Taxono-genomics description of Olsenella lakotia SW165 T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken

Supapit Wongkuna; Sudeep Ghimire; Tavan Janvilisri; Kinchel Doerner; Surang Chankhamhaengdecha; Joy Scaria

doi:10.12688/f1000research.25823.1

Taxono-genomics description of Olsenella lakotia SW165 ^T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken

F1000Res. 2020 Sep 8:9:1103. doi: 10.12688/f1000research.25823.1. eCollection 2020.

Authors

Supapit Wongkuna^{1

2}, Sudeep Ghimire^{2

3}, Tavan Janvilisri⁴, Kinchel Doerner⁵, Surang Chankhamhaengdecha⁶, Joy Scaria^{2

3}

Affiliations

¹ Doctor of Philosophy Program in Biochemistry (International Program), Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
² Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA.
³ South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, 57007, USA.
⁴ Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
⁵ Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, 57007, USA.
⁶ Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.

Abstract

Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165 ^T. Methods: For the possible novel strain SW165 ^T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was Olsenella profusa DSM 13989 ^T (96.33% similarity) within the family Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45 ^oC and pH 6.0-7.5 respectively. This strain produced acetic acid as the primary fermentation product. Major fatty acids were C _12:0, C _14:0, C _14:0 DMA and summed feature 1 (C _13:1 at 12-13 and C _14:0 aldehyde). Strain SW165 ^T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165 ^T and DSM 13989 ^T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus Olsenella, and name it Olsenella lakotia SW165 ^T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.

Keywords: Olsenella lakotia SW165T sp. nov.; chicken gut microbiota; culturomics; taxono-genomics.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Actinobacteria
Anaerobiosis
Animals
Bacterial Typing Techniques
Base Composition
Cecum
Chickens*
DNA, Bacterial
Genomics*
Phylogeny
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA

Substances

DNA, Bacterial
RNA, Ribosomal, 16S

Supplementary concepts

Olsenella profusa

Associated data

figshare/10.6084/m9.figshare.12793544.v1
figshare/10.6084/m9.figshare.12793610.v1

Grants and funding

This research project was supported by Mahidol University to SC and TJ, and was funded in part 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 to JS.