Matilde, the holobiont

Dr. Patricia Valdespino

Have you ever had a pet? This is Matilde when she was young. She came to my door one day and never left, so we adopted her. Cats are so much fun, so I played with her as much as I could, and by doing so, everything happened to me! I got scratched, found fleas and other parasites, and read up on all the different diseases pets can get. But it didn’t matter…I wanted to bond with the kitten, even with all her associated bugs.

This relates to something we have recently realized: we are not alone. Basically every plant and animal live in association with a unique collection of microbes. We are not individual organisms, instead we are systems, what we call holobionts (meaning the whole collection of life in a unit). In these systems, microbes are in the majority, and until recently, an unseen majority. For example you can find a million microbes in a bucket of seawater and there are ten-fold the number of human cells in your body. Hosts and microbiota have managed to walk together through time in a very dynamic and complex equilibrium.

If you live in Berkeley you probably know that having different people living together in the same house is not easy. Though we can now roughly predict (using bulk sequencing analyses), the role of microbes in the holobiont or in the environment, the structure, function, and interactions of microbes need clarification more than ever.

This has been a revolution for biology. And in the middle of this era of discovery, here at Berkeley Lab you can find exciting strategies to study microbes, such as synchrotron-based infrared spectroscopy. This is the strategy I use to study live microbial cell processes at micro to nanometric scale. Biomolecules are infrared visible, so my job is to integrate the chemical dimension synchrontron technologies provide, to lipidomics, proteomics, and other powerful analyses to try to unravel some of the deepest secrets of the microbial world.

Specifically, I study the microbes that mediate the transfer of atmospheric carbon into time stable mineral structures, the carbonates. This is the way I study microbes at the Berkeley Lab, but at home I keep studying them by doing things like taking probiotics, drinking kombucha, or playing with Matilde.