Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity
Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properti...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.910390/full |
| _version_ | 1797960441848135680 |
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| author | Firas S. Midani Firas S. Midani Lawrence A. David Lawrence A. David |
| author_facet | Firas S. Midani Firas S. Midani Lawrence A. David Lawrence A. David |
| author_sort | Firas S. Midani |
| collection | DOAJ |
| description | Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properties. However, quantifying abundance of more than two microbes in a community in a high throughput fashion requires rapid, inexpensive assays. Here, we show that multicolor flow cytometry combined with a machine learning-based classifier can rapidly quantify species abundances in simple, synthetic microbial communities. Our approach measures community structure over time and detects the exchange of metabolites in a four-member community of fluorescent Bacteroides species. Notably, we quantified species abundances in co-cultures and detected evidence of cooperation in polysaccharide processing and competition for monosaccharide utilization. We also observed that co-culturing on simple sugars, but not complex sugars, reduced microbial productivity, although less productive communities maintained higher community diversity. In summary, our multicolor flow cytometric approach presents an economical, tractable model system for microbial ecology using well-studied human bacteria. It can be extended to include additional species, evaluate more complex environments, and assay response of communities to a variety of disturbances. |
| first_indexed | 2024-04-11T00:45:42Z |
| format | Article |
| id | doaj.art-5fd1c381c6d14375b8d57375ef56f28f |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T00:45:42Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-5fd1c381c6d14375b8d57375ef56f28f2023-01-05T17:01:09ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-01-011310.3389/fmicb.2022.910390910390Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversityFiras S. Midani0Firas S. Midani1Lawrence A. David2Lawrence A. David3Center for Genomic and Computational Biology, Duke University, Durham, NC, United StatesDepartment of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United StatesCenter for Genomic and Computational Biology, Duke University, Durham, NC, United StatesDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC, United StatesCross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properties. However, quantifying abundance of more than two microbes in a community in a high throughput fashion requires rapid, inexpensive assays. Here, we show that multicolor flow cytometry combined with a machine learning-based classifier can rapidly quantify species abundances in simple, synthetic microbial communities. Our approach measures community structure over time and detects the exchange of metabolites in a four-member community of fluorescent Bacteroides species. Notably, we quantified species abundances in co-cultures and detected evidence of cooperation in polysaccharide processing and competition for monosaccharide utilization. We also observed that co-culturing on simple sugars, but not complex sugars, reduced microbial productivity, although less productive communities maintained higher community diversity. In summary, our multicolor flow cytometric approach presents an economical, tractable model system for microbial ecology using well-studied human bacteria. It can be extended to include additional species, evaluate more complex environments, and assay response of communities to a variety of disturbances.https://www.frontiersin.org/articles/10.3389/fmicb.2022.910390/fullBacteroidescross feedingflow cytometrycarbon sourcesmicrobial ecology |
| spellingShingle | Firas S. Midani Firas S. Midani Lawrence A. David Lawrence A. David Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity Frontiers in Microbiology Bacteroides cross feeding flow cytometry carbon sources microbial ecology |
| title | Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity |
| title_full | Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity |
| title_fullStr | Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity |
| title_full_unstemmed | Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity |
| title_short | Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity |
| title_sort | tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity |
| topic | Bacteroides cross feeding flow cytometry carbon sources microbial ecology |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.910390/full |
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