The answer is different for different types of bacteria. The enterobacteria like Salmonella, Shigella, Escherichia don't necessarily follow the same nomenclature/classification rules as the Clostridia or other groups of bacteria.

In general, the terms "strain" and "Genus" and "species" are not very easy to define in a consistent manner across all types of bacteria. There are some very good reasons why the various serotypes or lineages of Shigella are named differently that the shiga-toxin producing E. coli (STEC) lineages. Likewise there are slightly less good reasons why very divergent lineages of Clostridia are all named "Clostridium botulinum" if they kill a human but may be named as "toxin-producing Clostridium sporogenes" if they do not kill a human.

Lack of consistency does not make the nomenclature wrong or useless, but it does make it a little frustrating to sort out.

Hi Brian

thank you for your feedback. I agree and understand that nomenclature is not as easy in bacteria and for sure there is also a problem with misclassifications, as it also happens with fungi.

But let's say that I need to "label" my genome with the most probable strain ID. What to do in that case? Is there a "general" rule?

The general rule I observe in GenBank data is that if sequences are obtained from environmental samples and not isolated as a single colony and biochemically classified by something like Bergey's Manual methods, they get labelled as "Uncultured enterobacteria" or "Clostridium species, uncultured environmental isolate nn" or similar.

See:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=91347 or

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=544

for examples

For most purposes, it is far more helpful to the global bacteriology community, for you to describe the environment than to put a specific isolate name on each sequence. A name like "Citrobacter braakii" is less informative than "Citrobacter sp. from salted Italy cheese 2011"

https://www.ncbi.nlm.nih.gov/nuccore/354720708

Article Effect of different salting technologies on the chemical and...

The sample data, sample location, etc does not all go in the name, there are specific database annotations for that in the FEATURES table:

FEATURES Location/Qualifiers source 1..396 /organism="Citrobacter sp. 102(2011)" /mol_type="genomic DNA" /strain="102" /isolation_source="PDO Pecorino Siciliano cheese" /db_xref="taxon:1091590" /country="Italy" /collection_date="15-Mar-2011" /collected_by="Luca Settanni" /identified_by="Luca Settanni"

In your case, you say you have cultured "isolates", that have already been given a name. In that case, you really need to keep the same name so that other people working with with alliquots of the same isolate (such as Citrobacter freundii NBRC 12681 for example

https://www.ncbi.nlm.nih.gov/nuccore/?term=txid1114920[Organism:noexp] ) can look up the sequences.