Host-Diet Effect on the Metabolism of

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2021 Apr 30

PMID 33924280

Citations 8

Authors

Maria Satti

Monica Modesto

Akihito Endo

Takeshi Kawashima

Paola Mattarelli

Masanori Arita

Affiliations

Soon will be listed here.

Abstract

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 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.

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References

Letunic I, Bork P . Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016; 44(W1):W242-5. PMC: 4987883. DOI: 10.1093/nar/gkw290. View

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

Contreras-Moreira B, Vinuesa P . GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013; 79(24):7696-701. PMC: 3837814. DOI: 10.1128/AEM.02411-13. View

Trovatelli L, Crociani F, Pedinotti M, Scardovi V . Bifidobacterium pullorum sp. nov.: a new species isolated from chicken feces and a related group of bifidobacteria isolated from rabbit feces. Arch Microbiol. 1974; 98(3):187-98. DOI: 10.1007/BF00425281. View

Ward R, Ninonuevo M, Mills D, Lebrilla C, German J . In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria. Mol Nutr Food Res. 2007; 51(11):1398-405. DOI: 10.1002/mnfr.200700150. View

Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P . Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol. 2019; 69(8):2477-2485. DOI: 10.1099/ijsem.0.003518. View

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D . Comparative genomics of the genus Bifidobacterium. Microbiology (Reading). 2010; 156(Pt 11):3243-3254. DOI: 10.1099/mic.0.039545-0. View

Milani C, Lugli G, Duranti S, Turroni F, Bottacini F, Mangifesta M . Genomic encyclopedia of type strains of the genus Bifidobacterium. Appl Environ Microbiol. 2014; 80(20):6290-302. PMC: 4178644. DOI: 10.1128/AEM.02308-14. View

10.

Keck F, Rimet F, Bouchez A, Franc A . phylosignal: an R package to measure, test, and explore the phylogenetic signal. Ecol Evol. 2016; 6(9):2774-80. PMC: 4799788. DOI: 10.1002/ece3.2051. View

11.

Blomberg S, Garland Jr T, Ives A . Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution. 2003; 57(4):717-45. DOI: 10.1111/j.0014-3820.2003.tb00285.x. View

12.

Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang C . 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(6):126017. DOI: 10.1016/j.syapm.2019.126017. View

13.

Duranti S, Lugli G, Napoli S, Anzalone R, Milani C, Mancabelli L . 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..... Int J Syst Evol Microbiol. 2019; 69(5):1288-1298. DOI: 10.1099/ijsem.0.003306. View

14.

Lugli G, Milani C, Duranti S, Alessandri G, Turroni F, Mancabelli L . Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol. 2019; 20(1):96. PMC: 6524291. DOI: 10.1186/s13059-019-1711-6. View

15.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

16.

Satti M, Tanizawa Y, Endo A, Arita M . Comparative analysis of probiotic bacteria based on a new definition of core genome. J Bioinform Comput Biol. 2018; 16(3):1840012. DOI: 10.1142/S0219720018400127. View

17.

Tanizawa Y, Fujisawa T, Nakamura Y . DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2017; 34(6):1037-1039. PMC: 5860143. DOI: 10.1093/bioinformatics/btx713. View

18.

Bottacini F, Milani C, Turroni F, Sanchez B, Foroni E, Duranti S . Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut. PLoS One. 2012; 7(9):e44229. PMC: 3447821. DOI: 10.1371/journal.pone.0044229. View

19.

Alberoni D, Gaggia F, Baffoni L, Modesto 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. 2018; 42(2):205-216. DOI: 10.1016/j.syapm.2018.11.005. View

20.

Capella-Gutierrez S, Silla-Martinez J, Gabaldon T . trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009; 25(15):1972-3. PMC: 2712344. DOI: 10.1093/bioinformatics/btp348. View