With the advent of new molecular techniques, we have been able to investigate bacterial diversity in different microhabitats using molecular fingerprinting methods and sequence analysis of microbial small subunit ribosomal (r) RNA genes (16S rRNA) and other universal targets (such as cpn60) [ 13, 36, 37].
Mycobacteria spp. were further identified by 16S rRNA gene sequence analysis (MicroSeq ID Microbial Indentification Software, version 2.0; Applied Biosystems, Foster City, CA, USA) to the species level as described (5 ).
This study supports mounting evidence that culture-independent 454-based 16S rDNA sequencing is necessary as a diagnostic tool in gallstone-associated bacterial infection, because it provides more detailed information than cultivation or other molecular finger-printing methods currently employed [ 37] and sequence analysis of cloned microbial 16S rDNA [ 17, 19, 21].
By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome.
Interestingly, the other rhodopsin gene appears to encode a new type of microbial rhodopsin according to the amino acid sequence analysis.
As expected, analysis with the environmental virus and eukaryotic microbial sequence databases produced either zero or very small numbers of cross-hybridizing hits (fewer than 10).
Microbial diversity in the gastrointestinal tract of these animals was characterized by sequence analysis of 16S rRNA gene libraries.
Notably, many microbial ecologists using these tools are not formally trained in phylogenetics or comparative sequence analysis.
Comparative sequence analysis of 16S rDNA genes is a popular method of investigating microbial communities but problems arise when the subjects are rhizoplane consortia.
Sequence analysis of the PCR product is time-consuming, but has improved the rate of microbial detection.
