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Annotation-free discovery of functional groups in microbial communities

Nature Ecology & Evolution volume 7, pages 716–724 (2023)Cite this article

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Abstract

Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa whose abundance is more stable and better-associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent of error-prone functional gene annotations remains a major open problem. Here we tackle this structure–function problem by developing a novel unsupervised approach that coarse-grains taxa into functional groups, solely on the basis of the patterns of statistical variation in species abundances and functional read-outs. We demonstrate the power of this approach on three distinct datasets. On data of replicate microcosms with heterotrophic soil bacteria, our unsupervised algorithm recovered experimentally validated functional groups that divide metabolic labour and remain stable despite large variation in species composition. When leveraged against the ocean microbiome data, our approach discovered a functional group that combines aerobic and anaerobic ammonia oxidizers whose summed abundance tracks closely with nitrate concentrations in the water column. Finally, we show that our framework can enable the detection of species groups that are probably responsible for the production or consumption of metabolites abundant in animal gut microbiomes, serving as a hypothesis-generating tool for mechanistic studies. Overall, this work advances our understanding of structure–function relationships in complex microbiomes and provides a powerful approach to discover functional groups in an objective and systematic manner.

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Fig. 1: Schematic illustration of Ensemble Quotient Optimization (EQO).
Fig. 2: Coarse-graining functional groups in replicate microcosms.
Fig. 3: Functional guilds of nitrogen cycling in the ocean microbiome.
Fig. 4: Predicting the level of metabolites with minimal assemblages in gut microbiome.

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Data availability

Data used for EQO in this study are provided as supplementary tables. Access to the raw source data is available in original publications of microbiome datasets3,4,20,21.

Code availability

R scripts are available at https://github.com/Xiaoyu2425/Ensemble-Quotient-Optimization. An R package for EQO, mEQO, is available at https://github.com/Xiaoyu2425/mEQO with an accompanying vignette illustrating how to use the package.

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Acknowledgements

We thank S. Louca, J. Goldford, I. Mizrahi and coworkers for sharing their datasets; B. Liu, M. Tikhonov, Q. Wang, C. Song and all Cordero lab members for helpful suggestions. X.S. thanks S. W. Chisholm, M. Follows and R. Juanes for encouraging feedback. X.S. and O.X.C. were supported by a seed grant from the Abdul Latif Jameel Water and Food Systems Lab. O.X.C. was supported by the Simons Collaboration: Principles of Microbial Ecosystems, award number 542395. A.G. was supported by the Gordon and Betty Moore Foundation as a Physics of Living Systems Fellow through grant number GBMF4513. R.G. was supported by Simons Foundation Postdoctoral Fellowship Award 653410.

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Authors and Affiliations

  1. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Xiaoyu Shan, Rachel Gregor & Otto X. Cordero

  2. Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA

    Akshit Goyal

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Contributions

O.X.C. conceived the study. X.S. and O.X.C. designed the algorithm and performed data analysis. X.S., A.G., R.G. and O.X.C. wrote the manuscript.

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Correspondence to Otto X. Cordero.

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Extended data

Extended Data Fig. 1 Schematic illustration of different types of environmental/phenotypic variables that can be leveraged by EQO to predict functional groups.

Bar plots show relative abundance of different taxa. Appropriate grouping of taxa leads to strong coupling with the phenotypic variable. For a continuous phenotypic variable such as measured concentration of a metabolite across samples, the coupling can be captured by a strong correlation. For a uniform phenotypic variable, the coupling can be marked as high stability or low variability. For a categorical phenotypic variable, the coupling can be interpreted as significant discrimination between treatments.

Extended Data Fig. 2 EQO for Tara Ocean microbiome.

(a) The best group size for EQO was determined to be 11 based on an AIC minimization criterion. (b) Relative abundance distribution of the 11 taxa selected by the algorithm across all sampling sites (left y-axis). Nitrate concentration measured at each sampling site was shown as black dots (right y-axis).

Extended Data Fig. 3 Statistical tests for predictability of metabolites in the gut microbiome dataset.

Metabolites with cross-validated R2 lower than 0.2 as well as adjusted P-value higher than 0.01 were filtered out from further analysis (Methods).

Extended Data Fig. 4 Distribution of predicted putrescine functional group in samples ranked according to host phylogeny.

1, hyena; 2, tiger; 3, leopard; 4, lion; 5, sand cat; 6, jungle cat; 7, wolf; 8, coati; 9, black bear; 10, brown bear; 11, donkey; 12, zebra; 13, rhino; 14, goat; 15, sheep; 16, lemur; 17, capuchin; 18, mandrill; 19, gibbon; 20, gorilla; 21, chimpanzee; 22, African elephant; 23, Asian elephant.

Extended Data Fig. 5 Functional groups identified for lactate production and butyrate production.

Species that are confirmed to be lactate producers or butyrate producers in previous experimental studies are highlighted in red. The two Streptococcus luteciae species in the left panel are well-known lactate producers in the Lactobacillales clade. Faecalibacterium prausnitzii and Blautia producta as well as Lachnospiraceae species have been reported to be butyrate producers.

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Supplementary Tables 1–3.

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Shan, X., Goyal, A., Gregor, R. et al. Annotation-free discovery of functional groups in microbial communities. Nat Ecol Evol 7, 716–724 (2023). https://doi.org/10.1038/s41559-023-02021-z

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