The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
Modifying and reacting to the environmental pH can drive bacterial interactions
Open accessAbstract
Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects the growth of both themselves and also other microbes. We show here that the way microbes modify their environment and react to it sets the interactions within single-species populations and also between different species. A very common environmental modification is a change of the environmental pH. We find experimentally that these pH changes create feedback loops that can determine the fate of bacterial populations; they can either facilitate or inhibit growth, and in extreme cases will cause extinction of the bacterial population. Understanding how single species change the pH and react to these changes allowed us to estimate their pairwise interaction outcomes. Those interactions lead to a set of generic interaction motifs-bistability, successive growth, extended suicide, and stabilization-that may be independent of which environmental parameter is modified and thus may reoccur in different microbial systems.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
(1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,715
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
The diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
Soil bacterial and fungal communities across a pH gradient in an arable soil
Rousk, J., Bååth, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., Knight, R., & Fierer, N. (2010) · The ISME Journal · doi:10.1038/ismej.2010.58 · Cited by 4,223
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,141
Atkins, P., Paula, J. D., & Keeler, J. (2022) · Oxford University Press eBooks · doi:10.1093/hesc/9780198847816.001.0001 · Cited by 3,044
Bacterial competition: surviving and thriving in the microbial jungle
Hibbing, M. E., Fuqua, C., Parsek, M. R., & Peterson, S. B. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2259 · Cited by 2,689
Succession of microbial consortia in the developing infant gut microbiome
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540
Rousk, J., Brookes, P. C., & Bååth, E. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02775-08 · Cited by 1,673
Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors
Kerr, B., Riley, M. A., Feldman, M. W., & Bohannan, B. J. M. (2002) · Nature · doi:10.1038/nature00823 · Cited by 1,623
Inverse density dependence and the Allee effect
Courchamp, F., Clutton-Brock, T., & Grenfell, B. (1999) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(99)01683-3 · Cited by 1,548
Microbial community structure and its functional implications
Fuhrman, J. A. (2009) · Nature · doi:10.1038/nature08058 · Cited by 1,382
Stephens, P. A., Sutherland, W. J., & Freckleton, R. P. (1999) · Oikos · doi:10.2307/3547011 · Cited by 1,379
The Physiological Ecology of Plant Succession
Bazzaz, F. A. (1979) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.10.110179.002031 · Cited by 1,310
Nicol, G. W., Leininger, S., Schleper, C., & Prosser, J. I. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01701.x · Cited by 1,306
Gugale, G. S., Pujari‐Palmer, S., Basutkar, P. H., Jadhav, S., Shinde, V., & Ubale, V. P. (2019) · Cited by 1,281
Microbial Ecology: Fundamentals and Applications
Atlas, R. M., & Bartha, R. (1978) · Cited by 1,255
Bacteriocins: Evolution, Ecology, and Application
Riley, M. A., & Wertz, J. E. (2002) · Annual Review of Microbiology · doi:10.1146/annurev.micro.56.012302.161024 · Cited by 1,236
Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · The ISME Journal · doi:10.1038/ismej.2008.127 · Cited by 1,230
Factors That Alter Rumen Microbial Ecology
Russell, J. B., & Rychlik, J. L. (2001) · Science · doi:10.1126/science.1058830 · Cited by 946
Edwards, J. S., Ibarra, R. U., & Palsson, B. O. (2001) · Nature Biotechnology · doi:10.1038/84379 · Cited by 939
The Ecology and Evolution of Microbial Competition
Ghoul, M., & Mitri, S. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.06.011 · Cited by 917
Pitelka, F. A. (1951) · Evolution · doi:10.1111/j.1558-5646.1951.tb02762.x · Cited by 687
Snowdrift game dynamics and facultative cheating in yeast
Gore, J., Youk, H., & van Oudenaarden, A. (2009) · Nature · doi:10.1038/nature07921 · Cited by 668
Self-citationFlint, H. J., Duncan, S. H., Scott, K. P., & Louis, P. (2007) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01281.x · Cited by 635
Syntrophic exchange in synthetic microbial communities
Mee, M. T., Collins, J. J., Church, G. M., & Wang, H. H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405641111 · Cited by 616
Competitive and cooperative metabolic interactions in bacterial communities
Freilich, S., Zarecki, R., Eilam, O., Segal, E. S., Henry, C. S., Kupiec, M., Gophna, U., Sharan, R., & Ruppin, E. (2011) · Nature Communications · doi:10.1038/ncomms1597 · Cited by 566
Effect of pH on the efficiency of growth by pure cultures of rumen bacteria in continuous culture
Russell, J. B., & Dombrowski, D. B. (1980) · Applied and Environmental Microbiology · doi:10.1128/aem.39.3.604-610.1980 · Cited by 458
Synthetic cooperation in engineered yeast populations
Shou, W., Ram, S., & Vilar, J. M. G. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610575104 · Cited by 449
The Introduction, Increase, and Crash of Reindeer on St. Matthew Island
Klein, D. R. (1968) · The Journal of Wildlife Management · doi:10.2307/3798981 · Cited by 447
Microbial interactions lead to rapid micro-scale successions on model marine particles
Datta, M. S., Sliwerska, E., Gore, J., Polz, M. F., & Cordero, O. X. (2016) · Nature Communications · doi:10.1038/ncomms11965 · Cited by 432
Self-citationSpatial Ecology of Bacteria at the Microscale in Soil
Raynaud, X., & Nunan, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087217 · Cited by 401
Molecular eco-systems biology: towards an understanding of community function
Raes, J., & Bork, P. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1935 · Cited by 395
The ecological role of bacteriocins in bacterial competition
Riley, M. A., & Gordon, D. M. (1999) · Trends in Microbiology · doi:10.1016/s0966-842x(99)01459-6 · Cited by 385
Rosenzweig, R. F., Sharp, R. R., Treves, D. S., & Adams, J. (1994) · Genetics · doi:10.1093/genetics/137.4.903 · Cited by 360
Solutions to the Public Goods Dilemma in Bacterial Biofilms
Drescher, K., Nadell, C. D., Stone, H. A., Wingreen, N. S., & Bassler, B. L. (2014) · Current Biology · doi:10.1016/j.cub.2013.10.030 · Cited by 354
Tipping elements in the human intestinal ecosystem
Lahti, L., Salojärvi, J., Salonen, A., Scheffer, M., & de Vos, W. M. (2014) · Nature Communications · doi:10.1038/ncomms5344 · Cited by 325
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria
Pande, S., Merker, H., Bohl, K., Reichelt, M., Schuster, S., de Figueiredo, L. F., Kaleta, C., & Kost, C. (2014) · The ISME Journal · doi:10.1038/ismej.2013.211 · Cited by 321
Understanding ecological community succession: Causal models and theories, a review
McCook, L. J. (1994) · Vegetatio · doi:10.1007/bf00033394 · Cited by 291
Microbial Ecology of Ocean Biogeochemistry: A Community Perspective
Strom, S. L. (2008) · Science · doi:10.1126/science.1153527 · Cited by 266
Brook, I. (1989) · Clinical Infectious Diseases · doi:10.1093/clinids/11.3.361 · Cited by 241
Community genomics in microbial ecology and evolution
Allen, E. E., & Banfield, J. F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1157 · Cited by 234
Bacterial Unculturability and the Formation of Intercellular Metabolic Networks
Pande, S., & Kost, C. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.02.015 · Cited by 232
Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids
Chao, H. X., Artemova, T., Gore, J., Yurtsev, E. A., & Datta, M. S. (2013) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 229
Self-citationBacterial interactions in biofilms
Moons, P., Michiels, C. W., & Aertsen, A. (2009) · Critical Reviews in Microbiology · doi:10.1080/10408410902809431 · Cited by 211
Fu, W., & Mathews, A. P. (1999) · Biochemical Engineering Journal · doi:10.1016/s1369-703x(99)00014-5 · Cited by 209
Recent advances in reconstruction and applications of genome-scale metabolic models
Kim, T. Y., Sohn, S. B., Kim, Y. B., Kim, W. J., & Lee, S. Y. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.10.007 · Cited by 202
Interspecies bacterial interactions in biofilms
James, G. A., Beaudette, L., & Costerton, J. W. (1995) · Journal of Industrial Microbiology · doi:10.1007/bf01569978 · Cited by 190
The Rise and Fall of a Reindeer Herd
Scheffer, V. B. (1951) · The Scientific monthly/Scientific monthly · Cited by 136
Oscillatory dynamics in a bacterial cross-protection mutualism
Yurtsev, E. A., Conwill, A., & Gore, J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523317113 · Cited by 124
Self-citationpH of Drinking Water Influences the Composition of Gut Microbiome and Type 1 Diabetes Incidence
Sofi, M. H., Gudi, R. R., Karumuthil‐Melethil, S., Perez, N., Johnson, B. M., & Vasu, C. (2013) · Diabetes · doi:10.2337/db13-0981 · Cited by 123
Adaptation of oral streptococci to low pH
(2000) · Advances in Microbial Physiology · doi:10.1016/s0065-2911(00)42004-7 · Cited by 118
Dugatkin, L. A., Perlin, M. H., Lucas, J. S., & Atlas, R. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2004.2916 · Cited by 111
Ecological suicide in microbes
Ratzke, C., Denk, J., & Gore, J. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0535-1 · Cited by 104
Self-citationCellular cooperation: insights from microbes
Celiker, H., & Gore, J. (2012) · Trends in Cell Biology · doi:10.1016/j.tcb.2012.08.010 · Cited by 97
Self-citationADVANCES IN CARBOHYDRATE CHEMISTRY
(1962) · Elsevier eBooks · doi:10.1016/b978-0-08-009654-4.50007-8 · Cited by 80
Ratzke, C., & Gore, J. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.22 · Cited by 74
Self-citationBowden, G. H., & Hamilton, I. R. (1987) · Canadian Journal of Microbiology · doi:10.1139/m87-143 · Cited by 61
Solé, M., Rius, N., & Lorén, J. G. (2000) · PubMed · Cited by 51
MEHTA, N. C., Dubach, P., & Deuel, H. (1962) · Advances in carbohydrate chemistry · doi:10.1016/s0096-5332(08)60266-0 · Cited by 49
Stability of Cross-Feeding Polymorphisms in Microbial Communities
Gudelj, I., Kinnersley, M. A., Rashkov, P., Schmidt, K., & Rosenzweig, F. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005269 · Cited by 45
Collins, M. D. (1987) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-37-4-442 · Cited by 38
Higgins, L. M., Friedman, J., Shen, H., & Gore, J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/175737 · Cited by 33
Self-citationBiochemical factors affecting symbiosis among bacteria
Nurmikko, V. (1956) · Cellular and Molecular Life Sciences · doi:10.1007/bf02157327 · Cited by 27
Cited by
Gut microbial metabolites as multi-kingdom intermediates
Krautkramer, K. A., Fan, J., & Bäckhed, F. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0438-4 · Cited by 1,398
Understanding Competition and Cooperation within the Mammalian Gut Microbiome
Coyte, K. Z., & Rakoff-Nahoum, S. (2019) · Current Biology · doi:10.1016/j.cub.2019.04.017 · Cited by 329
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
Blasche, S., Kim, Y., Mars, R. A. T., Machado, D., Maansson, M., Kafkia, E., Milanese, A., Zeller, G., Teusink, B., Nielsen, J., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-020-00816-5 · Cited by 328
Tsukuda, N., Yahagi, K., Hara, T., Watanabe, Y., Matsumoto, H., Mori, H., Higashi, K., Tsuji, H., Matsumoto, S., Kurokawa, K., et al. (2021) · The ISME Journal · doi:10.1038/s41396-021-00937-7 · Cited by 319
High-throughput microbial culturomics using automation and machine learning
Huang, Y., Sheth, R. U., Zhao, S., Cohen, L. A., Dabaghi, K., Moody, T., Sun, Y., Ricaurte, D., Richardson, M., Velez-Cortes, F., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01674-2 · Cited by 283
Metadata
- Authors
- Ratzke, C., & Gore, J.
- Venue
- PLOS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-03-14
- Volume
- 16
- Issue
- 3
- Pages
- e2004248
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2938797415
- Cited by
- 455
- References
- 64
- FWCI
- 20.27
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.