page_title: Pathogenomics
section_title: Host microbe analysis
hierarchical_section_title: Pathogenomics / Host microbe analysis
caption_attribution_description: English: This is a summary of the host-pathogen analysis approaches which were outlined in the article: "Pathogenomics: An Updated European Research Agenda". The reference for that article is here: Demuth, A., Aharonowitz, Y., Bachmann, T.T., Blum-Oehler, G., Buchrieser, C., Covacci, A., Dbrindt, G., Emody, L., et al. (2008). "Pathogenomics: An updated European Research Agenda". Infection Genetic and Evolution 8: 386-393. doi:10.1016/j.meegid.2008.01.005. PMID 18321793. http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6W8B-4RM7N0K-2&amp;_user=1022551&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_acct=C000050484&amp;_version=1&amp;_urlVersion=0&amp;_userid=1022551&amp;md5=07de65f47b981b04fc7842cb37f3f3af.
context_page_description: Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors, which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for making the vast amounts of data accessible to researchers in the form of databases, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
context_section_description: Pathogens have the ability to adapt and manipulate host cells, taking full advantage of a host cell's cellular processes and mechanisms.
  A microbe may be influenced by hosts to either adapt to its new environment or learn to evade it. An insight into these behaviours will provide beneficial insight for potential therapeutics. The most detailed outline of host-microbe interaction initiatives is outlined by the Pathogenomics European Research Agenda. Its report emphasizes the following features:
  Microarray analysis of host and microbe gene expression during infection. This is important for identifying the expression of virulence factors that allow a pathogen to survive a host's defense mechanism. Pathogens tend to undergo an assortment of changed in order to subvert and hosts immune system, in some case favoring a hyper variable genome state. The genomic expression studies will be complemented with protein-protein interaction networks studies.
  Using RNA interference (RNAi) to identify host cell functions in response to infections.  Infection depends on the balance between the characteristics of the host cell and the pathogen cell. In some cases, there can be an overactive host response to infection, such as in meningitis, which can overwhelm the host's body. Using RNA, it will be possible to more clearly identify how a host cell defends itself during times of acute or chronic infection. This has also been applied successfully is Drosophila.
  Not all microbe interactions in host environment are malicious.  Commensal flora, which exists in various environments in animals and humans may actually help combating microbial infections. The human flora, such as the gut for example, is home to a myriad of microbes.
  The diverse community within the gut has been heralded to be vital for human health. There are a number of projects under way to better understand the ecosystems of the gut. The sequence of commensal Escherichia coli strain SE11, for example, has already been determined from the faecal matter of a healthy human and promises to be the first of many studies. Through genomic analysis and also subsequent protein analysis, a better understanding of the beneficial properties of commensal flora will be investigated in hopes of understanding how to build a better therapeutic.
caption: Summary of host-microbe project goals in the Pathogenomics European Research Agenda[9]
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