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A PCR Primer Bias Free Examination of Microbial Community Composition and Co-Occurrence
Başlık:
A PCR Primer Bias Free Examination of Microbial Community Composition and Co-Occurrence
Yazar:
Banks-Richardson, David Joshua, author.
ISBN:
9780438038134
Yazar Ek Girişi:
Fiziksel Tanımlama:
1 electronic resource (93 pages)
Genel Not:
Source: Masters Abstracts International, Volume: 57-06M(E).
Advisors: Christopher S. Miller Committee members: Michael Ferrara; Laurel Hartley; Annika Mosier.
Özet:
Microbial communities drive biogeochemical cycling, maintain human health, and produce useful compounds. Studies relying on the Polymerase Chain Reaction (PCR) to amplify the conserved small subunit of the Ribosome (SSU) gene have been utilized to study the structure of these communities. The primers used in these studies detect some taxa more readily than others. To overcome PCR primer-bias, we utilized the SSU gene assembler EMRIGE to estimate the community composition of 3110 shotgun sequenced metagenomes. The primer quality evaluator PrimerProspector was used to predict the likelihood that the bacterial primer pair 338f*/1061r and the Earth Microbiome Project primer pair 515f/806 would amplify the reconstructed sequences. While these primer sets are anticipated to amplify many of the taxa they were designed to, the bacterial primer pair 338f*/1061r was not expected to amplify many members of the Verricumicrobia and the Earth Microbiome Project primers were predicted to under amplify some members of the Actinobacteria. Some members of the Candidate Phyla Radiation (CPR) were not predicted to amplify using either primer pair. Beta-Diversity analyses of the communities detected widespread taxonomic similarities between samples collected from similar environments. Co-occurrence analyses were performed using the primer-bias-free estimates of marine and saline water associated microbial communities as well as soil and sediment associated microbial communities. Additionally, a network analysis curriculum was developed for high school students. The methods used to generate this data could be used as a taxonomic composition companion database to the Sequence Read Archive and serve as a valuable resource to the broader scientific community.
Notlar:
School code: 0765
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Yer Numarası | Demirbaş Numarası | Shelf Location | Lokasyon / Statüsü / İade Tarihi |
---|---|---|---|
XX(691236.1) | 691236-1001 | Proquest E-Tez Koleksiyonu | Arıyor... |
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