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Appl Environ Microbiol. 2019 Apr 4;85(8). pii: e03065-18. doi: 10.1128/AEM.03065-18. Print 2019 Apr 15.

Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom.

Author information

1
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
2
Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA.
3
Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA.
4
GenProbio srl, Parma, Italy.
5
Microbiome Research Hub, University of Parma, Parma, Italy.
6
Department of Veterinary Medical Science, University of Parma, Parma, Italy.
7
Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
8
APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
9
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy marco.ventura@unipr.it.
#
Contributed equally

Abstract

Bifidobacteria are commensals of the animal gut and are commonly found in mammals, birds, and social insects. Specifically, strains of Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium longum, and Bifidobacterium pseudolongum are widely distributed in the mammalian gut. In this context, we investigated the genetic variability and metabolic abilities of the B. pseudolongum taxon, whose genomic characterization has so far not received much attention. Phylogenomic analysis of the genome sequences of 60 B. pseudolongum strains revealed that B. pseudolongum subsp. globosum and B. pseudolongum subsp. pseudolongum may actually represent two distinct bifidobacterial species. Furthermore, our analysis highlighted metabolic differences between members of these two subspecies. Moreover, comparative analyses of genetic strategies to prevent invasion of foreign DNA revealed that the B. pseudolongum subsp. globosum group exhibits greater genome plasticity. In fact, the obtained findings indicate that B. pseudolongum subsp. globosum is more adaptable to different ecological niches such as the mammalian and avian gut than is B. pseudolongum subsp. pseudolongum IMPORTANCE Currently, little information exists on the genetics of the B. pseudolongum taxon due to the limited number of sequenced genomes belonging to this species. In order to survey genome variability within this species and explore how members of this taxon evolved as commensals of the animal gut, we isolated and decoded the genomes of 51 newly isolated strains. Comparative genomics coupled with growth profiles on different carbohydrates has further provided insights concerning the genotype and phenotype of members of the B. pseudolongum taxon.

KEYWORDS:

Bifidobacterium; animal commensals; bifidobacteria; genomics; next-generation sequencing

PMID:
30737347
PMCID:
PMC6450028
[Available on 2019-10-04]
DOI:
10.1128/AEM.03065-18

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