Nooij S, Plomp N, Sanders I M J G, Schout L, van der Meulen A E, Terveer E M, Norman J M, Karcher N, Larralde M F, Vossen R H A M, Kloet S L, Faber K N, Harmsen H J M, Zeller G F, Kuijper E J, Smits W K, Ducarmon Q R
Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands.
Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.
Nat Commun. 2025 Jan 30;16(1):1182. doi: 10.1038/s41467-025-56449-x.
Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.
迟缓瘤胃球菌是一种在90%以上的健康个体肠道中都能发现的细菌，但其丰度增加也与慢性炎症性疾病有关，尤其是克罗恩病。然而，其全球分布和种内基因组变异仍未得到充分研究。通过对12791个肠道宏基因组进行调查，我们总结了与代谢疾病和炎症性肠病的已知关联。我们发现西方化人群中迟缓瘤胃球菌的患病率和丰度更高，并且在新生儿中观察到该细菌的相对丰度高达83%。接下来，我们构建了一份来自健康个体和克罗恩病患者的迟缓瘤胃球菌分离株资源（N = 45），并使用PacBio环形一致序列测序生成了完整的迟缓瘤胃球菌基因组。对这些基因组以及公开可用的高质量草图基因组（N = 333个基因组）进行分析后，发现了多个分支，这些分支将来自克罗恩病患者的分离株与来自健康个体的分离株区分开来。推测的迟缓瘤胃球菌毒力因子无法解释这种分离现象。细菌全基因组关联研究表明，来自克罗恩病患者的分离株在与移动元件和黏蛋白觅食相关的基因中富集。我们共同提供了一份大型的迟缓瘤胃球菌资源，可供科学界使用，并为迟缓瘤胃球菌的全球分布和基因组变异提供了新的生物学见解。
