Use of 16S rRNA sequencing to determine phylum Chloroflexi diversity in substratum habitats.
16S rRNA sequencing was used to determine Chloroflexi diversity on 12 soil samples taken from an underground tunnel in Sweden. Out of the 64 novel sequences obtained, 9 were confirmed to be of Chloroflexi origin, with the other 55 sequences classified as either unknown or of other species by the Nat...
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| Format: | Final Year Project |
| Language: | English |
| Published: |
2011
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| Online Access: | http://hdl.handle.net/10356/44753 |
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| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | 16S rRNA sequencing was used to determine Chloroflexi diversity on 12 soil samples taken from an underground tunnel in Sweden. Out of the 64 novel sequences obtained, 9 were confirmed to be of Chloroflexi origin, with the other 55 sequences classified as either unknown or of other species by the National Centre for Biotechnology Information (NCBI), showing the large microbial diversity in the substratum. However, this method has its own disadvantages such as being unable to differentiate strains at the intra-species level and also the problem of lack of coordination of current classification standards in databases such as NCBI, ARB-Silva and Ribosomal Database Project (RDP). Single molecular methods alone are insufficient for such studies and are usually coupled with Fluorescence In-Situ Hybridization (FISH) and other molecular tools. FISH is a good technique for visualization purposes but not without its problems, such as lack of specificity and auto-fluorescence of certain species. Thus, better culture-independent methods should be developed for such studies. Package software such as ARB can be used for sequence analysis and this work is currently ongoing for the 64 sequences obtained. |
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