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.
