TY - JOUR

T1 - Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae

AU - Lin, Xiaoqian

AU - Hu, Tongyuan

AU - Wu, Zhinan

AU - Li, Lingne

AU - Wang, Yuhao

AU - Wen, Dingyang

AU - Liu, Xudong

AU - Li, Wenxi

AU - Liang, Hewei

AU - Jin, Xin

AU - Xu, Xun

AU - Wang, Jian

AU - Yang, Huanming

AU - Kristiansen, Karsten

AU - Xiao, Liang

AU - Zou, Yuanqiang

N1 - Funding Information: The authors also appreciate the colleagues at BGI Research for discussions and the support of Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome. This work was supported by grants from the National Natural Science Foundation of China (No. 32100009), the Natural Science Foundation of Guangdong Province, China (No. 2019B020230001), and Shenzhen Municipal Government of China (No. XMHT20220104017). Publisher Copyright: © 2024 The Authors. iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.

PY - 2024

Y1 - 2024

N2 - The Lachnospiraceae family holds promise as a source of next-generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in-depth genomic and functional analysis of 1868 high-quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization-selective species-level clusters, of which eight genera represented multilineage clusters. Pan-genome analysis, single-nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge-based selection of strains for the development of next-generation probiotics holding promise for improving human health and disease management.

AB - The Lachnospiraceae family holds promise as a source of next-generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in-depth genomic and functional analysis of 1868 high-quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization-selective species-level clusters, of which eight genera represented multilineage clusters. Pan-genome analysis, single-nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge-based selection of strains for the development of next-generation probiotics holding promise for improving human health and disease management.

KW - genomic analysis

KW - Lachnospiraceae

KW - next-generation probiotics

KW - probiotic functional predictions

U2 - 10.1002/imt2.174

DO - 10.1002/imt2.174

M3 - Journal article

AN - SCOPUS:85185459310

VL - 3

JO - iMeta

JF - iMeta

SN - 2770-5986

IS - 2

M1 - e174

ER -