Maybe this could help you? 

Article Complete Genome Sequence of Bacillus bombysepticus, a Pathog...

 Hey Victoria, thank you for your answer. I have read this paper before, it doesn't have the information I need on the "biochemical profile" of Bacillus bombysepticus. The paper in which the description is supposed to be is:

Hartman E. 1931. A flacherie disease of silkworm caused by Bacillus bombysepticus.

Lignan Sci. J. 10:279 –289

But I can not find it anywhere. :(

I'm not even sure that any bug with the name Bacillus bombysepticus has been formally/oficially described: It does not show up at the LPSN and neither it does in the list of approved bacterial names of 1980 (considering it is an old taxa, based on the paper you cite)

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

http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-30-1-225

Interesting. So, how should I proceed in this case? Simply ignore that "bombysepticus" result from my molecular analysis?

Usually you would say is a Bacillus sp., because you cannot further refine the identification.

What did you use to identify based on the 16S?

Did you use the 16S database from BLAST at NCBI?

It includes only sequences from reference material, which may help to resolve the issue, as many times the sequences are not properly annotated

You can also try EzTaxon.

Edit: I found that B. cereus, B. thuringiensis, B. anthracis, B. mycoides, B. pseudomycoides, B. weihenstephanensis, B. toyonensis and B. cytotoxicus  all belong to the 'B. cereus group' with no possible direct differentiation by 16S sequence, so forget about what said before. Check the paper below for more details.

http://www.ezbiocloud.net/eztaxon/taxonomic_group

Article Description of Bacillus toyonensis sp. nov., a novel species...

You typed the name of the journal wrong (as Lignan Sci J). The citation you might have seen is: Hartman E (1931) A flacherie disease of silkworm caused by Bacillus bombysepticus. Lignan Science Journal 10: 279–289. It is spelled wrong because I think the citing authors typed it wrong! And the proofreaders didn't see the mistake. The citing article may be:

Huang et al. (2009) A Genome-Wide Survey for Host Response of Silkworm, Bombyx mori during Pathogen Bacillus bombyseptieus Infection. PLOS ONE 4(12): e8098. DOI: 10.1371/journal.pone.0008098

You should write to the corresponding author of that article: [email protected]  The journal you are looking for is a Chinese journal, and that corresponding author should have a copy of the article. Well, they cited it, so they must have read it, right :-) I think the journal's real name is Lingnan Science Journal (not Lignan). Here's what i get from Worldcat:

Author: Ling nan da xue (Guangzhou, China)

Publisher: Canton, China : Lingnan University, 1928-1942.

Edition/Format: Journal, magazine : Periodical : Microfilm : Master microform : EnglishView all editions and formats

Database: WorldCat

Rating: (not yet rated) 0 with reviews - Be the first.

Subjects Agriculture -- China -- Periodicals.

Agriculture.

China.

To answer your next question: "Interesting. So, how should I proceed in this case? Simply ignore that "bombysepticus" result from my molecular analysis?"

Yes. Ignore it. Don't believe everything you read in a BLAST result. Limit your searches to those of type strains. Not only to the 16S database, but check the box for type material only (maybe not the exact term, but something like that). And Xabier Vázquez Campos is correct about LPSN, IJSEM and EzTaxon. All good resources.

The previous answers are correct. This species name has no standing in nomenclature. The standard approach is to refer to the organism in your formal papers or your thesis with quotation marks surrounding the genus-species name: "Bacillus bombysepticus."  It would be tempting to assume that "B. bombysepticus" is actually an isolate of B. thuringiensis (Bt), since it shows pathogenicity to the larvae of a lepidopteran, the hallmark of many Bt isolates. But we shouldn't jump to that conclusion. There are no apparent crystal toxin genes in the genome sequence, and Bt is essentially a B. cereus isolate that makes a parasporal crystal. Further, I analyzed the "B. bombysepticus" genome with the Genome to Genome Distance Calculator (ggdc..dsmz.de), comparing it to sequences of the type strains for B. thuringiensis (ACNF01) and B. cereus (AE016877). The results showed that while "B. bombysepticus" is indeed closely related to Bt (distance 0.0378), it is even more closely related to "B. cereus" (distance 0.0307).

Anyway, to recap:

(1) The recommended way to refer to a taxon without standing in nomenclature is with quotes around the full genus-species name.

(2) "B. bombysepticus" is clearly a member of the B. cereus species group, but is probably displaying pathogenicity through some other mechanism than that employed by B. thuringiensis.

OK, part 2 of my answer...

Based on the sequence results that you already have, your isolate is certainly a member of the B. cereus group. The taxonomy of that group has some difficulties. If we were starting over from scratch, we would probably consider B. cereus, B. thuringienisis, and even B. anthracis as members of a single species. But we do not have that luxury. The species names include important human pathogens with a long standing in the literature, and the Bacteriological Code mandates that we don't change such names. Yet the upshot is that there are no biochemical tests that will help us assign a novel isolate to one of these species, and 16S rRNA gene sequences are of little help. In practice, it is approximately correct to say that B. thuringiensis makes a parasporal crystal, while B. mycoides forms "hairy" colonies, and that most (not all) other isolates are B. cereus. But if you want to be more precise, I would strongly suggest that you perform MLST analysis. There are already standardized primers and reaction conditions and a database covering hundreds of isolates from every species in the group. Please see see http://pubmlst.org/bcereus/ for more information. For a very reasonable cost, you can determine partial sequences for 7 housekeeping genes and place your isolate precisely on the phylogenetic tree for the group. You may be able to make inferences about its species and some of its properties by looking at the closest neighbors on the tree. If you can afford to do a whole genome sequence, do that and perform WGS comparisons such as those described in PMID: 26373441. If not, consider MLST analysis as a lower cost, faster option.

http://pubmlst.org/bcereus/

http://www.ncbi.nlm.nih.gov/pubmed/26373441

@Stuart, I copied the citation the way it was published, and I think the journal name was written using standard abbreviations... Thanks for correcting. I performed my blast using 16S rRNA database only, but did not check the "type material" option. Thank you for the tip, I will try it to see if results will get a little bit less confusing :)

@Daniel, thank you for your considerations! I am finding the hard way how difficult taxonomy of Bacillus can be! I am not trying to place my isolate particularly as a B. bombysepticus, since most of the blast results were B. thuringiensis, I just want to make sure I am not making mistakes in the identification. I was kind of mounting huge spreadsheets with the biochemical/physiological characteristics of the closest matches (based on the original descriptions for each species) to see if I could find differences that would allow me to distinguish them, but then I saw that the test results are not 100% the same to all strains... =/  Not even malditof gave reliable results. Well, I'll see if I can try the MLST approach and also give a thought about the pathogenicity mechanism...

Thank you all for your great help!