Computational meta'omics for microbial community studies

Molecular Systems Biology
Nicola SegataCurtis Huttenhower


Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.


Jul 1, 1991·Journal of Bacteriology·T M SchmidtN R Pace
May 1, 1993·Applied Microbiology and Biotechnology·K MollyW Verstraete
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 24, 1997·Science·R L TatusovD J Lipman
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SchultzC P Ponting
Jul 31, 1999·Applied and Environmental Microbiology·Floyd E DewhirstJ G Fox
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Aug 10, 2000·Cell·T R HughesS H Friend
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fredrik BäckhedJeffrey I Gordon
Dec 15, 2004·Advances in Marine Biology·Alan J SouthwardStephen J Hawkins
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
Jan 13, 2006·Trends in Microbiology·Paul Wilmes, Philip L Bond
Mar 4, 2006·Science·Francesca D CiccarelliPeer Bork
Jun 24, 2006·Science·Alexander I CulleyCurtis A Suttle
Jul 18, 2006·Nucleic Acids Research·Christopher HylandDavid R Westhead
Nov 17, 2006·Applied Microbiology and Biotechnology·Thomas KvistPeter Westermann
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Mar 16, 2007·PLoS Biology·Rekha SeshadriMarvin Frazier
Jul 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Yann MarcyStephen R Quake
Feb 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Min LiLiping Zhao
Mar 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jorge Frias-LopezEdward F DeLong
Mar 12, 2008·Proceedings of the National Academy of Sciences of the United States of America·Marios GiannakisJeffrey I Gordon
Sep 9, 2008·Cell·Peter J Turnbaugh, Jeffrey I Gordon
Sep 17, 2008·Nature Reviews. Microbiology·Ruth E LeyJeffrey I Gordon
Sep 27, 2008·Current Opinion in Microbiology·Susannah G Tringe, Philip Hugenholtz
Oct 9, 2008·PloS One·Daniel C RichterDaniel H Huson
Oct 31, 2008·The ISME Journal·Nathan C VerberkmoesJanet K Jansson
Nov 6, 2008·Annual Review of Genetics·Nancy A MoranAtsushi Nakabachi
Dec 2, 2008·Nature·Peter J TurnbaughJeffrey I Gordon
Jan 3, 2009·Science·John Chen, Richard P Novick
Apr 11, 2009·PLoS Computational Biology·James Robert WhiteMihai Pop
Apr 25, 2009·PloS One·Tanja WoykeRamunas Stepanauskas
Jun 10, 2009·Journal of Bioinformatics and Computational Biology·Yuzhen Ye, Haixu Tang
Jul 29, 2009·PloS One·Janet K JanssonPhilippe Schmitt-Kopplin
Aug 7, 2009·The ISME Journal·Allan E Konopka
Aug 22, 2009·Bioinformatics·Erik KristianssonDaniel Dalevi
Oct 20, 2009·Cell·Ivaylo I IvanovDan R Littman
Dec 8, 2009·Nature Reviews. Microbiology·Matthew A Croxen, B Brett Finlay
Dec 17, 2009·Bioinformatics·Matthew HortonJoy Bergelson
Dec 25, 2009·Nature·Dongying WuJonathan A Eisen
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Feb 5, 2010·Bioinformatics·Donovan H Parks, Robert G Beiko
Feb 23, 2010·Bioinformatics·Fabian SchreiberPeter Meinicke
Apr 7, 2010·Proceedings of the National Academy of Sciences of the United States of America·Peter J TurnbaughJeffrey I Gordon
Apr 7, 2010·Science Translational Medicine·Peter J TurnbaughJeffrey I Gordon
Apr 30, 2010·PloS One·Tanja WoykeJan-Fang Cheng
May 12, 2010·Genome Research·Samuel ChaffronChristian von Mering
May 22, 2010·Science·Karen E NelsonDianhui Zhu
Jun 23, 2010·Proceedings of the National Academy of Sciences of the United States of America·Maria Gloria Dominguez-BelloRob Knight
Jul 17, 2010·Mutagenesis·David Lovell
Jul 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jeremy E KoenigRuth E Ley
Aug 17, 2010·Bioinformatics·Robert C Edgar
Sep 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jay McCarrenEdward F DeLong
Sep 18, 2010·Proceedings of the National Academy of Sciences of the United States of America·Les Dethlefsen, David A Relman
Oct 12, 2010·Science·Lauren D McDanielJohn H Paul
Oct 21, 2010·Bioinformatics·Manimozhiyan ArumugamPeer Bork
Oct 23, 2010·Bioinformatics·Eoghan D HarringtonDavid A Relman
Oct 30, 2010·Bioinformatics·Monzoorul Haque MohammedSharmila S Mande
Nov 26, 2010·Nature Methods·Can AlkanEvan E Eichler
Dec 9, 2010·BMC Bioinformatics·Tarini Shankar GhoshSharmila S Mande
Dec 3, 2010·PLoS Computational Biology·Niels Klitgord, Daniel Segrè
Jan 29, 2011·Science·Nicholas J CroucherStephen D Bentley
Jan 29, 2011·Science·Matthias HessEdward M Rubin
Mar 5, 2011·BMC Bioinformatics·Suparna MitraDaniel H Huson
Mar 2, 2011·Nature Methods·Kaustubh Raosaheb PatilAlice Carolyn McHardy
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jonathan LasersonDaphne Koller
Mar 12, 2011·Genome Medicine·James M KinrossJeremy K Nicholson
Mar 15, 2011·Current Protocols in Bioinformatics·Todd TreangenMihai Pop
Mar 17, 2011·PloS One·María José GosalbesAndrés Moya
Mar 25, 2011·Methods in Molecular Biology·Jack A Gilbert, Margaret Hughes
Mar 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·Andrew L GoodmanJeffrey I Gordon
Apr 30, 2011·Nature Methods·Arthur Brady, Steven L Salzberg
May 19, 2011·Nucleic Acids Research·Wolfgang Gerlach, Jens Stoye
May 21, 2011·Science·Jeremiah J FaithJeffrey I Gordon
Jun 4, 2011·Bioinformatics·Simon A Berger, Alexandros Stamatakis
Jun 17, 2011·Nature·Andrew L KauJeffrey I Gordon
Jun 21, 2011·Bioinformatics·Yu PengFrancis Y L Chin
Jun 28, 2011·Genome Biology·Nicola SegataCurtis Huttenhower
Jul 19, 2011·Nature Methods·Dan KnightsScott T Kelley
Aug 6, 2011·Current Opinion in Microbiology·Kay D Bidle, Assaf Vardi
Aug 11, 2011·BMC Bioinformatics·Donovan H ParksRobert G Beiko
Oct 20, 2011·Genome Research·Aleksandar D KosticMatthew Meyerson
Oct 28, 2011·Science Translational Medicine·Nathan P McNultyJeffrey I Gordon
Nov 17, 2011·Nucleic Acids Research·Victor M MarkowitzNikos Kyrpides
Nov 29, 2011·Nucleic Acids Research·Kim D PruittDonna R Maglott
Dec 1, 2011·Nucleic Acids Research·Marco PuntaRobert D Finn
Dec 14, 2011·Seminars in Immunology·Margaret McFall-NgaiElizabeth A Harvie
Dec 20, 2011·Standards in Genomic Sciences·Amrita PatiNatalia N Ivanova
Dec 24, 2011·Nucleic Acids Research·Victor M MarkowitzNikos Kyrpides
Feb 4, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yi WangFrancis Y L Chin
Feb 15, 2012·Bioinformatics·Martin Wu, Alexandra J Scott
Feb 18, 2012·BMC Genomics·Kerensa E McElroyTorsten Thomas
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Mar 28, 2012·Nature Reviews. Microbiology·Karsten Zengler, Bernhard O Palsson
Mar 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jiangchao ZhaoJohn J LiPuma
Apr 17, 2012·Nature Methods·Peter E LarsenJack A Gilbert
May 4, 2012·Science Translational Medicine·Pawel GajerJacques Ravel
May 12, 2012·PLoS Computational Biology·Vanni BucciJoao B Xavier
Jan 1, 2011·Microbial Informatics and Experimentation·Peter E LarsenJack A Gilbert
Jun 8, 2012·Science·Lora V HooperAndrew J Macpherson
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Jun 16, 2012·Nature·Human Microbiome Project Consortium
Jun 16, 2012·Nature·Human Microbiome Project Consortium
Jun 16, 2012·Nature·Tanya YatsunenkoJeffrey I Gordon
Jun 22, 2012·PLoS Computational Biology·Sahar AbubuckerCurtis Huttenhower
Jun 30, 2012·PloS One·Kaustubh Raosaheb PatilAlice Carolyn McHardy
Jul 5, 2012·Genome Biology·Serena DolliveFrederic D Bushman
Jul 19, 2012·PLoS Computational Biology·Karoline FaustCurtis Huttenhower
Jul 24, 2012·Nucleic Acids Research·Toshiaki NamikiYasubumi Sakakibara
Aug 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jason PellC Titus Brown
Aug 1, 2012·PloS One·Anthony A FodorAshlee M Earl
Aug 15, 2012·Nature Reviews. Microbiology·Roger S Lasken
Sep 1, 2012·Science·Kevin J ForsbergGautam Dantas
Sep 7, 2012·Journal of Cystic Fibrosis : Official Journal of the European Cystic Fibrosis Society·Yan Wei LimForest Rohwer
Sep 28, 2012·Genome Biology·Xochitl C MorganCurtis Huttenhower
Oct 3, 2012·PLoS Computational Biology·Jonathan Friedman, Eric J Alm
Oct 20, 2012·PloS One·Jens Roat KultimaPeer Bork


Aug 15, 2013·Nature Communications·Nicola SegataCurtis Huttenhower
Feb 8, 2014·PloS One·Daniela LangfeldtRuth A Schmitz
Apr 5, 2014·PLoS Computational Biology·Paul J McMurdie, Susan Holmes
Oct 22, 2014·International Journal of Molecular Sciences·Magda DudekJoe Gallagher
Jan 27, 2016·Proceedings of the National Academy of Sciences of the United States of America·Jessica L Mark WelchGary G Borisy
Dec 10, 2013·Nucleic Acids Research·Tatiana TatusovaIgor Tolstoy
Apr 23, 2015·Proceedings of the National Academy of Sciences of the United States of America·Sahand HormozBoris I Shraiman
Jan 7, 2016·Frontiers in Genetics·Alejandra Escobar-ZepedaAlejandro Sanchez-Flores
Sep 28, 2015·BMC Research Notes·Se-Ran JunAndrey A Gorin
Apr 14, 2016·Nature Communications·Peter MenzelAnders Krogh
Mar 20, 2014·Virulence·Ping Xu, John Gunsolley
May 6, 2016·Frontiers in Microbiology·Juan JovelGane K-S Wong
Apr 29, 2015·Nature Reviews. Microbiology·Eric A FranzosaCurtis Huttenhower
May 7, 2016·Bioinformatics·Jens Roat KultimaPeer Bork
May 28, 2016·Nature Reviews. Immunology·Michelle G Rooks, Wendy S Garrett
Jun 9, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Surojit BiswasVladimir Jojic
Jul 12, 2016·PLoS Computational Biology·Edoardo PasolliNicola Segata
Aug 17, 2016·International Journal of Molecular Sciences·Da-Zhi WangZhang-Xian Xie
Jan 17, 2017·Expert Review of Molecular Diagnostics·Jeremy Davis-TurakGary Hardiman
Jun 13, 2015·Critical Reviews in Food Science and Nutrition·Youzhong LiuHervé Alexandre
Jan 26, 2017·Journal of Biotechnology·Lutz WiehlmannBurkhard Tümmler
Feb 25, 2017·Immunologic Research·Nurit Katz-Agranov, Gisele Zandman-Goddard
Sep 5, 2015·Current Opinion in Biotechnology·Smitha KrishnanKyongbum Lee
Jun 1, 2017·Critical Reviews in Microbiology·Johanna GutlebenDetmer Sipkema
Feb 25, 2014·Biotechnology Letters·Jagroop Pandhal, Josselin Noirel
Jun 20, 2014·Journal of Biotechnology·Nina Jagmann, Bodo Philipp
Jul 16, 2014·Chemical Society Reviews·Hao SongYing-Jin Yuan
Mar 13, 2014·Molecular Ecology·Clio Der SarkissianLudovic Orlando
Jan 5, 2018·Genes·Sandra Christine Andersen, Jeffrey Hoorfar
Nov 10, 2013·Nucleic Acids Research·Katherine HuangNicola Segata
May 21, 2016·Evolutionary Bioinformatics Online·Vanessa Aguiar-PulidoGiri Narasimhan
Dec 1, 2017·Briefings in Bioinformatics·Aitor Blanco-MíguezAnália Lourenço
Nov 9, 2018·Tissue Barriers·Ashfaqul Alam, Andrew Neish
Jan 18, 2018·Nature Microbiology·Galeb S Abu-AliCurtis Huttenhower
Sep 13, 2017·Nature Biotechnology·Christopher QuinceNicola Segata
Feb 14, 2014·Applied Microbiology and Biotechnology·Chiranjib ChakrabortySanghamitra Bandyopadhyay
May 31, 2015·American Journal of Epidemiology·Betsy Foxman, Emily T Martin
Aug 3, 2017·Biological Reviews of the Cambridge Philosophical Society·W Daniel KisslingAlex R Hardisty
Apr 25, 2018·Mediators of Inflammation·Anna PiccaEmanuele Marzetti
Feb 5, 2019·Database : the Journal of Biological Databases and Curation·Gerhard RamboldDagmar Triebel
Jan 21, 2015·PLoS Biology·Matthew K WaldorHamilton Smith
Sep 14, 2016·Experimental Dermatology·Pamela FerrettiNicola Segata
Jul 25, 2015·Applied Microbiology and Biotechnology·João Pinto da CostaRui Vitorino
Jun 11, 2020·International Journal of Molecular Sciences·Bruno TiloccaViviana Greco
Apr 3, 2019·FEMS Microbiology Letters·Alejandra Hernandez-AgredaTracy D Ainsworth
Mar 1, 2015·FEMS Microbiology Reviews·Thulani P MakhalanyaneDon A Cowan
Sep 4, 2015·Molecular Ecology·Anastasia BraginaGabriele Berg
Mar 8, 2016·Annals of the New York Academy of Sciences·Stanislas Mondot, Patricia Lepage
Jun 11, 2016·Journal of Animal Science·B C Guard, J S Suchodolski
Sep 10, 2017·Scientific Reports·Yihwan KimMina Rho
May 30, 2019·Frontiers in Cellular and Infection Microbiology·Diego J CastilloMarnie Potgieter
Jul 19, 2019·Nature Communications·Himel MallickCurtis Huttenhower
Apr 11, 2017·Molecular Ecology Resources·Clio Der SarkissianLudovic Orlando
Mar 30, 2017·Microbial Genomics·Aravind SankarAntti Honkela
Nov 30, 2018·Frontiers in Physiology·Sarah C PearceKenneth Racicot
Jan 11, 2019·Microbiology and Molecular Biology Reviews : MMBR·Aislinn D Rowan-NashPeter Belenky
Jun 27, 2017·NPJ Biofilms and Microbiomes·Adrian TettNicola Segata
May 27, 2015·Alimentary Pharmacology & Therapeutics·H L Simpson, B J Campbell
Jan 31, 2019·Metabolites·Partho Sen, Matej Orešič
Oct 8, 2020·Animal Models and Experimental Medicine·Inbal Cahana, Fuad A Iraqi
Nov 3, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Ovidiu PopaOliver Ebenhöh
Oct 9, 2019·The Veterinary Clinics of North America. Food Animal Practice·Diego E GomezMarcio C Costa
Jan 29, 2021·FEMS Microbiology Letters·Álvaro Del MoralAsunción de Los Ríos
Feb 5, 2021·International Journal of Molecular Sciences·Marc OlivaVictor Moreno

Related Concepts

In Silico
Computer Programs and Programming
Gene Expression Regulation, Bacterial
MRNA Differential Display
Microbial Consortia
Base Sequence

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

The Tendon Seed Network

Tendons are rich in the extracellular matrix and are abundant throughout the body providing essential roles including structure and mobility. The transcriptome of tendons is being compiled to understand the micro-anatomical functioning of tendons. Discover the latest research pertaining to the Tendon Seed Network here.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.


Incretins are metabolic hormones that stimulate a decrease in glucose levels in the blood and they have been implicated in glycemic regulation in the remission phase of type 1 diabetes. Here is the latest research.

Chromatin Regulation and Circadian Clocks

The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.

Long COVID-19

“Long Covid-19” describes illness in patients who are reporting long-lasting effects of the SARS-CoV-19 infection, often long after they have recovered from acute Covid-19. Ongoing health issues often reported include low exercise tolerance and breathing difficulties, chronic tiredness, and mental health problems such as post-traumatic stress disorder and depression. This feed follows the latest research into Long Covid.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.