Describing a novel species involves justification like 16S r RNA sequencing, FAME analysis etc. Is DNA _DNA hybridization essential if the FAME suggests 87% similarity with the available strains in the database? Still the 34% query coverage of the 16 S rRNA gives 98.9 percent similarity. So what are the other categories I should fullfill to describe the strain as a novel species?
Dear Balaji,
Bacterial taxonomy is a very interesting field. Usually, to describe a novel species you have to use a polyphasic approach, i.e., a combination of molecular, phenotypic and chemical features which assures that your isolate merits to be recognised as a new species.
Also, for streptomycetes it is highly desirable that the species distinguish by means of phenotypic properties, i.e., growth on sole carbon source, pH and temperature tolerance, etc.
Furthermore, you have to check the chemical properties of your isolates and these properties have to be in line for its classification in the Streptomyces genus.
DDH relatedness studies is only mandatory if your 16S rRNA gene similarity is below 99.0% (in a 1400 bp gene sequence comparison). Check the reference:
Meier-Kolthoff, Jan P., et al. "When should a DDH experiment be mandatory in microbial taxonomy?." Archives of microbiology 195.6 (2013): 413-418.
Thus, based on your results, 34% coverage in 16S rRNA comparison is not enough. The 16S rRNA sequence should be at least 1400 bp to ensure a robust phylogenetic history between your isolate and the closest neighbours.
The FAME analysis is used only to demonstrate the differences or simarities in the isolate profile and the major components are rather constant between members of the same genus. Do not consider this result as indicative of species because this analysis suffers a lot of external influences which may give you a wrong result.
Finally, I reckon you to follow the instruction at the ad hoc commitee for bacterial taxonomy:
Stackebrandt, Erko, et al. "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology." International journal of systematic and evolutionary microbiology 52.3 (2002): 1043-1047.
or some of Streptomyces description papers:
Kim, Byung-Yong, et al. "Streptomyces cocklensis sp. nov., a dioxamycin-producing actinomycete." International journal of systematic and evolutionary microbiology 62.2 (2012): 279-283.
Kim, Byung-Yong, et al. "Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., isolated from the soil of a hay meadow." International journal of systematic and evolutionary microbiology 62.Pt 8 (2012): 1908-1913.
Good lucky with your research,
Zucchi
In time, MLST is considered as an additional test and in most case it can't replace the DDH relatedness studies...
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