Correction: Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3(PLoS ONE (2018) 13:2 (e0192452) DOI: 10.1371/journal.pone.0192452);Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

PLoS ONE

Volumn 13, Issue 2, 2018, Pages

  Douillard, François P ^a   Mora, Diego ^b   Eijlander, Robyn T ^c   Wels, Michiel ^c   De Vos, Willem M ^a,d  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF MILAN   (Italy)

^c NIZO FOOD RESEARCH   (Netherlands)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

PROBIOTIC AGENT; SORTASE;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM PILUS; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BREVE; COMPARATIVE STUDY; CONTROLLED STUDY; CRISPR CAS SYSTEM; DENDRITIC CELL; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; HOST CELL; INTESTINE MUCOSA; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS HELVETICUS; LACTOBACILLUS PARACASEI; LACTOBACILLUS PLANTARUM; NONHUMAN; PHYLOGENY; SIGNAL TRANSDUCTION; STREPTOCOCCUS THERMOPHILUS; BACTERIUM ADHERENCE; BIFIDOBACTERIUM; CLASSIFICATION; GENETICS; HUMAN; LACTOBACILLUS; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY;

BACTERIAL ADHESION; BIFIDOBACTERIUM; CRISPR-CAS SYSTEMS; GENOME, BACTERIAL; GENOMICS; HUMANS; INTESTINAL MUCOSA; LACTOBACILLUS; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS PARACASEI; LACTOBACILLUS PLANTARUM; MICROBIAL SENSITIVITY TESTS; PHYLOGENY; PROBIOTICS;

EID: 85042236692     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0203548     Document Type: Erratum

References (96)

1. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, et al. (2014) 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 11: 506–514. https://doi.org/10.1038/nrgastro.2014.66 PMID: 24912386
2. Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, et al. (2009) Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci U S A 106: 17193–17198. https://doi.org/10.1073/pnas.0908876106 PMID: 19805152
3. Douillard FP, Ribbera A, Kant R, Pietilä TE, Järvinen HM, et al. (2013) Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet 9: e1003683. https://doi.org/10.1371/journal.pgen.1003683 PMID: 23966868
4. Nissilä E, Douillard FP, Ritari J, Paulin L, Järvinen HM, et al. (2017) Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system. PLoS One 12: e0176739. https://doi.org/10.1371/journal.pone.0176739 PMID: 28493885
5. Tytgat HL, Douillard FP, Reunanen J, Rasinkangas P, Hendrickx AP, et al. (2016) Lactobacillus rhamnosus GG outcompetes Enterococcus faecium via mucus-binding pili: Evidence for a novel and hetero-specific probiotic mechanism. Appl Environ Microbiol 82: 5756–5762. https://doi.org/10.1128/AEM.01243-16 PMID: 27422834
6. Tytgat HL, van Teijlingen NH, Sullan RM, Douillard FP, Rasinkangas P, et al. (2016) Probiotic gut microbiota isolate interacts with dendritic cells via glycosylated heterotrimeric pili. PLoS One 11: e0151824. https://doi.org/10.1371/journal.pone.0151824 PMID: 26985831
7. Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, et al. (2005) Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A 102: 3906–3912. https://doi.org/10.1073/pnas.0409188102 PMID: 15671160
8. Konstantinov SR, Smidt H, de Vos WM, Bruijns SC, Singh SK, et al. (2008) S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci U S A 105: 19474–19479. https://doi.org/10.1073/pnas.0810305105 PMID: 19047644
9. Johnson B, Selle K, O’Flaherty S, Goh YJ, Klaenhammer T (2013) Identification of extracellular surface-layer associated proteins in Lactobacillus acidophilus NCFM. Microbiology 159: 2269–2282. https://doi.org/10.1099/mic.0.070755-0 PMID: 24002751
10. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, et al. (2003) Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A 100: 1990–1995. https://doi.org/10.1073/pnas.0337704100 PMID: 12566566
11. van den Nieuwboer M, van Hemert S, Claassen E, de Vos WM (2016) Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome. Microb Biotechnol 9: 452–465. https://doi.org/10.1111/1751-7915.12368 PMID: 27231133
12. van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, et al. (2009) Differential NF-kap-paB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci U S A 106: 2371–2376. https://doi.org/10.1073/pnas.0809919106 PMID: 19190178
13. Mujagic Z, de Vos P, Boekschoten MV, Govers C, Pieters HH, et al. (2017) The effects of Lactobacillus plantarum on small intestinal barrier function and mucosal gene transcription; a randomized double-blind placebo controlled trial. Sci Rep 7: 40128. https://doi.org/10.1038/srep40128 PMID: 28045137
14. Garrigues C, Johansen E, Pedersen MB (2010) Complete genome sequence of Bifidobacterium animalis subsp. lactis BB-12, a widely consumed probiotic strain. J Bacteriol 192: 2467–2468. https://doi.org/10.1128/JB.00109-10 PMID: 20190051
15. Loquasto JR, Barrangou R, Dudley EG, Stahl B, Chen C, et al. (2013) Bifidobacterium animalis subsp. lactis ATCC 27673 is a genomically unique strain within its conserved subspecies. Appl Environ Microbiol 79: 6903–6910. https://doi.org/10.1128/AEM.01777-13 PMID: 23995933
16. Ventura M, O’Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, et al. (2009) Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol 7: 61–71. https://doi.org/10.1038/nrmicro2047 PMID: 19029955
17. O’Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, et al. (2011) Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A 108: 11217–11222. https://doi.org/10.1073/pnas.1105380108 PMID: 21690406
18. Milani C, Mangifesta M, Mancabelli L, Lugli GA, Mancino W, et al. (2017) The sortase-dependent fim-briome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue. Appl Environ Microbiol. 83(19):e01295–17. https://doi.org/10.1128/AEM.01295-17 PMID: 28754709
19. Fanning S, Hall LJ, van Sinderen D (2012) Bifidobacterium breve UCC2003 surface exopolysaccharide production is a beneficial trait mediating commensal-host interaction through immune modulation and pathogen protection. Gut Microbes 3: 420–425. https://doi.org/10.4161/gmic.20630 PMID: 22713271
20. Douillard FP, de Vos WM (2014) Functional genomics of lactic acid bacteria: from food to health. Microb Cell Fact 13 Suppl 1: S8.
21. Sun Z, Harris HM, McCann A, Guo C, Argimon S, et al. (2015) Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun 6: 8322. https://doi.org/10.1038/ncomms9322 PMID: 26415554
22. Douillard FP, Ribbera A, Xiao K, Ritari J, Rasinkangas P, et al. (2016) Polymorphisms, chromosomal rearrangements, and mutator phenotype development during experimental evolution of Lactobacillus rhamnosus GG. Appl Environ Microbiol 82: 3783–3792. https://doi.org/10.1128/AEM.00255-16 PMID: 27084020
23. Douillard FP, Kant R, Ritari J, Paulin L, Palva A, et al. (2013) Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin. Microb Biotechnol 6: 576–587. https://doi.org/10.1111/1751-7915.12062 PMID: 23815335
24. Mimura T, Rizzello F, Helwig U, Poggioli G, Schreiber S, et al. (2004) Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis. Gut 53: 108–114. PMID: 14684584
25. Sood A, Midha V, Makharia GK, Ahuja V, Singal D, et al. (2009) The probiotic preparation, VSL#3 induces remission in patients with mild-to-moderately active ulcerative colitis. Clin Gastroenterol Hepatol 7: 1202–1209, 1209 e1201. https://doi.org/10.1016/j.cgh.2009.07.016 PMID: 19631292
26. Kim HJ, Vazquez Roque MI, Camilleri M, Stephens D, Burton DD, et al. (2005) A randomized controlled trial of a probiotic combination VSL# 3 and placebo in irritable bowel syndrome with bloating. Neurogas-troenterol Motil 17: 687–696. https://doi.org/10.1111/j.1365-2982.2005.00695.x PMID: 16185307
27. Caballero-Franco C, Keller K, De Simone C, Chadee K (2007) The VSL#3 probiotic formula induces mucin gene expression and secretion in colonic epithelial cells. Am J Physiol Gastrointest Liver Physiol 292: G315–322. https://doi.org/10.1152/ajpgi.00265.2006 PMID: 16973917
28. Massi M, Vitali B, Federici F, Matteuzzi D, Brigidi P (2004) Identification method based on PCR combined with automated ribotyping for tracking probiotic Lactobacillus strains colonizing the human gut and vagina. J Appl Microbiol 96: 777–786. PMID: 15012816
29. Vitali B, Candela M, Matteuzzi D, Brigidi P (2003) Quantitative detection of probiotic Bifidobacterium strains in bacterial mixtures by using real-time PCR. Syst Appl Microbiol 26: 269–276. https://doi.org/10.1078/072320203322346128 PMID: 12866854
30. Lewis ZT, Shani G, Masarweh CF, Popovic M, Frese SA, et al. (2016) Validating bifidobacterial species and subspecies identity in commercial probiotic products. Pediatr Res 79: 445–452. https://doi.org/10.1038/pr.2015.244 PMID: 26571226
31. Vandamme P, Peeters C (2014) Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 106: 57–65. https://doi.org/10.1007/s10482-014-0148-x PMID: 24633913
32. Tursi A, Brandimarte G, Papa A, Giglio A, Elisei W, et al. (2010) Treatment of relapsing mild-to-moderate ulcerative colitis with the probiotic VSL#3 as adjunctive to a standard pharmaceutical treatment: a double-blind, randomized, placebo-controlled study. Am J Gastroenterol 105: 2218–2227. https://doi.org/10.1038/ajg.2010.218 PMID: 20517305
33. Alisi A, Bedogni G, Baviera G, Giorgio V, Porro E, et al. (2014) Randomised clinical trial: The beneficial effects of VSL#3 in obese children with non-alcoholic steatohepatitis. Aliment Pharmacol Ther 39: 1276–1285. https://doi.org/10.1111/apt.12758 PMID: 24738701
34. Dhiman RK, Rana B, Agrawal S, Garg A, Chopra M, et al. (2014) Probiotic VSL#3 reduces liver disease severity and hospitalization in patients with cirrhosis: a randomized, controlled trial. Gastroenterology 147: 1327–1337 e1323. https://doi.org/10.1053/j.gastro.2014.08.031 PMID: 25450083
35. Rajkumar H, Mahmood N, Kumar M, Varikuti SR, Challa HR, et al. (2014) Effect of probiotic (VSL#3) and omega-3 on lipid profile, insulin sensitivity, inflammatory markers, and gut colonization in overweight adults: a randomized, controlled trial. Mediators Inflamm 2014: 348959. https://doi.org/10.1155/2014/348959 PMID: 24795503
36. Hart AL, Lammers K, Brigidi P, Vitali B, Rizzello F, et al. (2004) Modulation of human dendritic cell phenotype and function by probiotic bacteria. Gut 53: 1602–1609. https://doi.org/10.1136/gut.2003.037325PMID: 15479680
37. Mariman R, Tielen F, Koning F, Nagelkerken L (2014) The probiotic mixture VSL#3 dampens LPS-induced chemokine expression in human dendritic cells by inhibition of STAT-1 phosphorylation. PLoS One 9: e115676. https://doi.org/10.1371/journal.pone.0115676 PMID: 25546330
38. Pagnini C, Saeed R, Bamias G, Arseneau KO, Pizarro TT, et al. (2010) Probiotics promote gut health through stimulation of epithelial innate immunity. Proc Natl Acad Sci U S A 107: 454–459. https://doi.org/10.1073/pnas.0910307107 PMID: 20018654
39. Kahlmeter G, Brown DF, Goldstein FW, MacGowan AP, Mouton JW, et al. (2003) European harmonization of MIC breakpoints for antimicrobial susceptibility testing of bacteria. J Antimicrob Chemother 52: 145–148. https://doi.org/10.1093/jac/dkg312 PMID: 12837738
40. EFSA Panel on Additives Products or Substances used in Animal Feed (FEEDAP) (2012) Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance. EFSA Journal 10(6): 2740.
41. International Dairy Federation (2012) Milk and milk products—Determination of the minimal inhibitory concentration (MIC) of antibiotics applicable to bifidobacteria and non-enterococcal lactic acid bacteria (LAB). Brussels, Belgium.: International Dairy Federation.
42. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, et al. (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9: e112963. https://doi.org/10.1371/journal.pone.0112963 PMID: 25409509
43. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578–579. https://doi.org/10.1093/bioinformatics/btq683 PMID: 21149342
44. Boetzer M, Pirovano W (2012) Toward almost closed genomes with GapFiller. Genome Biol 13: R56. https://doi.org/10.1186/gb-2012-13-6-r56 PMID: 22731987
45. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068–2069. https://doi.org/10.1093/bioinformatics/btu153 PMID: 24642063
46. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119. https://doi.org/10.1186/1471-2105-11-119 PMID: 20211023
47. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11–16. https://doi.org/10.1093/nar/gkh152 PMID: 14704338
48. Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785–786. https://doi.org/10.1038/nmeth.1701 PMID: 21959131
49. Mistry J, Finn RD, Eddy SR, Bateman A, Punta M (2013) Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res 41: e121. https://doi.org/10.1093/nar/gkt263 PMID: 23598997
50. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069–5072. https://doi.org/10.1128/AEM.03006-05 PMID: 16820507
51. Li L, Stoeckert CJ Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178–2189. https://doi.org/10.1101/gr.1224503 PMID: 12952885
52. Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, et al. (2013) Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One 8: e68731. https://doi.org/10.1371/journal.pone.0068731 PMID: 23894338
53. Gibson MK, Forsberg KJ, Dantas G (2015) Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J 9: 207–216. https://doi.org/10.1038/ismej.2014.106 PMID: 25003965
54. Chen L, Yang J, Yu J, Yao Z, Sun L, et al. (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33: D325–328. https://doi.org/10.1093/nar/gki008 PMID: 15608208
55. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410. PMID: 2231712
56. Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly inter-spaced short palindromic repeats. Nucleic Acids Res 35: W52–57. https://doi.org/10.1093/nar/gkm360PMID: 17537822
57. Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM (2013) CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol 10: 817–827. https://doi.org/10.4161/rna.24046 PMID: 23492433
58. Boekhorst J, de Been MW, Kleerebezem M, Siezen RJ (2005) Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. J Bacteriol 187: 4928–4934. https://doi.org/10.1128/JB.187.14.4928-4934.2005 PMID: 15995208
59. Litou ZI, Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ (2008) Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes. J Bioinform Comput Biol 6: 387–401. PMID: 18464329
60. Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, et al. (2009) Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol 191: 4144–4151. https://doi.org/10.1128/JB.00155-09 PMID: 19376856
61. Delorme C, Bartholini C, Luraschi M, Pons N, Loux V, et al. (2011) Complete genome sequence of the pigmented Streptococcus thermophilus strain JIM8232. J Bacteriol 193: 5581–5582. https://doi.org/10.1128/JB.05404-11 PMID: 21914889
62. Siefert JL (2009) Defining the mobilome. Methods Mol Biol 532: 13–27. https://doi.org/10.1007/978-1-60327-853-9_2 PMID: 19271177
63. Hoffmann FG, McGuire LP, Counterman BA, Ray DA (2015) Transposable elements and small RNAs: Genomic fuel for species diversity. Mob Genet Elements 5: 63–66. https://doi.org/10.1080/2159256X.2015.1066919 PMID: 26904375
64. Casacuberta E, Gonzalez J (2013) The impact of transposable elements in environmental adaptation. Mol Ecol 22: 1503–1517. https://doi.org/10.1111/mec.12170 PMID: 23293987
65. Stapley J, Santure AW, Dennis SR (2015) Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol 24: 2241–2252. https://doi.org/10.1111/mec.13089 PMID: 25611725
66. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brussow H (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6: 417–424. PMID: 12941415
67. Lecomte X, Gagnaire V, Briard-Bion V, Jardin J, Lortal S, et al. (2014) The naturally competent strain Streptococcus thermophilus LMD-9 as a new tool to anchor heterologous proteins on the cell surface. Microb Cell Fact 13: 82. https://doi.org/10.1186/1475-2859-13-82 PMID: 24902482
68. Marco MB, Moineau S, Quiberoni A (2012) Bacteriophages and dairy fermentations. Bacteriophage 2: 149–158. https://doi.org/10.4161/bact.21868 PMID: 23275866
69. Garneau JE, Moineau S (2011) Bacteriophages of lactic acid bacteria and their impact on milk fermentations. Microb Cell Fact 10 Suppl 1: S20.
70. Ventura M, Sozzi T, Turroni F, Matteuzzi D, van Sinderen D (2011) The impact of bacteriophages on probiotic bacteria and gut microbiota diversity. Genes Nutr 6: 205–207. https://doi.org/10.1007/s12263-010-0188-4 PMID: 21484155
71. Ai L, Chen C, Zhou F, Wang L, Zhang H, et al. (2011) Complete genome sequence of the probiotic strain Lactobacillus casei BD-II. J Bacteriol 193: 3160–3161. https://doi.org/10.1128/JB.00421-11PMID: 21478345
72. Hochwind K, Weinmaier T, Schmid M, van Hemert S, Hartmann A, et al. (2012) Draft genome sequence of Lactobacillus casei W56. J Bacteriol 194: 6638. https://doi.org/10.1128/JB.01386-12 PMID: 23144392
73. Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E, et al. (2017) Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel clade-associated features. mSystems 2(4) e00061–17. https://doi.org/10.1128/mSystems.00061-17 PMID: 28845461
74. Jang SE, Han MJ, Kim SY, Kim DH (2014) Lactobacillus plantarum CLP-0611 ameliorates colitis in mice by polarizing M1 to M2-like macrophages. Int Immunopharmacol 21: 186–192. https://doi.org/10.1016/j.intimp.2014.04.021 PMID: 24815859
75. Charnchai P, Jantama SS, Prasitpuriprecha C, Kanchanatawee S, Jantama K (2016) Effects of the food manufacturing chain on the viability and functionality of Bifidobacterium animalis through simulated gastrointestinal conditions. PLoS One 11: e0157958. https://doi.org/10.1371/journal.pone.0157958PMID: 27333286
76. Dupuis ME, Villion M, Magadan AH, Moineau S (2013) CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance. Nat Commun 4: 2087. https://doi.org/10.1038/ncomms3087 PMID: 23820428
77. Price VJ, Huo W, Sharifi A, Palmer KL (2016) CRISPR-Cas and Restriction-Modification act additively against conjugative antibiotic resistance plasmid transfer in Enterococcus faecalis. mSphere 1 (3) e00064–16. https://doi.org/10.1128/mSphere.00064-16 PMID: 27303749
78. Gueimonde M, Florez AB, van Hoek AH, Stuer-Lauridsen B, Stroman P, et al. (2010) Genetic basis of tetracycline resistance in Bifidobacterium animalis subsp. lactis. Appl Environ Microbiol 76: 3364–3369. https://doi.org/10.1128/AEM.03096-09 PMID: 20348299
79. Perez PF, Minnaard Y, Disalvo EA, De Antoni GL (1998) Surface properties of bifidobacterial strains of human origin. Appl Environ Microbiol 64: 21–26. PMID: 9435057
80. Hidalgo-Cantabrana C, Sanchez B, Milani C, Ventura M, Margolles A, et al. (2014) Genomic overview and biological functions of exopolysaccharide biosynthesis in Bifidobacterium spp. Appl Environ Microbiol 80: 9–18. https://doi.org/10.1128/AEM.02977-13 PMID: 24123746
81. Tytgat HL, de Vos WM (2016) Sugar Coating the Envelope: Glycoconjugates for microbe-host crosstalk. Trends Microbiol 24: 853–861. https://doi.org/10.1016/j.tim.2016.06.004 PMID: 27374775
82. Filloux A (2010) A variety of bacterial pili involved in horizontal gene transfer. J Bacteriol 192: 3243–3245. https://doi.org/10.1128/JB.00424-10 PMID: 20418394
83. Mandlik A, Swierczynski A, Das A, Ton-That H (2008) Pili in Gram-positive bacteria: assembly, involvement in colonization and biofilm development. Trends Microbiol 16: 33–40. https://doi.org/10.1016/j.tim.2007.10.010 PMID: 18083568
84. Sengupta R, Altermann E, Anderson RC, McNabb WC, Moughan PJ, et al. (2013) The role of cell surface architecture of lactobacilli in host-microbe interactions in the gastrointestinal tract. Mediators Inflamm 2013: 237921. https://doi.org/10.1155/2013/237921 PMID: 23576850
85. Chen C, Ai L, Zhou F, Wang L, Zhang H, et al. (2011) Complete genome sequence of the probiotic bacterium Lactobacillus casei LC2W. J Bacteriol 193: 3419–3420. https://doi.org/10.1128/JB.05017-11PMID: 21515769
86. Buntin N, Hongpattarakere T, Ritari J, Douillard FP, Paulin L, et al. (2017) An inducible operon is involved in inulin utilization in Lactobacillus plantarum strains, as revealed by comparative proteoge-nomics and metabolic profiling. Appl Environ Microbiol 83(2):e02402–16. https://doi.org/10.1128/AEM.02402-16 PMID: 27815279
87. Fredriksen L, Moen A, Adzhubei AA, Mathiesen G, Eijsink VG, et al. (2013) Lactobacillus plantarum WCFS1 O-linked protein glycosylation: an extended spectrum of target proteins and modification sites detected by mass spectrometry. Glycobiology 23: 1439–1451. https://doi.org/10.1093/glycob/cwt071PMID: 24000282
88. Turroni F, Serafini F, Foroni E, Duranti S, O’Connell Motherway M, et al. (2013) Role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions. Proc Natl Acad Sci U S A 110: 11151–11156. https://doi.org/10.1073/pnas.1303897110 PMID: 23776216
89. Lebeer S, Claes I, Tytgat HL, Verhoeven TL, Marien E, et al. (2012) Functional analysis of Lactobacillus rhamnosus GG pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells. Appl Environ Microbiol 78: 185–193. https://doi.org/10.1128/AEM.06192-11 PMID: 22020518
90. Hynonen U, Palva A (2013) Lactobacillus surface layer proteins: structure, function and applications. Appl Microbiol Biotechnol 97: 5225–5243. https://doi.org/10.1007/s00253-013-4962-2 PMID: 23677442
91. Johnson BR, O’Flaherty S, Goh YJ, Carroll I, Barrangou R, et al. (2017) The S-layer associated serine protease homolog PrtX impacts cell surface-mediated microbe-host interactions of Lactobacillus acidophilus NCFM. Front Microbiol 8: 1185. https://doi.org/10.3389/fmicb.2017.01185 PMID: 28713337
92. Taverniti V, Stuknyte M, Minuzzo M, Arioli S, De Noni I, et al. (2013) S-layer protein mediates the stimulatory effect of Lactobacillus helveticus MIMLh5 on innate immunity. Appl Environ Microbiol 79: 1221–1231. https://doi.org/10.1128/AEM.03056-12 PMID: 23220964
93. Mora D, Arioli S (2014) Microbial urease in health and disease. PLoS Pathog 10: e1004472. https://doi.org/10.1371/journal.ppat.1004472 PMID: 25501953
94. Millward DJ, Forrester T, Ah-Sing E, Yeboah N, Gibson N, et al. (2000) The transfer of 15N from urea to lysine in the human infant. Br J Nutr 83: 505–512. PMID: 10953675
95. Wilson CM, Loach D, Lawley B, Bell T, Sims IM, et al. (2014) Lactobacillus reuteri 100–23 modulates urea hydrolysis in the murine stomach. Appl Environ Microbiol 80: 6104–6113. https://doi.org/10.1128/AEM.01876-14 PMID: 25063664
96. Power DA, Burton JP, Chilcott CN, Dawes PJ, Tagg JR (2008) Preliminary investigations of the coloni-sation of upper respiratory tract tissues of infants using a paediatric formulation of the oral probiotic Streptococcus salivarius K12. Eur J Clin Microbiol Infect Dis 27: 1261–1263. https://doi.org/10.1007/s10096-008-0569-4 PMID: 18560907