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Published Articles from USDA ARS National Program 108: Food Safety
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Title: Estimation of viral richness from shotgun metagenomes using a frequency count approach
Authors: Allen HK, Bunge J, Foster JA, Bayles DO, Stanton TB
Journal: BMC Microbiome
Accepted date: 2012 Nov 2
Interpretive summary: Phages, the viruses that infect bacteria, are the most abundant biological entities on earth. Studying them relies on the culturability of their host bacteria, but most bacteria are not readily culturable by standard laboratory techniques. The study of the collective genome of an assemblage of phages, which is called phage metagenomics, is one way to access the vast diversity of phages. The number of phage species in an environment (phage richness) is one important aspect of phage diversity. However, previous tools to study the richness of phage metagenomes are limited by their underlying mathematical principles. To improve calculations of phage richness from metagenomes, we recently developed a program called Catchall to analyze the richness of any population data. In this study we apply Catchall to the analysis of phage metagenomic data. The results show much greater estimates of phage species richness than previously reported in all environments analyzed, including swine feces and fresh water. For example, Catchall revealed roughly 1000 to 100,000 phage species per swine fecal phage metagenome, whereas previous tools estimated fewer than 1000 species. Using Catchall to analyze phage metagenomic data will improve estimations of species richness, particularly from large datasets.
Publication date: 2013 Feb 4
Volume: 1
Pages: 5