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Scientists sequence genome of pathogen responsible for pneumocystis pneumonia
Date:12/25/2012

ganism simply extract DNA from thick cultures of cells they grow in the lab. Since they were unable to grow P. jirovecii cells for their genomic DNA, Hauser and his colleagues took a different approach. They took a sample of bronchoalveolar lavage fluid from an individual infected with Pneumocystis pneumonia, then concentrated the P. jirovecii cells using immuno-precipitation and created copies of the DNA in the sample using a technique called random DNA amplification. This mixture of DNA strands, from P. jirovecii, human, and other microbes from the lungs of the infected patient, was then sequenced using high throughput technologies.

According to Hauser and his colleagues, the fact that the sequence data represented DNA from many different species created the biggest challenge they faced. "The major challenge of the study was the in silico sorting of the reads out of a mixture representing the human host and different organisms present in the lung microbiome," he says. This challenge was met through a collaboration with Marco Pagni of the Vital-IT group of the SIB Swiss Institute of Bioinformatics, who provided indispensable expertise and infrastructure.

Once the sorting task was accomplished, the researchers assembled the sequences into a genome and attempted to identify the functions of P. jirovecii's genes. This is the first time scientists have assembled the genome of a fungus from a mixed pool of DNA from a single source, often called a metagenome. Their analyses reveal a surprising fact: P. jirovecii is a parasite that must live within the human body to survive.

P. jirovecii lacks the genes necessary for creating some of the essential ingredients of life, a hallmark of obligate parasites, organisms that must rely on another creature for sustenance. "It implies that they need their host to provide these molecules. Thus, this has been quite an important finding which implied that human bein
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Contact: Garth Hogan
ghogan@asmusa.org
American Society for Microbiology
Source:Eurekalert

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