The social network of microorganisms — how auxotrophies shape complex communities

Zengler, Karsten; Zaramela, Livia S.

doi:10.1038/s41579-018-0004-5

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

Journal Article · 28 March 2018 · Nature Reviews Microbiology

DOI: https://doi.org/10.1038/s41579-018-0004-5 · OSTI ID:1485597

^[1]; Zaramela, Livia S. ^[2]

Univ. of California, San Diego, CA (United States); University of California, San Diego
Univ. of California, San Diego, CA (United States)

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Johns Hopkins Univ., Baltimore, MD (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: SC0012658

OSTI ID:: 1485597

Journal Information:: Nature Reviews Microbiology, Journal Name: Nature Reviews Microbiology Journal Issue: 6 Vol. 16; ISSN 1740-1526

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (92)

Metabolic costs of amino acid and protein production in Escherichia coli Kaleta, Christoph; Schäuble, Sascha; Rinas, Ursula Biotechnology Journal, Vol. 8, Issue 9 https://doi.org/10.1002/biot.201200267	journal	July 2013
Agent‐based models in translational systems biology An, Gary; Mi, Qi; Dutta‐Moscato, Joyeeta Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 1, Issue 2 https://doi.org/10.1002/wsbm.45	journal	September 2009
Family Propionibacteriaceae: The Genus Propionibacterium Stackebrandt, Erko; Cummins, Cecil S.; Johnson, John L. The Prokaryotes https://doi.org/10.1007/0-387-30743-5_19	book	January 2006
Bacterial amino acid transport proteins: occurrence, functions, and significance for biotechnological applications Krämer, A. Burkovski, R. Applied Microbiology and Biotechnology, Vol. 58, Issue 3 https://doi.org/10.1007/s00253-001-0869-4	journal	March 2002
The association between vaginal microbiota and female infertility: a systematic review and meta-analysis Hong, Xiang; Ma, Jun; Yin, Jiechen Archives of Gynecology and Obstetrics, Vol. 302, Issue 3 https://doi.org/10.1007/s00404-020-05675-3	journal	July 2020
The Traveling Microbiome Riddle, Mark S.; Connor, Bradley A. Current Infectious Disease Reports, Vol. 18, Issue 9 https://doi.org/10.1007/s11908-016-0536-7	journal	July 2016
Unraveling interactions in microbial communities - from co-cultures to microbiomes Tan, Justin; Zuniga, Cristal; Zengler, Karsten Journal of Microbiology, Vol. 53, Issue 5 https://doi.org/10.1007/s12275-015-5060-1	journal	May 2015
Elemental Economy Merchant, Sabeeha S.; Helmann, John D. Advances in Microbial Physiology https://doi.org/10.1016/B978-0-12-398264-3.00002-4	book	January 2012
Sequential batch thermophilic solid-state anaerobic digestion of lignocellulosic biomass via recirculating digestate as inoculum – Part II: Microbial diversity and succession Lin, Long; Yu, Zhongtang; Li, Yebo Bioresource Technology, Vol. 241 https://doi.org/10.1016/j.biortech.2017.06.011	journal	October 2017
Algae acquire Vitamin B12 through a symbiotic relationship with bacteria Hodson, S.; Croft, M.; Deery, E. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, Vol. 146, Issue 4 https://doi.org/10.1016/j.cbpa.2007.01.489	journal	April 2007
Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations Thaiss, Christoph A.; Levy, Maayan; Korem, Tal Cell, Vol. 167, Issue 6 https://doi.org/10.1016/j.cell.2016.11.003	journal	December 2016
Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut Fischbach, Michael A.; Sonnenburg, Justin L. Cell Host & Microbe, Vol. 10, Issue 4 https://doi.org/10.1016/j.chom.2011.10.002	journal	October 2011
Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut Degnan, Patrick H.; Barry, Natasha A.; Mok, Kenny C. Cell Host & Microbe, Vol. 15, Issue 1 https://doi.org/10.1016/j.chom.2013.12.007	journal	January 2014
Vitamin B 12 as a Modulator of Gut Microbial Ecology Degnan, Patrick H.; Taga, Michiko E.; Goodman, Andrew L. Cell Metabolism, Vol. 20, Issue 5 https://doi.org/10.1016/j.cmet.2014.10.002	journal	November 2014
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome Shoaie, Saeed; Ghaffari, Pouyan; Kovatcheva-Datchary, Petia Cell Metabolism, Vol. 22, Issue 2 https://doi.org/10.1016/j.cmet.2015.07.001	journal	August 2015
Quantifying the effects of the division of labor in metabolic pathways Harvey, Emily; Heys, Jeffrey; Gedeon, Tomáš Journal of Theoretical Biology, Vol. 360 https://doi.org/10.1016/j.jtbi.2014.07.011	journal	November 2014
Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts Yu, Xue-Jie; Walker, David H.; Liu, Yan Infection, Genetics and Evolution, Vol. 9, Issue 4 https://doi.org/10.1016/j.meegid.2009.02.002	journal	July 2009
How bacterial pathogens colonize their hosts and invade deeper tissues Ribet, David; Cossart, Pascale Microbes and Infection, Vol. 17, Issue 3 https://doi.org/10.1016/j.micinf.2015.01.004	journal	March 2015
Collect reliable data on embryo selection Thompson, Charis Nature, Vol. 551, Issue 7678 https://doi.org/10.1038/551033a	journal	November 2017
Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics Lopez-Siles, Mireia; Duncan, Sylvia H.; Garcia-Gil, L. Jesús The ISME Journal, Vol. 11, Issue 4 https://doi.org/10.1038/ismej.2016.176	journal	January 2017
Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities Romine, Margaret F.; Rodionov, Dmitry A.; Maezato, Yukari The ISME Journal, Vol. 11, Issue 6 https://doi.org/10.1038/ismej.2017.2	journal	February 2017
Algae acquire vitamin B12 through a symbiotic relationship with bacteria Croft, Martin T.; Lawrence, Andrew D.; Raux-Deery, Evelyne Nature, Vol. 438, Issue 7064 https://doi.org/10.1038/nature04056	journal	November 2005
The Human Microbiome Project Turnbaugh, Peter J.; Ley, Ruth E.; Hamady, Micah Nature, Vol. 449, Issue 7164 https://doi.org/10.1038/nature06244	journal	October 2007
Bacterial colonization factors control specificity and stability of the gut microbiota Lee, S. Melanie; Donaldson, Gregory P.; Mikulski, Zbigniew Nature, Vol. 501, Issue 7467 https://doi.org/10.1038/nature12447	journal	August 2013
Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism Cuskin, Fiona; Lowe, Elisabeth C.; Temple, Max J. Nature, Vol. 517, Issue 7533 https://doi.org/10.1038/nature13995	journal	January 2015
Diet-induced extinctions in the gut microbiota compound over generations Sonnenburg, Erica D.; Smits, Samuel A.; Tikhonov, Mikhail Nature, Vol. 529, Issue 7585 https://doi.org/10.1038/nature16504	journal	January 2016
The evolution of cooperation within the gut microbiota Rakoff-Nahoum, Seth; Foster, Kevin R.; Comstock, Laurie E. Nature, Vol. 533, Issue 7602 https://doi.org/10.1038/nature17626	journal	April 2016
Persistent microbiome alterations modulate the rate of post-dieting weight regain Thaiss, Christoph A.; Itav, Shlomik; Rothschild, Daphna Nature, Vol. 540, Issue 7634 https://doi.org/10.1038/nature20796	journal	November 2016
Dietary trehalose enhances virulence of epidemic Clostridium difficile Collins, J.; Robinson, C.; Danhof, H. Nature, Vol. 553, Issue 7688 https://doi.org/10.1038/nature25178	journal	January 2018
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V. Nature Biotechnology, Vol. 34, Issue 8 https://doi.org/10.1038/nbt.3597	journal	August 2016
Functional mining of transporters using synthetic selections Genee, Hans J.; Bali, Anne P.; Petersen, Søren D. Nature Chemical Biology, Vol. 12, Issue 12 https://doi.org/10.1038/nchembio.2189	journal	October 2016
Metabolic network analysis reveals microbial community interactions in anammox granules Lawson, Christopher E.; Wu, Sha; Bhattacharjee, Ananda S. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15416	journal	May 2017
Harnessing the landscape of microbial culture media to predict new organism–media pairings Oberhardt, Matthew A.; Zarecki, Raphy; Gronow, Sabine Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9493	journal	October 2015
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
An insider's perspective: Bacteroides as a window into the microbiome Wexler, Aaron G.; Goodman, Andrew L. Nature Microbiology, Vol. 2, Issue 5 https://doi.org/10.1038/nmicrobiol.2017.26	journal	April 2017
Constraint-based models predict metabolic and associated cellular functions Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A. Nature Reviews Genetics, Vol. 15, Issue 2 https://doi.org/10.1038/nrg3643	journal	January 2014
The resilience of the intestinal microbiota influences health and disease Sommer, Felix; Anderson, Jacqueline Moltzau; Bharti, Richa Nature Reviews Microbiology, Vol. 15, Issue 10 https://doi.org/10.1038/nrmicro.2017.58	journal	June 2017
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling Franzosa, Eric A.; Hsu, Tiffany; Sirota-Madi, Alexandra Nature Reviews Microbiology, Vol. 13, Issue 6 https://doi.org/10.1038/nrmicro3451	journal	April 2015
Mapping the ecological networks of microbial communities Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02090-2	journal	December 2017
Evolutionary adaptations of biofilms infecting cystic fibrosis lungs promote mechanical toughness by adjusting polysaccharide production Kovach, Kristin; Davis-Fields, Megan; Irie, Yasuhiko npj Biofilms and Microbiomes, Vol. 3, Issue 1 https://doi.org/10.1038/s41522-016-0007-9	journal	January 2017
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Engineering ecosystems and synthetic ecologies Mee, Michael T.; Wang, Harris H. Molecular BioSystems, Vol. 8, Issue 10 https://doi.org/10.1039/c2mb25133g	journal	January 2012
Ubiquinone deficiency in an auxotroph of Escherichia coli requiring 4-hydroxybenzoic acid Jones, Rgw Biochemical Journal, Vol. 103, Issue 3 https://doi.org/10.1042/bj1030714	journal	June 1967
Synthetic cooperation in engineered yeast populations Shou, W.; Ram, S.; Vilar, J. M. G. Proceedings of the National Academy of Sciences, Vol. 104, Issue 6 https://doi.org/10.1073/pnas.0610575104	journal	January 2007
Metabolic niche of a prominent sulfate-reducing human gut bacterium Rey, F. E.; Gonzalez, M. D.; Cheng, J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 33 https://doi.org/10.1073/pnas.1312524110	journal	July 2013
Syntrophic exchange in synthetic microbial communities Mee, M. T.; Collins, J. J.; Church, G. M. Proceedings of the National Academy of Sciences, Vol. 111, Issue 20 https://doi.org/10.1073/pnas.1405641111	journal	April 2014
Model-driven discovery of underground metabolic functions in Escherichia coli Guzmán, Gabriela I.; Utrilla, José; Nurk, Sergey Proceedings of the National Academy of Sciences, Vol. 112, Issue 3 https://doi.org/10.1073/pnas.1414218112	journal	January 2015
Networks of energetic and metabolic interactions define dynamics in microbial communities Embree, Mallory; Liu, Joanne K.; Al-Bassam, Mahmoud M. Proceedings of the National Academy of Sciences, Vol. 112, Issue 50 https://doi.org/10.1073/pnas.1506034112	journal	November 2015
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K. Proceedings of the National Academy of Sciences, Vol. 113, Issue 26 https://doi.org/10.1073/pnas.1523199113	journal	June 2016
Nonlinear partial differential equations and applications: Cultivating the uncultured Zengler, K.; Toledo, G.; Rappe, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 24 https://doi.org/10.1073/pnas.252630999	journal	November 2002
Spatial Structure and Interspecific Cooperation: Theory and an Empirical Test Using the Mycorrhizal Mutualism Verbruggen, Erik; El Mouden, Claire; Jansa, Jan The American Naturalist, Vol. 179, Issue 5 https://doi.org/10.1086/665032	journal	May 2012
Identification and quantitation of cobalamin and cobalamin analogues in human feces Allen, Robert H.; Stabler, Sally P. The American Journal of Clinical Nutrition, Vol. 87, Issue 5 https://doi.org/10.1093/ajcn/87.5.1324	journal	May 2008
Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis Heizer, Esley M.; Raiford, Douglas W.; Raymer, Michael L. Molecular Biology and Evolution, Vol. 23, Issue 9 https://doi.org/10.1093/molbev/msl029	journal	June 2006
IMG: the integrated microbial genomes database and comparative analysis system Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1044	journal	December 2011
Biofilms promote altruism Kreft, J. -U. Microbiology, Vol. 150, Issue 8 https://doi.org/10.1099/mic.0.26829-0	journal	August 2004
Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris Zuñiga, Cristal; Levering, Jennifer; Antoniewicz, Maciek R. Plant Physiology, Vol. 176, Issue 1 https://doi.org/10.1104/pp.17.00605	journal	September 2017
The human gut microbiome in health: establishment and resilience of microbiota over a lifetime: The human gut microbiome in health Greenhalgh, Kacy; Meyer, Kristen M.; Aagaard, Kjersti M. Environmental Microbiology, Vol. 18, Issue 7 https://doi.org/10.1111/1462-2920.13318	journal	July 2016
Microbial syntrophy: interaction for the common good Morris, Brandon E. L.; Henneberger, Ruth; Huber, Harald FEMS Microbiology Reviews, Vol. 37, Issue 3 https://doi.org/10.1111/1574-6976.12019	journal	May 2013
Lactic acid bacteria as a cell factory for riboflavin production Thakur, Kiran; Tomar, Sudhir Kumar; De, Sachinandan Microbial Biotechnology, Vol. 9, Issue 4 https://doi.org/10.1111/1751-7915.12335	journal	December 2015
Elucidation of complexity and prediction of interactions in microbial communities Zuñiga, Cristal; Zaramela, Livia; Zengler, Karsten Microbial Biotechnology, Vol. 10, Issue 6 https://doi.org/10.1111/1751-7915.12855	journal	August 2017
Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the C hloroflexi phylum : B-vitamin biosynthesis and transport in Rodionova, Irina A.; Li, Xiaoqing; Plymale, Andrew E. Environmental Microbiology Reports, Vol. 7, Issue 2 https://doi.org/10.1111/1758-2229.12227	journal	December 2014
Less is More: Selective Advantages can Explain the Prevalent loss of Biosynthetic Genes in Bacteria: Adaptive loss of Biosynthetic Genes in Bacteria D'Souza, Glen; Waschina, Silvio; Pande, Samay Evolution, Vol. 68, Issue 9 https://doi.org/10.1111/evo.12468	journal	July 2014
Genome-scale models of bacterial metabolism: reconstruction and applications Durot, Maxime; Bourguignon, Pierre-Yves; Schachter, Vincent FEMS Microbiology Reviews, Vol. 33, Issue 1 https://doi.org/10.1111/j.1574-6976.2008.00146.x	journal	January 2009
Sewage Treatment with Anammox Kartal, B.; Kuenen, J. G.; van Loosdrecht, M. C. M. Science, Vol. 328, Issue 5979 https://doi.org/10.1126/science.1185941	journal	May 2010
The ecology of the microbiome: Networks, competition, and stability Coyte, K. Z.; Schluter, J.; Foster, K. R. Science, Vol. 350, Issue 6261 https://doi.org/10.1126/science.aad2602	journal	November 2015
Adapting Koch's postulates Byrd, A. L.; Segre, J. A. Science, Vol. 351, Issue 6270 https://doi.org/10.1126/science.aad6753	journal	January 2016
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania Smits, Samuel A.; Leach, Jeff; Sonnenburg, Erica D. Science, Vol. 357, Issue 6353 https://doi.org/10.1126/science.aan4834	journal	August 2017
Temporal Dynamics of the Human Vaginal Microbiota Gajer, P.; Brotman, R. M.; Bai, G. Science Translational Medicine, Vol. 4, Issue 132 https://doi.org/10.1126/scitranslmed.3003605	journal	May 2012
Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis Nakatsuji, Teruaki; Chen, Tiffany H.; Narala, Saisindhu Science Translational Medicine, Vol. 9, Issue 378 https://doi.org/10.1126/scitranslmed.aah4680	journal	February 2017
The effects of micronutrient deficiencies on bacterial species from the human gut microbiota Hibberd, Matthew C.; Wu, Meng; Rodionov, Dmitry A. Science Translational Medicine, Vol. 9, Issue 390 https://doi.org/10.1126/scitranslmed.aal4069	journal	May 2017
Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis Byrd, Allyson L.; Deming, Clay; Cassidy, Sara K. B. Science Translational Medicine, Vol. 9, Issue 397 https://doi.org/10.1126/scitranslmed.aal4651	journal	July 2017
Short Peptide Induces an "Uncultivable" Microorganism To Grow In Vitro Nichols, D.; Lewis, K.; Orjala, J. Applied and Environmental Microbiology, Vol. 74, Issue 15 https://doi.org/10.1128/AEM.00393-08	journal	May 2008
Facilitation of Robust Growth of Prochlorococcus Colonies and Dilute Liquid Cultures by "Helper" Heterotrophic Bacteria Morris, J. J.; Kirkegaard, R.; Szul, M. J. Applied and Environmental Microbiology, Vol. 74, Issue 14 https://doi.org/10.1128/AEM.02479-07	journal	May 2008
Metabolism of Fructooligosaccharides by Lactobacillus paracasei 1195 Kaplan, H.; Hutkins, R. W. Applied and Environmental Microbiology, Vol. 69, Issue 4 https://doi.org/10.1128/AEM.69.4.2217-2222.2003	journal	April 2003
Bacillus anthracis Overcomes an Amino Acid Auxotrophy by Cleaving Host Serum Proteins Terwilliger, Austen; Swick, Michelle C.; Pflughoeft, Kathryn J. Journal of Bacteriology, Vol. 197, Issue 14 https://doi.org/10.1128/JB.00073-15	journal	May 2015
A Novel Class of Modular Transporters for Vitamins in Prokaryotes Rodionov, D. A.; Hebbeln, P.; Eudes, A. Journal of Bacteriology, Vol. 191, Issue 1 https://doi.org/10.1128/JB.01208-08	journal	October 2008
The Genotypic View of Social Interactions in Microbial Communities Mitri, Sara; Richard Foster, Kevin Annual Review of Genetics, Vol. 47, Issue 1 https://doi.org/10.1146/annurev-genet-111212-133307	journal	November 2013
Ecological Resilience—In Theory and Application Gunderson, Lance H. Annual Review of Ecology and Systematics, Vol. 31, Issue 1 https://doi.org/10.1146/annurev.ecolsys.31.1.425	journal	November 2000
Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities Little, Ainslie E. F.; Robinson, Courtney J.; Peterson, S. Brook Annual Review of Microbiology, Vol. 62, Issue 1 https://doi.org/10.1146/annurev.micro.030608.101423	journal	October 2008
The last generation of bacterial growth in limiting nutrient Bren, Anat; Hart, Yuval; Dekel, Erez BMC Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1752-0509-7-27	journal	January 2013
Moving pictures of the human microbiome Caporaso, J. Gregory; Lauber, Christian L.; Costello, Elizabeth K. Genome Biology, Vol. 12, Issue 5 https://doi.org/10.1186/gb-2011-12-5-r50	journal	January 2011
The gut microbiome in human immunodeficiency virus infection Zilberman-Schapira, Gili; Zmora, Niv; Itav, Shlomik BMC Medicine, Vol. 14, Issue 1 https://doi.org/10.1186/s12916-016-0625-3	journal	June 2016
Experimental design and quantitative analysis of microbial community multiomics Mallick, Himel; Ma, Siyuan; Franzosa, Eric A. Genome Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s13059-017-1359-z	journal	November 2017
Metabolic capability and in situ activity of microorganisms in an oil reservoir Liu, Yi-Fan; Galzerani, Daniela Domingos; Mbadinga, Serge Maurice Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-017-0392-1	journal	January 2018
Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism Hoek, Tim A.; Axelrod, Kevin; Biancalani, Tommaso PLOS Biology, Vol. 14, Issue 8 https://doi.org/10.1371/journal.pbio.1002540	journal	August 2016
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities Germerodt, Sebastian; Bohl, Katrin; Lück, Anja PLOS Computational Biology, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pcbi.1004986	journal	June 2016
Clostridium difficile Is an Autotrophic Bacterial Pathogen Köpke, Michael; Straub, Melanie; Dürre, Peter PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0062157	journal	April 2013
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking M., Waters, Katrina; Yao, Peng,; L., McPhail, Kerry The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/dd92-mf79	text	January 2016
Nutrient cross-feeding in the microbial world Seth, Erica C.; Taga, Michiko E. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00350	journal	July 2014
The Role of Microbial Amino Acid Metabolism in Host Metabolism Neis, Evelien; Dejong, Cornelis; Rensen, Sander Nutrients, Vol. 7, Issue 4 https://doi.org/10.3390/nu7042930	journal	April 2015
Mathematical Modeling of Microbial Community Dynamics: A Methodological Review Song, Hyun-Seob; Cannon, William; Beliaev, Alexander Processes, Vol. 2, Issue 4 https://doi.org/10.3390/pr2040711	journal	October 2014
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities Germerodt, Sebastian; Bohl, Katrin; Lück, Anja ETH Zurich https://doi.org/10.3929/ethz-b-000117248	text	January 2016

Cited By (42)

Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology McCarty, Nicholas S.; Ledesma-Amaro, Rodrigo Trends in Biotechnology, Vol. 37, Issue 2 https://doi.org/10.1016/j.tibtech.2018.11.002	journal	February 2019
Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments Dombrowski, Nina; Teske, Andreas P.; Baker, Brett J. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07418-0	journal	November 2018
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates Zaramela, Livia S.; Martino, Cameron; Alisson-Silva, Frederico Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0564-9	journal	September 2019
Dynamics of ColicinE2 production and release determine the competitive success of a toxin-producing bacterial population Weiß, Anna S.; Götz, Alexandra; Opitz, Madeleine Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-61086-z	journal	March 2020
Ecological drivers of bacterial community assembly in synthetic phycospheres Fu, He; Uchimiya, Mario; Gore, Jeff Proceedings of the National Academy of Sciences, Vol. 117, Issue 7 https://doi.org/10.1073/pnas.1917265117	journal	February 2020
Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism Hidalgo‐Ahumada, Catalina A. P.; Nobu, Masaru K.; Narihiro, Takashi Environmental Microbiology, Vol. 20, Issue 12 https://doi.org/10.1111/1462-2920.14388	journal	October 2018
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria Garcia, Sarahi L.; Buck, Moritz; Hamilton, Joshua J. mSphere, Vol. 3, Issue 3 https://doi.org/10.1128/msphere.00202-18	journal	May 2018
Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing Mu, Da-Shuai; Liang, Qi-Yun; Wang, Xiao-Man Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0613-2	journal	December 2018
Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells Hart, Samuel F. M.; Mi, Hanbing; Green, Robin PLOS Biology, Vol. 17, Issue 2 https://doi.org/10.1371/journal.pbio.3000135	journal	February 2019
The genetic basis for adaptation of model-designed syntrophic co-cultures Lloyd, Colton J.; King, Zachary A.; Sandberg, Troy E. PLOS Computational Biology, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pcbi.1006213	journal	March 2019
Core Gut Bacteria Analysis of Healthy Mice Wang, Jingjing; Lang, Tao; Shen, Jian Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00887	journal	April 2019
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions Islam, Mohammad Mazharul; Fernando, Samodha C.; Saha, Rajib Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02412	journal	October 2019
Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities Rodríguez Amor, Daniel; Dal Bello, Martina Life, Vol. 9, Issue 1 https://doi.org/10.3390/life9010022	journal	February 2019
A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium A., Hernandez-Valdes, Jhonatan; Jordi, van Gestel,; P., Kuipers, Oscar ETH Zurich https://doi.org/10.3929/ethz-b-000405676	text	January 2020
The advantage of leakage of essential metabolites and resultant symbiosis of diverse species Yamagishi, Jumpei F.; Saito, Nen; Kaneko, Kunihiko arXiv https://doi.org/10.48550/arxiv.1811.10172	text	January 2018
Additional file 1 of Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle Liu, Sijia; Yu, Zhongtang; Zhong, Huiyue figshare https://doi.org/10.6084/m9.figshare.22637932	dataset	January 2023
Additional file 2 of Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle Liu, Sijia; Yu, Zhongtang; Zhong, Huiyue figshare https://doi.org/10.6084/m9.figshare.22637935.v1	dataset	January 2023
Additional file 3 of Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle Liu, Sijia; Yu, Zhongtang; Zhong, Huiyue figshare https://doi.org/10.6084/m9.figshare.22637938	dataset	January 2023
Additional file 4 of Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle Liu, Sijia; Yu, Zhongtang; Zhong, Huiyue figshare https://doi.org/10.6084/m9.figshare.22637941	dataset	January 2023
Additional file 5 of Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle Liu, Sijia; Yu, Zhongtang; Zhong, Huiyue figshare https://doi.org/10.6084/m9.figshare.22637944	dataset	January 2023
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel eLife, Vol. 8 https://doi.org/10.7554/elife.39733	journal	June 2019
Nanocatalytic Medicine Yang, Bowen; Chen, Yu; Shi, Jianlin Advanced Materials, Vol. 31, Issue 39 https://doi.org/10.1002/adma.201901778	journal	July 2019
Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization Cai, Peng; Sun, Xiaojie; Wu, Yichao Soil Ecology Letters, Vol. 1, Issue 3-4 https://doi.org/10.1007/s42832-019-0017-7	journal	July 2019
Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community Fritts, Ryan K.; Bird, Jordan T.; Behringer, Megan G. The ISME Journal, Vol. 14, Issue 11 https://doi.org/10.1038/s41396-020-00737-5	journal	August 2020
Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments Dombrowski, Nina; Teske, Andreas P.; Baker, Brett J. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07418-0	journal	November 2018
Polarization of microbial communities between competitive and cooperative metabolism Machado, Daniel; Maistrenko, Oleksandr M.; Andrejev, Sergej Nature Ecology & Evolution, Vol. 5, Issue 2 https://doi.org/10.1038/s41559-020-01353-4	journal	January 2021
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates Zaramela, Livia S.; Martino, Cameron; Alisson-Silva, Frederico Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0564-9	journal	September 2019
Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities Zuñiga, Cristal; Li, Chien-Ting; Yu, Geng Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0567-6	journal	October 2019
Common principles and best practices for engineering microbiomes Lawson, Christopher E.; Harcombe, William R.; Hatzenpichler, Roland Nature Reviews Microbiology, Vol. 17, Issue 12 https://doi.org/10.1038/s41579-019-0255-9	journal	September 2019
Ecological drivers of bacterial community assembly in synthetic phycospheres Fu, He; Uchimiya, Mario; Gore, Jeff Proceedings of the National Academy of Sciences, Vol. 117, Issue 7 https://doi.org/10.1073/pnas.1917265117	journal	February 2020
Can dynamic network modelling be used to identify adaptive microbiomes? Garcia, Joshua; Kao‐Kniffin, Jenny Functional Ecology, Vol. 34, Issue 10 https://doi.org/10.1111/1365-2435.13491	journal	December 2019
Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism Hidalgo‐Ahumada, Catalina A. P.; Nobu, Masaru K.; Narihiro, Takashi Environmental Microbiology, Vol. 20, Issue 12 https://doi.org/10.1111/1462-2920.14388	journal	October 2018
Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes Goberna, Marta; Montesinos‐Navarro, Alicia; Valiente‐Banuet, Alfonso Molecular Ecology Resources, Vol. 19, Issue 6 https://doi.org/10.1111/1755-0998.13079	journal	September 2019
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria Garcia, Sarahi L.; Buck, Moritz; Hamilton, Joshua J. mSphere, Vol. 3, Issue 3 https://doi.org/10.1128/msphere.00202-18	journal	May 2018
Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing Mu, Da-Shuai; Liang, Qi-Yun; Wang, Xiao-Man Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0613-2	journal	December 2018
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics Wang, Yulin; Niu, Qigui; Zhang, Xu Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0730-6	journal	August 2019
Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss Haange, Sven-Bastiaan; Jehmlich, Nico; Krügel, Ute Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-0788-1	journal	February 2020
Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria Garcia, Sarahi L.; Buck, Moritz; Hamilton, Joshua J. Universität Potsdam https://doi.org/10.25932/publishup-42729	text	January 2019
Metabolic Overlap in Environmentally Diverse Microbial Communities Hester, Eric R.; Jetten, Mike S. M.; Welte, Cornelia U. Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00989	journal	October 2019
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions Islam, Mohammad Mazharul; Fernando, Samodha C.; Saha, Rajib Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02412	journal	October 2019
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel eLife, Vol. 8 https://doi.org/10.7554/elife.39733	journal	June 2019
Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community Hart, Samuel Frederick Mock; Pineda, Jose Mario Bello; Chen, Chi-Chun eLife, Vol. 8 https://doi.org/10.7554/elife.44812	journal	June 2019

Similar Records

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Journal Article · 2023 · Nature Communications · OSTI ID:2217635

Ramoneda, Josep; Jensen, Thomas B. N.; Price, Morgan N.; +2 more

Metabolic capability and in situ activity of microorganisms in an oil reservoir

Journal Article · 2018 · Microbiome · OSTI ID:1510971

Liu, Yi-Fan; Galzerani, Daniela Domingos; Mbadinga, Serge Maurice; +4 more

Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton

Journal Article · 2011 · Frontiers in Microbiology · OSTI ID:1628075

Bertrand, Erin M.; Allen, Andrew E.

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

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

Citation Formats

References (92)

Cited By (42)

Similar Records

Related Subjects