I would like to identify the difference of microbiome in asthmatic and non asthmatic subjects. Which available technique is most efficient for this study.
Dear Neeraj,sorroy, I am not yet very familiar with microbiome in asthma.
If you want to find differences microbial communities and just want to know "who is there" and want to have a clue about abundances of different groups, 16S rRNA analysis by New Generation Sequencing might be a good method. For this you need sterile samples from the desired area to extract total DNA, followed by sequencing of the 16S rRNA gene. You could use other genes as well but the database for comparing the received sequences is biggest for 16S rRNA gene. I am sure there are many other good methods but this is one that I know and for analysis of microbial communities it works good as far as I can say. You can look for publications about "microbial community analysis" and "new generation sequencing". qPCR for validation of gene copy numbers might also help. I hope this helps, kind regards from Vienna
http://www.nature.com/ismej/journal/v6/n1/full/ismej201174a.html
http://www.illumina.com/areas-of-interest/microbiology/microbial-sequencing-methods/16s-rrna-sequencing.html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045242/
http://www.ncbi.nlm.nih.gov/pubmed/18828852
Thank you, Dear Stefanie Urimare Wetzels. These information are quit enough for my work. Once again thanks for your informative reply.
I used 16S rRNA for a study in premature infants with and without BPD V3-V5 targets. Studies in adults show that sputum can be as good as BALs. As Bhoj Singh mentions, that would exclusively be for bacterial DNA, and not viruses, fungal or other organisms.