F13 lecture 24(2)

some studies use pcr amplica6on of samples some do

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Unformatted text preview: Ruminococcus bromii Rothia dentocariosa Ruminococcus spp Sarcina spp Staphylococcus aureus Staphylococcus epidermidis Streptococcus anginosus Streptococcus mutans Streptococcus oralis Streptococcus pneumoniae Streptococcus sobrinus Streptococcus viridans Torulopsis glabrata Treponema denticola Treponema refringens Veillonella spp Vibrio spp Vibrio sputorum Wolinella succinogenes Yersinia enterocolitica Location Mouth Sputum Mouth Mouth Mouth, Saliva Mouth Feces Large intestine, small intestine (Ileon) Large intestine, small intestine (Ileon) Mouth, Amygdala Mouth Sputum Mouth Saliva, sputum Mouth, large intestine Mouth, amygdala General distribution Mouth Large intestine General distribution Feces Large intestine, small intestine (Ileon) Large intestine Mouth Cecum, large intestine Large intestine Mouth, large intestine, small intestine (Ileon) Mouth General distribution Teeth: Dental plaque Teeth: Dental plaque Amygdala Teeth: Dental plaque Mouth, large intestine, small intestine (Ileon) Mouth Mouth Mouth Mouth, amygdala, large Intestine Large intestine, Small intestine (Ileon) Mouth Mouth Large intestine how metagenomics is done •  microarrays •  shotgun cloning and sequencing of environmental DNA samples •  PCR amplifica6on and direct high throughput sequencing •  isola6on of RNA samples and reverse transcriptase shotgun cloning/sequecing –  reverse transcrip6on: RNA - > DNA; by enzyme reverse transcriptase from retroviruses using microarrays in an ecological context •  func6onal gene microarrays – detect presence of genes with specific func6ons in the environment –  DNA sample from nature (water, soil, etc.) •  some studies use PCR amplifica6on of samples, some do not •  can detect genes with 80% of more sequence homology to probe sequences on microarray •  detec6ng func6onal mRNAs from the environment is much harder early studies •  Wu et al. 2001 –  array of 104 probes represen6ng genes involved in the nitrogen cycle •  used PCR amplifica6on of environmental DNA sample •  strong signals from marine sediment and surface soil •  diversity of nitrate reductase and ammonium monooxygenase genes in both environments was similar –  => both environments have similar capaci6es for denitrifica6on –  (denitrifica6on: nitrite, nitrate = > N2) h]p://bioh.wikispaces.com/file/view/36- 16- NitrogenCycle- L.gif/31445777/36- 16- NitrogenCycle- L.gif early studies •  Tiquia et al. 2004 –  did not use PCR amplifica6on of samples •  several hundred proves of genes in nitrogen, carbon, and sulfur cycle –  demonst...
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