Dear all,
I am looking for some current databases of ancient firmicute ganomes.
I saw 7 posts in Biostars. I hope someone may have some new information.
TYVM!
Have you tried just searching for firmicutes genomes at PubMed Genomes: https://www.ncbi.nlm.nih.gov/genome/?term=Firmicutes
No, I never used this approach. It looks very nice, thank you! Usually I use the information from this post (where can I get environmental bacteria genome in fasta format (as many as possible)? ) to find some bacterial genomes. But what about time scale? How to distinguish between current strains and ancient strains? Firmicutes are not human-friendly as most of bacteria, (Bacillus antracis as an example), but gram-negative Proteobacteria, like Yersinia pestis (“Black death” from Middle Ages) look more dangerous. Now scientists have determined their sequence and can estimate their age. I’ve never heard about such examples for firmicutes.
If you have seen a publication where the genomic sequence of an ancient strain was being reported, then the authors should mention (in the publication text) the accession number of the genome and where to obtain the sequence. If you cannot find a publication, then the genomic sequence may not exist.
So, are you sure that the genomes that you seek exist (or are you just trying to find out if they do indeed exist)?
Exactly! I am just trying to find out if they do indeed exist. There are thousands of bacterial papers, this particular aspect may not be essential for the authors. That's why I've asked the question - someone could read someting about. Yesterday I saw an article about many E.coli generations. But I need the same for some firmicutes.
Hi! Well, this area is certainly very interesting. I studied microbiology extensively at undergrad level but then branched into cancer and other diseases at doctoral level.
I was able to find these, which may be of relevance (I've ordered them by how relevant I believe they are):
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
Can you further define
ancient? You are only going to see sequences of extant bacteria in databases.Thank you for your question! I would be happy to be able to compare bacterial genomes from the 1st and several hundred generation. I found less than 10 papers mentioning it, and most are about E.coli only. But I need some information about gram-positive bacteria.
Sounds like you are interested in finding a dataset where an organism is monitored/sampled over many generations like the E. coli study you have referred to but for a fermicute?
Yes! I would like to find a database or whatever it is with some firmicute genomes of many generations. But I need to have a starting genome, a middle point genome and a final genome. I am afraid it has not been done yet, it implies a hard wet-lab work.
That is my guess as well.