REFERENCES
1. Wilson BC, Vatanen T, Cutfield WS, O’Sullivan JM. The super-donor phenomenon in fecal microbiota transplantation. Front Cell Infect Microbiol 2019;9:2.
2. Allegretti JR, Mullish BH, Kelly C, Fischer M. The evolution of the use of faecal microbiota transplantation and emerging therapeutic indications. Lancet 2019;394:420-31.
3. Schmidt TSB, Li SS, Maistrenko OM, et al. Drivers and determinants of strain dynamics following fecal microbiota transplantation. Nat Med 2022;28:1902-12.
4. Ianiro G, Punčochář M, Karcher N, et al. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nat Med 2022;28:1913-23.
5. Cammarota G, Ianiro G, Tilg H, et al; European FMT Working Group. European consensus conference on faecal microbiota transplantation in clinical practice. Gut 2017;66:569-80.
6. Drewes JL, Corona A, Sanchez U, et al. Transmission and clearance of potential procarcinogenic bacteria during fecal microbiota transplantation for recurrent Clostridioides difficile. JCI Insight 2019;4:e130848.
7. DeFilipp Z, Bloom PP, Torres Soto M, et al. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N Engl J Med 2019;381:2043-50.
8. Kao D, Wong K, Franz R, et al. The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial. Lancet Gastroenterol Hepatol 2021;6:282-91.
9. Duranti S, Longhi G, Ventura M, van Sinderen D, Turroni F. Exploring the ecology of bifidobacteria and their genetic adaptation to the mammalian gut. Microorganisms 2020;9:8.
10. 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.
11. Binda S, Hill C, Johansen E, et al. Criteria to qualify microorganisms as “probiotic” in foods and dietary supplements. Front Microbiol 2020;11:1662.
12. Zúñiga M, Monedero V, Yebra MJ. Utilization of host-derived glycans by intestinal Lactobacillus and Bifidobacterium species. Front Microbiol 2018;9:1917.
13. Derrien M, van Passel MW, van de Bovenkamp JH, Schipper RG, de Vos WM, Dekker J. Mucin-bacterial interactions in the human oral cavity and digestive tract. Gut Microbes 2010;1:254-68.
14. Westermann C, Gleinser M, Corr SC, Riedel CU. A critical evaluation of bifidobacterial adhesion to the host tissue. Front Microbiol 2016;7:1220.
15. Yu JY, He XL, Puthiyakunnon S, et al. Mucin2 is required for probiotic agents-mediated blocking effects on meningitic E. coli-induced pathogenicities. J Microbiol Biotechnol 2015;25:1751-60.
16. Turroni F, Milani C, van Sinderen D, Ventura M. Genetic strategies for mucin metabolism in Bifidobacterium bifidum PRL2010: an example of possible human-microbe co-evolution. Gut Microbes 2011;2:183-9.
17. Glover JS, Ticer TD, Engevik MA. Characterizing the mucin-degrading capacity of the human gut microbiota. Sci Rep 2022;12:8456.
18. Gutierrez A, Pucket B, Engevik MA. Bifidobacterium and the intestinal mucus layer. Microbiome Res Rep 2023;2:36.
19. Paone P, Cani PD. Mucus barrier, mucins and gut microbiota: the expected slimy partners? Gut 2020;69:2232-43.
20. Garrido D, Nwosu C, Ruiz-Moyano S, et al. Endo-β-N-acetylglucosaminidases from infant gut-associated bifidobacteria release complex N-glycans from human milk glycoproteins. Mol Cell Proteomics 2012;11:775-85.
21. Duranti S, Lugli GA, Mancabelli L, et al. Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria. Appl Environ Microbiol 2017;83:e02894-16.
22. Sharma M, Wasan A, Sharma RK. Recent developments in probiotics: an emphasis on Bifidobacterium. Food Biosci 2021;41:100993.
23. Jouhten H, Ronkainen A, Aakko J, et al. Cultivation and genomics prove long-term colonization of donor’s bifidobacteria in recurrent Clostridioides difficile patients treated with fecal microbiota transplantation. Front Microbiol 2020;11:1663.
24. Ronkainen A, Khan I, Krzyżewska-Dudek E, Hiippala K, Freitag TL, Satokari R. In vitro adhesion, pilus expression, and in vivo amelioration of antibiotic-induced microbiota disturbance by Bifidobacterium spp. strains from fecal donors. Gut Microbes 2023;15:2229944.
25. Jalanka J, Mattila E, Jouhten H, et al. Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection. BMC Med 2016;14:155.
26. Mattila E, Uusitalo-Seppälä R, Wuorela M, et al. Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology 2012;142:490-6.
27. Vesterlund S, Karp M, Salminen S, Ouwehand AC. Staphylococcus aureus adheres to human intestinal mucus but can be displaced by certain lactic acid bacteria. Microbiology 2006;152:1819-26.
28. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018;34:i884-90.
29. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016;32:3047-8.
30. Andrews S. FastQC: a quality control tool for high throughput sequence data. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. [Last accessed on 16 Oct 2024].
31. Page AJ, Cummins CA, Hunt M, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015;31:3691-3.
32. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60.
33. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011;12:323.
34. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26:139-40.
35. Florensa AF, Kaas RS, Clausen PTLC, Aytan-aktug D, Aarestrup FM. ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microbial Genomics 2022;8:000748.
36. Keller B, Mühlenkamp M, Deuschle E, et al. Yersinia enterocolitica exploits different pathways to accomplish adhesion and toxin injection into host cells. Cell Microbiol 2015;17:1179-204.
37. Hoffman CL, Lalsiamthara J, Aballay A. Host mucin is exploited by pseudomonas aeruginosa to provide monosaccharides required for a successful infection. mBio 2020;11:e00060-20.
38. Wijesinghe G, Dilhari A, Gayani B, Kottegoda N, Samaranayake L, Weerasekera M. Influence of laboratory culture media on in vitro growth, adhesion, and biofilm formation of Pseudomonas aeruginosa and Staphylococcus aureus. Med Princ Pract 2019;28:28-35.
39. Co JY, Cárcamo-Oyarce G, Billings N, et al. Mucins trigger dispersal of Pseudomonas aeruginosa biofilms. NPJ Biofilms Microbiomes 2018;4:23.
40. Wheeler KM, Cárcamo-Oyarce G, Turner BS, et al. Mucin glycans attenuate the virulence of Pseudomonas aeruginosa in infection. Nat Microbiol 2019;4:2146-54.
41. Vazquez-Gutierrez P, de Wouters T, Werder J, Chassard C, Lacroix C. High iron-sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro. Front Microbiol 2016;7:1480.
42. Collado MC, Gueimonde M, Hernández M, Sanz Y, Salminen S. Adhesion of selected Bifidobacterium strains to human intestinal mucus and the role of adhesion in enteropathogen exclusion. J Food Prot 2005;68:2672-8.
43. Serafini F, Strati F, Ruas-Madiedo P, et al. Evaluation of adhesion properties and antibacterial activities of the infant gut commensal Bifidobacterium bifidum PRL2010. Anaerobe 2013;21:9-17.
44. Poole J, Day CJ, von Itzstein M, Paton JC, Jennings MP. Glycointeractions in bacterial pathogenesis. Nat Rev Microbiol 2018;16:440-52.
45. Biavati B, Mattarelli P. Bifidobacterium. In: Whitman WB, editor. Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2015. pp. 1-57.
46. Masco L, Van Hoorde K, De Brandt E, Swings J, Hugs G. Antimicrobial susceptibility of Bifidobacterium strains from humans, animals and probiotic products. J Antimicrob Chemother 2006;58:85-94.
47. Saturio S, Nogacka AM, Alvarado-Jasso GM, et al. Role of bifidobacteria on infant health. Microorganisms 2021;9:2415.
48. Gueimonde M, Sánchez B, G de Los Reyes-Gavilán C, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol 2013;4:202.
49. Klein RD, Hultgren SJ. Urinary tract infections: microbial pathogenesis, host–pathogen interactions and new treatment strategies. Nat Rev Microbiol 2020;18:211-26.
50. Woerther PL, Andremont A, Kantele A. Travel-acquired ESBL-producing Enterobacteriaceae: impact of colonization at individual and community level. J Travel Med 2017;24:S29-34.
