Modulation of antibiotic effects on microbial communities by resource competition
Abstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigate community responses to species-specific death ra...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-04-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-37895-x |
| _version_ | 1827956732274409472 |
|---|---|
| author | Daniel P. Newton Po-Yi Ho Kerwyn Casey Huang |
| author_facet | Daniel P. Newton Po-Yi Ho Kerwyn Casey Huang |
| author_sort | Daniel P. Newton |
| collection | DOAJ |
| description | Abstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigate community responses to species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such as bacteriophages. Our analyses highlight the complex dependence of species coexistence that can arise from the interplay of resource competition and antibiotic activity, independent of other biological mechanisms. In particular, we identify resource competition structures that cause richness to depend on the order of sequential application of antibiotics (non-transitivity), and the emergence of synergistic and antagonistic effects under simultaneous application of multiple antibiotics (non-additivity). These complex behaviors can be prevalent, especially when generalist consumers are targeted. Communities can be prone to either synergism or antagonism, but typically not both, and antagonism is more common. Furthermore, we identify a striking overlap in competition structures that lead to non-transitivity during antibiotic sequences and those that lead to non-additivity during antibiotic combination. In sum, our results establish a broadly applicable framework for predicting microbial community dynamics under deleterious perturbations. |
| first_indexed | 2024-04-09T15:08:22Z |
| format | Article |
| id | doaj.art-4039c7418f3a4f7a9bba6daa8128765a |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-09T15:08:22Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-4039c7418f3a4f7a9bba6daa8128765a2023-04-30T11:19:59ZengNature PortfolioNature Communications2041-17232023-04-0114111210.1038/s41467-023-37895-xModulation of antibiotic effects on microbial communities by resource competitionDaniel P. Newton0Po-Yi Ho1Kerwyn Casey Huang2Department of Bioengineering, Stanford UniversityDepartment of Bioengineering, Stanford UniversityDepartment of Bioengineering, Stanford UniversityAbstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigate community responses to species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such as bacteriophages. Our analyses highlight the complex dependence of species coexistence that can arise from the interplay of resource competition and antibiotic activity, independent of other biological mechanisms. In particular, we identify resource competition structures that cause richness to depend on the order of sequential application of antibiotics (non-transitivity), and the emergence of synergistic and antagonistic effects under simultaneous application of multiple antibiotics (non-additivity). These complex behaviors can be prevalent, especially when generalist consumers are targeted. Communities can be prone to either synergism or antagonism, but typically not both, and antagonism is more common. Furthermore, we identify a striking overlap in competition structures that lead to non-transitivity during antibiotic sequences and those that lead to non-additivity during antibiotic combination. In sum, our results establish a broadly applicable framework for predicting microbial community dynamics under deleterious perturbations.https://doi.org/10.1038/s41467-023-37895-x |
| spellingShingle | Daniel P. Newton Po-Yi Ho Kerwyn Casey Huang Modulation of antibiotic effects on microbial communities by resource competition Nature Communications |
| title | Modulation of antibiotic effects on microbial communities by resource competition |
| title_full | Modulation of antibiotic effects on microbial communities by resource competition |
| title_fullStr | Modulation of antibiotic effects on microbial communities by resource competition |
| title_full_unstemmed | Modulation of antibiotic effects on microbial communities by resource competition |
| title_short | Modulation of antibiotic effects on microbial communities by resource competition |
| title_sort | modulation of antibiotic effects on microbial communities by resource competition |
| url | https://doi.org/10.1038/s41467-023-37895-x |
| work_keys_str_mv | AT danielpnewton modulationofantibioticeffectsonmicrobialcommunitiesbyresourcecompetition AT poyiho modulationofantibioticeffectsonmicrobialcommunitiesbyresourcecompetition AT kerwyncaseyhuang modulationofantibioticeffectsonmicrobialcommunitiesbyresourcecompetition |