Metagenomic Analysis of the Astronaut Microbiome
Posted in Internship Presentations | Tagged Summer 2020
Mentors: Drs. Crystal Jaing and Michael Morrison, Lawrence Livermore National Laboratory Genomics Group.
Date/Time: August 25, 2020 at 1-5pm
Abstract: The human microbiome plays an important role in maintaining homeostasis in several biological systems. Environmental stresses can alter the delicate balance and subsequentially alter our health. Astronauts onboard the International Space Station (ISS) are exposed to a unique combination of environmental stresses (i.e. microgravity and cosmic radiation) which could cause serious health risks by disrupting biological systems or by altering bacterial communities. In order to characterize the effect of spaceflight on the astronaut microbiome, NASA approved the Microbial Tracking-2 mission. Samples were collected from 4 ISS crewmembers across four consecutive flights prior to, during, and post spaceflight. DNA was collected for these crew samples for metagenomic sequencing.
Taxonomic classification of the microbial reads using the Livermore Metagenomic Analysis Toolkit (LMAT) and Kraken 2. Results were then compared to ensure the data consistency from the two taxonomy classification pipelines. The results showed that because of the different k-mer lengths and database versions that the programs use, the results were drastically different. Kraken failed to show many bacteria species that were present in LMAT. Crew samples were also run in MIDAS to calculate species abundance that was then used to conduct enrichment analysis. Flight status were used to find which species were specific to them. They were then grouped to seven phylum using the program Phylogenize. The outputs also showed that there is a change in gene expressed within the bacteria when compared to before, during, and after the astronauts were in space which continued to show differences in functional enrichment between pre, during, and post flight.