Since the invention of high-throughput sequencing, the majority of experiments studying bacterial microbiomes have relied on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiomic sample. Several computational methods exist for analyzing 16S amplicon based metagenomics, but the most commonly used bioinformatics tools are unable to produce quality genus-level or species-level taxonomic calls and may underestimate the degree to which such calls are possible. In this thesis, I have used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, with a focus on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads. With the efficacy of these tools established, I then applied them in the analysis of data from two studies into human microbiomes.
I evaluated the metagenomics analysis tools Qiime 2, Mothur, PathoScope 2, and Kraken 2, in conjunction with reference libraries from GreenGenes, Silva, Kraken, and RefSeq, using publicly available mock community data from several sources, comprising 137 samples with varied species richness and evenness, several different amplified regions within the 16S gene, and both DNA spike-ins and cDNA from collections of plated cells. PathoScope 2 and Kraken 2, both tools designed for whole genome metagenomics, outperformed Qiime 2 and Mothur, which are theoretically specialized in 16S analyses.
I used PathoScope 2 to analyze longitudinal 16S data from infants in Zambia, exploring the maturation of nasopharyngeal microbiomes in healthy infants, establishing a range of typical healthy taxonomic profiles, and identifying dysbiotic patterns which are associated with the development of severe lower respiratory tract infections in early childhood.
I used Qiime 2 to analyze 16S data from human subjects in a controlled dietary intervention study with a focus on dietary carbohydrate quality. I correlated alterations in the gut microbiome with various cardiometabolic risk factors, and identified increases in some butyrate-producing bacteria in response to complex carbohydrates. I also constructed a metatranscriptomics pipeline to analyze paired rRNA-depleted RNAseq data.
My evaluation of 16S methods should improve 16S amplicon analyses by advocating for the modernization of computational tools; my analysis of infant nasopharyngeal microbiomes lays groundwork for future predictive models for childhood disease and longitudinal microbiomic studies; my analysis of gut microbes illuminates the mechanisms through which bacteria can mediate cardiovascular health. Taken together, the research I present here represents a significant contribution to 16S metagenomics and its application to epidemiology, clinical nutritional science.
| Identifer | oai:union.ndltd.org:bu.edu/oai:open.bu.edu:2144/42640 |
| Date | 26 May 2021 |
| Creators | Faits, Tyler |
| Contributors | Johnson, William E., Campbell, Joshua D. |
| Source Sets | Boston University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis/Dissertation |
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