title: Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG.
abstract: 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.
authors: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland. francois.douillard@helsinki.fi
authors: François P
authors: FP
authors: Douillard
authors: Angela
authors: A
authors: Ribbera
authors: Ravi
authors: R
authors: Kant
authors: Taija E
authors: TE
authors: Pietilä
authors: Hanna M
authors: HM
authors: Järvinen
authors: Marcel
authors: M
authors: Messing
authors: Cinzia L
authors: CL
authors: Randazzo
authors: Lars
authors: L
authors: Paulin
authors: Pia
authors: P
authors: Laine
authors: Jarmo
authors: J
authors: Ritari
authors: Cinzia
authors: C
authors: Caggia
authors: Tanja
authors: T
authors: Lähteinen
authors: Stan J J
authors: SJ
authors: Brouns
authors: Reetta
authors: R
authors: Satokari
authors: Ingemar
authors: I
authors: von Ossowski
authors: Justus
authors: J
authors: Reunanen
authors: Airi
authors: A
authors: Palva
authors: Willem M
authors: WM
authors: de Vos
mesh_terms: D000818:Animals; D056726:Genetic Association Studies; D016680:Genome, Bacterial; D023281:Genomics; D052201:Lacticaseibacillus rhamnosus / Q000145:classification / Q000235:genetics*; D008892:Milk / Q000382:microbiology; D010641:Phenotype; D010802:Phylogeny; D011156:Population Density
references: Nat Rev Genet. 2010 Mar;11(3):181-90
references: 20125085
references: Lancet. 2003 May 31;361(9372):1869-71
references: 12788576
references: Environ Microbiol. 2007 Sep;9(9):2125-36
references: 17686012
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: Infect Immun. 2008 Apr;76(4):1340-8
references: 18227169
references: Benef Microbes. 2010 Nov;1(4):335-42
references: 21831772
references: Environ Microbiol. 2010 Mar;12(3):758-73
references: 20002138
references: Int J Food Microbiol. 2009 Apr 30;131(1):62-70
references: 18635282
references: Trends Microbiol. 2007 Dec;15(12):546-53
references: 18024129
references: Mol Microbiol. 2002 Mar;43(6):1565-75
references: 11952905
references: Food Microbiol. 2012 Aug;31(1):57-63
references: 22475943
references: J Bacteriol. 2008 Feb;190(4):1390-400
references: 18065545
references: J Microbiol Methods. 2005 Feb;60(2):225-33
references: 15590097
references: Clin Infect Dis. 2002 Nov 15;35(10):1155-60
references: 12410474
references: Microbiol Mol Biol Rev. 2008 Dec;72(4):728-64, Table of Contents
references: 19052326
references: Nat Rev Microbiol. 2010 Mar;8(3):171-84
references: 20157338
references: J Appl Microbiol. 2007 Aug;103(2):427-35
references: 17650203
references: J Clin Gastroenterol. 2005 Oct;39(9):786-90
references: 16145341
references: BMC Infect Dis. 2009 Oct 14;9:167
references: 19828036
references: Cell. 2012 Mar 16;148(6):1258-70
references: 22424233
references: Appl Environ Microbiol. 2010 Apr;76(7):2049-57
references: 20118368
references: Curr Opin Biotechnol. 2005 Apr;16(2):204-11
references: 15831388
references: Lancet. 2001 Apr 7;357(9262):1076-9
references: 11297958
references: Appl Environ Microbiol. 2012 Jan;78(1):185-93
references: 22020518
references: Microb Biotechnol. 2011 May;4(3):323-32
references: 21375712
references: Appl Environ Microbiol. 2013 Mar;79(6):1923-33
references: 23315726
references: Genome Biol. 2004;5(2):R12
references: 14759262
references: J Bacteriol. 2008 Feb;190(4):1401-12
references: 18065539
references: Clin Microbiol Infect. 2012 Jul;18 Suppl 4:16-20
references: 22647042
references: FEMS Microbiol Rev. 2006 Jul;30(4):487-513
references: 16774584
references: PLoS Genet. 2011 Feb;7(2):e1001314
references: 21379339
references: Appl Environ Microbiol. 2003 Nov;69(11):6908-22
references: 14602655
references: Annu Rev Genet. 2012;46:311-39
references: 23145983
references: Appl Environ Microbiol. 2013 Apr;79(7):2233-9
references: 23354703
references: ISME J. 2012 Jul;6(7):1415-26
references: 22258098
references: BMC Microbiol. 2009 Mar 05;9:50
references: 19265535
references: Annu Rev Microbiol. 2009;63:269-90
references: 19575569
references: Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S3
references: 21995294
references: Science. 2008 Dec 19;322(5909):1843-5
references: 19095942
references: Curr Issues Intest Microbiol. 2000 Mar;1(1):1-12
references: 11709849
references: Int J Food Microbiol. 2004 Apr 15;92(2):141-51
references: 15109791
references: FEMS Microbiol Lett. 2005 Mar 1;244(1):129-37
references: 15727832
references: Gut. 2003 Jun;52(6):827-33
references: 12740338
references: J Clin Microbiol. 2012 Dec;50(12):4035-40
references: 23035199
references: Science. 2007 Mar 23;315(5819):1709-12
references: 17379808
references: Methods Mol Biol. 2012;804:35-55
references: 22144147
references: Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5
references: 16172379
references: Mol Cell Proteomics. 2011 Feb;10(2):M110.002741
references: 21078892
references: Antimicrob Agents Chemother. 1987 Aug;31(8):1231-3
references: 3307619
references: J Gen Appl Microbiol. 2008 Jun;54(3):141-8
references: 18654035
references: Appl Environ Microbiol. 2012 Apr;78(7):2337-44
references: 22247175
references: Bioinformatics. 2002 Jan;18(1):207-8
references: 11836235
references: Clin Infect Dis. 2006 Mar 1;42(5):e35-44
references: 16447101
references: Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17193-8
references: 19805152
references: Nat Rev Immunol. 2012 Oct;12(10):728-34
references: 23007572
references: Appl Environ Microbiol. 2002 Jan;68(1):114-23
references: 11772617
references: Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S2
references: 21995776
references: FEMS Immunol Med Microbiol. 1997 Jun;18(2):125-32
references: 9223617
references: Curr Opin Gastroenterol. 2012 Jan;28(1):63-9
references: 22080827
references: FEMS Microbiol Lett. 2006 Jun;259(1):89-96
references: 16684107
references: Mol Biol Evol. 2007 Aug;24(8):1596-9
references: 17488738
references: Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4645-52
references: 20615995
references: J Med Microbiol. 2010 Mar;59(Pt 3):285-294
references: 19959631
references: Res Microbiol. 2001 Mar;152(2):157-65
references: 11316369
references: Transl Res. 2012 Oct;160(4):267-82
references: 22683415
references: Annu Rev Food Sci Technol. 2010;1:397-414
references: 22129342
references: J Food Sci. 2010 Oct;75(8):M521-7
references: 21535508
references: Microbiology (Reading). 2006 Jun;152(Pt 6):1819-1826
references: 16735744
references: PLoS One. 2012;7(5):e36995
references: 22623967
references: Appl Environ Microbiol. 1999 Jan;65(1):351-4
references: 9872808
references: Appl Environ Microbiol. 2008 Aug;74(16):4985-96
references: 18539818
references: J Bacteriol. 2012 Feb;194(3):726
references: 22247527
references: J Bacteriol. 2009 Dec;191(24):7630-1
references: 19820099
references: Genome Biol Evol. 2009 Jul 14;1:239-57
references: 20333194
references: Arch Dis Child. 1993 Nov;69(5 Spec No):483-7
references: 8285750
references: BMC Genomics. 2012 Oct 05;13:533
references: 23035691
references: PLoS One. 2009 Aug 20;4(8):e6669
references: 19693277
references: J Bacteriol. 2008 Jan;190(2):727-35
references: 17993529
references: Annu Rev Microbiol. 2001;55:283-303
references: 11544357