Human microbiome and other zoo-omes – Section of Microbiology - University of Copenhagen

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Human microbiome and other zoo-omes

Microbial communities colonize various habitats on the earth including some of the harshest environments on Earth such deep-sea hydrothermal vents to hypersaline lakes and acidic hot springs. In humans, it is estimated that the gut may hold approximately 1014 cells (mostly prokaryotic), which is 10-fold greater than the human cells. Furthermore, the human microbiome harbours around 3,000,000 genes compared to the approximately 30,000 genes of the human genome, demonstrating coevolutionary pathways. Similar situations in know found in all studied animals.

The microbiomal species have been shown to interact with each other and with the host organism in several ways affecting health and disease, including (1) modulating the inflammatory host response, (2) synthesizing small molecules and proteins that are taken up other microorganisms and/or by the host cells.
In Section of Microbiology, we are working to understand and exploit the adaptive potential of natural microbial communities using cutting-edge molecular techniques. Our research is based on a holistic perception of the microorganisms as integrated members of complex microbial communities shaped by their physico-chemical microenvironment, and by social community interactions.

The section staff members have access to continuously updated state of the art facilities that currently include a fully automated nucleic acids extraction robot, qPCR instruments, a high throughput sequencing facility with two GS FLX Roche, two Illumina HiSeq, and an Illumina MiSeq Sequencers. Furthermore, Section of Microbiology has access to several powerful computers that can be used for quality check and analysis of the generated sequences and is currently in the process of developing new sequencing analysis pipelines with improved accuracy to better understand the microbial communities and their relation to health and disease. The current strategy includes 1. Amplicon sequencing of rRNA genes and ITS region, 2. Metagenome sequencing of microbiome DNA and 3. Metatranscriptome sequencing of microbiome RNA

Our present microbiome research includes:

  • Designing and optimization of PCR primers and analysis tools for investigation microbial communities.
  • Screening microbial community and structure in human and a broad range of animals from fruit flies to giraffes.
  • Finding correlations between members of microbial community and humans and animals health and disease.

Write a project on Human microbiome and other zoo-omes

Microbiome in healthy and sick children
We investigate microbiome structure, diversity and activities of samples from healthy and sick children and animal model systems in order to identify the microbial factor in important illnesses such as asthma and diarrhea and others.

Techniques covered:
Classic culturing
Profiling of antibiotic resistance
PCR and qPCR analysis
Metagenomics sequencing
Bioinformatic analysis

Keywords:  Microbiomes, human health, network analysis
Supervisor(s): Søren J. Sørensen