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Comparative Study
. 2021 Apr 20;12(4):609.
doi: 10.3390/genes12040609.

Host-Diet Effect on the Metabolism of Bifidobacterium

Maria Satti  1 , Monica Modesto  2 , Akihito Endo  3 , Takeshi Kawashima  4 , Paola Mattarelli  2 , Masanori Arita  4   5
Affiliations
Comparative Study

Host-Diet Effect on the Metabolism of Bifidobacterium

Maria Satti et al. Genes (Basel). .

Abstract

Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts' dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts' feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts' dietary pattern is the key determinant of the distribution and evolution of GH genes.

Keywords: Bifidobacterium; comparative genomics; evolution; glycoside hydrolase; phylogenetics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree based on concatenated amino acid sequences of 362 core genes of the 84 type strains. Bootstrap percentages of >70 are shown. Eleven phylogenetic groups are highlighted in different colors and the new group is the second rightmost (rose).
Figure 2
Figure 2
Genome sizes of the strains in each dietary group. The box plot indicates the mean and standard deviation. Compro: Commercial probiotic; Exudi: Exudativore; Fermen: Fermented food; Frugi: Frugivore; Grani: Granivore; Gumi: Gummivore; Herbi: Herbivore; Infant: Infant food; Ins&Frugi: Frugivore eating insects; Insec: Nectarivore, palynivore; Omni: Omnivore; Oppori: Opportunistic omnivore eating fruits, leaves and insects; Sewg: Sewage. Exudi, gumi, and grani eat insects too. The colors in the boxplot show different host groups; Dark red: bats, Pink: monkey/apes, Blue: human/pigs, Yellow: other animals.
Figure 3
Figure 3
Distribution of the number of glycoside hydrolase genes in the different dietary groups. CAZyme families in >80% of the strains are shown. The significance by Kruskal-Wallis test is shown by asterisks. * p < 0.05, ** p < 0.01, *** p < 0.001.
Figure 4
Figure 4
Clustering of bifidobacterial species based on GH family genes. The heatmap shows the gene number for the selected GH families (families present in 20% of the strains). Pink: Group I with the opportunistic omnivores; Orange: Group II with omnivore, herbivore or insectivore; Gold: Group III with nectarivore; Red: Group IV with insectivore and frugivore; Green: Group V with herbivore and mixed diet. Each strain is highlighted with the color of the corresponding diet class.
Figure 5
Figure 5
Clustering of 66 strains isolated from different sources based on their GHs. Heatmap displays the number of genes in GH families. Strains were colored according to their host dietary patterns as in the upper box. Strains were clustered in seven major groups: Cluster (i) Opportunistic omnivore; Cluster (ii) and Cluster (vi) Herbivore; Cluster (iii) and Cluster (v) Omnivore; Cluster (iv) Infant food; and Cluster (vii) Granivore and Insectivore.
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References

    1. Alberoni D., Gaggìa F., Baffoni L., Modesto M.M., Biavati B., Di Gioia D. Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract. Syst. Appl. Microbiol. 2019;42:205–216. doi: 10.1016/j.syapm.2018.11.005. - DOI - PubMed
    1. Modesto M., Watanabe K., Arita M., Satti M., Oki K., Sciavilla P., Patavino C., Cammà C., Michelini S., Sgorbati B., et al. Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus) Int. J. Syst. Evol. Microbiol. 2019;69:2477–2485. doi: 10.1099/ijsem.0.003518. - DOI - PubMed
    1. Modesto M., Satti M., Watanabe K., Puglisi E., Morelli L., Huang C.-H., Liou J.-S., Miyashita M., Tamura T., Saito S., et al. Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov. Syst. Appl. Microbiol. 2019;42:126017. doi: 10.1016/j.syapm.2019.126017. - DOI - PubMed
    1. Duranti S., Lugli G.A., Napoli S., Anzalone R., Milani C., Mancabelli L., Alessandri G., Turroni F., Ossiprandi M.C., Van Sinderen D., et al. Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. Int. J. Syst. Evol. Microbiol. 2019;69:1288–1298. doi: 10.1099/ijsem.0.003306. - DOI - PubMed
    1. Lugli G.A., Mangifesta M., Duranti S., Anzalone R., Milani C., Mancabelli L., Alessandri G., Turroni F., Ossiprandi M.C., van Sinderen D., et al. Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. Syst. Appl. Microbiol. 2018;41:173–183. doi: 10.1016/j.syapm.2018.01.002. - DOI - PubMed

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