The essential genomic landscape of the commensal Bifidobacterium breve UCC2003

• Published in: Scientific reports Vol. 7; no. 1; pp. 5648 - 13
• Main Authors: Ruiz, Lorena, Bottacini, Francesca, Boinett, Christine J., Cain, Amy K., O’Connell-Motherway, Mary, Lawley, Trevor D., van Sinderen, Douwe
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17-07-2017; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/70; 631/326/1320; 631/61/191/1908; Adaptation; Astrophysics; Bacterial Proteins - genetics; Bifidobacterium breve; Bifidobacterium breve - genetics; Bifidobacterium breve - growth & development; Biosynthesis; Commensals; DNA Transposable Elements; Evolution, Molecular; Gene expression; Genes, Essential; Genetic engineering; Genome, Plant; Genomes; Genomic analysis; Genomics; Health promotion; Humanities and Social Sciences; Insertion; Laboratories; Metabolism; Microorganisms; Molecular Sequence Annotation; multidisciplinary; Mutagenesis; Mutagenesis, Insertional; Phylogeny; Physics; Science; Science (multidisciplinary); Sequence Homology, Nucleic Acid; Statistical analysis; Symbiosis; Transposons
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-05795-y

Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn
5
transposon mutant library of the commensal
Bifidobacterium breve
UCC2003 that was further characterized by means of a
Tra
nsposon
D
irected
I
nsertion
S
equencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the
Bifidobacterium
and
B. breve
core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.