1887

Abstract

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.

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2016-02-09
2019-08-25
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References

  1. Alikhan N. F., Petty N. K., Ben Zakour N. L., Beatson S. A.. 2011; blast Ring Image Generator (brig): simple prokaryote genome comparisons. BMC Genomics12:402 [CrossRef][PubMed]
    [Google Scholar]
  2. Aminov R. I., Walker A. W., Duncan S. H., Harmsen H. J., Welling G. W., Flint H. J.. 2006; Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale . Appl Environ Microbiol72:6371–6376[CrossRef]
    [Google Scholar]
  3. Balamurugan R., Rajendiran E., George S., Samuel G. V., Ramakrishna B. S.. 2008; Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer. J Gastroenterol Hepatol23:1298–1303[CrossRef]
    [Google Scholar]
  4. Barcenilla A., Pryde S. E., Martin J. C., Duncan S. H., Stewart C. S., Henderson C., Flint H. J.. 2000; Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol66:1654–1661 [CrossRef][PubMed]
    [Google Scholar]
  5. Ben David Y., Dassa B., Borovok I., Lamed R., Koropatkin N. M., Martens E. C., White B. A., Bernalier-Donadille A., Duncan S. H., other authors. 2015; Ruminococcal cellulosome systems from rumen to human. Environ Microbiol17:3407–3426 [CrossRef][PubMed]
    [Google Scholar]
  6. Bendtsen J. D., Kiemer L., Fausbøll A., Brunak S.. 2005; Non-classical protein secretion in bacteria. BMC Microbiol5:58 [CrossRef][PubMed]
    [Google Scholar]
  7. Boetzer M., Pirovano W.. 2012; Toward almost closed genomes with GapFiller. Genome Biol13:R56 [CrossRef][PubMed]
    [Google Scholar]
  8. Boraston A. B., Healey M., Klassen J., Ficko-Blean E., Lammerts van Bueren A., Law V.. 2006; A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J Biol Chem281:587–598 [CrossRef][PubMed]
    [Google Scholar]
  9. Bryant M. P.. 1972; Commentary on the Hungate technique for culture of anaerobic bacteria. Am J Clin Nutr25:1324–1328[PubMed]
    [Google Scholar]
  10. Chassard C., Goumy V., Leclerc M., Del'homme C., Bernalier-Donadille A.. 2007; Characterization of the xylan-degrading microbial community from human faeces. FEMS Microbiol Ecol61:121–131 [CrossRef][PubMed]
    [Google Scholar]
  11. Cid M., Pedersen H. L., Kaneko S., Coutinho P. M., Henrissat B., Willats W. G., Boraston A. B.. 2010; Recognition of the helical structure of beta-1,4-galactan by a new family of carbohydrate-binding modules. J Biol Chem285:35999–36009 [CrossRef][PubMed]
    [Google Scholar]
  12. Cockburn D. W., Orlovsky N. I., Foley M. H., Kwiatkowski K. J., Bahr C. M., Maynard M., Demeler B., Koropatkin N. M.. 2015; Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale . Mol Microbiol95:209–230 [CrossRef][PubMed]
    [Google Scholar]
  13. Cuskin F., Flint J. E., Gloster T. M., Morland C., Baslé A., Henrissat B., Coutinho P. M., Strazzulli A., Solovyova A. S., other authors. 2012; How nature can exploit nonspecific catalytic and carbohydrate binding modules to create enzymatic specificity. Proc Natl Acad Sci U S A109:20889–20894 [CrossRef][PubMed]
    [Google Scholar]
  14. Cuskin F., Lowe E. C., Temple M. J., Zhu Y., Cameron E. A., Pudlo N. A., Porter N. T., Urs K., Thompson A. J., other authors. 2015; Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature517:165–169 [CrossRef][PubMed]
    [Google Scholar]
  15. D'Elia J. N., Salyers A. A.. 1996; Contribution of a neopullulanase, a pullulanase, and an alpha-glucosidase to growth of Bacteroides thetaiotaomicron on starch. J Bacteriol178:7173–7179[PubMed]
    [Google Scholar]
  16. David L. A., Maurice C. F., Carmody R. N., Gootenberg D. B., Button J. E., Wolfe B. E., Ling A. V., Devlin A. S., Varma Y., other authors. 2014; Diet rapidly and reproducibly alters the human gut microbiome. Nature505:559–563 [CrossRef][PubMed]
    [Google Scholar]
  17. Duncan S. H., Aminov R. I., Scott K. P., Louis P., Stanton T. B., Flint H. J.. 2006; Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces. Int J Syst Evol Microbiol56:2437–2441 [CrossRef][PubMed]
    [Google Scholar]
  18. Duncan S. H., Belenguer A., Holtrop G., Johnstone A. M., Flint H. J., Lobley G. E.. 2007; Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol73:1073–1078 [CrossRef][PubMed]
    [Google Scholar]
  19. Eckburg P. B., Bik E. M., Bernstein C. N., Purdom E., Dethlefsen L., Sargent M., Gill S. R., Nelson K. E., Relman D. A.. 2005; Diversity of the human intestinal microbial flora. Science308:1635–1638 [CrossRef][PubMed]
    [Google Scholar]
  20. El Kaoutari A., Armougom F., Gordon J. I., Raoult D., Henrissat B.. 2013; The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol11:497–504 [CrossRef][PubMed]
    [Google Scholar]
  21. Flint H. J., Bayer E. A., Rincon M. T., Lamed R., White B. A.. 2008; Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol6:121–131 [CrossRef][PubMed]
    [Google Scholar]
  22. Flint H. J., Scott K. P., Duncan S. H., Louis P., Forano E.. 2012a; Microbial degradation of complex carbohydrates in the gut. Gut Microbes3:289–306 [CrossRef][PubMed]
    [Google Scholar]
  23. Flint H. J., Scott K. P., Louis P., Duncan S. H.. 2012b; The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol9:577–589 [CrossRef][PubMed]
    [Google Scholar]
  24. Gregg K. J., Finn R., Abbott D. W., Boraston A. B.. 2008; Divergent modes of glycan recognition by a new family of carbohydrate-binding modules. J Biol Chem283:12604–12613 [CrossRef][PubMed]
    [Google Scholar]
  25. Hold G. L., Schwiertz A., Aminov R. I., Blaut M., Flint H. J.. 2003; Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces. Appl Environ Microbiol69:4320–4324 [CrossRef][PubMed]
    [Google Scholar]
  26. Hyatt D., Chen G. L., Locascio P. F., Land M. L., Larimer F. W., Hauser L. J.. 2010; Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics11:119 [CrossRef][PubMed]
    [Google Scholar]
  27. Kanehisa M., Goto S.. 2000; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res28:27–30 [CrossRef][PubMed]
    [Google Scholar]
  28. Kumar S., Nei M., Dudley J., Tamura K.. 2008; mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform9:299–306 [CrossRef][PubMed]
    [Google Scholar]
  29. Lagesen K., Hallin P., Rødland E. A., Staerfeldt H. H., Rognes T., Ussery D. W.. 2007; RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  30. Lammerts van Bueren A., Finn R., Ausió J.. 2004; α-Glucan recognition by a new family of carbohydrate-binding modules found primarily in bacterial pathogens. Biochemistry43:15633–15642 [CrossRef][PubMed]
    [Google Scholar]
  31. Larsbrink J., Rogers T. E., Hemsworth G. R., McKee L. S., Tauzin A. S., Spadiut O., Klinter S., Pudlo N. A., Urs K., other authors. 2014; A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature506:498–502 [CrossRef][PubMed]
    [Google Scholar]
  32. Lopez-Siles M., Khan T. M., Duncan S. H., Harmsen H. J., Garcia-Gil L. J., Flint H. J.. 2012; Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol78:420–428 [CrossRef][PubMed]
    [Google Scholar]
  33. Louis P., Flint H. J.. 2009; Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett294:1–8 [CrossRef][PubMed]
    [Google Scholar]
  34. Louis P., Duncan S. H., McCrae S. I., Millar J., Jackson M. S., Flint H. J.. 2004; Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J Bacteriol186:2099–2106 [CrossRef][PubMed]
    [Google Scholar]
  35. Louis P., Young P., Holtrop G., Flint H. J.. 2010; Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environ Microbiol12:304–314 [CrossRef][PubMed]
    [Google Scholar]
  36. Louis P., Hold G. L., Flint H. J.. 2014; The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol12:661–672 [CrossRef][PubMed]
    [Google Scholar]
  37. Machiels K., Joossens M., Sabino J., De Preter V., Arijs I., Eeckhaut V., Ballet V., Claes K., Van Immerseel F., other authors. 2014; A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut63:1275–1283 [CrossRef][PubMed]
    [Google Scholar]
  38. Martens E. C., Chiang H. C., Gordon J. I.. 2008; Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe4:447–457 [CrossRef][PubMed]
    [Google Scholar]
  39. Martens E. C., Lowe E. C., Chiang H., Pudlo N. A., Wu M., McNulty N. P., Abbott D. W., Henrissat B., Gilbert H. J., other authors. 2011; Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol9:e1001221 [CrossRef][PubMed]
    [Google Scholar]
  40. Martínez I., Kim J., Duffy P. R., Schlegel V. L., Walter J.. 2010; Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One5:e15046 [CrossRef][PubMed]
    [Google Scholar]
  41. Martínez I., Lattimer J. M., Hubach K. L., Case J. A., Yang J., Weber C. G., Louk J. A., Rose D. J., Kyureghian G., other authors. 2013; Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J7:269–280 [CrossRef][PubMed]
    [Google Scholar]
  42. McNulty N. P., Wu M., Erickson A. R., Pan C., Erickson B. K., Martens E. C., Pudlo N. A., Muegge B. D., Henrissat B., other authors. 2013; Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol11:e1001637 [CrossRef][PubMed]
    [Google Scholar]
  43. Miyazaki K., Martin J. C., Marinsek-Logar R., Flint H. J.. 1997; Degradation and utilization of xylans by the rumen anaerobe Prevotella bryantii (formerly P. ruminicola subsp. brevis) B14. Anaerobe3:373–381 [CrossRef][PubMed]
    [Google Scholar]
  44. Neville B. A., Sheridan P. O., Harris H. M., Coughlan S., Flint H. J., Duncan S. H., Jeffery I. B., Claesson M. J., Ross R. P., other authors. 2013; Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans. PLoS One8:e68919 [CrossRef][PubMed]
    [Google Scholar]
  45. Otto T. D., Sanders M., Berriman M., Newbold C.. 2010; Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics26:1704–1707 [CrossRef][PubMed]
    [Google Scholar]
  46. Petersen T. N., Brunak S., von Heijne G., Nielsen H.. 2011; SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods8:785–786 [CrossRef][PubMed]
    [Google Scholar]
  47. Punta M., Coggill P. C., Eberhardt R. Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., other authors. 2012; The Pfam protein families database. Nucleic Acids Res40:(D1)D290–D301 [CrossRef][PubMed]
    [Google Scholar]
  48. Ramsay A. G., Scott K. P., Martin J. C., Rincon M. T., Flint H. J.. 2006; Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon. Microbiology152:3281–3290 [CrossRef][PubMed]
    [Google Scholar]
  49. Reeves A. R., Wang G. R., Salyers A. A.. 1997; Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron . J Bacteriol179:643–649[PubMed]
    [Google Scholar]
  50. Rincon M. T., Dassa B., Flint H. J., Travis A. J., Jindou S., Borovok I., Lamed R., Bayer E. A., Henrissat B., other authors. 2010; Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium. Ruminococcus flavefaciens FD-1.PLoS One5:e12476 [CrossRef][PubMed]
    [Google Scholar]
  51. Saeed A. I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., other authors. 2003; tm4: a free, open-source system for microarray data management and analysis. Biotechniques34:374–378[PubMed]
    [Google Scholar]
  52. Salonen A., Lahti L., Salojärvi J., Holtrop G., Korpela K., Duncan S. H., Date P., Farquharson F., Johnstone A. M., other authors. 2014; Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J8:2218–2230 [CrossRef][PubMed]
    [Google Scholar]
  53. Scott K. P., Martin J. C., Campbell G., Mayer C. D., Flint H. J.. 2006; Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium Roseburia inulinivorans . J Bacteriol188:4340–4349 [CrossRef][PubMed]
    [Google Scholar]
  54. Scott K. P., Martin J. C., Chassard C., Clerget M., Potrykus J., Campbell G., Mayer C. D., Young P., Rucklidge G., other authors. 2011; Substrate-driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch. Proc Natl Acad Sci U S A 108 (Suppl1:4672–4679 [CrossRef][PubMed]
    [Google Scholar]
  55. Scott K. P., Martin J. C., Duncan S. H., Flint H. J.. 2014; Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. FEMS Microbiol Ecol87:30–40 [CrossRef][PubMed]
    [Google Scholar]
  56. Sekirov I., Russell S. L., Antunes L. C., Finlay B. B.. 2010; Gut microbiota in health and disease. Physiol Rev90:859–904 [CrossRef][PubMed]
    [Google Scholar]
  57. Shipman J. A., Berleman J. E., Salyers A. A.. 2000; Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. J Bacteriol182:5365–5372 [CrossRef][PubMed]
    [Google Scholar]
  58. Sigrist C. J., Cerutti L., de Castro E., Langendijk-Genevaux P. S., Bulliard V., Bairoch A., Hulo N.. 2010; PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res38:D161–D166 [CrossRef][PubMed]
    [Google Scholar]
  59. Sonnenburg E. D., Sonnenburg J. L., Manchester J. K., Hansen E. E., Chiang H. C., Gordon J. I.. 2006; A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc Natl Acad Sci U S A103:8834–8839 [CrossRef][PubMed]
    [Google Scholar]
  60. Stam M. R., Danchin E. G., Rancurel C., Coutinho P. M., Henrissat B.. 2006; Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel19:555–562 [CrossRef][PubMed]
    [Google Scholar]
  61. Tap J., Mondot S., Levenez F., Pelletier E., Caron C., Furet J. P., Ugarte E., Muñoz-Tamayo R., Paslier D. L., other authors. 2009; Towards the human intestinal microbiota phylogenetic core. Environ Microbiol11:2574–2584 [CrossRef][PubMed]
    [Google Scholar]
  62. Travis A. J., Kelly D., Flint H. J., Aminov R. I.. 2015; Complete genome sequence of the human gut symbiont Roseburia hominis . Genome Announc3:e01286–e01215 [CrossRef][PubMed]
    [Google Scholar]
  63. Walker A. W., Ince J., Duncan S. H., Webster L. M., Holtrop G., Ze X., Brown D., Stares M. D., Scott P., other authors. 2011; Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J5:220–230 [CrossRef][PubMed]
    [Google Scholar]
  64. Wang T., Cai G., Qiu Y., Fei N., Zhang M., Pang X., Jia W., Cai S., Zhao L.. 2012; Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J6:320–329 [CrossRef][PubMed]
    [Google Scholar]
  65. Wegmann U., Louis P., Goesmann A., Henrissat B., Duncan S. H., Flint H. J.. 2014; Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota (‘Ruminococcus bicirculans’) reveals two chromosomes and a selective capacity to utilize plant glucans. Environ Microbiol16:2879–2890[PubMed][CrossRef]
    [Google Scholar]
  66. Yin Y., Mao X., Yang J., Chen X., Mao F., Xu Y.. 2012; dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res40:(W1)W445–W451 [CrossRef][PubMed]
    [Google Scholar]
  67. Yu C., Zavaljevski N., Desai V., Reifman J.. 2011; QuartetS: a fast and accurate algorithm for large-scale orthology detection. Nucleic Acids Res39:e88 [CrossRef][PubMed]
    [Google Scholar]
  68. Ze X., Duncan S. H., Louis P., Flint H. J.. 2012; Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J6:1535–1543 [CrossRef][PubMed]
    [Google Scholar]
  69. Ze X., Ben David Y., Laverde-Gomez J. A., Dassa B., Sheridan P. O., Duncan S. H., Louis P., Henrissat B., Juge N., other authors. 2015; Unique organization of extracellular amylases into amylosomes in the resistant starch-utilizing human colonic Firmicutes bacterium Ruminococcus bromii . MBio6:e01058–e01015 [CrossRef][PubMed]
    [Google Scholar]
  70. Zerbino D. R., Birney E.. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res18:821–829 [CrossRef][PubMed]
    [Google Scholar]
  71. Eubacterium rectale T1-815 genome (2015); CVRQ01000001–CVRQ01000090http://www.ebi.ac.uk/ena/data/view/PRJEB9320
  72. Roseburia faecis M72/1 genome (2015); CVRR01000001–CVRR01000101http://www.ebi.ac.uk/ena/data/view/PRJEB9321
  73. Roseburia inulinivorans L1-83 genome (2015); CVRS01000001–CVRS01000151http://www.ebi.ac.uk/ena/data/view/PRJEB9322
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