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

Blanco, Guillermo; Ruiz, Lorena; Tamé; s, Hector; Ruas-Madiedo, Patricia; Fdez-Riverola, Florentino; Sá; nchez, Borja; Lourenç; o, Aná; lia; Margolles, Abelardo

doi:10.3390/microorganisms8050723

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

Microorganisms, v.8 no.5, 2020년, pp.723 -

Blanco, Guillermo (Escuela Superior de Ingenierí) , Ruiz, Lorena (a Informá) , Tamés, Hector (tica, Edificio Polité) , Ruas-Madiedo, Patricia (cnico, Campus Universitario As Lagoas s) , Fdez-Riverola, Florentino (guillermo@guillermoblanco.es (G.B.)) , Sánchez, Borja (riverola@uvigo.es (F.F.-R.)) , Lourenço, Anália (Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lá) , Margolles, Abelardo (cteos de Asturias (IPLA), Consejo Superior de Investigaciones Cientí)

Abstract ▼ AI-Helper

Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

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참고문헌 (46)

1. Bottacini F. Ventura M. van Sinderen D. O’Connell Motherway M. Diversity, ecology and intestinal function of bifidobacteria Microb. Cell Fact. 2014 13 Suppl. 1 S4 10.1186/1475-2859-13-S1-S4 25186128

상세보기
2. Qin J. Li R. Raes J. Arumugam M. Burgdorf K.S. Manichanh C. Nielsen T. Pons N. Levenez F. Yamada T. A human gut microbial gene catalogue established by metagenomic sequencing Nature 2010 464 59 65 10.1038/nature08821 20203603

상세보기
3. Koutsoumanis K. Allende A. Alvarez-Ordonez A. Bolton D. Bover-Cid S. Chemaly M. Davies R. De Cesare A. Hilbert F. Lindqvist R. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA EFSA J. 2019 15 5753
4. Hidalgo-Cantabrana C. Delgado S. Ruiz L. Ruas-Madiedo P. Sanchez B. Margolles A. Bifidobacteria and Their Health-Promoting Effects Microbiol. Spectr. 2018 10.1128/9781555819705.ch3
5. Mattarelli P. Bonaparte C. Pot B. Biavati B. Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov Int. J. Syst. Evol. Microbiol. 2008 58 767 772 10.1099/ijs.0.65319-0 18398167

상세보기
6. Yanokura E. Oki K. Makino H. Modesto M. Pot B. Mattarelli P. Biavati B. Watanabe K. 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 Syst. Appl. Microbiol. 2015 38 305 314 10.1016/j.syapm.2015.05.001 26007614

상세보기
7. Milani C. Duranti S. Bottacini F. Casey E. Turroni F. Mahony J. Belzer C. Delgado-Palacio S. Arboleya-Montes S. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol. Biol. Rev. 2017 81 e00036-17 10.1128/MMBR.00036-17 29118049

상세보기
8. Turroni F. Milani C. Duranti S. Mancabelli L. Mangifesta M. Viappiani A. Lugli G.A. Ferrario C. Gioiosa L. Ferrarini A. Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach ISME J. 2016 10 1656 1668 10.1038/ismej.2015.236 26859770

상세보기
9. Schell M.A. Karmirantzou M. Snel B. Vilanova D. Berger B. Pessi G. Zwahlen M.C. Desiere F. Bork P. Delley M. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract Proc. Natl. Acad. Sci. USA 2002 99 14422 14427 10.1073/pnas.212527599 12381787

상세보기
10. Sela D.A. Chapman J. Adeuya A. Kim J.H. Chen F. Whitehead T.R. Lapidus A. Rokhsar D.S. Lebrilla C.B. German J.B. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome Proc. Natl. Acad. Sci. USA 2008 105 18964 18969 10.1073/pnas.0809584105 19033196

상세보기
11. Sela D.A. Li Y. Lerno L. Wu S. Marcobal A.M. German J.B. Chen X. Lebrilla C.B. Mills D.A. An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides J. Biol. Chem. 2011 286 11909 11918 10.1074/jbc.M110.193359 21288901

상세보기
12. Zabel B. Yde C.C. Roos P. Marcussen J. Jensen H.M. Salli K. Hirvonen J. Ouwehand A.C. Morovic W. Novel Genes and Metabolite Trends in Bifidobacterium longum subsp. infantis Bi-26 Metabolism of Human Milk Oligosaccharide 2’-fucosyllactose Sci. Rep. 2019 9 7983 10.1038/s41598-019-43780-9 31138818

상세보기
13. O’Callaghan A. Bottacini F. O’Connell Motherway M. van Sinderen D. Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems BMC Genom. 2015 16 832 10.1186/s12864-015-1968-4 26489930

상세보기
14. Milani C. Turroni F. Duranti S. Lugli G.A. Mancabelli L. Ferrario C. van Sinderen D. Ventura M. Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment Appl. Environ. Microbiol. 2015 82 980 991 10.1128/AEM.03500-15 26590291

상세보기
15. Quast C. Pruesse E. Yilmaz P. Gerken J. Schweer T. Yarza P. Peplies J. Glockner F.O. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools Nucleic Acids Res. 2013 41 D590 D596 10.1093/nar/gks1219 23193283

상세보기
16. Sievers F. Wilm A. Dineen D. Gibson T.J. Karplus K. Li W. Lopez R. McWilliam H. Remmert M. Soding J. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Mol. Syst. Biol. 2011 7 539 10.1038/msb.2011.75 21988835

상세보기
17. Letunic I. Bork P. Interactive Tree Of Life (iTOL) v4: Recent updates and new developments Nucleic Acids Res. 2019 47 W256 W259 10.1093/nar/gkz239 30931475

상세보기
18. Seemann T. Prokka: Rapid prokaryotic genome annotation Bioinformatics 2014 30 2068 2069 10.1093/bioinformatics/btu153 24642063

상세보기
19. Page A.J. Cummins C.A. Hunt M. Wong V.K. Reuter S. Holden M.T. Fookes M. Falush D. Keane J.A. Parkhill J. Roary: Rapid large-scale prokaryote pan genome analysis Bioinformatics 2015 31 3691 3693 10.1093/bioinformatics/btv421 26198102

상세보기
20. Blanco G. Sanchez B. Ruiz L. Fdez-Riverola F. Margolles A. Lourenco A. Computational approach to the systematic prediction of glycolytic abilities: Looking into human microbiota IEEE/ACM Trans. Comput. Biol. Bioinform. 2020 10.1109/TCBB.2020.2978461

상세보기
21. Cantarel B.L. Coutinho P.M. Rancurel C. Bernard T. Lombard V. Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): An expert resource for Glycogenomics Nucleic Acids Res. 2009 37 D233 D238 10.1093/nar/gkn663 18838391

상세보기
22. Kanehisa M. Goto S. KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 2000 28 27 30 10.1093/nar/28.1.27 10592173

상세보기
23. NCBI Resource Coordinators Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 2018 46 D8 D13 10.1093/nar/gkx1095 29140470

상세보기
24. Altschul S.F. Gish W. Miller W. Myers E.W. Lipman D.J. Basic local alignment search tool J. Mol. Biol. 1990 215 403 410 10.1016/S0022-2836(05)80360-2 2231712

상세보기
25. Skuta C. Bartnk P. Svozil D. InCHlib-interactive cluster heatmap for web applications J. Cheminform. 2014 6 44 10.1186/s13321-014-0044-4 25264459

상세보기
26. Bottacini F. Morrissey R. Esteban-Torres M. James K. van Breen J. Dikareva E. Egan M. Lambert J. van Limpt K. Knol J. Comparative genomics and genotype-phenotype associations in Bifidobacterium breve Sci. Rep. 2018 8 10633 10.1038/s41598-018-28919-4 30006593

상세보기
27. Kullen M.J. Brady L.J. O’Sullivan D.J. Evaluation of using a short region of the recA gene for rapid and sensitive speciation of dominant bifidobacteria in the human large intestine FEMS Microbiol. Lett. 1997 154 377 383 10.1016/S0378-1097(97)00356-X 9311137

상세보기
28. Roy D. Sirois S. Molecular differentiation of Bifidobacterium species with amplified ribosomal DNA restriction analysis and alignment of short regions of the ldh gene FEMS Microbiol. Lett. 2000 191 17 24 10.1111/j.1574-6968.2000.tb09313.x 11004394

상세보기
29. Sakanaka M. Nakakawaji S. Nakajima S. Fukiya S. Abe A. Saburi W. Mori H. Yokota A. A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS3 Family Insertion Sequence, ISBlo11 Appl. Environ. Microbiol. 2018 84 e00824-18 10.1128/AEM.00824-18 29934330

상세보기
30. Ventura M. Canchaya C. Meylan V. Klaenhammer T.R. Zink R. Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification Appl. Environ. Microbiol. 2003 69 6908 6922 10.1128/AEM.69.11.6908-6922.2003 14602655

상세보기
31. Chaplin A.V. Efimov B.A. Smeianov V.V. Kafarskaia L.I. Pikina A.P. Shkoporov A.N. Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum PLoS ONE 2015 10 e0135658 10.1371/journal.pone.0135658 26275230

상세보기
32. Munoz J.A. Chenoll E. Casinos B. Bataller E. Ramon D. Genoves S. Montava R. Ribes J.M. Buesa J. Fabrega J. Novel probiotic Bifidobacterium longum subsp. infantis CECT 7210 strain active against rotavirus infections Appl. Environ. Microbiol. 2011 77 8775 8783 22003027

상세보기
33. Milani C. Lugli G.A. Duranti S. Turroni F. Mancabelli L. Ferrario C. Mangifesta M. Hevia A. Viappiani A. Scholz M. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut Sci. Rep. 2015 5 5782 10.1038/srep15782

상세보기
34. Arboleya S. Bottacini F. O’Connell-Motherway M. Ryan C.A. Ross R.P. van Sinderen D. Stanton C. Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains BMC Genom. 2018 19 33 10.1186/s12864-017-4388-9 29310579

상세보기
35. Riviere A. Selak M. Geirnaert A. Van den Abbeele P. De Vuyst L. Complementary Mechanisms for Degradation of Inulin-Type Fructans and Arabinoxylan Oligosaccharides among Bifidobacterial Strains Suggest Bacterial Cooperation Appl. Environ. Microbiol. 2018 84 e02893-17 10.1128/AEM.02893-17 29500265

상세보기
36. Pastell H. Westermann P. Meyer A.S. Tuomainen P. Tenkanen M. In vitro fermentation of arabinoxylan-derived carbohydrates by bifidobacteria and mixed fecal microbiota J. Agric. Food Chem. 2009 57 8598 8606 10.1021/jf901397b 19694435

상세보기
37. Ruiz-Aceituno L. Esteban-Torres M. James K. Moreno F.J. van Sinderen D. Metabolism of biosynthetic oligosaccharides by human-derived Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 8809 Int. J. Food Microbiol. 2020 316 108476 10.1016/j.ijfoodmicro.2019.108476 31874325

상세보기
38. Garrido D. Ruiz-Moyano S. Kirmiz N. Davis J.C. Totten S.M. Lemay D.G. Ugalde J.A. German J.B. Lebrilla C.B. Mills D.A. A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596 Sci. Rep. 2016 6 35045 10.1038/srep35045 27756904

상세보기
39. Sakanaka M. Hansen M.E. Gotoh A. Katoh T. Yoshida K. Odamaki T. Yachi H. Sugiyama Y. Kurihara S. Hirose J. Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis Sci. Adv. 2019 5 eaaw7696 10.1126/sciadv.aaw7696 31489370

상세보기
40. Margolles A. de los Reyes-Gavilan C.G. Purification and functional characterization of a novel alpha- l -arabinofuranosidase from Bifidobacterium longum B667 Appl. Environ. Microbiol. 2003 69 5096 5103 10.1128/AEM.69.9.5096-5103.2003 12957891

상세보기
41. Komeno M. Hayamizu H. Fujita K. Ashida H. Two Novel α- l -Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan Appl. Environ. Microbiol. 2019 85 e02582-18 10.1128/AEM.02582-18 30635377

상세보기
42. Fujita K. Sasaki Y. Kitahara K. Degradation of plant arabinogalactan proteins by intestinal bacteria: Characteristics and functions of the enzymes involved Appl. Microbiol. Biotechnol. 2019 103 7451 7457 10.1007/s00253-019-10049-0 31384991

상세보기
43. Van Laere K.M. Beldman G. Voragen A.G. A new arabinofuranohydrolase from Bifidobacterium adolescentis able to remove arabinosyl residues from double-substituted xylose units in arabinoxylan Appl. Microbiol. Biotechnol. 1997 47 231 235 10.1007/s002530050918 9114514

상세보기
44. Broekaert W.F. Courtin C.M. Verbeke K. Van de Wiele T. Verstraete W. Delcour J.A. Prebiotic and other health-related effects of cereal-derived arabinoxylans, arabinoxylan-oligosaccharides, and xylooligosaccharides Crit. Rev. Food Sci. Nutr. 2011 51 178 194 10.1080/10408390903044768 21328111

상세보기
45. Walton G.E. Lu C. Trogh I. Arnaut F. Gibson G.R. A randomised, double-blind, placebo controlled cross-over study to determine the gastrointestinal effects of consumption of arabinoxylan-oligosaccharides enriched bread in healthy volunteers Nutr. J. 2012 11 36 10.1186/1475-2891-11-36 22657950

상세보기
46. Riviere A. Gagnon M. Weckx S. Roy D. De Vuyst L. Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides Appl. Environ. Microbiol. 2015 81 7767 7781 26319874

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

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