Comparative genomics and genotype-phenotype associations in Bifidobacterium breve

Scientific Reports
Francesca BottaciniDouwe van Sinderen

Abstract

Bifidobacteria are common members of the gastro-intestinal microbiota of a broad range of animal hosts. Their successful adaptation to this particular niche is linked to their saccharolytic metabolism, which is supported by a wide range of glycosyl hydrolases. In the current study a large-scale gene-trait matching (GTM) effort was performed to explore glycan degradation capabilities in B. breve. By correlating the presence/absence of genes and associated genomic clusters with growth/no-growth patterns across a dataset of 20 Bifidobacterium breve strains and nearly 80 different potential growth substrates, we not only validated the approach for a number of previously characterized carbohydrate utilization clusters, but we were also able to discover novel genetic clusters linked to the metabolism of salicin and sucrose. Using GTM, genetic associations were also established for antibiotic resistance and exopolysaccharide production, thereby identifying (novel) bifidobacterial antibiotic resistance markers and showing that the GTM approach is applicable to a variety of phenotypes. Overall, the GTM findings clearly expand our knowledge on members of the B. breve species, in particular how their variable genetic features can be linke...Continue Reading

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Citations

Mar 14, 2019·Scientific Reports·Manish KumarIndu Shekhar Thakur
May 8, 2019·American Journal of Primatology·Celeste J BrownLarry J Forney
Nov 14, 2020·Environmental Microbiology·Jonathon A BriggsHarry Brumer
Apr 10, 2021·Frontiers in Microbiology·Emily C HoedtDouwe van Sinderen
Sep 2, 2021·Applied and Environmental Microbiology·Gerald W Tannock

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Datasets Mentioned

BETA
CP021558

Methods Mentioned

BETA
phosphotransferase
PCR

Software Mentioned

Cazy
GTM
PGAP
BLASTP
mclblastline
BLAST

Related Concepts

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