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A short course on the human microbiome for students, including background information, key concepts, and hands-on activities. Students will learn about the microbiome through discussions of current science and experiments, with a focus on analyzing real microbiome data using web-based tools. The course aims to inspire students to further explore the hidden communities of microbes that shape human health and the environment.
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Science Department Team Lead Mica Mountain High School
Associate Investigator Microbial Genomics Section Translational and Functional Genomics Branch National Human Genome Research Institute
“We can compare the gut of a person with inflammatory bowel disease to a dying coral reef or a fallow field: a battered ecosystem where the balance of organisms has gone awry.” (Ed Yong, I Contain Multitudes: The Microbes Within Us and a Grander View of Life) This quote from Ed Yong illustrates how the study of the human microbiome is comparable to the way in which ecologists study complex communities. While people are probably most familiar with the human microbiome, every ecological niche on Earth has its own collection of distinctive microorganisms. This includes coral reefs and barnyard soils, as well as hostile environments like hot springs or acidic outflows from mining operations. These microbial communities are critical to important planet-wide processes like carbon sequestration, nitrogen fixation and the breakdown of toxic chemicals. These wildly differing environments and functions reflect another important feature of the microbiome: diversity. Despite a bias for focusing on the bacterial component of the microbiome, microbial communities are complex and draw organisms from across the tree of life, including fungi, viruses, protists and metazoans. Bacteria are often the focus of microbiome studies because microbiologists have developed robust tools for growing and identifying bacteria. Part of this stems from our frequently adversarial relationship with bacteria. Pathogens like Yersinia pestis, the causative agent of the Black Plague, have fundamentally shaped human history. The careers of famous microbiologists like Louis Pasteur (1822-1895), Robert Koch (1843-1910) and Alexander Fleming (1881-1955) were built on understanding and eradicating bacterial infections. While modern life wouldn’t be possible without medical advances to treat bacterial infections, it’s important to understand that bacteria far more often play a beneficial role in the world. Unlike pathogenic bacteria, which usually act alone, beneficial bacteria often function as a community made up of tens or hundreds of different microbes. Consortia of bacteria (and also fungi) are indispensable for making bread, cheese, yogurt, kimchi and many other foods. The microbiome is important to human health and the development of a strong immune system. Microbial communities are critical for nitrogen fixation and the health of our crops and livestock. This collection of lesson plans is designed to introduce students to the microbiome through discussions of current science and hands-on experiments.
HS-LS4-1. Communicate scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence.
For the teacher
One of the most basic questions a microbiome researcher can ask is: “What is in my sample?” There are many ways to answer this question, and the method you choose will determine how much biological detail you can elicit. The microbiome refers to the collection of bacteria, fungi, viruses, protists and metazoans in a sample, but researchers are often specifically interested in the bacterial component. Identification of bacteria is based on a taxonomic hierarchy. For instance, most people are familiar with the bacteria Escherichia coli. The bacteria E. coli is in the family Enterobacteriaceae and the phylum Proteobacteria; the full taxonomic hierarchy for E. coli is: Bacteria (Kingdom) Proteobacteria (Phylum) Gammaproteobacteria (Class) Enterobacterales (Order) Enterobacteriaceae (Family) Escherichia (Genus) Escherichia coli (Species) While taxonomic levels often stop at “species," additional taxonomic levels that allow scientists to categorize bacteria in finer detail (e.g., strains). The level of detail you can get from a microbiome experiment depends on the experimental method. For instance, figure 2 from Maiden et al., Nature Reviews 2013 (PMID: 23979428) (Maiden, Martin C. J., et al. (2012) “MLST revisited: the gene-by-gene approach to bacterial genomics.” Nature Reviews Microbiology, 11(10), pp. 728–736., doi:10.1038/nrmicro3093.) shows the level of resolution provided by various sequencing experiments. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980634/figure/F2/ In the experiment below, you will receive 16S rRNA sequence data. These sequences are derived from a fragment of the 16S rRNA gene and can be easily read with standard DNA sequencers. From the figure above you can see that short 16S rRNA sequences allow you to identify bacteria to the level of genus; full-length 16S rRNA sequences often allow classification to the species level. For those who are interested, the 16S rRNA is an RNA molecule that forms part of the structure of the bacterial ribosome, the molecular machine used to synthesize protein from mRNA. The 16S rRNA has
This is an example of the RDP Classifier output for sequences from a soil sample (associated with this paper: https://www.ncbi.nlm.nih.gov/pubmed/17041161, sequence accessions DQ827724:DQ829627). Soil is complex and has a lot of different bacterial taxa. A small section of the RDP report is below While this may look somewhat complicated, focus on the genus-level classifications. The sequences for the full analysis are included in the DOK03 file should you want to use this example in class.
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Students have been asked to connect many things and explore many new ideas. Ideas for closure:
Figure 2. Genus- and phylum-level classification of bacteria colonizing a composite subject, showing that human microbiome diversity is dependent on the site sampled. Sites in the oral cavity share greater similarity than other types of sites, such as the skin, vagina, and gut. Data derived from the NIH Human Microbiome Project study (http://commonfund.nih.gov/hmp).
