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Chapter 8 : The Future of Microbial Source Tracking Studies
Category: Environmental Microbiology; Applied and Industrial Microbiology
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This chapter summarizes some of the challenges that people interested in source identification are currently facing, provides information on the microbial ecology of the gut and potential microorganisms to use in source-tracking studies, discusses research tools that will likely improve marker discovery, and offers some suggestions on the future needs for determining sources of microorganisms impacting waterways. There is considerable debate as to the choice of organism(s) to be used as an indicator of fecal contamination of waterways and for microbial source tracking (MST) studies. There are four basic types of digestive systems in animals: simple stomach or monogastric (man, pig), equine-modified simple stomach (horse), ruminant or polygastric (sheep, cow, goat, deer), and avian (chicken, turkey). Genome sequence analyses, as well as the emergence of other ‘’omic ‘’ based technologies including metagenomics, proteomics, and transcriptomics, will enhance one’s understanding of the molecular and biochemical diversity of the animal GI tract. While genome sequence information for protozoa is not as wide ranging as that for bacteria and viruses, sequence analyses have shown strong host dependence due to the lack of biosynthetic pathways. The study of the gut metagenome has clear implications to human health. In this study, sequencing analysis of cloned transcripts showed the presence of transcripts linked to sulfur, carbon, and nitrogen biogeochemical processes. Results from the microbial characterization of animal intestinal tracts have suggested that anatomical and physiological differences found in different digestive systems may lead to conditions that affect the structure of gut microbial communities.
One strategy for identifying library-independent MST markers using microarrays and comparative genomics.