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Title: Elucidation of complexity and prediction of interactions in microbial communities


Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. As a result, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.

 [1];  [1];  [1]
  1. Department of Pediatrics University of California, San Diego 9500 Gilman Drive La Jolla CA 92093‐0760 USA
Publication Date:
Research Org.:
Johns Hopkins Univ., Baltimore, MD (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1392704; OSTI ID: 1485598
Grant/Contract Number:  
Resource Type:
Published Article
Journal Name:
Microbial Biotechnology (Online)
Additional Journal Information:
Journal Name: Microbial Biotechnology (Online) Journal Volume: 10 Journal Issue: 6; Journal ID: ISSN 1751-7915
Country of Publication:
United Kingdom

Citation Formats

Zuñiga, Cristal, Zaramela, Livia, and Zengler, Karsten. Elucidation of complexity and prediction of interactions in microbial communities. United Kingdom: N. p., 2017. Web.
Zuñiga, Cristal, Zaramela, Livia, & Zengler, Karsten. Elucidation of complexity and prediction of interactions in microbial communities. United Kingdom.
Zuñiga, Cristal, Zaramela, Livia, and Zengler, Karsten. Tue . "Elucidation of complexity and prediction of interactions in microbial communities". United Kingdom.
title = {Elucidation of complexity and prediction of interactions in microbial communities},
author = {Zuñiga, Cristal and Zaramela, Livia and Zengler, Karsten},
abstractNote = {Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. As a result, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.},
doi = {10.1111/1751-7915.12855},
journal = {Microbial Biotechnology (Online)},
number = 6,
volume = 10,
place = {United Kingdom},
year = {2017},
month = {9}

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Fig. 1 Fig. 1: Milestones in microbiology and computational modelling for the study of microbial communities.

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Works referenced in this record:

Dynamic photosynthetic response of the microalga Scenedesmus obtusiusculus to light intensity perturbations
journal, September 2014

Networks of energetic and metabolic interactions define dynamics in microbial communities
journal, November 2015

  • Embree, Mallory; Liu, Joanne K.; Al-Bassam, Mahmoud M.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 50
  • DOI: 10.1073/pnas.1506034112

Microbial interactions: from networks to models
journal, July 2012

  • Faust, Karoline; Raes, Jeroen
  • Nature Reviews Microbiology, Vol. 10, Issue 8
  • DOI: 10.1038/nrmicro2832

Serum Metabolomics Profiling to Identify Biomarkers for Unstable Angina
journal, January 2017

  • Yao, Wei; Gao, Yuxia; Wan, Zheng
  • BioMed Research International, Vol. 2017
  • DOI: 10.1155/2017/7657306

Fluctuations in the Abundance of a Species considered Mathematically1
journal, October 1926

Dimension reduction techniques for the integrative analysis of multi-omics data
journal, March 2016

  • Meng, Chen; Zeleznik, Oana A.; Thallinger, Gerhard G.
  • Briefings in Bioinformatics, Vol. 17, Issue 4
  • DOI: 10.1093/bib/bbv108

You Are What You Host: Microbiome Modulation of the Aging Process
journal, January 2014

Systems biology guided by XCMS Online metabolomics
journal, April 2017

  • Huan, Tao; Forsberg, Erica M.; Rinehart, Duane
  • Nature Methods, Vol. 14, Issue 5
  • DOI: 10.1038/nmeth.4260

Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
journal, April 2014

  • Paddon, Chris J.; Keasling, Jay D.
  • Nature Reviews Microbiology, Vol. 12, Issue 5
  • DOI: 10.1038/nrmicro3240

Recovering complete and draft population genomes from metagenome datasets
journal, March 2016

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
journal, October 2013

  • Embree, Mallory; Nagarajan, Harish; Movahedi, Narjes
  • The ISME Journal, Vol. 8, Issue 4
  • DOI: 10.1038/ismej.2013.187

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
journal, November 2012

Metabolic modeling of a mutualistic microbial community
journal, January 2007

  • Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea
  • Molecular Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1038/msb4100131

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys
journal, December 2015

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen
journal, November 2012

Host-Bacterial Mutualism in the Human Intestine
journal, March 2005

Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013

  • Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1076

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
journal, July 2013

  • Levy, R.; Borenstein, E.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 31
  • DOI: 10.1073/pnas.1300926110

Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry
journal, June 2011

Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses
journal, June 2014

  • Gowda, Harsha; Ivanisevic, Julijana; Johnson, Caroline H.
  • Analytical Chemistry, Vol. 86, Issue 14
  • DOI: 10.1021/ac500734c

A Whole-Cell Computational Model Predicts Phenotype from Genotype
journal, July 2012

The Human Microbiome Project
journal, October 2007

  • Turnbaugh, Peter J.; Ley, Ruth E.; Hamady, Micah
  • Nature, Vol. 449, Issue 7164
  • DOI: 10.1038/nature06244

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
journal, January 2017

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
journal, June 2016

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
journal, August 2011

  • Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
  • Nature Protocols, Vol. 6, Issue 9
  • DOI: 10.1038/nprot.2011.308

An analysis of models describing predator-prey interaction
journal, May 1970

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
journal, November 2013

  • Monk, J. M.; Charusanti, P.; Aziz, R. K.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 50
  • DOI: 10.1073/pnas.1307797110

Research priorities for harnessing plant microbiomes in sustainable agriculture
journal, March 2017

Bespoke microbiome therapy to manage plant diseases
journal, January 2013

A streamlined ribosome profiling protocol for the characterization of microorganisms
journal, June 2015

  • Latif, Haythem; Szubin, Richard; Tan, Justin
  • BioTechniques, Vol. 58, Issue 6
  • DOI: 10.2144/000114302

Rhizosphere microbiome assemblage is affected by plant development
journal, November 2013

  • Chaparro, Jacqueline M.; Badri, Dayakar V.; Vivanco, Jorge M.
  • The ISME Journal, Vol. 8, Issue 4
  • DOI: 10.1038/ismej.2013.196

Vitamin B 12 as a Modulator of Gut Microbial Ecology
journal, November 2014

Patterns and Processes of Microbial Community Assembly
journal, September 2013

  • Nemergut, D. R.; Schmidt, S. K.; Fukami, T.
  • Microbiology and Molecular Biology Reviews, Vol. 77, Issue 3
  • DOI: 10.1128/MMBR.00051-12

Constraint-based models predict metabolic and associated cellular functions
journal, January 2014

  • Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A.
  • Nature Reviews Genetics, Vol. 15, Issue 2
  • DOI: 10.1038/nrg3643

Systems approaches to microbial communities and their functioning
journal, August 2010

  • Röling, Wilfred FM; Ferrer, Manuel; Golyshin, Peter N.
  • Current Opinion in Biotechnology, Vol. 21, Issue 4
  • DOI: 10.1016/j.copbio.2010.06.007

Ribosome Footprint Profiling of Translation throughout the Genome
journal, March 2016

The role of the gut microbiota in nutrition and health
journal, September 2012

  • Flint, Harry J.; Scott, Karen P.; Louis, Petra
  • Nature Reviews Gastroenterology & Hepatology, Vol. 9, Issue 10
  • DOI: 10.1038/nrgastro.2012.156

Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton.
journal, January 1990

New insights into therapeutic strategies for gut microbiota modulation in inflammatory diseases
journal, June 2016

  • Vieira, Angélica Thomaz; Fukumori, Claudio; Ferreira, Caroline Marcantonio
  • Clinical & Translational Immunology, Vol. 5, Issue 6
  • DOI: 10.1038/cti.2016.38

Probiotics, prebiotics, and the host microbiome: the science of translation: Probiotics, prebiotics, and the host microbiome
journal, November 2013

  • Petschow, Bryon; Doré, Joël; Hibberd, Patricia
  • Annals of the New York Academy of Sciences, Vol. 1306, Issue 1
  • DOI: 10.1111/nyas.12303

Human Thanatomicrobiome Succession and Time Since Death
journal, July 2016

  • Javan, Gulnaz T.; Finley, Sheree J.; Can, Ismail
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep29598

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom
journal, May 2016

The challenges of integrating multi-omic data sets
journal, October 2010

  • Palsson, Bernhard; Zengler, Karsten
  • Nature Chemical Biology, Vol. 6, Issue 11
  • DOI: 10.1038/nchembio.462

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases
journal, January 2009

  • Brulc, Jennifer M.; Antonopoulos, Dionysios A.; Berg Miller, Margret E.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 6
  • DOI: 10.1073/pnas.0806191105

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni
journal, March 2017

  • Thibodeau, Alexandre; Letellier, Ann; Yergeau, Étienne
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.00451

A Glucose-Utilizing Strain, Cupriavidus euthrophus B-10646: Growth Kinetics, Characterization and Synthesis of Multicomponent PHAs
journal, February 2014

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
journal, February 2017

Protein production using recombinant yeast in an immobilized-cell-film airlift bioreactor
journal, July 1997

Syntrophic exchange in synthetic microbial communities
journal, April 2014

  • Mee, M. T.; Collins, J. J.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 20
  • DOI: 10.1073/pnas.1405641111

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
journal, March 2017

  • Bartell, Jennifer A.; Blazier, Anna S.; Yen, Phillip
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms14631

Evaluation of rate law approximations in bottom-up kinetic models of metabolism
journal, June 2016

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case
journal, July 2015

Context and the human microbiome
journal, November 2015

Microbial syntrophy: interaction for the common good
journal, May 2013

  • Morris, Brandon E. L.; Henneberger, Ruth; Huber, Harald
  • FEMS Microbiology Reviews, Vol. 37, Issue 3
  • DOI: 10.1111/1574-6976.12019

Novel bioactive from Lactobacillus brevis DSM17250 to stimulate the growth of Staphylococcus epidermidis : a pilot study
journal, February 2017

  • Holz, C.; Benning, J.; Schaudt, M.
  • Beneficial Microbes, Vol. 8, Issue 1
  • DOI: 10.3920/BM2016.0073

Metabolic interactions in microbial communities: untangling the Gordian knot
journal, October 2015

Atopic dermatitis: a disease of altered skin barrier and immune dysregulation: Immune response in atopic dermatitis
journal, June 2011

Draft Genome Sequence of Sphingobacterium sp. CZ-UAM, Isolated from a Methanotrophic Consortium
journal, August 2017

  • Steffani-Vallejo, José Luis; Zuñiga, Cristal; Cruz-Morales, Pablo
  • Genome Announcements, Vol. 5, Issue 33
  • DOI: 10.1128/genomeA.00792-17

MetaPhlAn2 for enhanced metagenomic taxonomic profiling
journal, September 2015

  • Truong, Duy Tin; Franzosa, Eric A.; Tickle, Timothy L.
  • Nature Methods, Vol. 12, Issue 10
  • DOI: 10.1038/nmeth.3589

Measurement of bacterial replication rates in microbial communities
journal, November 2016

  • Brown, Christopher T.; Olm, Matthew R.; Thomas, Brian C.
  • Nature Biotechnology, Vol. 34, Issue 12
  • DOI: 10.1038/nbt.3704

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
journal, November 2016

  • Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura
  • Nature Biotechnology, Vol. 35, Issue 1
  • DOI: 10.1038/nbt.3703

Competitive and cooperative metabolic interactions in bacterial communities
journal, September 2011

  • Freilich, Shiri; Zarecki, Raphy; Eilam, Omer
  • Nature Communications, Vol. 2, Issue 1
  • DOI: 10.1038/ncomms1597

A multi-omic future for microbiome studies
journal, April 2016

A new view of the tree of life
journal, April 2016

Microbial inoculation of seed for improved crop performance: issues and opportunities
journal, May 2016

Capturing the genetic makeup of the active microbiome in situ
journal, June 2017

  • Singer, Esther; Wagner, Michael; Woyke, Tanja
  • The ISME Journal, Vol. 11, Issue 9
  • DOI: 10.1038/ismej.2017.59

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Control analysis of microbial interactions in continuous culture: a simulation study
journal, October 1993

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
journal, January 2013

  • O'Brien, Edward J.; Lerman, Joshua A.; Chang, Roger L.
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.52

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
journal, April 2017

  • Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep46249

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
journal, August 2015

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
journal, July 2010

Relating the metatranscriptome and metagenome of the human gut
journal, May 2014

  • Franzosa, E. A.; Morgan, X. C.; Segata, N.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 22
  • DOI: 10.1073/pnas.1319284111

Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica
journal, March 2010

  • Ng, Charmaine; DeMaere, Matthew Z.; Williams, Timothy J.
  • The ISME Journal, Vol. 4, Issue 8
  • DOI: 10.1038/ismej.2010.28

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota
journal, May 2015

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association
journal, November 2013

  • Nagarajan, Harish; Embree, Mallory; Rotaru, Amelia-Elena
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3809

Novel major archaebacterial group from marine plankton
journal, March 1992

  • Fuhrman, Jed A.; McCallum, Kirk; Davis, Alison A.
  • Nature, Vol. 356, Issue 6365
  • DOI: 10.1038/356148a0

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013

  • Caspi, Ron; Altman, Tomer; Billington, Richard
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1103

Plankton networks driving carbon export in the oligotrophic ocean
journal, February 2016

  • Guidi, Lionel; Chaffron, Samuel; Bittner, Lucie
  • Nature, Vol. 532, Issue 7600
  • DOI: 10.1038/nature16942

Methods for the integration of multi-omics data: mathematical aspects
journal, January 2016

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms
journal, June 2017

  • von Kamp, Axel; Klamt, Steffen
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms15956

The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death
journal, February 2016

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales
journal, December 2016

  • Sierra-Garcia, Isabel Natalia; Dellagnezze, Bruna M.; Santos, Viviane P.
  • Extremophiles, Vol. 21, Issue 1
  • DOI: 10.1007/s00792-016-0897-8

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
journal, January 2010

  • Bordbar, Aarash; Lewis, Nathan E.; Schellenberger, Jan
  • Molecular Systems Biology, Vol. 6, Issue 1
  • DOI: 10.1038/msb.2010.68

Dynamics of the human gut microbiome in inflammatory bowel disease
journal, February 2017

  • Halfvarson, Jonas; Brislawn, Colin J.; Lamendella, Regina
  • Nature Microbiology, Vol. 2, Issue 5
  • DOI: 10.1038/nmicrobiol.2017.4

Microbiome Tools for Forensic Science
journal, September 2017

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
journal, June 2011

  • Martinez-Garcia, Manuel; Swan, Brandon K.; Poulton, Nicole J.
  • The ISME Journal, Vol. 6, Issue 1
  • DOI: 10.1038/ismej.2011.84

Metabolic dependencies drive species co-occurrence in diverse microbial communities
journal, May 2015

  • Zelezniak, Aleksej; Andrejev, Sergej; Ponomarova, Olga
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 20
  • DOI: 10.1073/pnas.1421834112

Perspectives in mathematical modelling for microbial ecology
journal, February 2016

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
journal, September 2014

  • Liu, Joanne K.; O’Brien, Edward J.; Lerman, Joshua A.
  • BMC Systems Biology, Vol. 8, Issue 1
  • DOI: 10.1186/s12918-014-0110-6

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics
journal, June 2013

  • McGibbon, Robert T.; Pande, Vijay S.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 7
  • DOI: 10.1021/ct400132h

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
journal, March 2015

Systems biology of host-microbe metabolomics: Host-microbe metabolomics
journal, April 2015

  • Heinken, Almut; Thiele, Ines
  • Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 7, Issue 4
  • DOI: 10.1002/wsbm.1301

Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica
journal, March 2016

  • Kerkhoven, Eduard J.; Pomraning, Kyle R.; Baker, Scott E.
  • npj Systems Biology and Applications, Vol. 2, Issue 1
  • DOI: 10.1038/npjsba.2016.5

Salivary Biomarkers: Toward Future Clinical and Diagnostic Utilities
journal, October 2013

  • Yoshizawa, J. M.; Schafer, C. A.; Schafer, J. J.
  • Clinical Microbiology Reviews, Vol. 26, Issue 4
  • DOI: 10.1128/CMR.00021-13

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
journal, January 2014

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
journal, July 2016

  • Wagner, Maggie R.; Lundberg, Derek S.; del Rio, Tijana G.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12151

High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

  • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1672

Bacteriophages and dairy fermentations
journal, July 2012

  • Marcó, Mariángeles Briggiler; Moineau, Sylvain; Quiberoni, Andrea
  • Bacteriophage, Vol. 2, Issue 3
  • DOI: 10.4161/bact.21868

A decade of metaproteomics: Where we stand and what the future holds: PROTEOMICS
journal, September 2015

  • Wilmes, Paul; Heintz-Buschart, Anna; Bond, Philip L.
  • PROTEOMICS, Vol. 15, Issue 20
  • DOI: 10.1002/pmic.201500183

Plant Succession: Life History and Competition
journal, August 1987

  • Huston, Michael; Smith, Thomas
  • The American Naturalist, Vol. 130, Issue 2
  • DOI: 10.1086/284704

Investigating the utility of human melanoma cell lines as tumour models
journal, January 2017

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

  • Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dion
  • Standards in Genomic Sciences, Vol. 3, Issue 3
  • DOI: 10.4056/sigs.1433550

Signaling in Host-Associated Microbial Communities
journal, March 2016

Metabolomic biomarkers as strong correlates of Parkinson disease progression
journal, February 2017

Correlation of mRNA and protein in complex biological samples
journal, October 2009

The Microbiome and Human Biology
journal, August 2017

Unraveling interactions in microbial communities - from co-cultures to microbiomes
journal, May 2015

Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis
journal, June 2015

  • Zielinski, Daniel C.; Filipp, Fabian V.; Bordbar, Aarash
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms8101

Fecal microbiota transplantation: in perspective
journal, October 2015

  • Gupta, Shaan; Allen-Vercoe, Emma; Petrof, Elaine O.
  • Therapeutic Advances in Gastroenterology, Vol. 9, Issue 2
  • DOI: 10.1177/1756283X15607414

The intestinal microbiome of the pig
journal, June 2012

A road map for the development of community systems (CoSy) biology
journal, March 2012

  • Zengler, Karsten; Palsson, Bernhard O.
  • Nature Reviews Microbiology, Vol. 10, Issue 5
  • DOI: 10.1038/nrmicro2763

Transcriptional interactions suggest niche segregation among microorganisms in the human gut
journal, August 2016

  • Plichta, Damian Rafal; Juncker, Agnieszka Sierakowska; Bertalan, Marcelo
  • Nature Microbiology, Vol. 1, Issue 11
  • DOI: 10.1038/nmicrobiol.2016.152

Reconstruction of genome-scale human metabolic models using omics data
journal, March 2015

  • Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup
  • Integrative Biology, Vol. 7, Issue 8
  • DOI: 10.1039/C5IB00002E

Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer
journal, February 2013

  • Dutilh, Bas E.; Backus, Lennart; van Hijum, Sacha A. F. T.
  • Best Practice & Research Clinical Gastroenterology, Vol. 27, Issue 1
  • DOI: 10.1016/j.bpg.2013.03.008

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling
journal, April 2015

  • Franzosa, Eric A.; Hsu, Tiffany; Sirota-Madi, Alexandra
  • Nature Reviews Microbiology, Vol. 13, Issue 6
  • DOI: 10.1038/nrmicro3451

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
journal, July 1995

In silico method for modelling metabolism and gene product expression at genome scale
journal, January 2012

  • Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem
  • Nature Communications, Vol. 3, Issue 1
  • DOI: 10.1038/ncomms1928

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli
journal, February 2014

  • Guimaraes, Joao C.; Rocha, Miguel; Arkin, Adam P.
  • Nucleic Acids Research, Vol. 42, Issue 8
  • DOI: 10.1093/nar/gku126

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota
journal, May 2017

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis
journal, February 2017

  • Nakatsuji, Teruaki; Chen, Tiffany H.; Narala, Saisindhu
  • Science Translational Medicine, Vol. 9, Issue 378
  • DOI: 10.1126/scitranslmed.aah4680

The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
journal, May 2000

  • Edwards, J. S.; Palsson, B. O.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 10
  • DOI: 10.1073/pnas.97.10.5528

Learning to Predict Chemical Reactions
journal, August 2011

  • Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.
  • Journal of Chemical Information and Modeling, Vol. 51, Issue 9
  • DOI: 10.1021/ci200207y

Adapting Koch's postulates
journal, January 2016

Prey bacteria shape the community structure of their predators
journal, February 2011

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
journal, August 2014

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics
journal, June 2017

  • Gibson, Glenn R.; Hutkins, Robert; Sanders, Mary Ellen
  • Nature Reviews Gastroenterology & Hepatology, Vol. 14, Issue 8
  • DOI: 10.1038/nrgastro.2017.75

Understanding the interactions between bacteria in the human gut through metabolic modeling
journal, August 2013

  • Shoaie, Saeed; Karlsson, Fredrik; Mardinoglu, Adil
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep02532

The role of bacterial outer membrane vesicles for intra- and interspecies delivery: Delivery of membrane vesicles
journal, December 2012

Modeling growth, lipid accumulation and lipid turnover in submerged batch cultures of Umbelopsis isabellina
journal, September 2011

  • Meeuwse, Petra; Akbari, Payman; Tramper, Johannes
  • Bioprocess and Biosystems Engineering, Vol. 35, Issue 4
  • DOI: 10.1007/s00449-011-0632-x

Antibiotic discovery is a walk in the park
journal, December 2016

  • Nothias, Louis-Félix; Knight, Rob; Dorrestein, Pieter C.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 51
  • DOI: 10.1073/pnas.1618221114

A cybernetic view of microbial growth: Modeling of cells as optimal strategists
journal, January 1985

  • Dhurjati, P.; Ramkrishna, D.; Flickinger, M. C.
  • Biotechnology and Bioengineering, Vol. 27, Issue 1
  • DOI: 10.1002/bit.260270102

The gut microbiota modulates host amino acid and glutathione metabolism in mice
journal, October 2015

  • Mardinoglu, Adil; Shoaie, Saeed; Bergentall, Mattias
  • Molecular Systems Biology, Vol. 11, Issue 10
  • DOI: 10.15252/msb.20156487

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
journal, March 2016

Dynamics of Predator-Prey Interactions in Continuous Cultures
journal, April 2005

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
journal, December 2011

  • Greenblum, S.; Turnbaugh, P. J.; Borenstein, E.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 2
  • DOI: 10.1073/pnas.1116053109

Metabolic network modeling of microbial communities: Metabolic network modeling
journal, June 2015

  • Biggs, Matthew B.; Medlock, Gregory L.; Kolling, Glynis L.
  • Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 7, Issue 5
  • DOI: 10.1002/wsbm.1308

Vitamin B 12 modulates the transcriptome of the skin microbiota in acne pathogenesis
journal, June 2015

Maintenance affects the stability of a two-tiered microbial ‘food chain’?
journal, May 2011

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
journal, October 1985

  • Lane, D. J.; Pace, B.; Olsen, G. J.
  • Proceedings of the National Academy of Sciences, Vol. 82, Issue 20
  • DOI: 10.1073/pnas.82.20.6955

The virus as metabolic engineer
journal, July 2010

  • Maynard, Nathaniel D.; Gutschow, Miriam V.; Birch, Elsa W.
  • Biotechnology Journal, Vol. 5, Issue 7
  • DOI: 10.1002/biot.201000080

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease
journal, April 2011

  • Wang, Zeneng; Klipfell, Elizabeth; Bennett, Brian J.
  • Nature, Vol. 472, Issue 7341
  • DOI: 10.1038/nature09922

Decoupling function and taxonomy in the global ocean microbiome
journal, September 2016

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
journal, June 2012

Characterizing complex reaction mechanisms using machine learning clustering techniques
journal, January 2003

  • Blurock, Edward S.
  • International Journal of Chemical Kinetics, Vol. 36, Issue 2
  • DOI: 10.1002/kin.10179

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
journal, March 2009

  • Mahowald, M. A.; Rey, F. E.; Seedorf, H.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 14
  • DOI: 10.1073/pnas.0901529106

Personalized nutrition through big data
journal, February 2016

  • McDonald, Daniel; Glusman, Gustavo; Price, Nathan D.
  • Nature Biotechnology, Vol. 34, Issue 2
  • DOI: 10.1038/nbt.3476

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
journal, August 2016

  • Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V.
  • Nature Biotechnology, Vol. 34, Issue 8
  • DOI: 10.1038/nbt.3597

Microbial Interactions in Food Fermentations
journal, February 2013

On enhancing productivity of bioethanol with multiple species
journal, January 2012

  • Geng, Jun; Song, Hyun-Seob; Yuan, Jingqi
  • Biotechnology and Bioengineering, Vol. 109, Issue 6
  • DOI: 10.1002/bit.24419

Abiotic Gas Formation Drives Nitrogen Loss from a Desert Ecosystem
journal, November 2009

Gut Microbiota in Health and Disease
journal, July 2010

  • Sekirov, Inna; Russell, Shannon L.; Antunes, L. Caetano M.
  • Physiological Reviews, Vol. 90, Issue 3
  • DOI: 10.1152/physrev.00045.2009

The rhizosphere microbiome and plant health
journal, August 2012

  • Berendsen, Roeland L.; Pieterse, Corné M. J.; Bakker, Peter A. H. M.
  • Trends in Plant Science, Vol. 17, Issue 8
  • DOI: 10.1016/j.tplants.2012.04.001

Transplantation of human skin microbiota in models of atopic dermatitis
journal, July 2016

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems
journal, May 2016

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
journal, August 2015

Microbial communities associated with plants: learning from nature to apply it in agriculture
journal, June 2017

  • Andreote, Fernando Dini; Pereira e. Silva, Michele de Cássia
  • Current Opinion in Microbiology, Vol. 37
  • DOI: 10.1016/j.mib.2017.03.011

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
journal, June 2016

  • Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 26
  • DOI: 10.1073/pnas.1523199113

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community
journal, July 2015

  • Hamilton, Joshua J.; Calixto Contreras, Montserrat; Reed, Jennifer L.
  • PLOS Computational Biology, Vol. 11, Issue 7
  • DOI: 10.1371/journal.pcbi.1004364

From next-generation sequencing to systematic modeling of the gut microbiome
journal, June 2015

The Infant Gut Microbiome: Evidence for Obesity Risk and Dietary Intervention
journal, March 2015

  • Koleva, Petya; Bridgman, Sarah; Kozyrskyj, Anita
  • Nutrients, Vol. 7, Issue 4
  • DOI: 10.3390/nu7042237

Linking modern coexistence theory and contemporary niche theory
journal, February 2017

  • Letten, Andrew D.; Ke, Po-Ju; Fukami, Tadashi
  • Ecological Monographs, Vol. 87, Issue 2
  • DOI: 10.1002/ecm.1242

Metabolomics for clinical use and research in chronic kidney disease
journal, March 2017

The Virome in Host Health and Disease
journal, May 2015

Archaea in coastal marine environments.
journal, June 1992

Metatranscriptomics of the Human Oral Microbiome during Health and Disease
journal, February 2014

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008

Recon 2.2: from reconstruction to model of human metabolism
journal, June 2016

Nonlinear Dynamics of a Controlled Stirred Tank Bioreactor With Predator-Prey Relationship
journal, September 2014

  • Tabiś, Bolesław; Skoneczny, Szymon; Stryjewski, Wojciech S.
  • Chemical and Process Engineering, Vol. 35, Issue 3
  • DOI: 10.2478/cpe-2014-0026

A simple biofilm model of bacterial competition for attached surface
journal, February 2002

Medicines from microbiota
journal, April 2013

Integrated analysis of root microbiomes of soybean and wheat from agricultural fields
journal, June 2016

  • Rascovan, Nicolás; Carbonetto, Belén; Perrig, Diego
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep28084

Control and Regulation of Mitochondrial Energetics in an Integrated Model of Cardiomyocyte Function
journal, March 2009

Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles
journal, May 2016

  • Zampieri, Elisa; Chiapello, Marco; Daghino, Stefania
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep25773

Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel
journal, September 2016

  • Cremer, Jonas; Segota, Igor; Yang, Chih-yu
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 41
  • DOI: 10.1073/pnas.1601306113

Rational identification of diet-derived postbiotics for improving intestinal microbiota function
journal, April 2014

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
journal, March 2016

Pathogen-mediated manipulation of arthropod microbiota to promote infection
journal, January 2017

  • Abraham, Nabil M.; Liu, Lei; Jutras, Brandon Lyon
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 5
  • DOI: 10.1073/pnas.1613422114

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.