Journal
GUT MICROBES
Volume 11, Issue 4, Pages -Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/19490976.2020.1740073
Keywords
Gut microbes; in vitro cultivation; insoluble fiber; natural products; zebrafish; metabolomics
Categories
Funding
- National Institute of General Medical Sciences of the National Institutes of Health [R01GM125943]
- University of Illinois at Chicago Startup Funds
- Icelandic Research Fund Grant [152336-051]
- American Society for Pharmacognosy research startup grant
- National Science Foundation Illinois Louis Stokes Alliance for Minority Participation Bridge [1500368]
- UIC Abraham Lincoln retention fellowship
- Division Of Human Resource Development
- Direct For Education and Human Resources [1500368] Funding Source: National Science Foundation
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There is a gap in measured microbial diversity when comparing genomic sequencing techniques versus cultivation from environmental samples in a laboratory setting. Standardized methods in artificial environments may not recapitulate the environmental conditions that native microbes require for optimal growth. For example, the intestinal tract houses microbes at various pH values as well as minimal oxygen and light environments. These microbes are also exposed to an atypical source of carbon: dietary fiber compacted in fecal matter. To investigate how the addition of insoluble fiber to isolation media could affect the cultivation of microbes from zebrafish intestines, an isolate library was built and analyzed using the bioinformatics pipeline IDBac. While all isolation media encouraged the growth of species from several phyla, the extent of growth was greater with the addition of fiber allowing for easier isolation. Furthermore, fiber addition altered the metabolism of the cultivated gut-derived microbes and induced the production of unique metabolites that were not produced when microbes were otherwise grown on standard isolation media. Addition of this inexpensive carbon source to the media supported the cultivation of a diverse community whose secondary metabolite production may more closely replicate their metabolite production in vivo.
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