I have read somewhere that similarity of 16S rRNA of the unknown isolate with reference species or strain below 97% represented the new type strain of the unknown isolate. 

But we cannot say it is a new species rather a new type strain. For determining an isolate as a new species certain analysis should be done along with 16S rRNA analysis. These are  DNA-DNA hybridization, %G+C content and Free fatty acid analysis. 

Also, morphological, biochemical and physiological characterization of the isolate (along with above said tests) determines the novelty of the bacterial isolate as a new species or type strain.

Hope this helps.

Regards,

Kunal

I have read somewhere that similarity of 16S rRNA of the unknown isolate with reference species or strain below 97% represented the new type strain of the unknown isolate. 

But we cannot say it is a new species rather a new type strain. For determining an isolate as a new species certain analysis should be done along with 16S rRNA analysis. These are  DNA-DNA hybridization, %G+C content and Free fatty acid analysis. 

Also, morphological, biochemical and physiological characterization of the isolate (along with above said tests) determines the novelty of the bacterial isolate as a new species or type strain.

Hope this helps.

Regards,

Kunal

It might be a new species. It might not be a new species. 16S rRNA sequences by themselves don't make it easy to define a new species as our idea of what is a species or a strain is mostly artificial anyway. If there is other evidence to suggest that your species is somehow different (like other genomic or phenotypic differences, for example) then it may complement the different 16S sequence. 

I've seen varying thresholds for what constitutes a different species or genus, anyway. I have linked a paper which suggests that 98.7 percent is the usual species cutoff. They do also note "These genetic criteria should always be accompanied by a discriminant phenotypic property".

http://www.nature.com/nrmicro/journal/v12/n9/full/nrmicro3330.html

Hi, how many sequences do you have? Did you sequenced it once? Cheers, Nadine

96% similarity index mean it is 96% similar to reference strains which have been indicated in BLAST results so it is a new strain of same species not a new species.  the morphological, physiological and biochemical characteristics results supporting the reference species than it is new strain of same species, if not than you have to utilize more techniques which have been mentioned by  Kunal Garg.

If you have complete sequence of 16S rRNA gene (approximately 1500 bp) and it is showing 96%  similarity with type strain (not with other strain), then it should be a new species.

I suggest you to follow the proposals of Kunal Garg. The 16S RNA sequence similarity is not enough by itself to talk about a new species. The analysis proposed by Kunal are commonly performed by some strain collections at relatively good prices. In case of DDH tests you have to be careful selecting the DNA strains to be compared by hybridization in order to get the information you need. Most of the strain collections where you can order the characterization services have good reference strains. Good luck

The proposal suggested by Kunal and Moran is generally followed if the similarity level of your strain with type strains is less than 97%. And to define a new species DNA-DNA hybridization is done with all the Type strains which have less than 97% similarity with your strain.

Dear all, I know that for determining new species , I have to do several techniques such as FAMES analysis, DNA DNA hybridization, biochem. morphology...   but problem is that few techniques such as DNA hybridization  and other are very costly techniques so before investing money I would like to know that whether tentatively  this  is new species or not.....

  I have also used eztaxon for its identity, there also i got 96 % . so is that new stain or species??

Yes, I agree with Kunal Garg. What him is suggesting is a complete characterizaction for a new strain, specie or pathovar bacterial. Perhaps, also would be a good idea, to obtain the complete sequence of the bacterial genome, if it is a new bacterial specie.

Cheers

Antonio Castillo

in my opinion dear friend the identity of two sequences not scale for saying new species but in same time it will give you indication for been separated species (very low identity)  and again based on the gene and part of genome which you are targeting for ex. in Animal evaluation of COI relatively very slow compare to ITS2 so Barcoding of animal today essential to be based on CoI not ITS2.

recent paper on this topic:

International Journal of Systematic and Evolutionary Microbiology (2014), 64, 346–351

There are several molecular testes that you should to test and calculate if your strain is novel species or not? I think that there is not any similarity percentage for 16S rRNA gene sequence to determine novel species. May be a strain with 99% similarity in 16S rRNA gene sequence with another strain will determine as a new species. Why?

DNA-DNA hybridization and G+C content are very important testes for the novel bacterial determination. Fro example when your 16S rRNA gene sequence similarity is around 99% if the DNA-DNA hybridization test show less than 70% your strain is a new species ....

I don't know about BLAST identities but I'm using an intersting method from the University of Nice (France), written in English, that is really useful to identify a new bacterial species uysing the 16S rRNA sequence.

Here is the link:  http://bioinfo.unice.fr/biodiv/16S_New_bacterial_species/16S_rRNA_Identification_of_a_bacterial_species.html

I hope it can help.

By the way if you want to get the exact result repeat your BLAST in the following website:

http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp

This site specialized just for 16srRNA gene sequence BLAST….

A BLAST result having 96% similarity to a known specie could only be indicative of a new strain to that specie not likely a new specie in itself. Please refer to Kunal and Mushtaq write up for adequate report. 

It's very good question.. I have few species which I identify recently having the similarity of 94 % and 95%.. so how can make it as a new species?

This percentage depends with the differents genus, but 98% is the percentage minimum to describe a species, and 97% is the minimum to describe a new generus. 

Following this interesting trait on bacterial species demarcation, I would like to ask a related question: how to define "STRAIN"? When we say that a bacterial isolate belongs to the same strain? Where is the upper limit, say >99% identity is the same strain?

A strain is considered when both bacteria have the same genetic information. This question is easy to resolve employing fingerprint techniques like RADP, Box-PCR...

>99% identity species level identity (same genus, same species)

for same genus, different species values between 99.5% to 97.0% were proposed in the past but since 2012, identity between 98.7% and 99.0% (same genus, different species) (ref 1,2,3).

I agree with Dr. Lingojwar, we have described a new species with a 98% similarity with P. viridiflava on the complete sequence of 16S RNA.

To describe a new species there are some papers that indicate the steps, for example:

Kampfer et al., 2003. Towards a standardized format for the description

of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. International Journal of Systematic and Evolutionary Microbiology 53, 893–896

Tindall et al., 2010. Notes on the characterization of prokaryote strains

for taxonomic purposes. International Journal of Systematic and Evolutionary Microbiology 60, 249–266

Ramasamy et al., 2014.  A polyphasic strategy incorporating genomic data

for the taxonomic description of novel bacterial species. International Journal of Systematic and Evolutionary Microbiology 64, 384–391

Good luck,

Ana

I got a new organism showing 99% similarity is it a new strain 

Dear Rajesh,

It may or may not be a new strain. You may consider it a new type strain. Also, you can do DNA-DNA hybridization, %G+C content and Free fatty acid analysis of your isolate for more confirmation. 

hope this article may help you

i guess it will be the same for actionobacterial species

< or = 97% may be novel species provided polyphasic taxonomic analysis as framed by Bergey's manual. 

This article may give you an elementary idea on the same

Notes on the characterization of prokaryote strains for taxonomic purposes

Authors: B. J. Tindall1, R. Rosselló-Móra2, H.-J. Busse3, W. Ludwig4, P. Kämpfer5

 All the best Milind 

What is a bacterial species? It may be a novel population that hasn't been described, and has a properties that segregate it from populations that have less than 96% 16S similarity?

I think context is needed. If you are finding that 16S at 96% similarity are segregated by some definable environmental factor (niche), then maybe something is going on. Using 16S as a definition of species is a dangerous, since we can't even clearly define a bacterial species. Maybe you have a population that is different from other described populations with 16S sequence data available.

Is this 97% rule also applicable for eukaryote sequence using the mitochondrial COI marker?

Hi: If your extent of 16S rRNA gene identity (>1400 nucleotides) is ≤ 97% with type strain of closest spp., be sure that your bacterial isolate is a new taxa. Read the following article:

Int J Syst Evol Microbiol 2014; 64, 346–351

The general rule of thumb is

I agree with Samy .However, both Milind and Samy are using wrong terminologies like identity or similarities. It is actually homology, which is pretty different from being identical or similar.