Application of phylogenetic microarrays to interrogation of human microbiota

FEMS Microbiology Ecology

Volumn 79, Issue 1, 2012, Pages 2-11

  Paliy, Oleg ^a   Agans, Richard ^a  

^a WRIGHT STATE UNIVERSITY   (United States)

Author keywords

HITChip; Microbial communities; Microbiota; Microbiota Array; PhyloChip; Phylogenetic microarray

Indexed keywords

RNA 16S;

ABUNDANCE; GENE EXPRESSION; GENETIC ANALYSIS; MICROBIAL COMMUNITY; NUCLEIC ACID; OPTIMIZATION; PHYLOGENETICS; QUANTITATIVE ANALYSIS; SAMPLING;

ARTICLE; BACTERIUM; CLASSIFICATION; DNA MICROARRAY; FECES; GENE EXPRESSION PROFILING; GENETICS; HUMAN; ILIAC BONE; ISOLATION AND PURIFICATION; METAGENOME; MICROBIAL CONSORTIUM; MICROBIOLOGY; OROPHARYNX; PHYLOGENY;

BACTERIA; FECES; GENE EXPRESSION PROFILING; HUMANS; ILIUM; METAGENOME; MICROBIAL CONSORTIA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OROPHARYNX; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 83555162602     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01222.x     Document Type: Article

References (83)

1. Agans R, Rigsbee L, Kenche H, Michail S, Khamis HJ & Paliy O (2011) Distal gut microbiota of adolescent children is different from that of adults. FEMS Microbiol Ecol 77: 404-412.
2. Arumugam M, Raes J, Pelletier E et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174-180.
3. Avarre JC, de Lajudie P & Bena G (2007) Hybridization of genomic DNA to microarrays: a challenge for the analysis of environmental samples. J Microbiol Methods 69: 242-248.
4. Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P, Lobley GE & Flint HJ (2006) Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol 72: 3593-3599.
5. Biagi E, Nylund L, Candela M et al. (2010) Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS ONE 5: e10667.
6. Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M & de Vos WM (2010a) Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol 76: 5533-5540.
7. Booijink CC, El-Aidy S, Rajilic-Stojanovic M et al. (2010b) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12: 3213-3227.
8. Brodie EL, Desantis TZ, Joyner DC et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288-6298.
9. Candela M, Consolandi C, Severgnini M et al. (2010) High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction-universal array approach. BMC Microbiol 10: 116.
10. Claesson MJ, O'Sullivan O, Wang Q et al. (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4: e6669.
11. Claesson MJ, Cusack S, O'Sullivan O et al. (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. P Natl Acad Sci USA 108 (Suppl 1): 4586-4591.
12. 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.
13. Cox MJ, Huang YJ, Fujimura KE et al. (2010a) Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS ONE 5: e8745.
14. Cox MJ, Allgaier M, Taylor B et al. (2010b) Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS ONE 5: e11044.
15. Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC & Keijser BJ (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics 4: 22.
16. de Graaf AA, Maathuis A, de Waard P, Deutz NE, Dijkema C, de Vos WM & Venema K (2009) Profiling human gut bacterial metabolism and its kinetics using [U-13C]glucose and NMR. NMR Biomed 23: 2-12.
17. De Vuyst L & Leroy F (2011) Cross-feeding between bifidobacteria and butyrate-producing colon bacteria explains bifdobacterial competitiveness, butyrate production, and gas production. Int J Food Microbiol 149: 73-80.
18. Deangelis KM, Allgaier M, Chavarria Y et al. (2011) Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS ONE 6: e19306.
19. Dols JA, Smit PW, Kort R et al. (2011) Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis. Am J Obstet Gynecol 204: 305.e1-7.
20. Duncan SH, Louis P & Flint HJ (2004) Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 70: 5810-5817.
21. Flint HJ, Bayer EA, Rincon MT, Lamed R & White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6: 121-131.
22. Gao Z, Tseng CH, Pei Z & Blaser MJ (2007) Molecular analysis of human forearm superficial skin bacterial biota. P Natl Acad Sci USA 104: 2927-2932.
23. Gao Z, Tseng CH, Strober BE, Pei Z & Blaser MJ (2008) Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS ONE 3: e2719.
24. Gill SR, Pop M, Deboy RT et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
25. Grice EA & Segre JA (2011) The skin microbiome. Nat Rev Microbiol 9: 244-253.
26. Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE & Mirzabekov AD (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63: 2397-2402.
27. Hamady M, Lozupone C & Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
28. Hashsham SA, Wick LM, Rouillard JM, Gulari E & Tiedje JM (2004) Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosens Bioelectron 20: 668-683.
29. Hazen TC, Dubinsky EA, DeSantis TZ et al. (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330: 204-208.
30. He Z, Gentry TJ, Schadt CW et al. (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1: 67-77.
31. Holmes S, Alekseyenko A, Timme A, Nelson T, Pasricha PJ & Spormann A (2011) Visualization and statistical comparisons of microbial communities using R packages on phylochip data. Pac Symp Biocomput 142-153.
32. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP & Lynch SV (2010) A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. Omics 14: 9-59.
33. Hultman J, Ritari J, Romantschuk M, Paulin L & Auvinen P (2008) Universal ligation-detection-reaction microarray applied for compost microbes. BMC Microbiol 8: 237.
34. Jalanka-Tuovinen J, Salonen A, Nikkila J et al. (2011) Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms. PLoS ONE 6: e23035.
35. Kajander K, Myllyluoma E, Rajilic-Stojanovic M et al. (2008) Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota. Aliment Pharmacol Ther 27: 48-57.
36. Kang S, Denman SE, Morrison M, Yu Z, Dore J, Leclerc M & McSweeney CS (2010) Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis 16: 2034-2042.
37. Kent AD & Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56: 211-236.
38. Klaassens ES, de Vos WM & Vaughan EE (2007) Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol 73: 1388-1392.
39. Larsen B & Monif GR (2001) Understanding the bacterial flora of the female genital tract. Clin Infect Dis 32: e69-e77.
40. Lee ZM, Bussema C III & Schmidt TM (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37: D489-D493.
41. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV & Kolter R (2010) Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio 1: e00129-10.
42. Letowski J, Brousseau R & Masson L (2004) Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods 57: 269-278.
43. Louis P & Flint HJ (2007) Development of a semiquantitative degenerate real-time pcr-based assay for estimation of numbers of butyryl-coenzyme A (CoA) CoA transferase genes in complex bacterial samples. Appl Environ Microbiol 73: 2009-2012.
44. Loy A & Bodrossy L (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363: 106-119.
45. Manges AR, Labbe A, Loo VG et al. (2010) Comparative metagenomic study of alterations to the intestinal microbiota and risk of nosocomial Clostridum difficile-associated disease. J Infect Dis 202: 1877-1884.
46. Marchesi JR, Holmes E, Khan F et al. (2007) Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 6: 546-551.
47. Martin FP, Sprenger N, Montoliu I, Rezzi S, Kochhar S & Nicholson JK (2010) Dietary modulation of gut functional ecology studied by fecal metabonomics. J Proteome Res 9: 5284-5295.
48. McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN & Sogin ML (2009) Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12: 378-392.
49. Mendes R, Kruijt M, de Bruijn I et al. (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332: 1097-1100.
50. Mitterer G, Huber M, Leidinger E, Kirisits C, Lubitz W, Mueller MW & Schmidt WM (2004) Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J Clin Microbiol 42: 1048-1057.
51. Neish AS (2009) Microbes in gastrointestinal health and disease. Gastroenterology 136: 65-80.
52. Olson JB & Kellogg CA (2010) Microbial ecology of corals, sponges, and algae in mesophotic coral environments. FEMS Microbiol Ecol 73: 17-30.
53. Olson JC, Cuff CF, Lukomski S et al. (2011) Use of 16S ribosomal RNA gene analyses to characterize the bacterial signature associated with poor oral health in West Virginia. BMC Oral Health 11: 7.
54. Paliy O & Foy B (2011) Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays. Bioinformatics 27: 2134-2140.
55. Paliy O, Kenche H, Abernathy F & Michail S (2009) High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. Appl Environ Microbiol 75: 3572-3579.
56. Palmer C, Bik EM, Digiulio DB, Relman DA & Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: e177.
57. Peplies J, Glockner FO & Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69: 1397-1407.
58. Peterson J, Garges S, Giovanni M et al. (2009) The NIH Human Microbiome Project. Genome Res 19: 2317-2323.
59. Preza D, Olsen I, Willumsen T, Grinde B & Paster BJ (2009a) Diversity and site-specificity of the oral microflora in the elderly. Eur J Clin Microbiol Infect Dis 28: 1033-1040.
60. Preza D, Olsen I, Willumsen T, Boches SK, Cotton SL, Grinde B & Paster BJ (2009b) Microarray analysis of the microflora of root caries in elderly. Eur J Clin Microbiol Infect Dis 28: 509-517.
61. Qin J, Li R, Raes J et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
62. Rajilic-Stojanovic 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.
63. Rigsbee L, Agans R, Foy BD & Paliy O (2011) Optimizing the analysis of human intestinal microbiota with phylogenetic microarray. FEMS Microbiol Ecol 75: 332-342.
64. Salonen A, Nikkila J, Jalanka-Tuovinen J et al. (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 81: 127-134.
65. Sartor RB (2008) Microbial influences in inflammatory bowel diseases. Gastroenterology 134: 577-594.
66. Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL & Ravel J (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Appl Environ Microbiol 76: 5636-5638.
67. Schena M, Shalon D, Davis RW & Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
68. Sekirov I, Russell SL, Antunes LC & Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90: 859-904.
69. Suau A (2003) Molecular tools to investigate intestinal bacterial communities. J Pediatr Gastroenterol Nutr 37: 222-224.
70. Van den Abbeele P, Grootaert C, Marzorati M et al. (2010) Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX. Appl Environ Microbiol 76: 5237-5246.
71. van den Bogert B, de Vos WM, Zoetendal EG & Kleerebezem M (2011) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77: 2071-2080.
72. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D & DeRisi JL (2002) Microarray-based detection and genotyping of viral pathogens. P Natl Acad Sci USA 99: 15687-15692.
73. Wang RF, Beggs ML, Erickson BD & Cerniglia CE (2004) DNA microarray analysis of predominant human intestinal bacteria in fecal samples. Mol Cell Probes 18: 223-234.
74. Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM & Zhou J (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67: 5780-5790.
75. Wu L, Thompson DK, Liu X, Fields MW, Bagwell CE, Tiedje JM & Zhou J (2004) Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci Technol 38: 6775-6782.
76. Wu CH, Sercu B, Van de Werfhorst LC et al. (2010) Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS ONE 5: e11285.
77. Xu W, Seok J, Mindrinos MN et al. (2011) Human transcriptome array for high-throughput clinical studies. P Natl Acad Sci USA 108: 3707-3712.
78. Yoo SM, Lee SY, Chang KH et al. (2009) High-throughput identification of clinically important bacterial pathogens using DNA microarray. Mol Cell Probes 23: 171-177.
79. Zabarovsky ER, Petrenko L, Protopopov A et al. (2003) Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems. Nucleic Acids Res 31: e95.
80. Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288-294.
81. Zhou J, He Z, Van Nostrand J, Wu L & Deng Y (2010) Applying GeoChip analysis to disparate microbial communities. Microbe 5: 60-65.
82. Zhou JZ, He ZL, Van Nostrand JD & Deng Y (2011) Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front Environ Sci Eng China 5: 1-20.
83. Zoetendal EG, Akkermans AD & De Vos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64: 3854-3859.