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Author ORCID Identifier

https://orcid.org/0000-0001-6026-273X

AccessType

Open Access Dissertation

Document Type

dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Food Science

Year Degree Awarded

2022

Month Degree Awarded

February

First Advisor

Ermin Zhao

Second Advisor

Hang Xiao

Third Advisor

John Gibbons

Subject Categories

Bioinformatics | Biotechnology | Computational Biology | Food Science | Genetics | Genomics | Microbial Physiology

Abstract

The human gut microbiome is a huge enzyme repository for dietary polyphenols metabolism, especially considering most of the polyphenols cannot be digested in the host and their biological functions are limited. Poor bioaccessibility based on traditional pharmaceutical ADME (absorption, distribution, metabolism, and excretion) assessment is the main problem facing the widely medical application of most polyphenols. Gut bacteria have the potential to mediate a wide range of biotransformation reactions of polyphenols, which leads to the production of many bioactive metabolites. In the past decades, mounting evidence in traditional ADME study have demonstrated gut bacteria play an irreplaceable role in dietary polyphenols metabolism, and the gastrointestinal tract (GIT) can be the therapeutic target for inflammatory disease. Microbial-mediated metabolites have a significant influence on host health and could account for variation in individual responses to supplements and environmental toxins. Although increasing evidence implicates that gut bacteria contribute to dietary compound metabolism, identifying the bacteria and genes responsible associated with host metabolism remains elusive. The objective of this study is to further understand the mechanism of gut microbial mediated dietary polyphenols metabolism at the genomic and genetic levels. Metabolic profiling, genomic, and transcriptomic approaches were applied to map eight selected polyphenols' metabolism with gut bacteria and their genes. First, in the metallic profiling study, we aimed to characterize gut microbiota-mediated biotransformation of eight selected polyphenols, namely curcumin, avicularin, resveratrol, dihydro-resveratrol, nobiletin, 3ˈ-demethylnobiletin, and 4ˈ-demethylnobiletin. First, anaerobic fermentation experiments were conducted using strains of human fecal bacteria. Next, cell-free supernatants were profiled for targeted metabolites using HPLC and LC-MS. At the same time, bacteria growth was evaluated. For the first time, we identified three bacterial strains that were capable of metabolizing curcumin by hydrogenation and cleavage reaction. These reactions have substrate specificity, they cannot hydrogenase resveratrol. We also discovered de-glucuronidation of avicularin by one bacterial strain that was isolated from a healthy volunteer. There were no substantial effects of these polyphenols on the growth of genera morphology of the bacteria. Next, to further identify the genomic basis of different microbial metabolic profiling, de novo genome assembly and comparative genomic analysis were conducted. After we sequenced the whole genome of each bacterium using Illumina NovoSeq platform, genome assembly, taxonomic classification, phylogenetic analysis, comparative genomic analysis, and enzyme protein homology detection were performed to identify the unique genes that were potentially involved in curcumin and avicularin metabolism. The whole-genome data provide a foundation to the survey of the transcriptomic landscape, global transcriptomics study of Lactobacillus gasseri and Ligilactobacillus salivarius in response to curcumin treatment were conducted. Curcumin generally shifted their transcriptomes compared with not curcumin treatment vehicle controls. The global transcriptome links the expression of putative curcumin degradation genes and networks and metabolic phenotypes. Overall, we use a combination of metabolic, genetics, and transcriptomic profiling to identify and characterize gut symbionts Lactobacillus gasseri, and Ligilactobacillus salivarius, and Bifidobacterium infantis that generated bioactive curcumin-metabolites. One bacterial strain that was isolated from a healthy person can metabolize avicularin. These results emphasized the importance of gut microbial genomes the in biotransformation of food components and their impact on human health. These results emphasized the importance of gut microbial biotransformation of food components and its impact on human health.

DOI

https://doi.org/10.7275/26363429.0

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

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