Diversity of human small intestinal Streptococcus and Veillonella populations

FEMS Microbiology Ecology

Volumn 85, Issue 2, 2013, Pages 376-388

  van den Bogert, Bartholomeus ^a,b   Erkus, Oylum ^a,b   Boekhorst, Jos ^c   de Goffau, Marcus ^d   Smid, Eddy J ^a,b   Zoetendal, Erwin G ^a,b   Kleerebezem, Michiel ^a,b,c  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c NIZO FOOD RESEARCH   (Netherlands)

^d UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

Genotyping; Human small intestine; Selective cultivation; Streptococcus spp.; Veillonella spp.

Indexed keywords

RNA 16S;

BACTERIOLOGY; BACTERIUM; DIGESTIVE SYSTEM; DNA FINGERPRINTING; PHYLOGENETICS; PHYLOGENY; RELATIVE ABUNDANCE; SPECIES RICHNESS;

AGED; ARTICLE; BIODIVERSITY; CARBOHYDRATE METABOLISM; CLASSIFICATION; FEMALE; GENETICS; GENOTYPE; HUMAN; HUMAN SMALL INTESTINE; ISOLATION AND PURIFICATION; MALE; MICROBIOLOGY; MIDDLE AGED; PHYLOGENY; SELECTIVE CULTIVATION; SMALL INTESTINE; STREPTOCOCCUS; STREPTOCOCCUS SPP.; VEILLONELLA; VEILLONELLA SPP.;

GENOTYPING; HUMAN SMALL INTESTINE; SELECTIVE CULTIVATION; STREPTOCOCCUS SPP.; VEILLONELLA SPP.;

AGED; BIODIVERSITY; CARBOHYDRATE METABOLISM; FEMALE; HUMANS; INTESTINE, SMALL; MALE; MIDDLE AGED; PHYLOGENY; RNA, RIBOSOMAL, 16S; STREPTOCOCCUS; VEILLONELLA;

STREPTOCOCCUS; STREPTOCOCCUS PARASANGUINIS; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS THERMOPHILUS; VEILLONELLA; VEILLONELLA ATYPICA; VEILLONELLA DISPAR; VEILLONELLA PARVULA;

EID: 84880135340     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12127     Document Type: Article

References (58)

1. Aas JA, Paster BJ, Stokes LN, Olsen I & Dewhirst FE (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721-5732.
2. Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P & Engstrand L (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3: e2836.
4. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ & Relman DA (2006) Molecular analysis of the bacterial microbiota in the human stomach. P Natl Acad Sci USA 103: 732-737.
5. Booijink CC, Zoetendal EG, Kleerebezem M & de Vos WM (2007) Microbial communities in the human small intestine: coupling diversity to metagenomics. Future Microbiol 2: 285-295.
6. Booijink CC, El-Aidy S, Rajilić-Stojanović M, Heilig HG, Troost FJ, Smidt H, Kleerebezem M, De Vos WM & Zoetendal EG (2010) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12: 3213-3227.
7. Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
8. Cheon K, Moser SA, Whiddon J, Osgood RC, Momeni S, Ruby JD, Cutter GR, Allison DB & Childers NK (2011) Genetic diversity of plaque mutans streptococci with rep-PCR. J Dent Res 90: 331-335.
9. Cole JR, Wang Q, Cardenas E et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
10. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI & Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
11. Cotter PD (2011) Small intestine and microbiota. Curr Opin Gastroenterol 27: 99-105.
12. Daims H, Bruhl A, Amann R, Schleifer KH & Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434-444.
13. De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K & Whitman WB (2009) Bergey's Manual of Systematic Bacteriology, 2nd edn. Springer, New York.
14. Do T, Jolley KA, Maiden MC, Gilbert SC, Clark D, Wade WG & Beighton D (2009) Population structure of Streptococcus oralis. Microbiology 155: 2593-2602.
15. Duerkop BA, Vaishnava S & Hooper LV (2009) Immune responses to the microbiota at the intestinal mucosal surface. Immunity 31: 368-376.
16. Dunbar J, White S & Forney L (1997) Genetic diversity through the looking glass: effect of enrichment bias. Appl Environ Microbiol 63: 1326-1331.
17. Dunne EM, Ong EK, Moser RJ, Siba PM, Phuanukoonnon S, Greenhill AR, Robins-Browne RM, Mulholland EK & Satzke C (2011) Multilocus sequence typing of Streptococcus pneumoniae by use of mass spectrometry. J Clin Microbiol 49: 3756-3760.
18. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
19. Egland PG, Palmer RJ Jr & Kolenbrander PE (2004) Interspecies communication in Streptococcus gordonii-Veillonella atypica biofilms: signaling in flow conditions requires juxtaposition. P Natl Acad Sci USA 101: 16917-16922.
20. Enright MC, Spratt BG, Kalia A, Cross JH & Bessen DE (2001) Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Infect Immun 69: 2416-2427.
21. Guindon S & Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
22. Haas BJ, Gevers D, Earl AM et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504.
23. Hamady M, Walker JJ, Harris JK, Gold NJ & Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237.
24. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M & Eisen JA (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. P Natl Acad Sci USA 106: 17187-17192.
25. Homan WL, Tribe D, Poznanski S, Li M, Hogg G, Spalburg E, Van Embden JD & Willems RJ (2002) Multilocus sequence typing scheme for Enterococcus faecium. J Clin Microbiol 40: 1963-1971.
26. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM & Crielaard W (2008) Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87: 1016-1020.
27. Kutahya OE, Starrenburg MJ, Rademaker JL, Klaassen CH, van Hylckama Vlieg JE, Smid EJ & Kleerebezem M (2011) High-resolution amplified fragment length polymorphism typing of Lactococcus lactis strains enables identification of genetic markers for subspecies-related phenotypes. Appl Environ Microbiol 77: 5192-5198.
28. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt MGE, ed.), pp. 115-175. Academic Press, Chichester.
29. Lawson RD & Coyle WJ (2010) The noncolonic microbiome: does it really matter? Curr Gastroenterol Rep 12: 259-262.
30. Leser TD & Molbak L (2009) Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol 11: 2194-2206.
31. Ludwig W, Strunk O, Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
32. Maslowski KM & Mackay CR (2011) Diet, gut microbiota and immune responses. Nat Immunol 12: 5-9.
33. Matsheka MI, Lastovica AJ, Zappe H & Elisha BG (2006) The use of (GTG)5 oligonucleotide as an RAPD primer to type Campylobacter concisus. Lett Appl Microbiol 42: 600-605.
34. McCartney AL, Wenzhi W & Tannock GW (1996) Molecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans. Appl Environ Microbiol 62: 4608-4613.
35. Meijerink M, Wells JM, Taverne N, de Zeeuw Brouwer ML, Hilhorst B, Venema K & van Bilsen J (2012) Immunomodulatory effects of potential probiotics in a mouse peanut sensitization model. FEMS Immunol Med Microbiol 65: 488-496.
36. Muniesa M, Blanch AR, Lucena F & Jofre J (2005) Bacteriophages may bias outcome of bacterial enrichment cultures. Appl Environ Microbiol 71: 4269-4275.
37. Ng SK & Hamilton IR (1971) Lactate metabolism by Veillonella parvula. J Bacteriol 105: 999-1005.
38. Pei Z, Bini EJ, Yang L, Zhou M, Francois F & Blaser MJ (2004) Bacterial biota in the human distal esophagus. P Natl Acad Sci USA 101: 4250-4255.
39. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J & Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
40. Qin J, Li R, Raes J et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
41. Rajilić-Stojanović M, Smidt H & de Vos WM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 2125-2136.
42. Rajilić-Stojanović M, Heilig HG, Molenaar D, Kajander K, Surakka A, Smidt H & de Vos WM (2009) Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 11: 1736-1751.
43. Rogosa M (1956) A selective medium for the isolation and enumeration of the veillonella from the oral cavity. J Bacteriol 72: 533-536.
44. Rogosa M, Fitzgerald RJ, Mackintosh ME & Beaman AJ (1958) Improved medium for selective isolation of Veillonella. J Bacteriol 76: 455-456.
45. Tap J, Mondot S, Levenez F et al. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11: 2574-2584.
46. Turnbaugh PJ, Hamady M, Yatsunenko T et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
47. van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, de Groot PJ, Hooiveld GJ, Brummer RJ & Kleerebezem M (2009) Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. P Natl Acad Sci USA 106: 2371-2376.
48. van Baarlen P, Troost F, van der Meer C, Hooiveld G, Boekschoten M, Brummer RJ & Kleerebezem M (2011) Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. P Natl Acad Sci USA 108(Suppl 1): 4562-4569.
49. van den Bogert B, de Vos WM, Zoetendal EG & Kleerebezem M (2011a) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77: 2071-2080.
50. van den Bogert B, Leimena MM, De Vos WM, Zoetendal EG & Kleerebezem M (2011b) Functional intestinal metagenomics. Handbook of Molecular Microbial Ecology, Vol II: Metagenomics in Different Habitats (De Bruin FJ, ed.), pp. 170-190. Wiley-Blackwell, Hoboken, NJ.
51. van Veen SQ, Claas EC & Kuijper EJ (2010) High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol 48: 900-907.
52. Veloo AC, Knoester M, Degener JE & Kuijper EJ (2011) Comparison of two matrix-assisted laser desorption ionisation-time of flight mass spectrometry methods for the identification of clinically relevant anaerobic bacteria. Clin Microbiol Infect 17: 1501-1506.
53. Walter J & Ley R (2011) The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol 65: 411-429.
54. Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
55. Waterhouse AM, Procter JB, Martin DM, Clamp M & Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
56. Zhou Q, Qin X, Qin M & Ge L (2011) Genotypic diversity of Streptococcus mutans and Streptococcus sobrinus in 3-4-year-old children with severe caries or without caries. Int J Paediatr Dent 21: 422-431.
57. Zoetendal EG, Booijink CC, Klaassens ES, Heilig HG, Kleerebezem M, Smidt H & de Vos WM (2006) Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat Protoc 1: 954-959.
58. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM & Kleerebezem M (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6: 1415-1426.