An in vitro model maintaining taxon-specific functional activities of the gut microbiome

Abstract

The gut microbiome is a new target for therapeutics. In vitro high-throughput culture models could provide time-and-cost saving solutions to discover microbiome responses to drugs. Unfortunately, there has been no report of in vitro models capable of maintaining functional and compositional profiles resembling the in vivo gut microbiome. Here, we developed and validated a high-throughput culturing model named Mipro to maintain individuals' microbiomes. The Mipro model quintupled viable bacteria count while maintained the functional and compositional profiles of individuals' gut microbiomes.Comparison of taxon-specific functions between pre -and-post culture microbiomes showed Pearson's correlation coefficient r of 0.83 ± 0.03. Moreover, the Mipro model also exhibited a high degree of in vitro -in vivo correlation (Pearson's r of 0.68 ± 0.09) in microbial responses to metformin in mice fed a high-fat diet. Mipro provides a highly simulated gut microbiome for high-throughput investigation of drug-microbiome interactions.

pepFunk, a tool for peptide-centric functional analysis in metaproteomic human gut microbiome studies

“…Metformin, a drug widely used in the treatment of type II diabetes, has previously been shown to alter gut microbiome taxonomic composition and functionality (De La Cuesta-Zuluaga et al, 2017; Ma et al, 2018; Li et al, 2019). In our study, we identified metformin-induced alterations to the same pathways as other studies, for example a decrease in fatty acid biosynthesis [PATH:KO00061] (Li et al, 2019), decrease in nitrogen metabolism [PATH:KO00910], increase in oxidative phosphorylation [PATH:KO00190], enrichment in lipopolysaccharide biosynthesis [PATH:KO00540] (Ma et al, 2018), and an increase in tRNA biosynthesis [BR:KO03016]. Metformin has also been shown to reduce folate metabolism (Cabreiro et al, 2013), thus lower “one carbon pool by folate” GSVA scores in metformin treated samples are expected.…”

“…We adopted an ex vivo microbiome assay, termed RapidAIM (rapid assay of individual’s microbiome) (Li et al, 2019) to assess the direct effects of the histone deacetylace (HDAC) inhibitor suberoulanilide hydroxamic acid (SAHA) on a human microbiome. Briefly, in a RapidAIM assay, a human gut microbiome (fecal) sample was cultured for 24 hours in anaerobic conditions in control conditions with dimethyl sulfoxide (DMSO) and treatment conditions with a low (0.125mg/ml), or high concentration of SAHA (0.25mg/ml).…”

“…A human fecal sample (microbiome) stored at -80° C was thawed quickly at 37° C and cultured using RapidAIM (Li et al, 2019) for 24 hours with 10mM metformin (MTFM) or DMSO as the control. Control and treatment samples were cultured in five replicates.…”

“…Control and treatment samples were cultured in five replicates. Cultured microbiome samples were subjected to protein extraction and tryptic digestion, and samples were analyzed using an Orbitrap Q-Exactive and a 90 min gradient as described previously (Li et al, 2019). Three technical replicates were run on the Q-Exactive for a single sample (MTFM_3).…”

A Chemoenzymatic Method for Glycoproteomic N-glycan Type Quantitation

“…Protein was pelleted by centrifugation at 16000g, 4 °C, 10 min and washed with the ice-cold acetone two times. For the in-solution trypsin digestion, the procedure was performed as the previously report 43 . Briefly, the resulting protein was dissolved in 50 mM ammonium bicarbonate and 8 M urea solution, reduced in 5 mM dithiothreitol (DTT) (56 °C, 30 min), and alkylated by with 10 mM iodoacetamide (25 °C, 40 min in the dark).…”