Integrative Analysis of the Gut Microbiota and Metabolome for In Vitro Human Gut Fermentation Modeling

Abstract

This study aimed to find the best in vitro fermentation method by integrative analysis of the gut microbiota and metabolome. We selected five different media: brain heart infusion broth, Luria–Bertani broth, Mueller–Hinton broth, anaerobe basal broth, and anaerobic medium base (AMB). After in vitro fermentation, the gut microbiota and metabolites were analyzed at different culture times. The results showed that different culture media have different effects on the bacterial community structure and metabolites. The integrative analysis of gut microbiota and metabolism also proved that AMB medium is effective in keeping a stable bacterial community structure and producing less metabolites and short-chain fatty acids by simulating the nutrient-poor microenvironment in the human gut during in vitro fermentation. Thus, culturing with AMB medium for 48 h is the most suitable in vitro model for human gut microbiota fermentation, which provides an alternative approach for diet and health research.

In vitro effects of two polysaccharide fractions from Laminaria japonica on gut microbiota and metabolome

“…In vitro fecal fermentation was conducted based on established methods. 21 The stool samples were divided into two groups, which were respectively collected from 4 healthy volunteers and 4 volunteers with hyperlipidemia (2 males and 2 females in each group, aged 20–40). The basic information of each volunteer is shown in Table S1 †.…”

“…The analysis method was performed according to the previously described method. 21 HPLC-MS/MS analysis was conducted on a Q Exactive Plus system (Thermo-Fisher Scientific), coupled online with the HPLC system and equipped with an ACQUITY UPLC BEH C18 column (2.1 × 5 mm, 1.7 μm, Waters, Ireland) at a temperature of 30 °C. The voltages of the positive mode (ESI+) and negative mode (ESI−) were both set as 30 V, and the mass spectra from 100 m / z to 1000 m / z were recorded.…”

“…The analysis method was performed according to the previously described method. 21 HPLC-MS/MS analysis was conducted on a Q Exactive Plus system (Thermo-Fisher Scientific), coupled online with the HPLC system and equipped with an…”

Effect of Bergamot and Laoxianghuang Polysaccharides on Gut Microbiota Derived from Patients with Hyperlipidemia: An Integrative Analysis of Microbiome and Metabolome during In Vitro Fermentation

“…Bacteria is a main factor that influences fermentation and related metabolites [ 41 ]. In this study, the gut microbiota was analyzed after 48 h of fermentation according to our previous study [ 24 ]. To identify the species of bacteria in the different groups, the relative abundance of bacteria in different groups was compared at the genus level.…”

“…The fundamental anaerobic culture medium (FAM) was prepared as described before, with slight modifications [ 24 ]. The FAM was composed of 1.6 mmol K 2 HPO 4 , 7.5 mmol NaCl, 1.3 mmol KH 2 PO 4 , 0.4 mmol CaCl 2 , 3.4 mmol (NH 4 ) 2 SO 4 , 0.7 mmol MgSO 4 , 4.0 mmol L-cysteine, 2.8 mmol L-ascorbic acids, 37.7 mmol Na 2 CO 3 , 1 g nutrient agar, 1 g beef extract, and 1 g peptone in 1 L water.…”