Compositional Lotka-Volterra describes microbial dynamics in the simplex.
Dynamic changes in microbial communities play an important role in human health and disease. Specifically, deciphering how microbial species in a community interact with each other and their environment can elucidate mechanisms of disease, a problem typically investigated using tools from community...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2020-05-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1007917 |
| _version_ | 1811237205939585024 |
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| author | Tyler A Joseph Liat Shenhav Joao B Xavier Eran Halperin Itsik Pe'er |
| author_facet | Tyler A Joseph Liat Shenhav Joao B Xavier Eran Halperin Itsik Pe'er |
| author_sort | Tyler A Joseph |
| collection | DOAJ |
| description | Dynamic changes in microbial communities play an important role in human health and disease. Specifically, deciphering how microbial species in a community interact with each other and their environment can elucidate mechanisms of disease, a problem typically investigated using tools from community ecology. Yet, such methods require measurements of absolute densities, whereas typical datasets only provide estimates of relative abundances. Here, we systematically investigate models of microbial dynamics in the simplex of relative abundances. We derive a new nonlinear dynamical system for microbial dynamics, termed "compositional" Lotka-Volterra (cLV), unifying approaches using generalized Lotka-Volterra (gLV) equations from community ecology and compositional data analysis. On three real datasets, we demonstrate that cLV recapitulates interactions between relative abundances implied by gLV. Moreover, we show that cLV is as accurate as gLV in forecasting microbial trajectories in terms of relative abundances. We further compare cLV to two other models of relative abundance dynamics motivated by common assumptions in the literature-a linear model in a log-ratio transformed space, and a linear model in the space of relative abundances-and provide evidence that cLV more accurately describes community trajectories over time. Finally, we investigate when information about direct effects can be recovered from relative data that naively provide information about only indirect effects. Our results suggest that strong effects may be recoverable from relative data, but more subtle effects are challenging to identify. |
| first_indexed | 2024-04-12T12:22:02Z |
| format | Article |
| id | doaj.art-5240174de84743169bdf1c704a15c5ff |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-12T12:22:02Z |
| publishDate | 2020-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-5240174de84743169bdf1c704a15c5ff2022-12-22T03:33:17ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-05-01165e100791710.1371/journal.pcbi.1007917Compositional Lotka-Volterra describes microbial dynamics in the simplex.Tyler A JosephLiat ShenhavJoao B XavierEran HalperinItsik Pe'erDynamic changes in microbial communities play an important role in human health and disease. Specifically, deciphering how microbial species in a community interact with each other and their environment can elucidate mechanisms of disease, a problem typically investigated using tools from community ecology. Yet, such methods require measurements of absolute densities, whereas typical datasets only provide estimates of relative abundances. Here, we systematically investigate models of microbial dynamics in the simplex of relative abundances. We derive a new nonlinear dynamical system for microbial dynamics, termed "compositional" Lotka-Volterra (cLV), unifying approaches using generalized Lotka-Volterra (gLV) equations from community ecology and compositional data analysis. On three real datasets, we demonstrate that cLV recapitulates interactions between relative abundances implied by gLV. Moreover, we show that cLV is as accurate as gLV in forecasting microbial trajectories in terms of relative abundances. We further compare cLV to two other models of relative abundance dynamics motivated by common assumptions in the literature-a linear model in a log-ratio transformed space, and a linear model in the space of relative abundances-and provide evidence that cLV more accurately describes community trajectories over time. Finally, we investigate when information about direct effects can be recovered from relative data that naively provide information about only indirect effects. Our results suggest that strong effects may be recoverable from relative data, but more subtle effects are challenging to identify.https://doi.org/10.1371/journal.pcbi.1007917 |
| spellingShingle | Tyler A Joseph Liat Shenhav Joao B Xavier Eran Halperin Itsik Pe'er Compositional Lotka-Volterra describes microbial dynamics in the simplex. PLoS Computational Biology |
| title | Compositional Lotka-Volterra describes microbial dynamics in the simplex. |
| title_full | Compositional Lotka-Volterra describes microbial dynamics in the simplex. |
| title_fullStr | Compositional Lotka-Volterra describes microbial dynamics in the simplex. |
| title_full_unstemmed | Compositional Lotka-Volterra describes microbial dynamics in the simplex. |
| title_short | Compositional Lotka-Volterra describes microbial dynamics in the simplex. |
| title_sort | compositional lotka volterra describes microbial dynamics in the simplex |
| url | https://doi.org/10.1371/journal.pcbi.1007917 |
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