REFERENCES

1. Hill C, Guarner F, Reid G, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014;11:506-14.

2. Aditya A, Peng M, Young A, Biswas D. Antagonistic mechanism of metabolites produced by lactobacillus casei on lysis of enterohemorrhagic escherichia coli. Front Microbiol 2020;11:574422.

3. Tomasik PJ, Tomasik P. Probiotics and prebiotics. Cereal Chemistry 2003;80:113-7.

4. Koutsoumanis K, Allende A, Alvarez-Ordóñez A, et al. EFSA Panel on Biological Hazards (BIOHAZ). Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021. EFSA J 2021;19:e06689.

5. Scheinbach S. Probiotics: functionality and commercial status. Biotechnology Advances 1998;16:581-608.

6. Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017;111:118-31.

7. McFarland LV. Efficacy of single-strain probiotics versus multi-strain mixtures: systematic review of strain and disease specificity. Dig Dis Sci 2021;66:694-704.

8. Ouwehand AC, Invernici MM, Furlaneto FAC, Messora MR. Effectiveness of multistrain versus single-strain probiotics: current status and recommendations for the future. J Clin Gastroenterol 2018;52 Suppl 1:S35-40.

9. Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation. FEMS Microbiol Lett 2016;363:fnw049.

10. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119.

11. Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 2012;28:125-6.

12. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955-64.

13. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100-8.

14. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. PGAP: pan-genomes analysis pipeline. Bioinformatics 2012;28:416-8.

15. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002;30:1575-84.

16. Huerta-Cepas J, Szklarczyk D, Forslund K, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016;44:D286-93.

17. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018;9:5114.

18. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30:3059-66.

19. Chenna R, Sugawara H, Koike T, et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003;31:3497-500.

20. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014;42:D490-5.

21. Wheeler TJ, Eddy SR. nhmmer: DNA homology search with profile HMMs. Bioinformatics 2013;29:2487-9.

22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-10.

23. Alcock BP, Raphenya AR, Lau TTY, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020;48:D517-25.

24. Saier MH Jr, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G. The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res 2016;44:D372-9.

25. Ye Y, Choi JH, Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 2011;12:159.

26. Milani C, Mangifesta M, Mancabelli L, et al. The Sortase-dependent fimbriome of the genus bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue. Appl Environ Microbiol 2017;83:e01295-17.

27. Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers OP. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res 2018;46:W278-81.

28. Chen L, Yang J, Yu J, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005;33:D325-8.

29. Tarracchini C, Milani C, Lugli GA, et al. Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon. Microb Genom 2021:7.

30. Blanco-Míguez A, Gutiérrez-Jácome A, Fdez-Riverola F, Lourenço A, Sánchez B. A peptidome-based phylogeny pipeline reveals differential peptides at the strain level within Bifidobacterium animalis subsp. lactis. Food Microbiol 2016;60:137-41.

31. Underwood MA, German JB, Lebrilla CB, Mills DA. Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut. Pediatr Res 2015;77:229-35.

32. Tan J, Mckenzie C, Potamitis M, Thorburn AN, Mackay CR, Macia L. The role of short-chain fatty acids in health and disease. Elsevier; 2014. p. 91-119.

33. Abdelhamid AG, El-Dougdoug NK. Comparative genomics of the gut commensal Bifidobacterium bifidum reveals adaptation to carbohydrate utilization. Biochem Biophys Res Commun 2021;547:155-61.

34. Sela DA, Garrido D, Lerno L, et al. Bifidobacterium longum subsp. infantis ATCC 15697 α-fucosidases are active on fucosylated human milk oligosaccharides. Appl Environ Microbiol 2012;78:795-803.

35. Katoh T, Ojima MN, Sakanaka M, Ashida H, Gotoh A, Katayama T. Enzymatic adaptation of bifidobacterium bifidum to Host Glycans, viewed from glycoside hydrolyases and carbohydrate-binding modules. Microorganisms 2020;8:481.

36. Sakurama H, Kiyohara M, Wada J, et al. Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression. J Biol Chem 2013;288:25194-206.

37. Odamaki T, Bottacini F, Kato K, et al. Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan. Sci Rep 2018;8:85.

38. Turroni F, Serafini F, Foroni E, et al. Role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions. Proc Natl Acad Sci U S A 2013;110:11151-6.

39. Nishiyama K, Yokoi T, Sugiyama M, Osawa R, Mukai T, Okada N. Roles of the cell surface architecture of Bacteroides and Bifidobacterium in the gut colonization. Front Microbiol 2021;12:754819.

40. Alessandri G, van Sinderen D, Ventura M. The genus bifidobacterium: from genomics to functionality of an important component of the mammalian gut microbiota running title: bifidobacterial adaptation to and interaction with the host. Comput Struct Biotechnol J 2021;19:1472-87.

41. Martinez FA, Balciunas EM, Converti A, Cotter PD, de Souza Oliveira RP. Bacteriocin production by Bifidobacterium spp. A review. Biotechnol Adv 2013;31:482-8.

42. Niederhäusern S, Camellini S, Sabia C, Iseppi R, Bondi M, Messi P. Antilisterial activity of bacteriocins produced by lactic bacteria isolated from dairy products. Foods 2020;9:1757.

43. Kanmani P, Satish Kumar R, Yuvaraj N, Paari KA, Pattukumar V, Arul V. Probiotics and its functionally valuable products-a review. Crit Rev Food Sci Nutr 2013;53:641-58.

44. Liévin V, Peiffer I, Hudault S, et al. Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity. Gut 2000;47:646-52.

45. O'Shea EF, Cotter PD, Stanton C, Ross RP, Hill C. Production of bioactive substances by intestinal bacteria as a basis for explaining probiotic mechanisms: bacteriocins and conjugated linoleic acid. Int J Food Microbiol 2012;152:189-205.

46. Gama JA, Zilhão R, Dionisio F. Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance. Plasmid 2018;99:82-8.

47. Lupski JR. Molecular mechanisms for transposition of drug-resistance genes and other movable genetic elements. Rev Infect Dis 1987;9:357-68.

48. Kiwaki M, Sato T. Antimicrobial susceptibility of Bifidobacterium breve strains and genetic analysis of streptomycin resistance of probiotic B. breve strain Yakult. Int J Food Microbiol 2009;134:211-5.

49. Sato T, Iino T. Genetic analyses of the antibiotic resistance of Bifidobacterium bifidum strain Yakult YIT 4007. Int J Food Microbiol 2010;137:254-8.

50. Gueimonde M, Sánchez B, G de Los Reyes-Gavilán C, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol 2013;4:202.

51. Franz CM, Huch M, Abriouel H, Holzapfel W, Gálvez A. Enterococci as probiotics and their implications in food safety. Int J Food Microbiol 2011;151:125-40.

52. Miller WR, Munita JM, Arias CA. Mechanisms of antibiotic resistance in enterococci. Expert Rev Anti Infect Ther 2014;12:1221-36.

53. Patel R. Enterococcal-type glycopeptide resistance genes in non-enterococcal organisms. FEMS Microbiol Lett 2000;185:1-7.

54. Vescovo M, Morelli L, Bottazzi V. Drug resistance plasmids in Lactobacillus acidophilus and Lactobacillus reuteri. Appl Environ Microbiol 1982;43:50-6.

55. Jarocki P, Podleśny M, Glibowski P, Targoński Z. A new insight into the physiological role of bile salt hydrolase among intestinal bacteria from the genus Bifidobacterium. PLoS One 2014;9:e114379.

56. Castro-Bravo N, Wells JM, Margolles A, Ruas-Madiedo P. Interactions of surface exopolysaccharides from Bifidobacterium and Lactobacillus within the intestinal environment. Front Microbiol 2018;9:2426.

57. Prasanna P, Grandison A, Charalampopoulos D. Bifidobacteria in milk products: an overview of physiological and biochemical properties, exopolysaccharide production, selection criteria of milk products and health benefits. Food Res Int 2014;55:247-62.

58. Fanning S, Hall LJ, Cronin M, et al. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc Natl Acad Sci U S A 2012;109:2108-13.

59. Provencher C, LaPointe G, Sirois S, Van Calsteren MR, Roy D. Consensus-degenerate hybrid oligonucleotide primers for amplification of priming glycosyltransferase genes of the exopolysaccharide locus in strains of the Lactobacillus casei group. Appl Environ Microbiol 2003;69:3299-307.

60. Ferrario C, Milani C, Mancabelli L, et al. Modulation of the eps-ome transcription of bifidobacteria through simulation of human intestinal environment. FEMS Microbiol Ecol 2016;92:fiw056.

61. Yan S, Zhao G, Liu X, Zhao J, Zhang H, Chen W. Production of exopolysaccharide by Bifidobacterium longum isolated from elderly and infant feces and analysis of priming glycosyltransferase genes. RSC Adv 2017;7:31736-44.

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