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Tag Archives: microbiology

Human genobiome and disease risk assesment

I’ve recently attended a talk on the advancements of human metagenomics projects. As the speaker admitted, the whole field is a researchers’ gold mine – almost all they find is new and interesting. There were couple of interesting points – mainly concerning how limited our knowledge about things in here is. For example, there was a unconfirmed feeling among microbiologists that in fact all modern microbiology is nothing more than biology of E. coli and relatives. Now we know that for sure – number of known to us microbial species is estimated at 0.5% of all existing microbial species. Also, I heard a nice story about polish doctor who described in 19th century Helicobacter pylori and its role in gastric diseases (there was a Nobel prize for that in 2005), wrote a book and then trashed the whole thing because he couldn’t grow the bacteria in a pure culture. Another important issue was amount of data and lack of new ways of handling them.

But the most interesting for me was a connection between human microbiome and diseases. Or rather a possibility of such connection. I am not aware of any single case when composition of human microbiome have been proven to influence chance of getting ill and I don’t think there will be a lots of such correlations found soon. My impression is that correlations are to be found when we have both, a complete human genome and a complete metagenome of all that lives on particular person – a human genobiome, as I’ve called it (BTW, word “genobiome” is not present in Google – is there a better word for that?). And I believe that getting the first full human genobiome will be the achievement compared to sequencing human genome for the first time. Not because of technical difficulties – because of the all discoveries that need to be made to make it happen. For example, human gut of all people carries a species doing some sulfur reaction – but its population is only up to few thousands cells. How many such cases are we have in our organisms? That is very good question. The field is brand new, and possibilities of speculations are endless.

SNPWatch: Researchers Find SNP Associated with Diffuse-type Gastric Cancer

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Posted by Pawel Szczesny on July 6, 2008 in bioinformatics, Research

Tags: biology, Helicobacter pylori, metagenomics, microbiology

Joining ONS club – classification and prediction of bacteriocins

03 May

It’s finally the time to jump in into Open Notebook Science pool with my small project: classification and prediction of bacteriocins. Main page of this project is on Freelancing Science wiki: freelancingscience.wikispaces.com/bacteriocins. After reading recent post by Michael Barton on ONS , I’ve decided to stick only to wiki – I had already another blog set up for this project, but if blog doesn’t work very well for Michael, I doubt it will work for me. Since it’s completely side project, updates on the project blog on would be embarassingly rare. So far the wiki doesn’t contain much of a data, nothing more than a plan in fact. But I think it’s important to at least start somewhere.
Direct inspiration for the project was this post at Microbiology Blog. It describes results of some experiments on growth inhibition of bacteria by haloarcheal organisms, which could be in some cases explained by novel archeocins, peptide or protein antibiotics from Archea. After quick look I realised, that I see sequence similarity between seemingly non-related bacteriocins. That of course lead to a question if I am able to repeat the procedure from my PhD project – understand the protein family, and then write an annotation/prediction tool. I don’t expect outstanding results but at least this will be a good occasion to document my approach to protein sequence annotation. So if not scientific, it should have at least a little of educational value.

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Posted by Pawel Szczesny on May 3, 2008 in bioinformatics, Research

Tags: bioinformatics, microbiology, ONS, open notebook science, wikispaces

Type VII secretion system

09 Oct

Yet another secretion system was described, this time from Gram-positive bacteria (types I to VI were from Gram-negative). I expect that the further microbiology will go from E. coli, the more secretion systems will be found. Within the large spectrum of bacterial species we still know very little on bacteria outside proteobacterial group.

This is from Nature Reviews Microbiology, and subscription may be required.

clipped from www.nature.com

Recent evidence shows that mycobacteria have developed novel and specialized secretion systems for the transport of extracellular proteins across their hydrophobic, and highly impermeable, cell wall. Strikingly, mycobacterial genomes encode up to five of these transport systems. Two of these systems, ESX-1 and ESX-5, are involved in virulence — they both affect the cell-to-cell migration of pathogenic mycobacteria. Here, we discuss this novel secretion pathway and consider variants that are present in various Gram-positive bacteria. Given the unique composition of this secretion system, and its general importance, we propose that, in line with the accepted nomenclature, it should be called type VII secretion.