I am carrying out a study of lactobacilli isolated from different samples. Genus and species are identified using a sequenced 1000pb long 16S fragment in BLASTn. I cannot distinguish between L. casei and L. paracasei because they have same score and query coverage when they appear as a hit for a sequence.

I read somewhere (cannot remember where) that L. casei and L. paracasei both should be itnegrated in a single L. casei species and their differences should be considered at strain level.

Should I focus my discussion on this fact? Or are they really different species?

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    $\begingroup$ My recommendation is to find that source you mention that you forget, check to see if it's a reputable source, and (if it is) use it to substantiate your discussion. Check to see if anyone else has ever cited the work, and if so, make sure the newer work doesnt contradict your first source. $\endgroup$ – theforestecologist Feb 21 '17 at 12:52
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    $\begingroup$ The definition of a bacterial species and (even worse) strain are somewhat debatable unfortunately. As far as I know there is no real single authority with a standardised decision process on what is a separate species or not. At least none that everybody agrees on. $\endgroup$ – skymningen Feb 21 '17 at 14:58
  • $\begingroup$ To me it seems like the OP asking whether the 2 "groups" (whatever the rank is species/ strain/ etc) of former-sense are same or not. $\endgroup$ – Always Confused Feb 22 '17 at 15:32

As far as I am concerned L. casei and L. paracasei can be differentiated by the amplification of the 16S rRNA gene of the aforementioned species using PCR - please see the work done by Ward and Timmins (1999). An alignment of the V1 region of the 16S rRNA genes of Lactobacillus casei and Lactobacillus paracasei shows the bases comprising the species-specific PCR primers - screenshot taken from Ward and Timmins (1999):

enter image description here

So, perhaps in your study you have not amplified the correct region of the 16S rRNA gene of L. casei and L. paracasei?

With regards to the classification of these organisms. Just as @skymningen has already mentioned in the comment section, the definition of a bacterial species (not even to mention strains) is somewhat debatable and tricky.

However, here is what Mori et al (1997) suggest:

The primary structures of the 16S rRNA genes of the type strains of Lactobacillus casei and related taxa were determined by PCR DNA-sequencing methods. The sequences of Lactobacillus casei, Lactobacillus zeae, Lactobacillus paracasei, and Lactobacillus rhamnosus were different. The K nuc values ranged from 0.0040 to 0.0126. On the basis of the K nuc values and the levels of DNA-DNA relatedness among the strains of these species, the L. casei-related taxa should be classified in the following three species: L. zeae, which includes the type strains of L. zeae and L. casei; a species that includes the strains of L. paracasei and L. casei ATCC 334; and L. rhamnosus.

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