DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The social network of microorganisms — how auxotrophies shape complex communities

Abstract

Microorganisms engage in complex interactions with other organisms and their environment. Recent studies have shown that these interactions are not limited to the exchange of electron donors. Most microorganisms are auxotrophs, thus relying on external nutrients for growth, including the exchange of amino acids and vitamins. Currently, we lack a deeper understanding of auxotrophies in microorganisms and how nutrient requirements differ between different strains and different environments. In this Opinion article, we describe how the study of auxotrophies and nutrient requirements among members of complex communities will enable new insights into community composition and assembly. Furthermore, understanding this complex network over space and time is crucial for developing strategies to interrogate and shape microbial communities.

Authors:
ORCiD logo [1];  [1]
  1. Univ. of California, San Diego, CA (United States)
Publication Date:
Research Org.:
Johns Hopkins Univ., Baltimore, MD (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE)
OSTI Identifier:
1485597
Grant/Contract Number:  
SC0012658
Resource Type:
Accepted Manuscript
Journal Name:
Nature Reviews Microbiology
Additional Journal Information:
Journal Volume: 16; Journal Issue: 6; Journal ID: ISSN 1740-1526
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zengler, Karsten, and Zaramela, Livia S. The social network of microorganisms — how auxotrophies shape complex communities. United States: N. p., 2018. Web. doi:10.1038/s41579-018-0004-5.
Zengler, Karsten, & Zaramela, Livia S. The social network of microorganisms — how auxotrophies shape complex communities. United States. https://doi.org/10.1038/s41579-018-0004-5
Zengler, Karsten, and Zaramela, Livia S. Thu . "The social network of microorganisms — how auxotrophies shape complex communities". United States. https://doi.org/10.1038/s41579-018-0004-5. https://www.osti.gov/servlets/purl/1485597.
@article{osti_1485597,
title = {The social network of microorganisms — how auxotrophies shape complex communities},
author = {Zengler, Karsten and Zaramela, Livia S.},
abstractNote = {Microorganisms engage in complex interactions with other organisms and their environment. Recent studies have shown that these interactions are not limited to the exchange of electron donors. Most microorganisms are auxotrophs, thus relying on external nutrients for growth, including the exchange of amino acids and vitamins. Currently, we lack a deeper understanding of auxotrophies in microorganisms and how nutrient requirements differ between different strains and different environments. In this Opinion article, we describe how the study of auxotrophies and nutrient requirements among members of complex communities will enable new insights into community composition and assembly. Furthermore, understanding this complex network over space and time is crucial for developing strategies to interrogate and shape microbial communities.},
doi = {10.1038/s41579-018-0004-5},
journal = {Nature Reviews Microbiology},
number = 6,
volume = 16,
place = {United States},
year = {Thu Mar 29 00:00:00 EDT 2018},
month = {Thu Mar 29 00:00:00 EDT 2018}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 165 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Temporal Dynamics of the Human Vaginal Microbiota
journal, May 2012


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

Sewage Treatment with Anammox
journal, May 2010


Clostridium difficile Is an Autotrophic Bacterial Pathogen
journal, April 2013


Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts
journal, July 2009


Agent‐based models in translational systems biology
journal, September 2009

  • An, Gary; Mi, Qi; Dutta‐Moscato, Joyeeta
  • Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 1, Issue 2
  • DOI: 10.1002/wsbm.45

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism
journal, August 2016


The resilience of the intestinal microbiota influences health and disease
journal, June 2017

  • Sommer, Felix; Anderson, Jacqueline Moltzau; Bharti, Richa
  • Nature Reviews Microbiology, Vol. 15, Issue 10
  • DOI: 10.1038/nrmicro.2017.58

Metabolism of Fructooligosaccharides by Lactobacillus paracasei 1195
journal, April 2003


Bacillus anthracis Overcomes an Amino Acid Auxotrophy by Cleaving Host Serum Proteins
journal, May 2015

  • Terwilliger, Austen; Swick, Michelle C.; Pflughoeft, Kathryn J.
  • Journal of Bacteriology, Vol. 197, Issue 14
  • DOI: 10.1128/JB.00073-15

The gut microbiome in human immunodeficiency virus infection
journal, June 2016


Functional mining of transporters using synthetic selections
journal, October 2016

  • Genee, Hans J.; Bali, Anne P.; Petersen, Søren D.
  • Nature Chemical Biology, Vol. 12, Issue 12
  • DOI: 10.1038/nchembio.2189

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis
journal, July 2017


Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
journal, August 2017


Nutrient cross-feeding in the microbial world
journal, July 2014


The Traveling Microbiome
journal, July 2016


Evolutionary adaptations of biofilms infecting cystic fibrosis lungs promote mechanical toughness by adjusting polysaccharide production
journal, January 2017

  • Kovach, Kristin; Davis-Fields, Megan; Irie, Yasuhiko
  • npj Biofilms and Microbiomes, Vol. 3, Issue 1
  • DOI: 10.1038/s41522-016-0007-9

Ecological Resilience—In Theory and Application
journal, November 2000


Bacterial amino acid transport proteins: occurrence, functions, and significance for biotechnological applications
journal, March 2002


Short Peptide Induces an "Uncultivable" Microorganism To Grow In Vitro
journal, May 2008

  • Nichols, D.; Lewis, K.; Orjala, J.
  • Applied and Environmental Microbiology, Vol. 74, Issue 15
  • DOI: 10.1128/AEM.00393-08

Model-driven discovery of underground metabolic functions in Escherichia coli
journal, January 2015

  • Guzmán, Gabriela I.; Utrilla, José; Nurk, Sergey
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 3
  • DOI: 10.1073/pnas.1414218112

The Human Microbiome Project
journal, October 2007

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

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


Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris
journal, September 2017

  • Zuñiga, Cristal; Levering, Jennifer; Antoniewicz, Maciek R.
  • Plant Physiology, Vol. 176, Issue 1
  • DOI: 10.1104/pp.17.00605

The Role of Microbial Amino Acid Metabolism in Host Metabolism
journal, April 2015

  • Neis, Evelien; Dejong, Cornelis; Rensen, Sander
  • Nutrients, Vol. 7, Issue 4
  • DOI: 10.3390/nu7042930

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review
journal, October 2014

  • Song, Hyun-Seob; Cannon, William; Beliaev, Alexander
  • Processes, Vol. 2, Issue 4
  • DOI: 10.3390/pr2040711

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


Engineering ecosystems and synthetic ecologies
journal, January 2012

  • Mee, Michael T.; Wang, Harris H.
  • Molecular BioSystems, Vol. 8, Issue 10
  • DOI: 10.1039/c2mb25133g

Quantifying the effects of the division of labor in metabolic pathways
journal, November 2014


The last generation of bacterial growth in limiting nutrient
journal, January 2013


Biofilms promote altruism
journal, August 2004


Bacterial colonization factors control specificity and stability of the gut microbiota
journal, August 2013

  • Lee, S. Melanie; Donaldson, Gregory P.; Mikulski, Zbigniew
  • Nature, Vol. 501, Issue 7467
  • DOI: 10.1038/nature12447

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

IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1044

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

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities
journal, February 2017

  • Romine, Margaret F.; Rodionov, Dmitry A.; Maezato, Yukari
  • The ISME Journal, Vol. 11, Issue 6
  • DOI: 10.1038/ismej.2017.2

Mapping the ecological networks of microbial communities
journal, December 2017


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


Metabolic network analysis reveals microbial community interactions in anammox granules
journal, May 2017

  • Lawson, Christopher E.; Wu, Sha; Bhattacharjee, Ananda S.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms15416

Adapting Koch's postulates
journal, January 2016


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

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut
journal, October 2011


An insider's perspective: Bacteroides as a window into the microbiome
journal, April 2017


Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities
journal, October 2008


Spatial Structure and Interspecific Cooperation: Theory and an Empirical Test Using the Mycorrhizal Mutualism
journal, May 2012

  • Verbruggen, Erik; El Mouden, Claire; Jansa, Jan
  • The American Naturalist, Vol. 179, Issue 5
  • DOI: 10.1086/665032

Synthetic cooperation in engineered yeast populations
journal, January 2007

  • Shou, W.; Ram, S.; Vilar, J. M. G.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 6
  • DOI: 10.1073/pnas.0610575104

Moving pictures of the human microbiome
journal, January 2011

  • Caporaso, J. Gregory; Lauber, Christian L.; Costello, Elizabeth K.
  • Genome Biology, Vol. 12, Issue 5
  • DOI: 10.1186/gb-2011-12-5-r50

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations
journal, December 2016


Dietary trehalose enhances virulence of epidemic Clostridium difficile
journal, January 2018


A Novel Class of Modular Transporters for Vitamins in Prokaryotes
journal, October 2008

  • Rodionov, D. A.; Hebbeln, P.; Eudes, A.
  • Journal of Bacteriology, Vol. 191, Issue 1
  • DOI: 10.1128/JB.01208-08

Metabolic niche of a prominent sulfate-reducing human gut bacterium
journal, July 2013

  • Rey, F. E.; Gonzalez, M. D.; Cheng, J.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 33
  • DOI: 10.1073/pnas.1312524110

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

Elucidation of complexity and prediction of interactions in microbial communities
journal, August 2017

  • Zuñiga, Cristal; Zaramela, Livia; Zengler, Karsten
  • Microbial Biotechnology, Vol. 10, Issue 6
  • DOI: 10.1111/1751-7915.12855

Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics
journal, January 2017

  • Lopez-Siles, Mireia; Duncan, Sylvia H.; Garcia-Gil, L. Jesús
  • The ISME Journal, Vol. 11, Issue 4
  • DOI: 10.1038/ismej.2016.176

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

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the C hloroflexi phylum : B-vitamin biosynthesis and transport in
journal, December 2014

  • Rodionova, Irina A.; Li, Xiaoqing; Plymale, Andrew E.
  • Environmental Microbiology Reports, Vol. 7, Issue 2
  • DOI: 10.1111/1758-2229.12227

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

Lactic acid bacteria as a cell factory for riboflavin production
journal, December 2015

  • Thakur, Kiran; Tomar, Sudhir Kumar; De, Sachinandan
  • Microbial Biotechnology, Vol. 9, Issue 4
  • DOI: 10.1111/1751-7915.12335

Ubiquinone deficiency in an auxotroph of Escherichia coli requiring 4-hydroxybenzoic acid
journal, June 1967


The evolution of cooperation within the gut microbiota
journal, April 2016

  • Rakoff-Nahoum, Seth; Foster, Kevin R.; Comstock, Laurie E.
  • Nature, Vol. 533, Issue 7602
  • DOI: 10.1038/nature17626

The ecology of the microbiome: Networks, competition, and stability
journal, November 2015


Nonlinear partial differential equations and applications: Cultivating the uncultured
journal, November 2002

  • Zengler, K.; Toledo, G.; Rappe, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 24
  • DOI: 10.1073/pnas.252630999

Harnessing the landscape of microbial culture media to predict new organism–media pairings
journal, October 2015

  • Oberhardt, Matthew A.; Zarecki, Raphy; Gronow, Sabine
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9493

Persistent microbiome alterations modulate the rate of post-dieting weight regain
journal, November 2016

  • Thaiss, Christoph A.; Itav, Shlomik; Rothschild, Daphna
  • Nature, Vol. 540, Issue 7634
  • DOI: 10.1038/nature20796

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

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


Genome-scale models of bacterial metabolism: reconstruction and applications
journal, January 2009


Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut
journal, January 2014


The human gut microbiome in health: establishment and resilience of microbiota over a lifetime: The human gut microbiome in health
journal, July 2016

  • Greenhalgh, Kacy; Meyer, Kristen M.; Aagaard, Kjersti M.
  • Environmental Microbiology, Vol. 18, Issue 7
  • DOI: 10.1111/1462-2920.13318

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

The Genotypic View of Social Interactions in Microbial Communities
journal, November 2013


Metabolic capability and in situ activity of microorganisms in an oil reservoir
journal, January 2018

  • Liu, Yi-Fan; Galzerani, Daniela Domingos; Mbadinga, Serge Maurice
  • Microbiome, Vol. 6, Issue 1
  • DOI: 10.1186/s40168-017-0392-1

Metabolic costs of amino acid and protein production in Escherichia coli
journal, July 2013

  • Kaleta, Christoph; Schäuble, Sascha; Rinas, Ursula
  • Biotechnology Journal, Vol. 8, Issue 9
  • DOI: 10.1002/biot.201200267

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
journal, September 2017

  • Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria
  • Nature Microbiology, Vol. 2, Issue 11
  • DOI: 10.1038/s41564-017-0012-7

Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis
journal, June 2006

  • Heizer, Esley M.; Raiford, Douglas W.; Raymer, Michael L.
  • Molecular Biology and Evolution, Vol. 23, Issue 9
  • DOI: 10.1093/molbev/msl029

Collect reliable data on embryo selection
journal, November 2017


Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism
journal, January 2015

  • Cuskin, Fiona; Lowe, Elisabeth C.; Temple, Max J.
  • Nature, Vol. 517, Issue 7533
  • DOI: 10.1038/nature13995

Identification and quantitation of cobalamin and cobalamin analogues in human feces
journal, May 2008

  • Allen, Robert H.; Stabler, Sally P.
  • The American Journal of Clinical Nutrition, Vol. 87, Issue 5
  • DOI: 10.1093/ajcn/87.5.1324

Diet-induced extinctions in the gut microbiota compound over generations
journal, January 2016

  • Sonnenburg, Erica D.; Smits, Samuel A.; Tikhonov, Mikhail
  • Nature, Vol. 529, Issue 7585
  • DOI: 10.1038/nature16504

How bacterial pathogens colonize their hosts and invade deeper tissues
journal, March 2015


Algae acquire vitamin B12 through a symbiotic relationship with bacteria
journal, November 2005

  • Croft, Martin T.; Lawrence, Andrew D.; Raux-Deery, Evelyne
  • Nature, Vol. 438, Issue 7064
  • DOI: 10.1038/nature04056

Experimental design and quantitative analysis of microbial community multiomics
journal, November 2017


The association between vaginal microbiota and female infertility: a systematic review and meta-analysis
journal, July 2020


Algae acquire Vitamin B12 through a symbiotic relationship with bacteria
journal, April 2007

  • Hodson, S.; Croft, M.; Deery, E.
  • Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, Vol. 146, Issue 4
  • DOI: 10.1016/j.cbpa.2007.01.489

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

  • M., Waters, Katrina; Yao, Peng,; L., McPhail, Kerry
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/dd92-mf79

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
text, January 2016


Works referencing / citing this record:

Nanocatalytic Medicine
journal, July 2019


Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization
journal, July 2019


Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments
journal, November 2018


Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates
journal, September 2019

  • Zaramela, Livia S.; Martino, Cameron; Alisson-Silva, Frederico
  • Nature Microbiology, Vol. 4, Issue 12
  • DOI: 10.1038/s41564-019-0564-9

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities
journal, October 2019


Common principles and best practices for engineering microbiomes
journal, September 2019

  • Lawson, Christopher E.; Harcombe, William R.; Hatzenpichler, Roland
  • Nature Reviews Microbiology, Vol. 17, Issue 12
  • DOI: 10.1038/s41579-019-0255-9

Ecological drivers of bacterial community assembly in synthetic phycospheres
journal, February 2020

  • Fu, He; Uchimiya, Mario; Gore, Jeff
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 7
  • DOI: 10.1073/pnas.1917265117

Can dynamic network modelling be used to identify adaptive microbiomes?
journal, December 2019


Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism
journal, October 2018

  • Hidalgo‐Ahumada, Catalina A. P.; Nobu, Masaru K.; Narihiro, Takashi
  • Environmental Microbiology, Vol. 20, Issue 12
  • DOI: 10.1111/1462-2920.14388

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes
journal, September 2019

  • Goberna, Marta; Montesinos‐Navarro, Alicia; Valiente‐Banuet, Alfonso
  • Molecular Ecology Resources, Vol. 19, Issue 6
  • DOI: 10.1111/1755-0998.13079

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria
journal, May 2018


Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
journal, December 2018


Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
journal, June 2019

  • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
  • eLife, Vol. 8
  • DOI: 10.7554/elife.39733

Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community
journal, June 2019

  • Hart, Samuel Frederick Mock; Pineda, Jose Mario Bello; Chen, Chi-Chun
  • eLife, Vol. 8
  • DOI: 10.7554/elife.44812

Metabolic Overlap in Environmentally Diverse Microbial Communities
journal, October 2019


Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions
journal, October 2019

  • Islam, Mohammad Mazharul; Fernando, Samodha C.; Saha, Rajib
  • Frontiers in Microbiology, Vol. 10
  • DOI: 10.3389/fmicb.2019.02412

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community
journal, August 2020


Polarization of microbial communities between competitive and cooperative metabolism
journal, January 2021

  • Machado, Daniel; Maistrenko, Oleksandr M.; Andrejev, Sergej
  • Nature Ecology & Evolution, Vol. 5, Issue 2
  • DOI: 10.1038/s41559-020-01353-4

Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria
text, January 2019


Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology
journal, February 2019


Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments
journal, November 2018


Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates
journal, September 2019

  • Zaramela, Livia S.; Martino, Cameron; Alisson-Silva, Frederico
  • Nature Microbiology, Vol. 4, Issue 12
  • DOI: 10.1038/s41564-019-0564-9

Dynamics of ColicinE2 production and release determine the competitive success of a toxin-producing bacterial population
journal, March 2020


Ecological drivers of bacterial community assembly in synthetic phycospheres
journal, February 2020

  • Fu, He; Uchimiya, Mario; Gore, Jeff
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 7
  • DOI: 10.1073/pnas.1917265117

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism
journal, October 2018

  • Hidalgo‐Ahumada, Catalina A. P.; Nobu, Masaru K.; Narihiro, Takashi
  • Environmental Microbiology, Vol. 20, Issue 12
  • DOI: 10.1111/1462-2920.14388

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria
journal, May 2018


Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
journal, December 2018


Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells
journal, February 2019


The genetic basis for adaptation of model-designed syntrophic co-cultures
journal, March 2019


Core Gut Bacteria Analysis of Healthy Mice
journal, April 2019


Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions
journal, October 2019

  • Islam, Mohammad Mazharul; Fernando, Samodha C.; Saha, Rajib
  • Frontiers in Microbiology, Vol. 10
  • DOI: 10.3389/fmicb.2019.02412

Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities
journal, February 2019


A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium
text, January 2020


The advantage of leakage of essential metabolites and resultant symbiosis of diverse species
text, January 2018


Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
journal, June 2019

  • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
  • eLife, Vol. 8
  • DOI: 10.7554/elife.39733