Genomic and functional diversity of the human-derived isolates of Faecalibacterium

Wenxi Li; Xiaoqian Lin; Hewei Liang; Zhinan Wu; Mengmeng Wang; Jingxi Sun; Xiaofang Li; Wenxin He; Xiaowei Gao; Tongyuan Hu; Liang Xiao; Yuanqiang Zou

doi:10.3389/fmicb.2024.1379500

Genomic and functional diversity of the human-derived isolates of Faecalibacterium

Front Microbiol. 2024 May 30:15:1379500. doi: 10.3389/fmicb.2024.1379500. eCollection 2024.

Authors

Wenxi Li^#^{1

2}, Xiaoqian Lin^#², Hewei Liang^{1

3}, Zhinan Wu^{1

4}, Mengmeng Wang^{1

4}, Jingxi Sun^{1

4}, Xiaofang Li^{1

5}, Wenxin He¹, Xiaowei Gao¹, Tongyuan Hu^{1

3}, Liang Xiao^{1

4

6}, Yuanqiang Zou^{1

5

6

7}

Affiliations

¹ BGI-Shenzhen, Shenzhen, China.
² School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
³ BGI Research, Wuhan, China.
⁴ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
⁵ BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
⁶ Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
⁷ Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark.

^# Contributed equally.

Abstract

Introduction: Faecalibacterium is one of the most abundant bacteria in the gut microbiota of healthy adults, highly regarded as a next-generation probiotic. However, the functions of Faecalibacterium genomes from cultured strains and the distribution of different species in populations may differ among different sources.

Methods: We here performed an extensive analysis of pan-genomes, functions, and safety evaluation of 136 Faecalibacterium genomes collected from 10 countries.

Results: The genomes are clustered into 11 clusters, with only five of them were characterized and validly nomenclated. Over 80% of the accessory genes and unique genes of Faecalibacterium are found with unknown function, which reflects the importance of expanding the collection of Faecalibacterium strains. All the genomes have the potential to produce acetic acid and butyric acid. Nine clusters of Faecalibacterium are found significantly enriched in the healthy individuals compared with patients with type II diabetes..

Discussion: This study provides a comprehensive view of genomic characteristic and functions and of culturable Faecalibacterium bacterium from human gut, and enables clinical advances in the future.

Keywords: Faecalibacterium; carbohydrate enzymes; gut microbiology; pan-genome; probiotics.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by a grant from the National Natural Science Foundation of China (No. 32100009) and the Shenzhen Municipal Government of China (No. XMHT20220104017).