I need to know to which taxonomic levels (from phylum to species) the following approaches allow prokaryote identification:
a) morphology-based approaches
b) chemotaxonomy
c) GC content
d) DNA-DNA hybridization
d) phylogeny
For instance, can morphology-based approaches be used to identify species?
Aia Oz Thanks for contributing.
yes I was referring to whole genome sequencing and rRNA gene sequencing.
by the way, does rRNA gene sequencing allow strain identification? or is it mostly applicable for species identification?
Kamyar Amirhosseini the identification depends on the database that you have, and also on the difference in the 16S sequences between the strains. So usually you cannot detect strains using 16S, but in few specific cases you might be able to see some strains.
If you are interested in strains, it is better to sequence metagenomes, and perhaps consider sequencing both with Illumina and with nanopore. But this is expensive, and really depends on the research question.
Some bacteria have very specific colony or cellular morphology. So yes, in some cases, you can use morphology to identify a bacterium to the genus or even species level. However, with most bacteria you can routinely cultivate, this isn't the case. You can use various phenotyping methods, such as biochemical testing, to get a better idea of what group of organisms you're working with and again, if the tested bacteria have some specific traits, you can identify them quite accurately this way.
In our lab where we work with a wide range of environmental and animal samples, we use 16S rRNA sequencing for routine identification. With a full-length 16S rRNA sequence, you can get very accurate identification to the genus or species level. Whole genome sequencing gives you even more information and you can identify to the species and even strain level.
I would say that in most bacteria, you cannot distinguish between strains based on the 16S rRNA sequence. When we need to differentiate between strains, we use fingerprinting methods, such as rep-PCR or MALDI-TOF. You can use these two methods for identification as well but you need a comprehensive database of reference strains to compare your strains with.
Vendula Koublová Thank you very much for your explanation. cleared up a lot.
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