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

Abstract

Summary In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem‐specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota – referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose–response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual‐specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria , Bacteroidetes and Firmicutes . Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.

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References 80

1. 1.

   Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol. 2005;71:8966-8969.

   Not in our library10.1128/aem.71.12.8966-8969.2005

2. 2.

   Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol. 1990;215:403-410.

   Not in our library10.1016/s0022-2836(05)80360-2

3. 3.
   Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing · 2008

   No notice
4. 4.

   Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–.

   Not in our library10.1126/science.1104816

5. 5.

   Bauer DF. Constructing confidence sets using rank statistics. J Am Stat Assoc. 1972;67:687-690.

   Not in our library

6. 6.

   Ben-Amor K, Heilig HG, Smidt H, Vaughan EE, Abee T, de Vos WM. Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis. Appl Environ Microbiol. 2005;71:4679-4689.

   Not in our library10.1128/aem.71.8.4679-4689.2005

7. 7.

   Bertilsson S, Cavanaugh CM, Polz MF. Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with deatachable primers. Appl Environ Microbiol. 2002;68:6077-6086.

   Not in our library10.1128/aem.68.12.6077-6086.2002

8. 8.

   Blanchard AP, Kaiser RJ, Hood LE. High-density oligonucleotide arrays. Biosens Bioelectron. 1996;11:687-690.

   Not in our library

9. 9.

   Bodrossy L, Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol. 2004;7:245-254.

   Not in our library10.1016/j.mib.2004.04.005

10. 10.

    Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol. 2003;5:566-582.

    Not in our library10.1046/j.1462-2920.2003.00450.x

11. 11.

    Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19:185-193.

    Not in our library10.1093/bioinformatics/19.2.185

12. 12.

    Bonnet R, Suau A, Doré J, Gibson GR, Collins MD. Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int J Syst Evol Microbiol. 2002;52:757-763.

    Not in our library10.1099/00207713-52-3-757

13. 13.

    ter Braak CJF, Šmilauer P. canoco Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination. 2002.

    Not in our library

14. 14.

    Button DK, Robertson BR. Determination of DNA content of aquatic bacteria by flow cytometry. Appl Environ Microbiol. 2001;67:1636-1645.

    Not in our library10.1128/aem.67.4.1636-1645.2001

15. 15.

    Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, et al. Accessing genetic information with high-density DNA arrays. Science. 1996;274:610-614.

    Not in our library10.1126/science.274.5287.610

16. 16.

    Cleveland WS, Grosse E, Shyu WM, Chambers JM, Hastie TJ. Local regression models. Statistical Models in S. 1992;309-376.

    Not in our library

17. 17.

    Collins M, Lawson P, Willems A, Cordoba J, Fernandez-Garayzabal J, Garcia P, et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol. 1994;44:812-826.

    Not in our library10.1099/00207713-44-4-812

18. 18.

    DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol. 2007;53:371-383.

    Not in our library10.1007/s00248-006-9134-9

19. 19.

    Dethlefsen L, Eckburg PB, Bik EM, Relman DA. Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006;21:517-523.

    Not in our library10.1016/j.tree.2006.06.013

20. 20.

    Dixon WJ. Analysis of extreme values. Ann Math Stat. 1950;21:488-506.

    Not in our library

21. 21.

    Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635-1638.

    Not in our library10.1126/science.1110591

22. 22.

    Emrich SJ, Lowe M, Delcher AL. PROBEmer: a web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res. 2003;31:3746-3750.

    Not in our library10.1093/nar/gkg569

23. 23.

    Favier CF, Vaughan EE, de Vos WM, Akkermans ADL. Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol. 2002;68:219-226.

    Not in our library10.1128/aem.68.1.219-226.2002

24. 24.

    Fogarty LR, Voytek MA. Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol. 2005;71:5999-6007.

    Not in our library10.1128/aem.71.10.5999-6007.2005

25. 25.

    Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J. Microarray applications in microbial ecology research. Microb Ecol. 2006;52:159-175.

    Not in our library10.1007/s00248-006-9072-6

26. 26.

    Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355-1359.

    Not in our library10.1126/science.1124234

27. 27.

    Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol. 1997;63:2397-2402.

    Not in our library10.1128/aem.63.6.2397-2402.1997

28. 28.

    Heuer H, Hartung K, Wieland G, Kramer I, Smalla K. Polynuclotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. Appl Environ Microbiol. 1999;65:1045-1049.

    Not in our library10.1128/aem.65.3.1045-1049.1999

29. 29.

    Horz HP, Vianna ME, Gomes BPFA, Conrads G. Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J Clin Microbiol. 2005;43:5332-5337.

    Not in our library10.1128/jcm.43.10.5332-5337.2005

30. 30.

    Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol. 1998;180:366-376.

    Not in our library10.1128/jb.180.2.366-376.1998

31. 31.

    Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 2001;29:181-184.

    Not in our library10.1093/nar/29.1.181

32. 32.

    Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007;14:169-181.

    Not in our library10.1093/dnares/dsm018

33. 33.

    Lane DJ, Stackebrandt E, Goodfellow M. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics. 1991;115-175.

    Not in our library

34. 34.

    Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J. Independence and reproducibility across microarray platforms. Nat Methods. 2005;2:337-344.

    Not in our library10.1038/nmeth757

35. 35.

    Lay C, Rigottier-Gois L, Holmstrom K, Rajilic M, Vaughan EE, de Vos WM, et al. Colonic microbiota signatures across five Northern European countries. Appl Environ Microbiol. 2005;71:4153-4155.

    Not in our library10.1128/aem.71.7.4153-4155.2005

36. 36.

    Leitch EC, Walker AW, Duncan SH, Holtrop G, Flint HJ. Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol. 2007;9:667-679.

    Not in our library10.1111/j.1462-2920.2006.01186.x

37. 37.

    Lepš J, Šmilauer P. Multivariate Analysis of Ecological Data Using CANOCO. 2003.

    Not in our library

38. 38.

    Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022-1023.

    Not in our library10.1038/4441022a

39. 39.

    Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A. 2008;105:2117-2122.

    Not in our library10.1073/pnas.0712038105

40. 40.

    Li X, He Z, Zhou J. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 2005;33:6114-6123.

    Not in our library10.1093/nar/gki914

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