AUTHOR=Park Ji-Hyeon , Song Won-Suk , Lee Jeongchan , Jo Sung-Hyun , Lee Jae-Seung , Jeon Hyo-Jin , Kwon Ji-Eun , Kim Ye-Rim , Baek Ji-Hyun , Kim Min-Gyu , Yang Yung-Hun , Kim Byung-Gee , Kim Yun-Gon 

TITLE=An Integrative Multiomics Approach to Characterize Prebiotic Inulin Effects on Faecalibacterium prausnitzii

JOURNAL=Frontiers in Bioengineering and Biotechnology

VOLUME=10

YEAR=2022

URL=https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2022.825399

DOI=10.3389/fbioe.2022.825399

ISSN=2296-4185

ABSTRACT=<p><italic>Faecalibacterium prausnitzii</italic>, a major commensal bacterium in the human gut, is well known for its anti-inflammatory effects, which improve host intestinal health. Although several studies have reported that inulin, a well-known prebiotic, increases the abundance of <italic>F. prausnitzii</italic> in the intestine, the mechanism underlying this effect remains unclear. In this study, we applied liquid chromatography tandem mass spectrometry (LC-MS/MS)-based multiomics approaches to identify biological and enzymatic mechanisms of <italic>F. prausnitzii</italic> involved in the selective digestion of inulin. First, to determine the preference for dietary carbohydrates, we compared the growth of <italic>F. prausnitzii</italic> in several carbon sources and observed selective growth in inulin. In addition, an LC-MS/MS-based intracellular proteomic and metabolic profiling was performed to determine the quantitative changes in specific proteins and metabolites of <italic>F. prausnitzii</italic> when grown on inulin. Interestingly, proteomic analysis revealed that the putative proteins involved in inulin-type fructan utilization by <italic>F. prausnitzii</italic>, particularly β-fructosidase and amylosucrase were upregulated in the presence of inulin. To investigate the function of these proteins, we overexpressed <italic>bfrA</italic> and <italic>ams,</italic> genes encoding β-fructosidase and amylosucrase, respectively, in <italic>Escherichia coli,</italic> and observed their ability to degrade fructan. In addition, the enzyme activity assay demonstrated that intracellular fructan hydrolases degrade the inulin-type fructans taken up by fructan ATP-binding cassette transporters. Furthermore, we showed that the fructose uptake activity of <italic>F. prausnitzii</italic> was enhanced by the fructose phosphotransferase system transporter when inulin was used as a carbon source. Intracellular metabolomic analysis indicated that <italic>F. prausnitzii</italic> could use fructose, the product of inulin-type fructan degradation, as an energy source for inulin utilization. Taken together, this study provided molecular insights regarding the metabolism of <italic>F. prauznitzii</italic> for inulin, which stimulates the growth and activity of the beneficial bacterium in the intestine.</p>