Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov

Monica Modesto; Maria Satti; Koichi Watanabe; Chien-Hsun Huang; Jong-Shian Liou; Tomohiko Tamura; Satomi Saito; Koji Mori; Lina Huang; Camillo Sandri; Caterina Spiezio; Barbara Sgorbati; Donatella Scarafile; Cesare Cammà; Massimo Ancora; Claudio Patavino; Masanori Arita; Paola Mattarelli

doi:10.1099/ijsem.0.004506

Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov

Int J Syst Evol Microbiol. 2020 Dec;70(12):6115-6125. doi: 10.1099/ijsem.0.004506.

Authors

Monica Modesto¹, Maria Satti², Koichi Watanabe^{3

4}, Chien-Hsun Huang³, Jong-Shian Liou³, Tomohiko Tamura⁵, Satomi Saito⁵, Koji Mori⁵, Lina Huang³, Camillo Sandri⁶, Caterina Spiezio⁶, Barbara Sgorbati¹, Donatella Scarafile¹, Cesare Cammà⁷, Massimo Ancora⁷, Claudio Patavino⁷, Masanori Arita^{8

9}, Paola Mattarelli¹

Affiliations

¹ Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
² Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan.
³ Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC.
⁴ Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC.
⁵ Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.
⁶ Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy.
⁷ National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy.
⁸ Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
⁹ RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.

PMID: 33052806
DOI: 10.1099/ijsem.0.004506

Abstract

Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth (Choloepus didactylus) housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dnaG) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854^T (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6^T), whereas the type strain of Bifidobacterium dentium DSM 20436^T (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6^T and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6^T combined with phenotypic analyses clearly revealed that the strain BRDM 6^T represents a novel species for which the names Bifidobacterium choloepi sp. nov. (BRDM 6^T=NBRC 114053^T=BCRC 81222^T) is proposed.

Keywords: Bifidobacterium; Bifidobacterium choloepi; Choloepus didactylus; new species; two-toed sloth.

MeSH terms

Animals
Bacterial Typing Techniques
Base Composition
Bifidobacterium / classification*
Bifidobacterium / isolation & purification
DNA, Bacterial / genetics
Fatty Acids / chemistry
Feces / microbiology
Genes, Bacterial
Italy
Male
Peptidoglycan / chemistry
Phylogeny*
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA
Sloths / microbiology*

Substances

DNA, Bacterial
Fatty Acids
Peptidoglycan
RNA, Ribosomal, 16S