This is a guest post by Carl Yeoman, a postdoctoral research fellow at the Institute for Genomic Biology at the University of Illinois Urbana-Champaign who will start as Assistant Professor in the Animal and Range Sciences Dept. at Montana State University in August (full bio below).
At this year’s Association of Biomolecular Resource Facilities (ABRF) 2012 conference, I will present the work that my colleagues and I have been doing at University of Illinois Urbana-Champaign using both 454 Life Sciences pyrosequencing and Illumina technologies to study the gastrointestinal and vaginal microbial ecosystems of humans and non-human wild primates.
Historically, microbiologists would interrogate these microbial ecosystems under a microscope or by trying to culture them in agar or broth containing nutrients. Microbes, however are extremely heterogeneous in their requirements for optimal growth. In fact, only ~1% of all microbes have been successfully grown in culture. Microbes grow at different rates (slower growing microbes will be outcompeted in non-replenishing culture), have different nutritional requirements and are often dependent upon other co-resident microbes for growth. These factors mean that culture-based analyses are inadequate for surveying microbial ecosystems, while the diversity of microbes in most ecosystems makes microscope-based analyses impossible.
Sequencing-based approaches overcome these confounding factors. Sequencing technologies have revolutionized our ability to analyze microbial ecosystems by reducing cost, increasing sequencing depth (the number of sequences you can generate), and removing bias. Through the targeting of phylogenetic markers, most prominently the 16S ribosomal RNA gene, we can establish which microbes are present. We can also sequence a representation of the entire DNA in an ecosystem and get an approximation of what these microbes are capable of metabolically. We can even get a peek at microbial intentions by using a representation of the entire messenger RNA in an ecosystem to look at what they are trying to do. Comparing this information among host species, environments or disease states we gain a greater understanding of the roles of microbes in host health and evolution.
Our work on wild primates has already shown that habitat destruction mediated by climate change and deforestation affects gut microbe communities and impacts host health; that the stress and dietary restrictions forced on captive primates have negative influences on gut microbiomes and host health; and that primate vaginal microbiomes are influenced by factors as disparate as promiscuity and gestation time, the later indicating an important evolutionary axis.
To be honest, I wasn’t familiar with the society or the conference before I was invited to present my work at ABRF 2012. So, I did the obvious and had a look at the conference website. The opportunity to rub shoulders with and learn from great scientists like George Church and Dion Antonopoulos (one of my predecessors at UIUC), made the decision to participate an easy one. The session topics are broad ranging which creates the type of environment I enjoy – one in which you can sit back and think about new and integrative ways to approach your own research. I will be developing my own research program later this year when I join the faculty at Montana State University, so I’m most looking forward to seeing what opportunities exist that could allow my lab to distinguish itself.
About the author
Carl Yeoman is currently a postdoctoral research fellow at the Institute for Genomic Biology at the University of Illinois Urbana-Champaign, but has recently been appointed to the position of Assistant Professor in the Animal and Range Sciences Dept. at Montana State University (starting August). He studies ecological and evolutionary dynamics of host-associated microbial ecosystems and genomes. He earned his Ph.D. at the Massey University in New Zealand investigating the genomes of fibrolytic, proteolytic and methanogenic rumen microbes and their symbiotic interactions. The Faculty of 1000 recently recognized his published work on Gardnerella vaginalis as being in the top 2% of biomedical research articles.