Medizinische Universität Graz Austria/Österreich - Forschungsportal - Medical University of Graz
Gewählte Publikation:
Bashir, M.
Unravelling the microbiome: From human gut to spacecraft assembly cleanrooms
PhD-Studium (Doctor of Philosophy); Humanmedizin; [ Dissertation ] Graz Medical University; 2016. pp.
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- Autor*innen der Med Uni Graz:
- Bashir Mina
- Betreuer*innen:
- Moissl-Eichinger Christine
- Pieber Thomas
- Altmetrics:
- Abstract:
- Although recent advances in microbiology have shed some light into the uncultivable biome, the majority of microorganisms still do not grow under laboratory conditions. Cultivation-independent techniques exploiting advances in next-generation sequencing are applied to sneak peak into the hidden microbial flora. This thesis describes a phylogeny based 16S rRNA amplicon sequencing study investigation the effects of an oral vitamin D3 supplementation on the mucosa associated gut microbiome and functional metagenomics study with focus on pathogens and their corresponding virulence factors in spacecraft assembly cleanrooms. Vitamin D is well-known for positively influencing human health but its impact on the human gut microbiome is still unknown. We performed an interventional pilot study, including 16 healthy volunteers (7 women, 9 men), who were endoscopically examined. A total of 7 sites, covering the major regions and stools were sampled before and after 8 weeks of vitamin D3 supplementation. Vitamin D3 supplementation changed the gut microbiome in the upper gastrointestinal tract, but lower regions including colon and stool showed no major changes. Gammaproteobacteria, including Pseudomonas spp. and Escherichia/Shigella spp. decreased while bacterial richness increased significantly. Modulation of the gut microbiome of the upper gastrointestinal tract might explain vitamin D’s positive influence on gastrointestinal diseases. The localized effects of vitamin D display distinct regional differences in the response of the GI-microbiome to confounders, which should be considered in future microbiome studies. Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: DAWN, Phoenix, and the Mars Science Laboratory (Curiosity). For Phoenix cleanroom was sampled at three time points: before arrival of the spacecraft, during the assembly and testing, and after removal of the spacecraft. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location. Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and virulence factors, which determine pathogenicity and in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, observed virulence factors were higher during assembly compared to before and after assembly, indicating a potential survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective and well implemented. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.