Experimental design for microbiome research in space.

Thanks to Project MERCCURI, I’ve been fortunate to develop a relationship with Sharmila Bhattacharya, a researcher at NASA Ames who is doing Drosophila research on the ISS. Her group is developing a “Fruit Fly Lab” for any researcher to run experiments on the ISS. She’s sending up her own experiments on several upcoming SpaceX flights, and when possible, she is providing me with samples of fly carcasses, dissected fly guts, and/or fly feces obtained from swabbing the interior of the enclosures. She is interested in (among other things) the affect of spaceflight on immune function. Dovetails nicely with my interest in microbiome research, right!?

So, the first experiment (HEARTFLIES) I got two groups of fly dissected guts, enclosure fecal swabs, and fly carcasses. I did 16S rDNA PCR sequencing from them and found a HUGE difference between the flies that went to the ISS and the flies that stayed on the ground. That was pretty exciting until I realized that the space fly gut microbiomes looked basically like regular old fly gut microbiomes and the ground fly microbiomes contained something like 99% of a single OTU of Lactobacillus.

As it turns out, the media for the ground flies dried up. The flies were very dehydrated (which affected their heart assays as well.) “Never fear,” they told me, “we are going to re-do those ground controls.” Huh? It’s been more than a month since the space flies were sent into space. A new batch of flies cannot be used asa control for those space flies. It doesn’t matter that they are the same genotype, maintained in the same conditions. They are a totally different population now with respect to their gut microbiomes.

For these ISS experiments, they always use this type of “asynchronous control.” Why? Because they cannot synchronously mimic on the ground the conditions that the flies are experiencing in space. Why not? Because ambient conditions on the ISS fluctuate and they don’t learn about those fluctuations on the ground until well after they’ve already occurred. Makes sense. So, in subsequent experiments, they have been running “best guess” synchronous ground controls in addition to their asynchronous controls.

Tomorrow, I’m finally going to get to tour her lab at NASA Ames. We’re going to chat about these kinds of issues. For one thing, flies can swap microbiomes, but not genotypes. Do their experimental enclosures separate the genotypes? I have no idea. We’ll see tomorrow. I wonder if anyone who has piggybacked on experiments in animals like this has any wisdom to share?

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