Bacterial species identification?

More Said Moukhlissi's questions See All

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Unable to detect a truncated protein variant, but I can observe a truncated cDNA from Sanger?

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Sourath E Calicut

Hi Said Moukhlissi,

I hope you are doing well. You can use nucleotide BLAST (NCBI) site for analyzing your result (https://goo.gl/q1Q8SM) . Before that, you have to check your 16srRNA sequence for identifying overlapping areas, mismatching pairs, and you can trim or make proper alignment of the sequence with the help of BioEdit software. If the query covering area and identity are 100% in the BLAST result, then you can confirm the species. but, you can't confirm the strain.

Kothari Vishal Vallabhbhai

I hope you are doing well.but please verify length of the sequence (1400bp to 1800bp for 16S) give more accurate result. Some time fatty acid profile and other morphological characters also need to check then you will conform strain.

Daniel R Zeigler

Unfortunately there is an error in the NCBI database. Brevibacterium halotolerans is a valid taxon. However, it is not part of the Bacillus subtilis group. It is not even a Firmicutes, but a member of the Actinobacteria, so it belongs to a completely different bacterial phylum/division than Bacillus subtilis. Yet there is an accession in the database for a 16S sequence (GenBank KR492903) that is annotated Brevibacterium halotolerans even though it is in truth from a Bacillus isolate. This error was then repeated with two WGS sequences, LUUT01 and LPVF01. That is the source of your confusion. Your sequence, therefore, is not actually from B. halotolerans if is 100% identical to KR492903.

To get a better idea of what these isolates actually are, I performed a Genome to Genome Distance Calculator analysis (ggdc.dsmz.de) of the "Brevibacterium halotolerans" WGS sequence LUUT01 against the genomes of the type species of the Bacillus subtilis group. According to this analysis, this genome probably belongs to Bacillus mojavensis. If I were describing your isolate, I would say that it is "closely related to the type strain of Bacillus mojavensis."

Said Moukhlissi

My sequence has 100% of similarity with Brevibacterium halotolerans DSM 8802 (T) (AM747812)

sequence from ExTaxon database.

My previous analysis still stands. AM747812 is not, in fact, a sequence from the genus Brevibacterium. (That is why NCBI has the genus name in square brackets.) This sequence is from the Bacillus subtilis group, from an isolate closely related to B. mojavensis and probably a member of that species. Your isolate is not Brevibacterium halotolerans.

Here is a little more information, which I obtained from www.bacterio.net:

"Note: According to J. Swiderski (DSMZ), the type strain DSM 8801 (= ATCC 25097= CCUG 43489 = CIP 67.20 = JCM 11681) is misclassified as Brevibacterium sp. This strain has been identified as Bacillus sp. at DSMZ. See (i) DSMZ, and (ii) NCBI, Entrez Nucleotide."

I would add that there are two simple tests that you can perform to confirm that your isolate is Bacillus:

Perform a Gram stain (Bacillus is Gram-positive);

Allow the cells to incubate on nutrient agar at 30°-37°C for several days. Examine them microscopically. If you have access to a phase-contrast microscope, you should see phase-bright endospores. If you only have a regular light microscope, you will have to perform staining. But you should easily identify endospores.

http://www.bacterio.net/brevibacterium.html

I saw this morning that Brevibacterium halotolerans has now been reclassified as Bacillus axarquiensis.

http://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.001048

Article Genome analysis shows Bacillus axarquiensis is not a later h...

Adán Chávez

Hi Said,

Could you share with me the sequence of universal primers and protocol to identify bacterial species by 16S rRNA. I need to identify bacterial species isolated from the nature using molecular tools.

Thank you.