Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov

Gabriele Andrea Lugli; Marta Mangifesta; Sabrina Duranti; Rosaria Anzalone; Christian Milani; Leonardo Mancabelli; Giulia Alessandri; Francesca Turroni; Maria Cristina Ossiprandi; Douwe van Sinderen; Marco Ventura

doi:10.1016/j.syapm.2018.01.002

Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov

Syst Appl Microbiol. 2018 May;41(3):173-183. doi: 10.1016/j.syapm.2018.01.002. Epub 2018 Jan 31.

Affiliations

¹ Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
² GenProbio srl, Parma, Italy.
³ Department of Veterinary Medical Science, University of Parma, Parma, Italy.
⁴ APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland.
⁵ Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy. Electronic address: [email protected].

PMID: 29395537
DOI: 10.1016/j.syapm.2018.01.002

Abstract

Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189^T=CCUG 70960^T), Bifidobacterium criceti sp. nov. (Ham19E=LMG 30188^T=CCUG 70962^T), Bifidobacterium imperatoris sp. nov. (Tam1G=LMG 30297^T=CCUG 70961^T), Bifidobacterium italicum sp. nov. (Rab10A=LMG 30187^T=CCUG 70963^T), Bifidobacterium margollesii sp. nov. (Uis1B=LMG 30296^T=CCUG 70959^T) and Bifidobacterium parmae sp. nov. (Uis4E=LMG 30295^T=CCUG 70964^T) are proposed as novel Bifidobacterium species.

Keywords: Bifidobacteria; Bifidobacterium; Genomics; Metagenomics; Next generation sequencing; Phylogenetic.

MeSH terms

Animals
Bacterial Typing Techniques
Base Sequence
Bifidobacterium / classification*
Bifidobacterium / genetics
Callithrix / microbiology
Cricetinae / microbiology
DNA, Bacterial / genetics
Fatty Acids / analysis
Feces / microbiology*
Geese / microbiology
High-Throughput Nucleotide Sequencing
Italy
Phylogeny*
RNA, Ribosomal, 16S / genetics
Rabbits / microbiology
Saguinus / microbiology
Sequence Analysis, DNA

Substances

DNA, Bacterial
Fatty Acids
RNA, Ribosomal, 16S