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Detecting (the Absence of) Species Interactions in Microbial Ecological Systems.

作者信息

Beardsley Thomas, Behringer Megan, Komarova Natalia L

机构信息

Department of Mathematics, University of California Irvine, Irvine, California, USA.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.

出版信息

Stud Appl Math. 2025 Feb;154(2). doi: 10.1111/sapm.70009. Epub 2025 Feb 9.


DOI:10.1111/sapm.70009
PMID:40894086
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12392786/
Abstract

Microbial communities are complex ecological systems of organisms that evolve in time, with new variants created, while others disappear. Understanding how species interact within communities can help us shed light into the mechanisms that drive ecosystem processes. We studied systems with serial propagation, where the community is kept alive by taking a subsample at regular intervals and replating it in fresh medium. The data that are usually collected consist of the % of the population for each of the species, at several time points. In order to utilize this type of data, we formulated a system of equations (based on the generalized Lotka-Volterra model) and derived conditions of species noninteraction. This was possible to achieve by reformulating the problem as a problem of finding feasibility domains, which can be solved by a number of efficient algorithms. This methodology provides a cost-effective way to investigate interactions in microbial communities.

摘要

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[1]
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.

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[2]
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[3]
Microbial interactions in theory and practice: when are measurements compatible with models?

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[4]
Ecological modelling approaches for predicting emergent properties in microbial communities.

Nat Ecol Evol. 2022-7

[5]
Conceptual strategies for characterizing interactions in microbial communities.

iScience. 2022-1-15

[6]
Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions.

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[7]
Network analysis methods for studying microbial communities: A mini review.

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[8]
Tractable models of ecological assembly.

Ecol Lett. 2021-5

[9]
Microbial communities as dynamical systems.

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[10]
Deciphering microbial interactions in synthetic human gut microbiome communities.

Mol Syst Biol. 2018-6-21

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