Tuesday, 15 May 2012

Genetic Advances in Human Gut Bacteria

Human Gut Bacteria.  Image source: <http://www.cosmosmagazine.com/files/imagecache/news/files/news/20110422_bacteria-with-guts.jpg>
This unsung hero is responsible for maintaining and regulating the wellbeing, disease and metabolism of the human body. The bacteria found in the gut of a human are however, not without its faithful sidekick; the virus. These viruses are an integral part of the upkeep the bacteria performs. Recent advances in this particular area of microbiology have led to discoveries in genetic variation in human gut viruses, which scientists believe could be used as raw material to inner evolution1. This was put into practise by Frederic D.Bushman, PhD, professor of microbiology, Perelem School of Medicine, Universitiy of Pennsylvania who sequenced DNA of viruses in the guts of healthy human test subjects1.
Initial data collection for the experiment was estimated to be at 48billion bases of the genetic building block, DNA, derived from the stool samples of 12 healthy human test subjects1. Collected samples were then taken by researchers working on the projected and the blocks were assembled, attempting to recreate a complete virus genome. Researchers expected to see only one type of the hundreds of thousands of distinct viruses to be a bacteriophage, essentially a virus that infects bacteria2. Human pathogen was found in a single test subject, Human papillomavirus, describes a group of viruses that have 100+ different types or strains3. Researchers then tested the variability of viral populations within the selected test subjects, led by Samuel Minot, Bushmans team searched for stretches of bases that varied the greatest1.
Identified were 51 hypervariable regions, the site on the immunoglobulin where most of the amino acid sequence variation occurs, were associated to reverse transcriptase genes1. Reverse transcript genes are associated with replication of retroviruses like HIV. From the original identified regions, another 29 had a sequence and structural similarity to reverse transcriptase, Bordetella bacteriophage, BBP-1 1.  BBP-1 uses the reverse transcriptase and a mechanism that acts as an error-prone copying machine, to modify a protein to help reproduce a myriad of viral targets1. Bushman and his team speculated that this new discovery could serve a function similar seen in the human virome and microbiome,
Minot speculated, ‘ natural selective pressure for rapid variation for this class of bacteriophage, implying there is a corresponding rapid environmental factor the phage must adapt to1. This change could be due to evading the immune system and maintaining pace with the bacterial hosts. This correlates with the evolutionary analysis done on the 185 reverse transcriptase found in the test population, which promotes the idea that a large fraction of enzymes are involved in generating diversity. The challenge now for scientist is to determine the function of these new regions and the link it has to the variability in relationship to disease.



References
1.      S. Minot, S. Grunberg, G. D. Wu, J. D. Lewis, F. D. Bushman. Hypervariable loci in the human gut virome. Proceedings of the National Academy of Sciences, 2012; 109 (10): 3962 DOI: 10.1073/pnas.1119061109 <http://www.sciencedaily.com/releases/2012/03/120319134212.htm>
2.  Unknown Author, (2009), ‘Bacteriophage’, Biology Online, United States <http://www.biology-online.org/dictionary/Bacteriophage>

3. Unknown Author, (2009), ‘Hypervariable Region’, Diction by Farlex, United States

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