This study was aimed at characterizing the complex microbial diversity profile of the patient with COPD and healthy individuals.
Obtaining accurate estimates of microbial diversity using rDNA profiling is the first step in most metagenomics projects.
In addition, all raw sequence reads recovered from the fosmid library were also exported to MG-RAST (Project No. mgp7584, access via http://tare.medisin.ntnu.no/data/mg-oil-compare/) to profile microbial diversity and abundance based on phylogeny and function (Meyer et al. 2008).
Since each organism can be uniquely characterized based on the 16s rRNA gene, aligning reads against the curated reference database of 16s rRNA will help in profiling the microbial diversity [ 8].
The DGGE profile suggests low microbial diversity because even when using several sets of primers to amplify different regions of the 16S rRNA, few amplicons were obtained.
Recently, 16S ribosomal RNA gene (rRNA) sequence profiles are used to elucidate microbial diversity, often to the phylotype level.
The hypervariable region(s) chosen for amplification can influence the PCR-DGGE profiles and diversity indices produced from community DNA samples, and even subtle differences in primer sequences can result in substantially different profiles and downstream assessments of microbial diversity.
A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers.
Our findings based on a comprehensive microbial community profiling technique support the decrease in microbial diversity reported previously in patients undergoing EEN therapy, but go further in that they associate these fluctuations in microbial OTUs with disease activity.
Our group 9 11 and others 12 15 have used diverse culture-independent approaches based on molecular profiling of 16S rRNA genes to compare the microbial diversity of intestinal or faecal samples from CD patients and healthy people.
Consistent with prior studies, we found that gut microbial diversity in this cohort increased with age, although the overall microbiota profile was distinct from cohorts in other regions of Africa, Asia and North America.
