Sunday, May 27, 2012

Discover the Microbes Within: The Wolbachia Project on CNN iReport

One of the most rewarding aspects of being a scientist is seeing its undeniable impacts on students. 

This is a brief mention that CNN iReport posted a panel of 10 high resolution images and a story with some good quotes on a Peyton, CO classroom doing our science education series called Discover the Microbes Within! The Wolbachia Project. 

The Wolbachia Project's website is here.

I consistently hear from students that this discovery-based project is the best lab they do all semester and this high school group is no exception. Kudos to the talented teacher, Paul Austin, and his 25 new microbiologists/Wolbachia fans. 

Notable quotes from the iReport:
“This is exciting,” said Jaren Prestwich, 16, an eleventh grade advanced placement student at Falcon High School. “We’re getting in there and being a part of the whole field of science... This is actually recorded at the national and international levels.”

“These students are doing high-end scientific research,” said science teacher Paul Austin, who brought the project to 25 AP students at the high school

“This project pulls students into real world scientific research that teaches critical thinking and lab skills,” said Austin

“I didn’t know it’d be this complicated... Everything is so precise, so exact,” said Reyes. “I never expected to participate in a nationwide project.”  


Friday, May 11, 2012

Is the microbiome part of the organism or part of the environment?

One of the central questions in the science of the microbiome is whether an animal’s genes or diet determine the composition of gut bacteria. This debate gets murky very quickly as it raises the fascinating question of whether you should consider your gut bacteria a part of you, just like the genes on your chromosomes in your gut cells, or a part of the environment that affects you, like a fruit that provides you nutrition on a daily basis or a parasite that occasionally makes you sick.

Approaches to studying gut bacteria in humans have largely been diet-centric, and we are reminded of this pattern by the news coverage this week of a heroic microbiome study by Rob Knight's and Jeff Gordon's labs. For starters, here's one good example published by Science Now - Your Inner Bugs are What You Eat

This study measured the number and types of gut bacteria in people from three very different populations - the Venezuelan Amazon, Malawian villages, and three American cities. Similarities and differences in their gut microbes were found but the news spin is that the microbial differences are driven by diet. This extrapolation goes too far, as these populations not only differ by diet, but also in so many other environmental and biological traits.

Diet clearly plays a role in shaping the microbiome. This fact is undeniable. But it is not the sole contributor. Genes are important and the relative importance of genes vs. diet remains a key question of the science of the gut microbiome. Before jumping too quickly into the diet camp, consider this observation.

  • We raised insect species on exactly the same diets (download here), yielding a null hypothesis that if diet is the sole player in shaping the gut bacteria, then each species would have the same microbiome. To the contrary, evidence supports the alternative hypothesis that the microbial assemblages were different between the species and in fact the assemblages were related to each other in the same manner that the insects' genes were related to each other. To put it simply, even when diet is controlled for, the species' genes select for variation in the microbiome.

As in most scientific debates, it will likely be the merger of opposing ideas that ultimately fashions the knowledge. Diet and genes shape the microbiome. But whether your gut microbes should be considered part of the environment or part of you is up for continued discourse. What do you think?

Tuesday, May 1, 2012

Science of a Superorganism - my article in Bare Essentials

Bare Essentials - A Free Online Magazine Promoting Life Science and Conservation:  Bare Essentials is an open access online journal that has a commitment to spreading scientific literacy along with some snazzy designs/layouts in their articles. The editor of Bare Essentials asked for a contribution on the relationships between the microbiota and evolution. The article, entitled Science of a Superorganism, is downloadable here.

BE has progressive principles that deserve giving a shot out to, including an affiliation with the Australian Zoo Wildlife Warriors, a conservationist organization that was established in 2002 by the late Steve Irwin and his wife Terri Irwin to involve and educate others in the protection of injured, threatened or endangered wildlife. From the Bare Essentials website:
"Beyond our online resources and publication, we help co-ordinate fundraising opportunities for our conservation partners inviting individuals, groups and sponsors to affiliate with and help raise awareness for preservation efforts through our Wildlife Warriors Initiative."
Spotlighting the Stories of the Microbiota: There's so much to say about the microbiota that it was impossible to cover all the work that should be covered; and there are many good articles already out there. My approach was to boil down the basics and shine the lights on the importance of the microbiota for the general audience. I included topics such as how microbes weigh over 5000x more than humans do on the planet, how microbes make you attractive to mosquitoes, how women's hands are microbial dirtier than men's hands, among others.

I also tried to pick up some of the things that my student is studying on gut microbiota and evolution. Here are two more scientific points that are touched upon towards the end of the Bare Essentials piece but dont get much real estate in the article:
  1. First, the influence of gut bacteria on animal speciation is one of the major foci of our lab's research. We are studying how changes in the number and types of gut bacteria change during the process of animal speciation, and how the gut bacterial community may in fact cause speciation events by reducing interbreeding between two animal species. Recently we published a paper in the journal Evolution in which we showed that gut bacteria in closely related species of insects, Nasonia parasitoid wasps, increases in diversity over development from larvae to pupae and adults. The gut bacteria essentially becomes more diverse by colonization of new bacterial types as the insects develop, similar to what happens within humans in which an infant rapidly accumulates different species of bacteria over the course of their first year. 
  2. We also test whether diet or animal genes have a more important impact on the composition of the types and abundance of bacterial species in their guts. If diet affects the gut microbiota, then by rearing closely related species on the same diet, the null hypothesis would be that all three species harbor the same types of bacteria. We did not observe this. Instead, what we observed is that when the Nasonia wasps were reared on the same diet (fleshfly hosts), the bacterial communities became slightly different in each of the wasp species; and the relationships of these slightly different gut communities between the Nasonia species parallels the relationships of the Nasonia chromosomal genes (see conceptual figure below based on findings in the Evolution paper). Therefore, we conclude that bacterial communities diverge in parallel with the wasp's genes over evolutionary time-frames that span the formation of new species. The implications are significant. In particular, a host's bacterial population is not transient or unstable. Instead, it is species-specific at some levels and likely selected for by the immune system to perform functions within the host that may be slightly different from the functions in closely-related host species. What happens to these bacterial communities in hybrids and how the bacteria affect hybrid problems such as mortality between Nasonia species is what we currently have our heads buried in.
The figure above by Robert Brucker and I shows the codivergence between the genes of the wasp on the left and their gut microbial communities on the right. The three Nasonia species differ in their wing sizes and the fleshfly host on the bottom is Sarcophaga bullata. The bolded colors on the circular trees indicate the different types of bacterial species present in the insects.