Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets

Yanokura, Emiko; Oki, Kaihei; Makino, Hiroshi; Modesto, Monica Marianna; Pot, Bruno; Mattarelli, Paola; Biavati, Bruno; Watanabe, Koichi

doi:10.1016/j.syapm.2015.05.001

Cited by 40 publications

(41 citation statements)

References 53 publications

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“…The main spectrum profile (MSP) dendrogram was reconstructed using the correlation distance measure with the weighted linkage algorithm settings of the MALDI BioTyper software package version 3.1 (Bruker Daltonics). It has been employed successfully for subspeciation of Bifidobacterium longum, L. paracasei, Lactobacillus delbrueckii and Lactococcus lactis using MALDI-TOF MS [9,[41][42][43]. Cluster analysis of MALDI-TOF MS spectra in the 2000-12000 m/z (70 peaks) region of strains in the L. casei group revealed the unambiguous grouping of four distinct clusters (A, B, C and D).…”

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Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Huang

Chen

Liou

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Taxonomic relationships between Lactobacillus casei , Lactobacillus paracasei and Lactobacillus zeae have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains L. casei ATCC 393T and L. zeae ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that L. casei could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the L. zeae strains, and supported an emended the description of the name of Lactobacillus zeae (ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.

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confidence: 99%

Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Huang

Chen

Liou

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…The amplification program for the hsp60 gene consisted of one cycle of 95 8C for 5 min, 30 cycles of 94 8C for 30 s, 61 8C for 1 min and 72 8C for 45 s, and a final amplification step at 72 8C for 10 min. The conditions for PCR amplification of the partial clpC gene have been described by Yanokura et al (2015), using primers clpC-F (59-GAGTACCGCAAGTACATCGAG-39) and clpC-R (59-TCATCGTCGAACAGGAAC-39). The amplification program for the clpC gene consisted of one cycle of 94 8C for 2 min, 32 cycles of 94 8C for 20 s, 51 8C for 20 s and 72 8C for 20 s, and a final amplification step at 72 8C for 3 min.…”

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“…The amplification program for the clpC gene consisted of one cycle of 94 8C for 2 min, 32 cycles of 94 8C for 20 s, 51 8C for 20 s and 72 8C for 20 s, and a final amplification step at 72 8C for 3 min. The PCR-amplified 16S rRNA, hsp60 and clpC genes were purified according to Yanokura et al (2015).…”

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Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.)

Michelini

Oki²,

Yanokura

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…Despite the shift in microbiota composition during weaning, specific strains of Bifidobacterium , and B. longum in particular, have previously been shown to persist in individuals over time ( 35, 36 ). B. longum is currently recognised as four subspecies: longum and infantis (characteristic of the human gut microbiota), and suis and suillum (from animal hosts) ( 37, 38 ). It is considered the most common and prevalent species found in the human gut, with B. longum subsp.…”

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confidence: 99%

Succession ofBifidobacterium longumstrains in response to the changing early-life nutritional environment reveals specific adaptations to distinct dietary substrates

Kujawska¹,

Rosa

et al. 2020

Preprint

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13 Diet-microbe interactions play a crucial role in infant development and modulation of the early-life 14 microbiota. The genus Bifidobacterium dominates the breast-fed infant gut, with strains of B. 15 longum subsp. longum (B. longum) and B. longum subsp. infantis (B. infantis) particularly prevalent. 16Although transition from milk to a more diversified diet later in infancy initiates a shift to a more 17 complex microbiome, specific strains of B. longum may persist in individual hosts for prolonged 18 periods of time. Here, we sought to investigate the adaptation of B. longum to the changing infant 19 diet. Genomic characterisation of 75 strains isolated from nine either exclusively breast-or formula-20 fed (pre-weaning) infants in their first 18 months revealed subspecies-and strain-specific intra-21 individual genomic diversity with respect to glycosyl hydrolase families and enzymes, which 22 2 persistence in a single host and may contribute to rational development of new dietary therapies for 31 this important developmental window. 32 33 35 particularly the ones involved in the degradation of breast milk-associated human milk 52 oligosaccharides (HMOs) (8). The presence of these genes is often species-and indeed strain-53 specific, and has been described in B. breve, B. bifidum, B. longum, B. infantis, and more rarely in B. 54 pseudocatenulatum (8,(25)(26)(27). However, previous studies have indicated co-existence of 55Bifidobacterium species and strains in individual hosts, resulting in interaction and metabolic co-56 operation within a single (HMO-associated) ecosystem (1, 28). 57Transition from breastfeeding to a more diversified diet and the introduction of solid foods has been 58 considered to initiate the development of a functionally more complex adult-like microbiome with 59 genes responsible for degradation of plant-derived complex carbohydrates, starches, and 60 xenobiotics, as well as production of vitamins (29, 30). Non-digestible complex carbohydrates such 61 as inulin-type fructans (ITF), arabino-xylans (AX) or arabinoxylo-oligosaccharides (AXOS) in 62 3 complementary foods have been proposed to potentially exert beneficial health effects through 63 their bifidogenic and prebiotic properties and resulting modulation of the intestinal microbiota and 64 metabolic end-products (31)(32)(33)(34). 65Despite the shift in microbiota composition during weaning, specific strains of Bifidobacterium, and 66 B. longum in particular, have previously been shown to persist in individuals over time (35, 36). B. 67 longum is currently recognised as four subspecies: longum and infantis (characteristic of the human 68 gut microbiota), and suis and suillum (from animal hosts) (37, 38). It is considered the most common 69 and prevalent species found in the human gut, with B. longum subsp. infantis detected in infants, 70 and B. longum subsp. longum widely distributed in both infants and adults (39, 40). The differences 71 in prevalence between the two subspecies, and the ability of infant, adult and elderly host t...

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Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets

Cited by 40 publications

References 53 publications

Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.)

Succession ofBifidobacterium longumstrains in response to the changing early-life nutritional environment reveals specific adaptations to distinct dietary substrates

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