Addition of insoluble fiber to isolation media allows for increased metabolite diversity of lab-cultivable microbes derived from zebrafish gut samples

Abstract

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.

Metabolomics of bacterial–fungal pairwise interactions reveal conserved molecular mechanisms

“…After at least 7 days of growth, a chemical extraction protocol was performed on biological replicates ( N = 4) of each strain as previously reported. 22 Data acquisition settings were based off of those previously developed by Clark et al 23…”

“…After at least 7 days of growth, a chemical extraction protocol was performed on biological replicates (N = 4) of each strain as previously reported. 22 Data acquisition settings were based off of those previously developed by Clark et al 23 For analysis of intact protein profiles via MALDI-TOF MS, the supernatant was co-crystallized 1 : 1 with 20 mg mL −1 sinapinic acid in 70 : 30 ACN : DI water with 0.1% TFA and 1.5 µL of each sample was spotted onto a MALDI ground steel plate. Measurements were performed using a Bruker Microflex LT mass spectrometer equipped with a nitrogen laser.…”

Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

“…After at least 7 days of growth, a chemical extraction protocol was performed on biological replicates (N=4) of each strain as previously reported 23 . Data acquisition settings were based off of those previously developed by Clark et al 24 .…”