Comparative Genomic and Functional Analysis of 100 Strains and Their Comparison with Strain GG

English version České info

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.

Vyšlo v časopise: Comparative Genomic and Functional Analysis of 100 Strains and Their Comparison with Strain GG. PLoS Genet 9(8): e32767. doi:10.1371/journal.pgen.1003683
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003683

Souhrn

Zdroje

1. Clemente JoseC, Ursell LukeK, Parfrey LauraW, KnightR (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148: 1258–1270.

2. Rajilić-StojanovićM, SmidtH, De VosWM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 2125–2136.

3. WilliamsonSJ, YoosephS (2011) From bacterial to microbial ecosystems (metagenomics) Bacterial Molecular Networks. Meth Mol Biol 35–55.

4. VaughanEE, SchutF, HeiligHG, ZoetendalEG, de VosWM, et al. (2000) A molecular view of the intestinal ecosystem. Curr Issues Intest Microbiol 1: 1–12.

5. KleerebezemM, VaughanEE (2009) Probiotic and gut lactobacilli and bifidobacteria: molecular approaches to study diversity and activity. Annu Rev Microbiol 63: 269–290.

6. ZoetendalEG, RaesJ, van den BogertB, ArumugamM, BooijinkCC, et al. (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6: 1415–1426.

7. ClaessonMJ, O'SullivanO, WangQ, NikkilaJ, MarchesiJR, et al. (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4 (8) e6669.

8. SalonenA, SalojarviJ, LahtiL, de VosWM (2012) The adult intestinal core microbiota is determined by analysis depth and health status. Clin Microbiol Infect 4: 16–20.

9. HeiligHG, ZoetendalEG, VaughanEE, MarteauP, AkkermansAD, et al. (2002) Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl Environ Microbiol 68: 114–123.

10. WalterJ (2008) Ecological Role of Lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol 74: 4985–4996.

11. WalterJ, BrittonRA, RoosS (2010) Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A 108 Suppl 1: 4645–4652.

12. KalliomakiM, SalminenS, ArvilommiH, KeroP, KoskinenP, et al. (2001) Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. Lancet 357: 1076–1079.

13. KalliomakiM, SalminenS, PoussaT, ArvilommiH, IsolauriE (2003) Probiotics and prevention of atopic disease: 4-year follow-up of a randomised placebo-controlled trial. Lancet 361: 1869–1871.

14. BernardeauM, GuguenM, VernouxJP (2006) Beneficial lactobacilli in food and feed: long-term use, biodiversity and proposals for specific and realistic safety assessments. FEMS Microbiol Rev 30: 487–513.

15. LebeerS, VanderleydenJ, De KeersmaeckerSC (2010) Adaptation factors of the probiotic Lactobacillus rhamnosus GG. Benef Microbes 1: 335–342.

16. SaxelinM, TynkkynenS, Mattila-SandholmT, de VosWM (2005) Probiotic and other functional microbes: from markets to mechanisms. Curr Opin Biotechnol 16: 204–211.

17. RandazzoCL, De LucaS, TodaroA, RestucciaC, LanzaCM, et al. (2007) Preliminary characterization of wild lactic acid bacteria and their abilities to produce flavour compounds in ripened model cheese system. J Appl Microbiol 103: 427–435.

18. PitinoI, RandazzoCL, CrossKL, ParkerML, BisignanoC, et al. (2012) Survival of Lactobacillus rhamnosus strains inoculated in cheese matrix during simulated human digestion. Food Microbiol 31: 57–63.

19. KankainenM, PaulinL, TynkkynenS, von OssowskiI, ReunanenJ, 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.

20. ReunanenJ, von OssowskiI, HendrickxAPA, PalvaA, de VosWM (2012) Characterization of the SpaCBA pilus fibers in the probiotic Lactobacillus rhamnosus GG. Appl Environ Microbiol 78: 2337–2344.

21. von OssowskiI, ReunanenJ, SatokariR, VesterlundS, KankainenM, et al. (2010) Mucosal adhesion properties of the probiotic Lactobacillus rhamnosus GG SpaCBA and SpaFED pilin subunits. Appl Environ Microbiol 76: 2049–2057.

22. MillarMR, BaconC, SmithSL, WalkerV, HallMA (1993) Enteral feeding of premature infants with Lactobacillus GG. Arch Dis Child 69: 483–487.

23. PetschowBW, FigueroaR, HarrisCL, BeckLB, ZieglerE, et al. (2005) Effects of feeding an infant formula containing Lactobacillus GG on the colonization of the intestine: a dose-response study in healthy infants. J Clin Gastroenterol 39: 786–790.

24. AlanderM, SatokariR, KorpelaR, SaxelinM, Vilpponen-SalmelaT, et al. (1999) Persistence of colonization of human colonic mucosa by a probiotic strain, Lactobacillus rhamnosus GG, after oral consumption. Appl Environ Microbiol 65: 351–354.

25. LebeerS, VanderleydenJ, De KeersmaeckerSCJ (2008) Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev 72: 728–764.

26. MackDR, AhrneS, HydeL, WeiS, HollingsworthMA (2003) Extracellular MUC3 mucin secretion follows adherence of Lactobacillus strains to intestinal epithelial cells in vitro. Gut 52: 827–833.

27. VesterlundS, KarpM, SalminenS, OuwehandAC (2006) Staphylococcus aureus adheres to human intestinal mucus but can be displaced by certain lactic acid bacteria. Microbiology 152: 1819–1826.

28. Johnson-HenryKC, DonatoKA, Shen-TuG, GordanpourM, ShermanPM (2008) Lactobacillus rhamnosus strain GG prevents enterohemorrhagic Escherichia coli O157:H7-induced changes in epithelial barrier function. Infect Immun 76: 1340–1348.

29. YoungVB (2012) The intestinal microbiota in health and disease. Curr Opin Gastroenterol 28: 63–69.

30. LebeerS, VanderleydenJ, De KeersmaeckerSC (2010) Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat Rev Microbiol 8: 171–184.

31. KlaenhammerTR, KleerebezemM, KoppMV, RescignoM (2012) The impact of probiotics and prebiotics on the immune system. Nat Rev Immunol 12: 728–734.

32. CallananM, KaletaP, O'CallaghanJ, O'SullivanO, JordanK, et al. (2008) Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. J Bacteriol 190: 727–735.

33. CaiH, ThompsonR, BudinichMF, BroadbentJR, SteeleJL (2009) Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution. Genome Biol Evol 1: 239–257.

34. SiezenR, TzenevaV, CastioniA, WelsM, PhanH, et al. (2010) Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ Microbiol 12: 758–773.

35. SiezenR, van Hylckama VliegJ (2011) Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microbial Cell Fact 10: S3.

36. SucciM, TremonteP, RealeA, SorrentinoE, GraziaL, et al. (2005) Bile salt and acid tolerance of Lactobacillus rhamnosus strains isolated from Parmigiano Reggiano cheese. FEMS Microbiol Lett 244: 129–137.

37. SalminenMK, TynkkynenS, RautelinH, SaxelinM, VaaraM, et al. (2002) Lactobacillus bacteremia during a rapid Increase in probiotic use of Lactobacillus rhamnosus GG in Finland. Clin Infect Dis 35: 1155–1160.

38. PascualLM, DanieleM, iacute, aB, RuizF, et al. (2008) Lactobacillus rhamnosus L60, a potential probiotic isolated from the human vagina. J Gen Appl Microbiol 54: 141–148.

39. RichardB, GroisillierA, BadetC, DorignacG, Lonvaud-FunelA (2001) Identification of salivary Lactobacillus rhamnosus species by DNA profiling and a specific probe. Res Microbiol 152: 157–165.

40. O'SullivanO, O'CallaghanJ, Sangrador-VegasA, McAuliffeO, SlatteryL, et al. (2009) Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol 9: 50.

41. BroadbentJ, Neeno-EckwallE, StahlB, TandeeK, CaiH, et al. (2012) Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 13: 533.

42. DouglasGL, KlaenhammerTR (2010) Genomic evolution of domesticated microorganisms. Annu Rev Food Sci Technol 1: 397–414.

43. KoskenniemiK, LaaksoK, KoponenJ, KankainenM, GrecoD, et al. (2011) Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Prot 10: M110.002741.

44. De KeersmaeckerSCJ, VerhoevenTLA, DesairJ, MarchalK, VanderleydenJ, et al. (2006) Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid. FEMS Microbiol Lett 259: 89–96.

45. FreseSA, BensonAK, TannockGW, LoachDM, KimJ, et al. (2011) The Evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 7: e1001314.

46. MoritaH, TohH, OshimaK, MurakamiM, TaylorTD, et al. (2009) Complete genome sequence of the probiotic Lactobacillus rhamnosus ATCC 53103. J Bacteriol 191: 7630–7631.

47. PittetV, EwenE, BushellBR, ZiolaB (2012) Genome Sequence of Lactobacillus rhamnosus ATCC 8530. J Bacteriol 194: 726.

48. de VosW (2011) Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact 10: S2.

49. TettelinH, MasignaniV, CieslewiczMJ, DonatiC, MediniD, et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102: 13950–13955.

50. KantR, BlomJ, PalvaA, SiezenRJ, de VosWM (2011) Comparative genomics of Lactobacillus. Microb Biotechnol 4: 323–332.

51. JansenR, EmbdenJDAv, GaastraW, SchoulsLM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43: 1565–1575.

52. HorvathP, RomeroDA, Coûté-MonvoisinA-C, RichardsM, DeveauH, et al. (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190: 1401–1412.

53. DeveauH, BarrangouR, GarneauJE, LabontéJ, FremauxC, et al. (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190: 1390–1400.

54. BarrangouR, FremauxC, DeveauH, RichardsM, BoyavalP, et al. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709–1712.

55. MarraffiniLA, SontheimerEJ (2008) CRISPR Interference limits horizontal gene transfer in Staphylococci by targeting DNA. Science 322: 1843–1845.

56. MarraffiniLA, SontheimerEJ (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11: 181–190.

57. WestraER, SwartsDC, StaalsRHJ, JoreMM, BrounsSJJ, et al. (2012) The CRISPRs, they are A-changin': how prokaryotes generate adaptive immunity. Annu Rev Genet 46: 311–339.

58. ZhangJ, AbadiaE, RefregierG, TafajS, BoschiroliML, et al. (2010) Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of ‘spoligotyping’ with new spacers and a microbead-based hybridization assay. J Med Microbiol 59: 285–294.

59. DelannoyS, BeutinL, FachP (2012) Use of CRISPR sequence polymorphisms for specific detection of enterohemorrhagic E. coli (EHEC) strains of serotypes O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28 and O157:H7 by real time PCR. J Clin Microbiol 12: 4035–4040.

60. FabreL, ZhangJ, GuigonG, Le HelloS, GuibertV, et al. (2012) CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS ONE 7: e36995.

61. HorvathP, Coûté-MonvoisinA-C, RomeroDA, BoyavalP, FremauxC, et al. (2009) Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int J Food Microbiol 131: 62–70.

62. El AilaN, TencyI, ClaeysG, VerstraelenH, SaerensB, et al. (2009) Identification and genotyping of bacteria from paired vaginal and rectal samples from pregnant women indicates similarity between vaginal and rectal microflora. BMC Infect Dis 9: 167.

63. DouillardFP, RibberaA, JärvinenHM, KantR, PietiläTE, et al. (2013) Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol 79 (6) 1923–1933.

64. SybesmaW, MolenaarD, van IJckenW, VenemaK, KortR (2013) Genome instability in Lactobacillus rhamnosus GG. Appl Environ Microbiol 79 (7) 2233–2239.

65. LebeerS, ClaesI, TytgatHL, VerhoevenTL, MarienE, 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 (1) 185–193.

66. HickeyRJ, ZhouX, PiersonJD, RavelJ, ForneyLJ (2012) Understanding vaginal microbiome complexity from an ecological perspective. Transl Res 160: 267–282.

67. PoznanskiE, CavazzaA, CappaF, CocconcelliPS (2004) Indigenous raw milk microbiota influences the bacterial development in traditional cheese from an alpine natural park. Int J Food Microbiol 92: 141–151.

68. SilvaM, JacobusNV, DenekeC, GorbachSL (1987) Antimicrobial substance from a human Lactobacillus strain. Antimicrob Agents Chemother 31: 1231–1233.

69. LehtoEM, SalminenSJ (1997) Inhibition of Salmonella typhimurium adhesion to Caco-2 cell cultures by Lactobacillus strain GG spent culture supernate: only a pH effect? FEMS Immunol Med Microbiol 18: 125–132.

70. BrüssowH (2001) Phages of dairy bacteria. Annu Rev Microbiol 55: 283–303.

71. PfeilerEA, KlaenhammerTR (2007) The genomics of lactic acid bacteria. Trends Microbiol 15: 546–553.

72. SheuS-J, HwangW-Z, ChiangY-C, LinW-H, ChenH-C, et al. (2010) Use of tuf gene-based primers for the PCR detection of probiotic Bifidobacterium species and enumeration of Bifidobacteria in fermented milk by cultural and quantitative Real-Time PCR methods. J Food Sci 75: M521–M527.

73. VenturaM, CanchayaC, MeylanV, KlaenhammerTR, ZinkR (2003) Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification. Appli Environ Microbiol 69: 6908–6922.

74. LiH, HandsakerB, WysokerA, FennellT, RuanJ, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079.

75. KurtzS, PhillippyA, DelcherA, SmootM, ShumwayM, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.

76. VesterlundS, PalttaJ, KarpM, OuwehandAC (2005) Measurement of bacterial adhesion— in vitro evaluation of different methods. J Microbiol Meth 60: 225–233.

77. SkyttäE, Mattila-SandholmT (1991) A quantitative method for assessing bacteriocins and other food antimicrobials by automated turbidometry. J Microbiol Meth 14: 77–88.

78. SturnA, QuackenbushJ, TrajanoskiZ (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18: 207–208.

79. TamuraK, DudleyJ, NeiM, KumarS (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596–1599.

80. SalminenMK, RautelinH, TynkkynenS, PoussaT, SaxelinM, et al. (2006) Lactobacillus bacteremia, species identification, and antimicrobial susceptibility of 85 blood isolates. Clinical Infect Dis 42: e35–e44.