Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov.

Modesto, Monica Marianna; Satti, Maria; Watanabe, Koichi; Puglisi, Edoardo; Morelli, L.; Huang, Chien‐Hsun; Liou, Jong‐Shian; Miyashita, Mika; Tamura, Tomohiko; Saito, Satomi; Mori, Koji; Huang, Lina; Sciavilla, Piero; Sandri, Camillo; Spiezio, Caterina; Vitali, Francesco; Cavalieri, Duccio; Perpetuini, Giorgia; Tofalo, Rosanna; Bonetti, Andrea; Arita, Masanori; Mattarelli, Paola

doi:10.1016/j.syapm.2019.126017

Cited by 23 publications

(5 citation statements)

References 26 publications

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“…Bifidobacteria are gram-positive anaerobes that inhabit animal digestive tracts and dairy products, with 78 species and 10 subspecies taxonomically identified to date (a total of 84 taxa) [1][2][3][4][5][6][7][8][9][10][11]. More than ten (sub)species were isolated from human stools, and among them, six (sub)species are known to be frequent colonizers of infant guts (described later) [1,[12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

et al. 2019

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The infant’s gut microbiome is generally rich in the Bifidobacterium genus. The mother’s milk contains natural prebiotics, called human milk oligosaccharides (HMOs), as the third most abundant solid component after lactose and lipids, and of the different gut microbes, infant gut-associated bifidobacteria are the most efficient in assimilating HMOs. Indeed, the fecal concentration of HMOs was found to be negatively correlated with the fecal abundance of Bifidobacterium in infants. Given these results, two HMO molecules, 2′-fucosyllactose and lacto-N-neotetraose, have recently been industrialized to fortify formula milk. As of now, however, our knowledge about the HMO consumption pathways in infant gut-associated bifidobacteria is still incomplete. The recent studies indicate that HMO assimilation abilities significantly vary among different Bifidobacterium species and strains. Therefore, to truly maximize the effects of prebiotic and probiotic supplementation in commercialized formula, we need to understand HMO consumption behaviors of bifidobacteria in more detail. In this review, we summarized how different Bifidobacterium species/strains are equipped with varied gene sets required for HMO assimilation. We then examined the correlation between the abundance of the HMO-related genes and bifidobacteria-rich microbiota formation in the infant gut through data mining analysis of a deposited fecal microbiome shotgun sequencing dataset. Finally, we shortly described future perspectives on HMO-related studies.

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Section: Introductionmentioning

confidence: 99%

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

et al. 2019

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“…These microorganisms were classified as Gram-positive, nonspore-forming, and nonmotile bacteria that belong to the phylum Actinobacteria [4]. To date, 88 different bifidobacterial (sub)species were classified, mostly isolated from the gastrointestinal tract of numerous animals, the human gut and oral cavity, and insect hindgut [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

et al. 2020

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Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR–Cas and restriction–modification systems may be responsible for the high genome synteny identified among members of this taxon.

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“…MARM_A1 also encodes two genes for the central metabolism of rhamnose at the PI-1 locus ( rhaW , encoding l -rhamnoate dehydratase, and rhaD , encoding 2-keto-3-deoxy- l -rhamnoate aldolase). Rhamnose utilization ( 53 ) and pectin degradation ( 54 , 55 ) are relatively rare traits among Bifidobacterium species, with the notable exception of the pectin-degrading capacity found in B. vespertilionis isolated from fruit bats ( 56 ). Although PI-1 and PI-2 were absent in the MARM_A3 genome, rhaW and rhaD were found adjacent to a 6×H family α- l -rhamnosidase, suggesting that this organism may cross-feed from the cleavage of rhamnose residues from the major pectin backbones by MARM_A1.…”

Section: Resultsmentioning

confidence: 99%

Captive Common Marmosets (Callithrix jacchus) Are Colonized throughout Their Lives by a Community of Bifidobacterium Species with Species-Specific Genomic Content That Can Support Adaptation to Distinct Metabolic Niches

Zhu

Yang

Haute

et al. 2021

mBio

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Bifidobacterium species are recognized as important, beneficial microbes in the human gut microbiome, and their ability colonize individuals at different stages of life is influenced by poorly understood interactions between host, dietary, environmental, and ecological factors. The common marmoset is an emerging nonhuman primate model with a short maturation period, making this model amenable to study of the microbiome throughout a life history.

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Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov.

Cited by 23 publications

References 26 publications

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

Captive Common Marmosets (Callithrix jacchus) Are Colonized throughout Their Lives by a Community of Bifidobacterium Species with Species-Specific Genomic Content That Can Support Adaptation to Distinct Metabolic Niches

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