Microbial Ecology

, Volume 72, Issue 4, pp 917–930 | Cite as

Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness

Genes and Genomes

Abstract

Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.

Keywords

Enterococcus hirae Ecotype Genome Competitive fitness index cpn60 

References

  1. 1.
    Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409(6819):529–533PubMedCrossRefGoogle Scholar
  2. 2.
    Ahmed A, Earl J, Retchless A, Hillier SL, Rabe LK, Cherpes TL, Powell E, Janto B, Eutsey R, Hiller NL, Boissy R, Dahlgren ME, Hall BG, Costerton JW, Post JC, Hu FZ, Ehrlich GD (2012) Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J Bacteriol 194(15):3922–3937PubMedPubMedCentralCrossRefGoogle Scholar
  3. 3.
    Mappley LJ, Black ML, AbuOun M, Darby AC, Woodward MJ, Parkhill J, Turner AK, Bellgard MI, La T, Phillips ND, La Ragione RM, Hampson DJ (2012) Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity. BMC Genomics 13:454PubMedPubMedCentralCrossRefGoogle Scholar
  4. 4.
    Wiedenbeck J, Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35(5):957–976PubMedCrossRefGoogle Scholar
  5. 5.
    Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6(12), e27310PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12(1):118–123PubMedCrossRefGoogle Scholar
  7. 7.
    Klatt CG, Wood JM, Rusch DB, Bateson MM, Hamamura N, Heidelberg JF, Grossman AR, Bhaya D, Cohan FM, Kuhl M, Bryant DA, Ward DM (2011) Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J 5(8):1262–1278PubMedPubMedCentralCrossRefGoogle Scholar
  8. 8.
    Cohan FM (2009) Tracking bacterial responses to global warming with an ecotype-based systematics. Clin Microbiol Infect 15(Suppl 1):54–59PubMedCrossRefGoogle Scholar
  9. 9.
    Cohan FM (2006) Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philos T R Soc B 361(1475):1985–1996CrossRefGoogle Scholar
  10. 10.
    Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM (2014) Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis. Appl Environ Microbiol 80(16):4842–4853PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE (2012) The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS ONE 7(11), e49755PubMedPubMedCentralCrossRefGoogle Scholar
  12. 12.
    Goh SH, Facklam RR, Chang M, Hill JE, Tyrrell GJ, Burns EC, Chan D, He C, Rahim T, Shaw C, Hemmingsen SM (2000) Identification of Enterococcus species and phenotypically similar Lactococcus and Vagococcus species by reverse checkerboard hybridization to chaperonin 60 gene sequences. J Clin Microbiol 38(11):3953–3959PubMedPubMedCentralGoogle Scholar
  13. 13.
    Bondici VF, Lawrence JR, Khan NH, Hill JE, Yergeau E, Wolfaardt GM, Warner J, Korber DR (2013) Microbial communities in low permeability, high pH uranium mine tailings: characterization and potential effects. J Appl Microbiol 114(6):1671–1686PubMedCrossRefGoogle Scholar
  14. 14.
    Chaban B, Albert A, Links MG, Gardy J, Tang P, Hill JE (2013) Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza. PLoS ONE 8(7), e69559PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Chaban B, Links MG, Hill JE (2012) A molecular enrichment strategy based on cpn60 for detection of Epsilon-Proteobacteria in the dog fecal microbiome. Microbial Ecol 63(2):348–357CrossRefGoogle Scholar
  16. 16.
    Desai AR, Links MG, Collins SA, Mansfield GS, Drew MD, Van Kessel AG, Hill JE (2012) Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss). Aquaculture 350:134–142CrossRefGoogle Scholar
  17. 17.
    Desai AR, Musil KM, Carr AP, Hill JE (2009) Characterization and quantification of feline fecal microbiota using cpn60 sequence-based methods and investigation of animal-to-animal variation in microbial population structure. Vet Microbiol 137:120–128PubMedCrossRefGoogle Scholar
  18. 18.
    Hill JE, Seipp RP, Betts M, Hawkins L, Van Kessel AG, Crosby WL, Hemmingsen SM (2002) Extensive profiling of a complex microbial community by high-throughput sequencing. Appl Environ Microbiol 68(6):3055–3066PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, Tyler S, Ball B, Severini A, Plummer FA (2009) Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl Environ Microbiol 75(9):2889–2898PubMedPubMedCentralCrossRefGoogle Scholar
  20. 20.
    Schellenberg J, Links MG, Hill JE, Hemmingsen SM, Peters GA, Dumonceaux TJ (2011) Pyrosequencing of chaperonin-60 (cpn60) amplicons as a means of determining microbial community composition. Methods Mol Biol 733:143–158PubMedCrossRefGoogle Scholar
  21. 21.
    Chaban B, Links MG, Paramel Jayaprakash T, Wagner EC, Bourque DK, Lohn Z, Albert AYK, van Schalkwyk J, Reid G, Hemmingsen SM, Hill JE, Money DM (2014) Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle. Microbiome 2:23PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Links MG, Demeke T, Gräfenhan T, Hill JE, Hemmingsen SM, Dumonceaux TJ (2014) Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds. New Phytologist 202(2):542–553PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Oliver KL, Hamelin RC, Hintz WE (2008) Effects of transgenic hybrid aspen overexpressing polyphenol oxidase on rhizosphere diversity. Appl Environ Microbiol 74(17):5340–5348PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Verbeke TJ, Sparling R, Hill JE, Links MG, Levin D, Dumonceaux TJ (2011) Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species. Syst Appl Microbiol 34:171–179PubMedCrossRefGoogle Scholar
  25. 25.
    Paramel Jayaprakash T, Schellenberg JJ, Hill JE (2012) Resolution and characterization of distinct cpn60-based subgroups of Gardnerella vaginalis in the vaginal microbiota. PLoS ONE 7(8), e43009PubMedPubMedCentralCrossRefGoogle Scholar
  26. 26.
    Vermette CJ, Russell AH, Desai AR, Hill JE (2009) Resolution of phenotypically distinct strains of Enterococcus spp. in a complex microbial community using cpn60 universal target sequencing. Microbial Ecol 59(1):14–24CrossRefGoogle Scholar
  27. 27.
    Martin-Platero AM, Valdivia E, Maqueda M, Martinez-Bueno M (2007) Fast, convenient, and economical method for isolating genomic DNA from lactic acid bacteria using a modification of the protein "salting-out" procedure. Anal Biochem 366(1):102–104PubMedCrossRefGoogle Scholar
  28. 28.
    Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75PubMedPubMedCentralCrossRefGoogle Scholar
  29. 29.
    Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Nat Acad Sci USA 106(45):19126–19131PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Hew CM, Korakli M, Vogel RF (2007) Expression of virulence-related genes by Enterococcus faecalis in response to different environments. Syst Appl Microbiol 30(4):257–267PubMedCrossRefGoogle Scholar
  31. 31.
    Travisano M (1997) Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence. Genetics 146(2):471–479PubMedPubMedCentralGoogle Scholar
  32. 32.
    Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T et al (2009) Genomics. Genome project standards in a new era of sequencing. Science 326(5950):236–237PubMedCrossRefGoogle Scholar
  33. 33.
    Lebreton F, Willems RJL, Gilmore MS (2014) Enterococcus Diversity, Origins in Nature, and Gut Colonization. In: Gilmore MS, Clewell DB, Ike Y, Shankar N (eds) Enterococci: From Commensals to Leading Causes of Drug Resistant Infection. Massachusetts Eye and Ear Infirmary, Boston, p 3–44Google Scholar
  34. 34.
    Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucl Acids Res 29(1):22–28PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Kandler O (1983) Carbohydrate metabolism in lactic acid bacteria. Antonie Van Leeuwenhoek 49(3):209–224PubMedCrossRefGoogle Scholar
  36. 36.
    Cases I, Velazquez F, de Lorenzo V (2007) The ancestral role of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics. Res Microbiol 158(8–9):666–670PubMedCrossRefGoogle Scholar
  37. 37.
    Palmer KL, Godfrey P, Griggs A, Kos VN, Zucker J, Desjardins C, Cerqueira G, Gevers D, Walker S, Wortman J, Feldgarden M, Haas B, Birren B, Gilmore MS (2012) Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. MBio 3(1):e00318–00311PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Clark ST, Diaz Caballero J, Cheang M, Coburn B, Wang PW, Donaldson SL, Zhang Y, Liu M, Keshavjee S, Yau YC, Waters VJ, Elizabeth Tullis D, Guttman DS, Hwang DM (2015) Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis. Sci Rep 5:10932PubMedPubMedCentralCrossRefGoogle Scholar
  39. 39.
    Hill JE, Town JR, Hemmingsen SM (2006) Improved template representation in cpn60 PCR product libraries generated from complex templates by application of a specific mixture of PCR primers. Environ Microbiol 8(4):741–746PubMedCrossRefGoogle Scholar
  40. 40.
    Hill JE, Penny SL, Crowell KG, Goh SH, Hemmingsen SM (2004) cpnDB: a chaperonin sequence database. Genome Res 14(8):1669–1675PubMedPubMedCentralCrossRefGoogle Scholar
  41. 41.
    Farrow JAE, Collins MD (1985) Enterococcus hirae, a new species that includes amino-acid assay strain NCDO-1258 and strains causing growth depression in young chickens. Int J Syst Bacteriol 35(1):73–75CrossRefGoogle Scholar
  42. 42.
    Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15(7):1713–1731PubMedCrossRefGoogle Scholar
  43. 43.
    Francl AL, Thongaram T, Miller MJ (2010) The PTS transporters of Lactobacillus gasseri ATCC 33323. BMC Microbiol 10:77PubMedPubMedCentralCrossRefGoogle Scholar
  44. 44.
    Thompson J (1979) Lactose metabolism in Streptococcus lactis: phosphorylation of galactose and glucose moieties in vivo. J Bacteriol 140(3):774–785PubMedPubMedCentralGoogle Scholar
  45. 45.
    McKay L, Miller A 3rd, Sandine WE, Elliker PR (1970) Mechanisms of lactose utilization by lactic acid streptococci: enzymatic and genetic analyses. J Bacteriol 102(3):804–809PubMedPubMedCentralGoogle Scholar
  46. 46.
    Francl AL, Hoeflinger JL, Miller MJ (2012) Identification of lactose phosphotransferase systems in Lactobacillus gasseri ATCC 33323 required for lactose utilization. Microbiology 158(Pt 4):944–952PubMedCrossRefGoogle Scholar
  47. 47.
    Dudkiewicz M, Szczepinska T, Grynberg M, Pawlowski K (2012) A novel protein kinase-like domain in a selenoprotein, widespread in the tree of life. PLoS ONE 7(2), e32138PubMedPubMedCentralCrossRefGoogle Scholar
  48. 48.
    Fu X, Liang W, Du P, Yan M, Kan B (2014) Transcript changes in Vibrio cholerae in response to salt stress. Gut Pathogens 6(1):47PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Veterinary MicrobiologyUniversity of SaskatchewanSaskatoonCanada
  2. 2.Department of Life SciencesImperial College LondonLondonUK

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