Complexity–stability trade-off in empirical microbial ecosystems
May, R. M. Will a large complex system be stable? Nature 238, 413–414 (1972).CAS
Article
PubMed
Google Scholar
May, R. M. & Mac Arthur, R. H. Niche overlap as a function of environmental variability. Proc. Natl Acad. Sci. USA 69, 1109–1113 (1972).CAS
Article
PubMed
PubMed Central
Google Scholar
May, R. M. Stability and Complexity in Model Ecosystems (Princeton Univ. Press, 2019).Sinha, S. Complexity vs. stability in small-world networks. Phys. A 346, 147–153 (2005).Article
Google Scholar
Thébault, E. & Fontaine, C. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853–856 (2010).Article
CAS
PubMed
Google Scholar
Mougi, A. & Kondoh, M. Diversity of interaction types and ecological community stability. Science 337, 349–351 (2012).CAS
Article
PubMed
Google Scholar
Allesina, S. & Tang, S. Stability criteria for complex ecosystems. Nature 483, 205–208 (2012).CAS
Article
PubMed
Google Scholar
Allesina, S. & Tang, S. The stability–complexity relationship at age 40: a random matrix perspective. Popul. Ecol. 57, 63–75 (2015).Article
Google Scholar
Qian, J. J. & Akçay, E. The balance of interaction types determines the assembly and stability of ecological communities. Nat. Ecol. Evol. 4, 356–365 (2020).Article
PubMed
Google Scholar
Landi, P., Minoarivelo, H. O., Brännström, Å., Hui, C. & Dieckmann, U. in Systems Analysis Approach for Complex Global Challenges (eds Mensah, P. et al.) 209–248 (Springer, 2018).Townsend, S. E., Haydon, D. T. & Matthews, L. On the generality of stability–complexity relationships in Lotka–Volterra ecosystems. J. Theor. Biol. 267, 243–251 (2010).Article
PubMed
Google Scholar
Pimm, S. L., Lawton, J. H. & Cohen, J. E. Food web patterns and their consequences. Nature 350, 669–674 (1991).Article
Google Scholar
Yodzis, P. The stability of real ecosystems. Nature 289, 674–676 (1981).Article
Google Scholar
Winemiller, K. O. Must connectance decrease with species richness? Am. Naturalist 134, 960–968 (1989).Article
Google Scholar
Warren, P. H. Variation in food-web structure: the determinants of connectance. Am. Nat. 136, 689–700 (1990).Article
Google Scholar
de Ruiter, P. C., Neutel, A.-M. & Moore, J. C. Energetics, patterns of interaction strengths, and stability in real ecosystems. Science 269, 1257–1260 (1995).Article
PubMed
Google Scholar
Schmid-Araya, J. M. et al. Connectance in stream food webs. J. Anim. Ecol. 71, 1056–1062 (2002).Article
Google Scholar
Neutel, A.-M. et al. Reconciling complexity with stability in naturally assembling food webs. Nature 449, 599–602 (2007).CAS
Article
PubMed
Google Scholar
James, A. et al. Constructing random matrices to represent real ecosystems. Am. Nat. 185, 680–692 (2015).Article
PubMed
Google Scholar
Jacquet, C. et al. No complexity–stability relationship in empirical ecosystems. Nat. Commun. 7, 12573 (2016).CAS
Article
PubMed
PubMed Central
Google Scholar
Thompson, L. R. et al. A communal catalogue reveals earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).CAS
Article
PubMed
PubMed Central
Google Scholar
Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207 (2012).CAS
Article
Google Scholar
Fricker, A. M., Podlesny, D. & Fricke, W. F. What is new and relevant for sequencing-based microbiome research? A mini-review. J. Adv. Res. 19, 105–112 (2019).CAS
Article
PubMed
PubMed Central
Google Scholar
Sander, E. L., Wootton, J. T. & Allesina, S. Ecological network inference from long-term presence-absence data. Sci. Rep. 7, 7154 (2017).Article
CAS
PubMed
PubMed Central
Google Scholar
Steinway, S. N., Biggs, M. B., Loughran Jr, T. P., Papin, J. A. & Albert, R. Inference of network dynamics and metabolic interactions in the gut microbiome. PLoS Comput. Biol. 11, e1004338 (2015).Article
CAS
PubMed
PubMed Central
Google Scholar
Bucci, V. et al. Mdsine: microbial dynamical systems inference engine for microbiome time-series analyses. Genome Biol. 17, 121 (2016).Article
CAS
PubMed
PubMed Central
Google Scholar
Stein, R. R. et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9, e1003388 (2013).Article
CAS
PubMed
PubMed Central
Google Scholar
Fisher, C. K. & Mehta, P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PloS ONE 9, e102451 (2014).Article
CAS
PubMed
PubMed Central
Google Scholar
Gerber, G. K., Onderdonk, A. B. & Bry, L. Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput. Biol. 8, e1002624 (2012).CAS
Article
PubMed
PubMed Central
Google Scholar
Cao, H.-T., Gibson, T. E., Bashan, A. & Liu, Y.-Y. Inferring human microbial dynamics from temporal metagenomics data: pitfalls and lessons. BioEssays 39, 1600188 (2017).Article
Google Scholar
David, L. A. et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15, R89 (2014).Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).Article
PubMed
PubMed Central
Google Scholar
Buffie, C. G. et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to clostridium difficile-induced colitis. Infect. Immun. 80, 62–73 (2012).CAS
Article
PubMed
PubMed Central
Google Scholar
Dohlman, A. B. & Shen, X. Mapping the microbial interactome: statistical and experimental approaches for microbiome network inference. Exp. Biol. Med. 244, 445–458 (2019).CAS
Article
Google Scholar
Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).CAS
Article
PubMed
Google Scholar
Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).CAS
Article
PubMed
PubMed Central
Google Scholar
Jiang, D. et al. Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities. Front. Genet. 10, 995 (2019).CAS
Article
PubMed
PubMed Central
Google Scholar
Faust, K. Open challenges for microbial network construction and analysis. ISME J. 15, 3111–3118 (2021).CAS
Article
PubMed
PubMed Central
Google Scholar
Bashan, A. et al. Universality of human microbial dynamics. Nature 534, 259–262 (2016).CAS
Article
PubMed
PubMed Central
Google Scholar
Vila, J. C., Liu, Y.-Y. & Sanchez, A. Dissimilarity–overlap analysis of replicate enrichment communities. ISME J. 14, 2505–2513 (2020).Article
PubMed
PubMed Central
Google Scholar
Moitinho-Silva, L. et al. The sponge microbiome project. Gigascience 6, gix077 (2017).Article
PubMed Central
Google Scholar
Swierts, T., Cleary, D. & de Voogd, N. Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny. FEMS Microbiol. Ecol. 94, fiy194 (2018).CAS
Article
PubMed Central
Google Scholar
Jost, L. Entropy and diversity. Oikos 113, 363–375 (2006).Article
Google Scholar
Suweis, S., Grilli, J., Banavar, J. R., Allesina, S. & Maritan, A. Effect of localization on the stability of mutualistic ecological networks. Nat. Commun. 6, 10179 (2015).CAS
Article
PubMed
Google Scholar
Grilli, J., Barabás, G., Michalska-Smith, M. J. & Allesina, S. Higher-order interactions stabilize dynamics in competitive network models. Nature 548, 210–213 (2017).CAS
Article
PubMed
Google Scholar
Butler, S. & O’Dwyer, J. P. Stability criteria for complex microbial communities. Nat. Commun. 9, 2970 (2018).Article
CAS
PubMed
PubMed Central
Google Scholar
Allesina, S. & Grilli, J. in Theoretical Ecology: Concepts and Applications (eds McCann, K. & Gellner, G.) Ch. 6 (Oxford Univ. Press, 2020).Jayant, P. & Shnerb, N. M. How temporal environmental stochasticity affects species richness: destabilization neutralization and the storage effect. J. Theor. Biol. 539, 111053 (2022).Article
Google Scholar
Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).Article
CAS
PubMed
PubMed Central
Google Scholar
Gajer, P. et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra52–132ra52 (2012).Article
PubMed
PubMed Central
Google Scholar
Van der Maaten, L. & Hinton, G. Visualizing data using t-sne. J. Mach. Learn. Res. 9, 2579–2605 (2008).
Google Scholar
Bunin, G. Ecological communities with Lotka-Volterra dynamics. Phys. Rev. E 95, 042414 (2017).Article
PubMed
Google Scholar More
