Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology.

Shuanghong Yang,Lingshuang Yang,Mingzhu Du,Longyan Li,Xingxiang He,Xinqiang Xie,Qingping Wu,Jun Ma,Jumei Zhang,Wei Chen,Ying Li

doi:10.3389/fmicb.2021.649698

Shuanghong Yang, Lingshuang Yang + Show 9 more

Open Access

https://doi.org/10.3389/fmicb.2021.649698

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Abstract

Bifidobacterium, an important genus for human health, is difficult to isolate. We applied metagenomics, pangenomics, and enzymology to determine the dominant glycoside hydrolase (GH) families of Bifidobacterium and designed selective medium for Bifidobacterium isolation. Pangenomics results showed that the GH13, GH3, GH42, and GH43 families were highly conserved in Bifidobacterium. Metagenomic analysis of GH families in human faecal samples was performed. The results indicated that Bifidobacterium contains core GHs for utilizing raffinose, D-trehalose anhydrous, D(+)-cellobiose, melibiose, lactulose, lactose, D(+)-sucrose, resistant starch, pullulan, xylan, and glucan. These carbohydrates as the main carbon sources were applied for selective media, which were more conducive to the growth of bifidobacteria. In the medium with lactose, raffinose and xylan as the main carbon sources, the ratio of cultivable bifidobacteria to cultivable microorganisms were 89.39% ± 2.50%, 71.45% ± 0.99%, and 53.95% ± 1.22%, respectively, whereas the ratio in the ordinary Gifu anaerobic medium was only 17.90% ± 0.58%. Furthermore, the species significantly (p < 0.05) varied among samples from different individuals. Results suggested that xylan might be a prebiotic that benefits host health, and it is feasible to screen and isolate bifidobacteria using the oligosaccharides corresponding to the specific GHs of bifidobacteria as the carbon sources of the selective media.

Highlights

Among the numerous microbial communities that colonise the human body, the intestinal microbiome plays a major role in maintaining host health
A total of 144 bifidobacterial genome sequences were downloaded from National Center for Biotechnology Information (NCBI) for pangenomic analysis (Figure 1A and Supplementary Table 2 sheets 1–3)
The total number of genes increased as the genomes increased, whereas conserved genes began to plateau at 20 genomes and remained constant thereafter. We used these whole genomes to find glycoside hydrolase (GH), which are abundant in bifidobacteria species

Summary

Introduction

Among the numerous microbial communities that colonise the human body, the intestinal microbiome plays a major role in maintaining host health. The intestinal microbiome of the gastrointestinal ecosystem comprises a collective genome of trillions of microorganisms. Interactions between the host and the intestinal microbiota are complex. Changes in the intestinal microbiota might be critical to prevent or treat various intestinal and non-intestinal diseases. Colonisation by intestinal microorganisms begins due to differences in microflora between the placenta and amniotic fluid; it continues post-partum via microorganisms in breast milk (Collado et al, 2016). A key function of the gut microbiota is to facilitate host food digestion, especially that of complex carbohydrates in mammalian diets (Armstrong et al, 2018; Cerqueira et al, 2020). The enzymes involved in polysaccharide decomposition are carbohydrate active enzymes (CAZymes), which consist of carbohydrate-binding modules, carbohydrate esterases, polysaccharide lyases, glycoside transferases, and glycoside hydrolases (GHs), the latter of which are the largest of the CAZymes

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