Boddeke, A.M. (2018) From realtive to quantitative microbial profiling improving microbial characterization. thesis, Medicine.
Full text available on request.Abstract
There is increasing interest in the gut microbial composition throughout the GI tract and its role in Inflammatory Bowel Disease (IBD). It is known that the microbial composition is not homogeneous throughout the GI tract. Also, although sequencing techniques have overcome laboratory limitations in investigating microbial composition, statistical biases originating from the use of relative abundances still pose a challenge. Therefore, the aim of this project was to investigate the microbial composition of the small intestines in IBD patients, taking into account cell densities to see whether combining quantitative and compositional data improved microbiome profiling. For this purpose, we used two IBD cohorts: 1) a subset of the UMCG 1000 IBD cohort. Samples of 40 patients, 20 with ileostomy, were used for implementing a flow cytometry protocol for absolute bacteria quantification of frozen fecal samples. 2) The RISE-UP cohort, consisting of data from 74 IBD patients including metagenomics reads and bacterial densities from Fluorescent In Situ Hybridization (FISH). Our results showed that the microbial composition of the colon differed from the ileum. The colon harbored more Actinobacteria and Bacteroidetes species, whereas the small intestine showed more Proteobacteria. In addition, QMP transformation showed a better correlation with the total bacterial load per sample than commonly used relative abundance. Moreover, when comparing associations between host phenotypes and gut microbiota, QMP profiles showed a reduction of false positive associations. Concluding, the composition of the gut microbiome varies throughout the GI tract. Also, flow cytometry on frozen fecal samples offers efficient bacteria quantification but warrants further investigation. Finally, we have shown generating a quantitative microbiome profile using metagenomics sequencing provides a more accurate view on microbiome composition.
| Item Type: | Thesis (Thesis) |
|---|---|
| Supervisor name: | Weersma, Prof. Dr. R.K. and Vich Vila, A. and Groningen Institute for Gastro Intestinal Genetics and Immun |
| Faculty: | Medical Sciences |
| Date Deposited: | 25 Jun 2020 10:49 |
| Last Modified: | 25 Jun 2020 10:49 |
| URI: | https://umcg.studenttheses.ub.rug.nl/id/eprint/1027 |
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