Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective

Blanco, Guillermo; Ruíz, Lorena; Tamés, Hector; Ruas‐Madiedo, Patricia; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, Anália; Margollés, Abelardo

doi:10.3390/microorganisms8050723

Cited by 12 publications

(8 citation statements)

References 48 publications

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“…longum subsp. longum strains have also been shown to encode members of glycosyl hydrolase (GH) families associated with the utilization of plant-derived carbohydrates (i.e., GH43, GH10, and GH5), reflecting their adaptation to plant glycan metabolism ( Arboleya et al, 2018 ; Blanco et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Plant Glycan Metabolism by Bifidobacteria

2021

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Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.

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Section: Introductionmentioning

confidence: 99%

Plant Glycan Metabolism by Bifidobacteria

2021

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“…Further, as expected, the subspecies corresponding to B.longum susbp. infantis was almost exclusively seen in infants (61/62) and contained a marker gene for the subspecies, sialidase ( Blanco et al , 2020 ; Supplementary Information S3 ).…”

Section: Resultsmentioning

confidence: 99%

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

et al. 2021

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Summary Taxonomic analysis of microbial communities is well supported at the level of species and strains. However, species can contain significant phenotypic diversity and strains are rarely widely shared across global populations. Stratifying the diversity between species and strains can identify ‘subspecies’, which are a useful intermediary. High-throughput identification and profiling of subspecies is not yet supported in the microbiome field. Here, we use an operational definition of subspecies based on single nucleotide variant (SNV) patterns within species to identify and profile subspecies in metagenomes, along with their distinctive SNVs and genes. We incorporate this method into metaSNV v2, which extends existing SNV-calling software to support further SNV interpretation for population genetics. These new features support microbiome analyses to link SNV profiles with host phenotype or environment and niche-specificity. We demonstrate subspecies identification in marine and fecal metagenomes. In the latter, we analyze 70 species in 7524 adult and infant subjects, supporting a common subspecies population structure in the human gut microbiome and illustrating some limits in subspecies calling. Availability and implementation Source code, documentation, tutorials and test data are available at https://github.com/metasnv-tool/metaSNV and https://metasnv.embl.de. Supplementary information Supplementary data are available at Bioinformatics online.

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“…Moreover, the ANI analysis of Albert et al clustered the B. longum SC664 genome conforming to subspecies infantis [ 8 ]. Notwithstanding, due to the large majority of B. longum genomes belonging to the subspecies longum , it is possible that fully sequenced of some strains such as B. longum SC664 and B. longum AH1206 indicated a different genomic architecture to adapt in their respective ecological niche [ 9 ].…”

Section: Discussionmentioning

confidence: 99%

“…longum and B. longum subsp. suis [ 7 , 8 , 9 ]. Among the key phylogenetic groups of Bifidobacterium , B. longum subsp.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota

et al. 2021

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Bifidobacterium longum subsp. longum is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies longum, as observed in phylogenetic analysis. B. longum SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among longum subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that B. longum M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of B. longum subsp. longum to colonize the human gut microbiota.

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Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective

Cited by 12 publications

References 48 publications

Plant Glycan Metabolism by Bifidobacteria

Plant Glycan Metabolism by Bifidobacteria

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota

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