What were the results of analysis of the sequence 16s rRNA sequence? And of biochemical studies? I think these are enough to claim a novel isolate!

Go for Polyphasic taxonomy and compare with nearest strain.

Polyphasic taxonomy is best method for identifying novel isolates. Molecular tool alone can't establish a novel isolate. It needs additional morphological, biochemical and chemotaxonomic traits to establish novelty of an isolate.

Have a look at some papers in IJSEM journal.

you would need all those tests.

briefly

16S

Genome hybridisation

% GC

Biolog

Lipid profile

etc.

One need to carry out polyphasic taxonomy study and compare the strain with already avilable one. Publications in IJSEM and AVL may be of your use.

Dear Shyam,

If your extent of 16S rRNA gene identity (>1400 nucleotides) is below the range of 98% (Read this paper:  International Journal of Systematic and Evolutionary Microbiology (2014), 64, 346–351) with type strain of closest sp. then for sure your bacterial isolate is a new taxa.Earlier this threshold limit was 97% (Stackebrandt & Goeble, 1994).

Carry out phylogentic analyses (do it first at Eztaxon site). You get result with type strains of spp. only and with % values. This site has extra advantage as it is connected with LPSN site. The latter gives you clear idea of taxonomic status of name (legitimate/illegitimate etc.). From phylogentic tree (use NJ, Pars and ML methods) noticthe over all topology and bootstrap values as well as clade of your strain in the question. If this is placed completely away from the cluster that defines your nearest genus (remember is a genus is naturally created then it is a monophylatic lineage so all its spp. must be clustered togather, if artificially, then this cluster will not be there). from this you will get priliminary idea. 

Now carry out comparative analyses as per polyphasic taxonomic approach after retrieving reference culture (i.e.Type strain) of 3 closest spp. This include whole cell fatty acid profile (must carried out using standard condition; look for Sherlock Midi,TSBA library). FAME analyses is now mandetary req. for description of taxa.

If you have a Gram positive isolate you must do cell wall amino acid, sugar, and glycoyl type (in case of actinobacterial culture),menaquinone type (homologous series for taxa excluding actino; while heterologous for actinobacterial isolates).

If your extent of similarity is less than 95% this is indication of novel genus (see Ludwig et al., 1998). But this may be sometime difficult as phenotypes may not give sufficient differences. You have to compare total lipid profiles (polar, amino etc.).

Taxonomic analyses is highly group/Taxa specific. 

I hope it will help you. Ifyou need more, read Bergey's manual of systematic bacteriology vol I (2000 edition) and some good papers on polyphasic taxonomy (Microbiol Rev 60, 407-438; Vandamme et al, 199). You also read some of my papers on new sp. Paeniballus assamensis, new genus Emticia oligotrophica etc. you will get valuable reference there as well.Read them all. These are available if you get problems, mail me at [email protected]  

Only by doing 16rRNA sequencing and further doing the homology alignment analysis.