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. Mazziotta C, Tognon M, Martini F, Torreggiani E, Rotondo JC. Probiotics mechanism of action on immune cells and beneficial effects on human health. Cells 2023;12:184.

3. Markowiak-Kopeć P, Śliżewska K. The effect of probiotics on the production of short-chain fatty acids by human intestinal microbiome. Nutrients 2020;12:1107.

4. Chávarri M, Diez-gutiérrez L, Marañón I, del Carmen Villarán M, Barrón LJR. Chapter 27 - The role of probiotics in nutritional health: probiotics as nutribiotics. In: Probiotics in the prevention and management of human diseases. Elsevier; 2022. pp. 397-415.

5. Barkhidarian B, Roldos L, Iskandar MM, Saedisomeolia A, Kubow S. Probiotic supplementation and micronutrient status in healthy subjects: a systematic review of clinical trials. Nutrients 2021;13:3001.

6. van Zyl WF, Deane SM, Dicks LMT. Molecular insights into probiotic mechanisms of action employed against intestinal pathogenic bacteria. Gut Microbes 2020;12:1831339.

7. Sanozky-Dawes R, Barrangou R. Lactobacillus, glycans and drivers of health in the vaginal microbiome. Microbiome Res Rep 2022;1:18.

8. Ruiz L, Margolles A, Sánchez B. Bile resistance mechanisms in Lactobacillus and Bifidobacterium. Front Microbiol 2013;4:396.

9. Bezkorovainy A. Probiotics: determinants of survival and growth in the gut. Am J Clin Nutr 2001;73:399S-405S.

10. Holzapfel WH, Haberer P, Geisen R, Björkroth J, Schillinger U. Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr 2001;73:365s-73s.

11. Fijan S. Microorganisms with claimed probiotic properties: an overview of recent literature. Int J Environ Res Public Health 2014;11:4745-67.

12. Goktepe I, Juneja VK, Ahmedna M. Probiotics in food safety and human health. 1st ed. CRC Press; 2005.

13. Chen L, Zou Y, Peng J, et al. Lactobacillus acidophilus suppresses colitis-associated activation of the IL-23/Th17 axis. J Immunol Res 2015;2015:909514.

14. Cortes-Perez NG, Lozano-Ojalvo D, Maiga MA, Hazebrouck S, Adel-Patient K. Intragastric administration of Lactobacillus casei BL23 induces regulatory FoxP3+RORγt+ T cells subset in mice. Benef Microbes 2017;8:433-8.

15. Karczewski J, Troost FJ, Konings I, et al. Regulation of human epithelial tight junction proteins by Lactobacillus plantarum in vivo and protective effects on the epithelial barrier. Am J Physiol Gastrointest Liver Physiol 2010;298:G851-9.

16. Garcia-Gonzalez N, Bottacini F, van Sinderen D, Gahan CGM, Corsetti A. Comparative genomics of Lactiplantibacillus plantarum: insights into probiotic markers in strains isolated from the human gastrointestinal tract and fermented foods. Front Microbiol 2022;13:854266.

17. Tarracchini C, Viglioli M, Lugli GA, et al. The Integrated Probiotic Database: a genomic compendium of bifidobacterial health-promoting strains. Microbiome Res Rep 2022;1:9.

18. Lugli GA, Fontana F, Tarracchini C, et al. MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes. Microbiome Res Rep 2023;2:15.

19. 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.

20. 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.

21. 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.

22. 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.

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

24. 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.

25. 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.

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

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. Blin K, Shaw S, Augustijn HE, et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023;51:W46-50.

29. Drula E, Garron ML, Dogan S, Lombard V, Henrissat B, Terrapon N. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 2022;50:D571-7.

30. Caspi R, Billington R, Keseler IM, et al. The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Res 2020;48:D445-53.

31. Zhang S, Li P, Lee S, Wang Y, Tan C, Shang N. Weizmannia coagulans: an ideal probiotic for gut health. Food Sci Hum Wellness 2024;13:16-226.

32. Zhu M, Zhu J, Fang S, Zhao B. Complete genome sequence of Heyndrickxia (Bacillus) coagulans BC99 isolated from a fecal sample of a healthy infant. Microbiol Resour Announc 2024;13:e0044923.

33. Zheng Z, Jiang T, Zou L, et al. Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons. Biotechnol Biofuels 2018;11:320.

34. Juturu V, Wu JC. Production of high concentration of l-lactic acid from oil palm empty fruit bunch by thermophilic Bacillus coagulans JI12. Biotechnol Appl Biochem 2018;65:145-9.

35. Loquasto JR, Barrangou R, Dudley EG, Stahl B, Chen C, Roberts RF. Bifidobacterium animalis subsp. lactis ATCC 27673 is a genomically unique strain within its conserved subspecies. Appl Environ Microbiol 2013;79:6903-10.

36. Han S, Lu Y, Xie J, et al. Probiotic gastrointestinal transit and colonization after oral administration: a long journey. Front Cell Infect Microbiol 2021;11:609722.

37. Mandlik A, Swierczynski A, Das A, Ton-That H. Pili in Gram-positive bacteria: assembly, involvement in colonization and biofilm development. Trends Microbiol 2008;16:33-40.

38. Lukaszczyk M, Pradhan B, Remaut H. The biosynthesis and structures of bacterial pili. Subcell Biochem 2019;92:369-413.

39. Scott JR, Zähner D. Pili with strong attachments: gram-positive bacteria do it differently. Mol Microbiol 2006;62:320-30.

40. Dempsey E, Corr SC. Lactobacillus spp. for gastrointestinal health: current and future perspectives. Front Immunol 2022;13:840245.

41. Ye Q, Lao L, Zhang A, et al. Multifunctional properties of the transmembrane LPxTG-motif protein derived from Limosilactobacillus reuteri SH-23. J Dairy Sci 2023;106:8207-20.

42. von Ossowski I, Reunanen J, Satokari R, et al. Mucosal adhesion properties of the probiotic Lactobacillus rhamnosus GG SpaCBA and SpaFED pilin subunits. Appl Environ Microbiol 2010;76:2049-57.

43. Kant R, Rintahaka J, Yu X, et al. A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus. PLoS One 2014;9:e102762.

44. Douillard FP, Ribbera A, Järvinen HM, et al. Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol 2013;79:1923-33.

45. Klotz C, Goh YJ, O’Flaherty S, Barrangou R. S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM. BMC Microbiol 2020;20:248.

46. Banić M, Uroić K, Leboš Pavunc A, et al. Characterization of S-layer proteins of potential probiotic starter culture Lactobacillus brevis SF9B isolated from sauerkraut. LWT 2018;93:257-67.

47. Kaushik JK, Kumar A, Duary RK, Mohanty AK, Grover S, Batish VK. Functional and probiotic attributes of an indigenous isolate of Lactobacillus plantarum. PLoS One 2009;4:e8099.

48. Sagmeister T, Gubensäk N, Buhlheller C, et al. The molecular architecture of Lactobacillus S-layer: assembly and attachment to teichoic acids. Proc Natl Acad Sci U S A 2024;121:e2401686121.

49. Martinović A, Cocuzzi R, Arioli S, Mora D. Streptococcus thermophilus: to survive, or not to survive the gastrointestinal tract, that is the question! Nutrients 2020;12:2175.

50. Zhang L, Yi H. Potential antitumor and anti-inflammatory activities of an extracellular polymeric substance (EPS) from Bacillus subtilis isolated from a housefly. Sci Rep 2022;12:1383.

51. Zhang J, Xiao Y, Wang H, Zhang H, Chen W, Lu W. Lactic acid bacteria-derived exopolysaccharide: formation, immunomodulatory ability, health effects, and structure-function relationship. Microbiol Res 2023;274:127432.

52. Ciszek-Lenda M, Nowak B, Sróttek M, Gamian A, Marcinkiewicz J. Immunoregulatory potential of exopolysaccharide from Lactobacillus rhamnosus KL37: effects on the production of inflammatory mediators by mouse macrophages. Int J Exp Pathol 2011;92:382-91.

53. Lu Q, Guo Y, Yang G, et al. Structure and anti-inflammation potential of lipoteichoic acids isolated from Lactobacillus strains. Foods 2022;11:1610.

54. Mizuno H, Arce L, Tomotsune K, et al. Lipoteichoic acid is involved in the ability of the immunobiotic strain Lactobacillus plantarum CRL1506 to modulate the intestinal antiviral innate immunity triggered by TLR3 activation. Front Immunol 2020;11:571.

55. Lightfoot YL, Mohamadzadeh M. Tailoring gut immune responses with lipoteichoic acid-deficient Lactobacillus acidophilus. Front Immunol 2013;4:25.

56. Li W, Ji J, Rui X, et al. Production of exopolysaccharides by Lactobacillus helveticus MB2-1 and its functional characteristics in vitro. LWT Food Sci Technol 2014;59:732-9.

57. Liu Z, Zhang Z, Qiu L, et al. Characterization and bioactivities of the exopolysaccharide from a probiotic strain of Lactobacillus plantarum WLPL04. J Dairy Sci 2017;100:6895-905.

58. Mizuno H, Tomotsune K, Islam MA, et al. Exopolysaccharides from Streptococcus thermophilus ST538 modulate the antiviral innate immune response in porcine intestinal epitheliocytes. Front Microbiol 2020;11:894.

59. Laiño J, Villena J, Kanmani P, Kitazawa H. Immunoregulatory effects triggered by lactic acid bacteria exopolysaccharides: new insights into molecular interactions with host cells. Microorganisms 2016;4:27.

60. Malick A, Khodaei N, Benkerroum N, Karboune S. Production of exopolysaccharides by selected Bacillus strains: optimization of media composition to maximize the yield and structural characterization. Int J Biol Macromol 2017;102:539-49.

61. Martino ME, Bayjanov JR, Caffrey BE, et al. Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats. Environ Microbiol 2016;18:4974-89.

62. Deo D, Davray D, Kulkarni R. A diverse repertoire of exopolysaccharide biosynthesis gene clusters in Lactobacillus revealed by comparative analysis in 106 sequenced genomes. Microorganisms 2019;7:444.

63. Parlindungan E, McDonnell B, Lugli GA, Ventura M, van Sinderen D, Mahony J. Dairy streptococcal cell wall and exopolysaccharide genome diversity. Microb Genom 2022;8:000803.

64. Prete R, Long SL, Gallardo AL, Gahan CG, Corsetti A, Joyce SA. Beneficial bile acid metabolism from Lactobacillus plantarum of food origin. Sci Rep 2020;10:1165.

65. Song Z, Feng S, Zhou X, Song Z, Li J, Li P. Taxonomic identification of bile salt hydrolase-encoding lactobacilli: modulation of the enterohepatic bile acid profile. Imeta 2023;2:e128.

66. Bernardeau M, Lehtinen MJ, Forssten SD, Nurminen P. Importance of the gastrointestinal life cycle of Bacillus for probiotic functionality. J Food Sci Technol 2017;54:2570-84.

67. Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021;19:726-39.

68. Aminov R, Aminova L. The role of the glycome in symbiotic host-microbe interactions. Glycobiology 2023;33:1106-16.

69. Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M. Glycan utilization and cross-feeding activities by bifidobacteria. Trends Microbiol 2018;26:339-50.

70. Seth ES, Taga ME. Nutrient cross-feeding in the microbial world. Front Microbiol 2014;5:350.

71. Singh JK, Devi PB, Reddy GB, Jaiswal AK, Kavitake D, Shetty PH. Biosynthesis, classification, properties, and applications of Weissella bacteriocins. Front Microbiol 2024;15:1406904.

72. O’Shea EF, O’Connor PM, O’Sullivan O, Cotter PD, Ross RP, Hill C. Bactofencin A, a new type of cationic bacteriocin with unusual immunity. mBio 2013;4:e00498-13.

73. Ryan MP, Rea MC, Hill C, Ross RP. An application in cheddar cheese manufacture for a strain of Lactococcus lactis producing a novel broad-spectrum bacteriocin, lacticin 3147. Appl Environ Microbiol 1996;62:612-9.

74. Holo H, Jeknic Z, Daeschel M, Stevanovic S, Nes IF. Plantaricin W from Lactobacillus plantarum belongs to a new family of two-peptide lantibiotics. The GenBank accession number for the sequence reported in this paper is AY007251. Microbiology 2001;147:643-51.

75. Latif A, Shehzad A, Niazi S, et al. Probiotics: mechanism of action, health benefits and their application in food industries. Front Microbiol 2023;14:1216674.

76. Lebeer S, Vanderleyden J, De Keersmaecker SC. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat Rev Microbiol 2010;8:171-84.

77. 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.

78. Domingues SZ, Timmers LFSM, Granada CE. Cellulase production by bacteria is a strain-specific characteristic with a high biotechnological potential. A review of cellulosome of highly studied strains. Cellulose 2022;29:8065-83.

79. Saqib S, Akram A, Halim SA, Tassaduq R. Sources of β-galactosidase and its applications in food industry. 3 Biotech 2017;7:79.

80. Cheng Y, Liu J, Ling Z. Short-chain fatty acids-producing probiotics: a novel source of psychobiotics. Crit Rev Food Sci Nutr 2022;62:7929-59.

81. Puertollano E, Kolida S, Yaqoob P. Biological significance of short-chain fatty acid metabolism by the intestinal microbiome. Curr Opin Clin Nutr Metab Care 2014;17:139-44.

82. Makras L, De Vuyst L. The in vitro inhibition of Gram-negative pathogenic bacteria by bifidobacteria is caused by the production of organic acids. Int Dairy J 2006;16:1049-57.

83. Makras L, Triantafyllou V, Fayol-Messaoudi D, et al. Kinetic analysis of the antibacterial activity of probiotic lactobacilli towards Salmonella enterica serovar Typhimurium reveals a role for lactic acid and other inhibitory compounds. Res Microbiol 2006;157:241-7.

84. Meng F, Zhao H, Nie T, et al. Acetate activates Lactobacillus bacteriocin synthesis by controlling quorum sensing. Appl Environ Microbiol 2021;87:e0072021.

85. Yan Y, Xu R, Li X, et al. Unexpected immunoregulation effects of D-lactate, different from L-lactate. Food Agr Immunol 2022;33:286-301.

86. McDonald B, Zucoloto AZ, Yu IL, et al. Programing of an intravascular immune firewall by the gut microbiota protects against pathogen dissemination during infection. Cell Host Microbe 2020;28:660-8.e4.

87. LeBlanc JG, Laiño JE, del Valle MJ, et al. B-group vitamin production by lactic acid bacteria - current knowledge and potential applications. J Appl Microbiol 2011;111:1297-309.

88. LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 2013;24:160-8.

89. Lin MY, Young CM. Folate levels in cultures of lactic acid bacteria. Int Dairy J 2000;10:409-13.

90. Salminen S, von Wright A, Morelli L, et al. Demonstration of safety of probiotics - a review. Int J Food Microbiol 1998;44:93-106.

91. Holzapfel WH, Schillinger U. Introduction to pre- and probiotics. Food Res Int 2002;35:109-16.

92. Smith LK, Mankin AS. Transcriptional and translational control of the mlr operon, which confers resistance to seven classes of protein synthesis inhibitors. Antimicrob Agents Chemother 2008;52:1703-12.

93. Toh SM, Xiong L, Arias CA, et al. Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid. Mol Microbiol 2007;64:1506-14.

94. Plant L, Sundqvist J, Zughaier S, Lövkvist L, Stephens DS, Jonsson AB. Lipooligosaccharide structure contributes to multiple steps in the virulence of Neisseria meningitidis. Infect Immun 2006;74:1360-7.

95. Vernocchi P, Del Chierico F, Putignani L. Gut microbiota metabolism and interaction with food components. Int J Mol Sci 2020;21:3688.

96. Hitch TCA, Hall LJ, Walsh SK, et al. Microbiome-based interventions to modulate gut ecology and the immune system. Mucosal Immunol 2022;15:1095-113.

97. Romero-Velarde E, Delgado-Franco D, García-Gutiérrez M, et al. The importance of lactose in the human diet: outcomes of a mexican consensus meeting. Nutrients 2019;11:2737.

98. Gökmen GG, Sarıyıldız S, Cholakov R, et al. A novel Lactiplantibacillus plantarum strain: probiotic properties and optimization of the growth conditions by response surface methodology. World J Microbiol Biotechnol 2024;40:66.

99. Goh YJ, Klaenhammer TR. Insights into glycogen metabolism in Lactobacillus acidophilus: impact on carbohydrate metabolism, stress tolerance and gut retention. Microb Cell Fact 2014;13:94.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/