Comparative genomics and genotype-phenotype associations in Bifidobacterium breve

Bottacini, Francesca; Morrissey, Ruth; Esteban-Torres, María; James, Kieran; Breen, Justin van; Dikareva, Evgenia; Egan, M.G.; Lambert, Jolanda; Limpt, Kees van; Knol, Jan; Motherway, Mary O’Connell; Sinderen, Douwe van

doi:10.1038/s41598-018-28919-4

Cited by 42 publications

(49 citation statements)

References 57 publications

(73 reference statements)

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“…infantis was the first bifidobacteria studied to carry a cluster of genes involved in the metabolism of HMOs [38], with B. longum ssp. longum [39] and B. breve [40] also able to utilize some types of HMOs. On the other hand, DHM-fed premature babies' feces exhibited increments over time of different species, such as B. bifidum, B. dentium, B. adolescentis, and B. animalis spp.…”

Section: Discussionmentioning

confidence: 99%

Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies

et al. 2020

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Correct establishment of the gut microbiome is compromised in premature babies, with Bifidobacterium being one of the most affected genera. Prematurity often entails the inability to successfully breastfeed, therefore requiring the implementation of other feeding modes; breast milk expression from a donor mother is the recommended option when their own mother’s milk is not available. Some studies showed different gut microbial profiles in premature infants fed with breast milk and donor human milk, however, it is not known how this affects the species composition of the genus Bifidobacterium. The objective of this study was to assess the effect of donated human milk on shaping the gut bifidobacterial populations of premature babies during the first three months of life. We analyzed the gut bifidobacterial communities of 42 premature babies fed with human donor milk or own-mother milk by the 16S rRNA–23S rRNA internal transcriber spaces (ITS) region sequencing and q-PCR. Moreover, metabolic activity was assessed by gas chromatography. We observed a specific bifidobacterial profile based on feeding type, with higher bifidobacterial diversity in the human donor milk group. Differences in specific Bifidobacterium species composition may contribute to the development of specific new strategies or treatments aimed at mimicking the impact of own-mother milk feeding in neonatal units.

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Section: Discussionmentioning

confidence: 99%

Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies

et al. 2020

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“…The predominant GH in all strains was GH13 which represents enzymes for the hydrolysis of alpha-glucosidic linkages in plant di-, oligo-, and polysaccharides [29]. Whilst, the second most abundant GH family present in infant V1 and V3 (but not infant V2) was GH43, which contains enzymes like beta-xylosidases (involved in xylan digestion).…”

Section: Functional Annotation Of Genomes Of Bifidobacterium From Infmentioning

confidence: 99%

“…V1 strains had the largest proportion of carbohydrate metabolism and transport genes (10.32%), whilst strains from infant V2 and V3 were slightly lower (10.06% and 9.53% respectively). Intraspecies gene differences in carbohydrate metabolism have been well described for B. pseudocatenulatum (albeit limited), and more so for B. longum and B. breve [29][30][31]. The B. pseudocatenulatum genome has a high proportion of glycosyl hydrolase family (GH)-43 enzymes that aid in the degradation of complex plant glycans, similar to other species including B. dentium and Bifidobacterium adolescentis [32].…”

Section: Functional Annotation Of Genomes Of Bifidobacterium From Infmentioning

confidence: 99%

Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem

et al. 2019

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Diet-microbe interactions play an important role in modulating the early-life microbiota, with Bifidobacterium strains and species dominating the gut of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating that within single infants there were differences in the ability to utilise 2′FL and LNnT HMOs between strains. Cross-feeding experiments were performed with HMO degraders and non-HMO users (using spent or 'conditioned' media and direct co-culture). Further 1 H-NMR analysis identified fucose, galactose, acetate, and N-acetylglucosamine as key by-products of HMO metabolism; as demonstrated by modest growth of non-HMO users on spend media from HMO metabolism. These experiments indicate how HMO metabolism permits the sharing of resources to maximise nutrient consumption from the diet and highlights the cooperative nature of bifidobacterial strains and their role as 'foundation' species in the infant ecosystem. The intra-and inter-infant bifidobacterial community behaviour may contribute to the diversity and dominance of Bifidobacterium in early life and suggests avenues for future development of new diet and microbiota-based therapies to promote infant health.

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“…Comparative genomics studies of members of the genus Bifidobacterium have provided valuable information regarding the characteristics that are unique to, shared between, or distinguish Bifidobacterium species from other gut microbiota. These characteristics likely evolved as a consequence of interspecies interactions among bacteria and adaptation to the host environment (Bottacini et al, ; Bottacini, O'Connell Motherway et al, ; Lee & O'Sullivan, ; Lugli et al, ; Schell et al, ; Sela et al, ). In view of what is known about the role of Bifidobacterium species in animal health, comparisons between species with different host specificity can provide information relevant to understanding adaptation to the host environment.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

Brown

Mtui

Oswald

et al. 2019

American J Primatol

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The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.

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Comparative genomics and genotype-phenotype associations in Bifidobacterium breve

Cited by 42 publications

References 57 publications

Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies

Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies

Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

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