Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut

Ventura, Marco; Turroni, Francesca; Sinderen, Douwe van

doi:10.4161/bbug.18540

Cited by 60 publications

(36 citation statements)

References 62 publications

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“…These genome-scale analyses have contributed significantly to our understanding as to how these bacteria colonize and adapt to the human gut [17], [18], [19], [20]. Nevertheless, until recently bifidobacteria have been rather recalcitrant to genetic manipulation, which represents one of the main reasons for our poor understanding of the molecular mechanisms underlying their probiotic attributes.…”

Section: Introductionmentioning

confidence: 99%

Transposon Mutagenesis in Bifidobacterium breve: Construction and Characterization of a Tn5 Transposon Mutant Library for Bifidobacterium breve UCC2003

et al. 2013

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Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.

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Section: Introductionmentioning

confidence: 99%

Transposon Mutagenesis in Bifidobacterium breve: Construction and Characterization of a Tn5 Transposon Mutant Library for Bifidobacterium breve UCC2003

et al. 2013

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“…However, the molecular mechanisms underlying these proclaimed health-promoting activities are still largely unknown. Recently, significant efforts have been made to decode and analyze bifidobacterial genome sequences, which is part of a novel discipline called probiogenomics, aimed at the discovery of genetic determinants responsible for the adaptation of these microorganisms to the gastrointestinal tract of their host (6)(7)(8)(9)(10)(11). In the context of probiogenomics attempts involving bifidobacterial strains, members of the Bifidobacterium animalis subsp.…”

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confidence: 99%

Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

Milani

Duranti²,

Lugli³

et al. 2013

Appl Environ Microbiol

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Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. In this article, we describe the complete genetic makeup of the B. animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. Moreover, a detailed comparative genomic analysis of B. animalis subsp. lactis genomes was performed, which revealed a closely related and isogenic nature of all currently available B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome structure of this bacterial group.

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“…Bifidobacteria have been shown to beneficially modulate the composition and activity of the intestinal microbiota, to prevent bacterial infections, and to exert anti-inflammatory and immunomodulation activities [9]. These beneficial traits depend strongly on the ability of a strain to survive and to adapt in the GI-tract [10]. Adaptation and survival involve the use of efficient and diverse nutrient uptake systems, enzymes, stress proteins, and factors that interact with the host and with other members of the gut microbiota [11].…”

Section: Introductionmentioning

confidence: 99%

“…Functional genomics is powerful to identify bifidobacterial mechanisms active in the gut, such as genes involved in host-microbe interactions, the degradation of human milk oligosaccharides, or pili encoding genes [10, 23]. Combined genomic and proteomic analyses of bifidobacteria revealed mechanisms of adaptation to the GI-tract and genetic functions that mediate specific host-microbe and microbe-microbe interactions [26, 27].…”

Section: Introductionmentioning

confidence: 99%

The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions

Vazquez-Gutierrez

Stevens

Gehrig³

et al. 2017

BMC Genomics

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BackgroundBifidobacteria are among the first anaerobic bacteria colonizing the gut. Bifidobacteria require iron for growth and their iron-sequestration mechanisms are important for their fitness and possibly inhibit enteropathogens. Here we used combined genomic and proteomic analyses to characterize adaptations to low iron conditions of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, 2 strains isolated from the feces of iron-deficient African infants and selected for their high iron-sequestering ability.ResultsAnalyses of the genome contents revealed evolutionary adaptation to low iron conditions. A ferric and a ferrous iron operon encoding binding proteins and transporters were found in both strains. Remarkably, the ferric iron operon of B. pseudolongum PV8-2 is not found in other B. pseudolongum strains and likely acquired via horizontal gene transfer. The genome B. kashiwanohense PV20-2 harbors a unique region encoding genes putatively involved in siderophore production.Additionally, the secretomes of the two strains grown under low-iron conditions were analyzed using a combined genomic-proteomic approach. A ferric iron transporter was found in the secretome of B. pseudolongum PV8-2, while ferrous binding proteins were detected in the secretome of B. kashiwanohense PV20-2, suggesting different strategies to take up iron in the strains. In addition, proteins such as elongation factors, a glyceraldehyde-3-phosphate dehydrogenase, and the stress proteins GroEL and DnaK were identified in both secretomes. These proteins have been previously associated with adhesion of lactobacilli to epithelial cells.ConclusionAnalyses of the genome and secretome of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 revealed different adaptations to low iron conditions and identified extracellular proteins for iron transport. The identified extracellular proteins might be involved in competition for iron in the gastrointestinal tract.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3472-x) contains supplementary material, which is available to authorized users.

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Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut

Cited by 60 publications

References 62 publications

Transposon Mutagenesis in Bifidobacterium breve: Construction and Characterization of a Tn5 Transposon Mutant Library for Bifidobacterium breve UCC2003

Transposon Mutagenesis in Bifidobacterium breve: Construction and Characterization of a Tn5 Transposon Mutant Library for Bifidobacterium breve UCC2003

Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions

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