar 30, 2017·Microbial Genomics·Aravind SankarAntti Honkela
Dec 10, 2016·The ISME Journal·Jinlyung ChoiAdina Howe
Sep 23, 2017·Genome Biology·Christopher QuinceA Murat Eren
Mar 30, 2017·Microbial Genomics·Kelly L WyresKathryn E Holt
May 26, 2017·Science Translational Medicine·Simon LaxJack A Gilbert
Nov 7, 2017·NPJ Biofilms and Microbiomes·Leah GuthrieLibusha Kelly
Feb 8, 2018·Molecular Ecology·Stefanie WagnerLudovic Orlando
Jun 27, 2018·Nature Medicine·Lesley HoylesMarc-Emmanuel Dumas
May 11, 2018·Translational Psychiatry·Loes M Olde LoohuisRoel A Ophoff
Apr 13, 2018·Viruses·Casandra W PhilipsonKimberly A Bishop-Lilly
Oct 5, 2018·Scientific Reports·Karen L OsmanAERIS Study Group
Nov 9, 2018·PeerJ·Juan C CastroKonstantinos T Konstantinidis
Jul 19, 2018·Scientific Reports·George TetzVictor Tetz
May 31, 2019·Nature Medicine·Myrna G SerranoGregory A Buck
May 30, 2019·Frontiers in Microbiology·Cindy H NakatsuMeredith B Nevers
Apr 20, 2019·Frontiers in Genetics·Wenxian YangRongshan Yu
Sep 12, 2019·Frontiers in Microbiology·Truc LyRegina Lamendella
Aug 17, 2019·Frontiers in Microbiology·Liliane Costa ContevilleAna Carolina Paulo Vicente
May 31, 2019·Nature Medicine·Jennifer M FettweisGregory A Buck
Dec 29, 2019·Scientific Reports·Thomas H A EderveenSacha A F T van Hijum
Aug 17, 2019·Microbiology Resource Announcements·Yuhao ChenLesley Hoyles
Mar 24, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Paul B Rainey, Steven D Quistad
Mar 7, 2020·Frontiers in Microbiology·Chad M CullenGail L Rosen
Jun 25, 2020·Briefings in Bioinformatics·Matteo CominFabio Vandin
Aug 15, 2020·Medicine·Éadaoin M ButlerWayne S Cutfield
Jun 20, 2020·Chemistry, an Asian Journal·Yuan QiaoSeng Chong Teo
May 25, 2020·Obesity Surgery·Naomi DaviesRinki Murphy
Feb 9, 2017·The Journal of Antimicrobial Chemotherapy·Will P M RoweGareth P Pearce
Dec 3, 2016·Proceedings of the National Academy of Sciences of the United States of America·Tze Guan TanDiane Mathis
Apr 11, 2017·Molecular Ecology Resources·Clio Der SarkissianLudovic Orlando
Jun 27, 2017·NPJ Biofilms and Microbiomes·Adrian TettNicola Segata
Sep 10, 2017·Scientific Reports·Yihwan KimMina Rho
Feb 3, 2017·Indian Journal of Microbiology·Anukriti Sharma, Rup Lal
May 26, 2017·Frontiers in Microbiology·Danillo O AlvarengaAlessandro M Varani
Apr 20, 2018·Scientific Reports·Quentin Le BastardEmmanuel Montassier
Dec 20, 2017·Nature Microbiology·Paul I CosteaPeer Bork
Sep 15, 2018·Frontiers in Public Health·Pauline TrinhPeter M Rabinowitz
Jan 9, 2019·Frontiers in Microbiology·Anukriti SharmaRup Lal
May 28, 2019·Frontiers in Microbiology·Ornella CarriónJonathan D Todd
Sep 29, 2018·Nature Reviews. Gastroenterology & Hepatology·Niv ZmoraEran Elinav
Dec 12, 2018·Nature Microbiology·Eric A FranzosaRamnik J Xavier
Sep 14, 2019·The American Journal of Clinical Nutrition·Angela McCannEibhlís M O'Connor
Feb 2, 2019·Environmental Science and Pollution Research International·Ying HanGuangfei Liu
Jan 9, 2019·Frontiers in Cellular and Infection Microbiology·Yuan-Liang HuChao-Jun Zhang
Mar 8, 2020·Scientific Reports·Maria De AngelisLuca Cocolin
Sep 19, 2019·Critical Reviews in Clinical Laboratory Sciences·Drew J SchwartzGautam Dantas
Mar 12, 2020·Microbiome·Michael C MaceyJ Colin Murrell
Jan 22, 2020·Scientific Reports·Reilly O Cooper, Clayton E Cressler
Feb 13, 2020·Microbiome·Philip BurnhamIwijn De Vlaminck
Aug 5, 2020·Proceedings of the National Academy of Sciences of the United States of America·Carolyn ZhangLingchong You
Aug 31, 2020·PeerJ·Matthieu J MiossecEduardo Castro-Nallar
Dec 18, 2013·Aging·Simone RampelliPatrizia Brigidi
Jan 1, 2013·Journal of Biomarkers·John P Jakupciak
Jul 21, 2017·Frontiers in Microbiology·Jessica D ForbesAleisha Reimer
Sep 30, 2017·Statistics in Biosciences·Eric Z ChenHongzhe Li
Sep 28, 2017·PeerJ·Michael Y LiuAaron E Darling
Apr 6, 2018·Journal of the Royal Society, Interface·Travers ChingCasey S Greene
Jun 7, 2019·Emerging Microbes & Infections·Tiffany HsuGeorgina L Hold
Mar 6, 2019·Genome Biology·Fernando MeyerDavid Koslicki
Oct 26, 2018·Bioinformatics·Rebecca RoseMattia Prosperi
Aug 27, 2019·Frontiers in Microbiology·Baiba VilneJuris Ķibilds
Jan 9, 2019·Frontiers in Microbiology·Ingrid HänelAnne Busch
Dec 11, 2019·Science Progress·Alexander Wy ChanHerb E Schellhorn
May 7, 2019·Frontiers in Microbiology·Alise J Ponsero, Bonnie L Hurwitz
Aug 15, 2019·Scientific Reports·Carlos Eduardo Posada-PerlazaMaría Mercedes Zambrano
Feb 7, 2020·Nature Genetics·Marc ZapatkaPCAWG Consortium
Jan 1, 2020·BMC Microbiology·Oleg V GoloshchapovBoris V Afanasyev
Jun 7, 2020·Applied and Environmental Microbiology·Pei-Ying HongChangzhi Wang
Aug 28, 2020·Brain : a Journal of Neurology·Yiwei QianQin Xiao
Dec 26, 2016·Briefings in Bioinformatics·Valentina GalataAndreas Keller
Oct 12, 2017·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Victor LeungAmee R Manges
Jul 10, 2020·Science Translational Medicine·Seung-Chul ChoiLaurence Morel
Oct 22, 2020·Environmental Science. Processes & Impacts·Dong LiJörg E Drewes
Nov 17, 2020·Frontiers in Microbiology·Gail L Rosen, Penny Hammrich
Dec 3, 2020·Frontiers in Cellular and Infection Microbiology·Otávio Guilherme Gonçalves de AlmeidaMarcia Regina von Zeska Kress
Jul 18, 2020·European Journal of Gastroenterology & Hepatology·Yann TouchefeuEmmanuel Montassier