Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces

Sudeep Ghimire; Supapit Wongkuna; Joy Scaria

doi:10.7717/peerj.10071

Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces

PeerJ. 2020 Oct 5:8:e10071. doi: 10.7717/peerj.10071. eCollection 2020.

Authors

Sudeep Ghimire¹, Supapit Wongkuna¹, Joy Scaria¹

Affiliation

¹ Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America.

Abstract

A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502^T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501^T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991^T and E. tortuosum DSM 3987^T(=ATCC 25548^T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502^T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502^T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4-22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, which is about half the size of C. innocuum genome and the G+C content revealed 10 mol% difference. Phenotypically, the optimal growth temperature and pH for the strain SG502^T were 37 °C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain when grown in BHI-M medium. The major cellular fatty acids produced were C_18:1 ω9c, C_18:0and C_16:0. Thus, based on the polyphasic analysis, for the type strain SG502^T (=DSM 107282^T= CCOS 1889^T), the name Dakotella fusiforme gen. nov., sp. nov., is proposed.

Keywords: Culturomics; Dakotella fusiforme; Erysipelotrichaceae; Genomic taxonomy; Gut microbiome; New genus; New species.

Grants and funding

This work was supported by the USDA National Institute of Food and Agriculture, Hatch projects SD00H532-14 and SD00R540-15, and a grant from the South Dakota Governor’s Office of Economic Development awarded to Joy Scaria. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.