Poop, prunes and proteomics: one of these is not discussed in this blog post

September 9, 2013 § Leave a comment

While much of the recent research focus has been on understanding what makes up a microbiome  in various parts of our bodies and how it impacts health and disease, there is less of a focus on how we respond to these communities of bacteria. But in order to do that, researchers need to know which proteins in the huge mix of proteins are actually ours. Teasing out the host proteins has been a technical challenge.

In a paper just out in Molecular & Cellular Proteomics, researchers tackled this issue by developing a method that can pick out the proteome of the host gut and see how it changes to shape the gut environment and nurture its teeming community of microbes. “While it is important to enumerate all the microbes that inhabit our bodies, it may be even more important to measure the ways in which we, as hosts, have evolved ways to shape the microbes’ environment, and how changes in that environment can, in turn, shape our own health,” says senior author Josh Elias of Stanford University.

The investigators studied feces by mass spectrometry to understand how a host proteome responds to a microbiome. The lead author on the paper, Josh Lichtman, had suggested the idea to Elias while he was interviewing for admission into the Stanford University chemical and systems biology graduate program.  “Immediately, I agreed that studying gut microbes with mass spectrometry would be a powerful tool for studying this hugely complex system, but that it could get ‘messy,’” notes Elias.

So when Lichtman joined the group, the investigators started on the project. “One of the biggest difficulties in understanding the gut environment is that there are potentially hundreds of thousands to millions of proteins from hundreds of distinct organisms that could be identified,” explains Elias. “The gut environment, with its active proteases, add a further layer of complexity” because the proteases generate peptides that complicate the signals obtained from the mass spectrometric analysis, which involves protease digestion steps. Because the number of bacterial species outnumbers the kinds of animal cells present in the gut, the proteomes of all the bacteria overwhelm that of the host.

To solely focus on proteins from the host, Lichtman devised an enrichment strategy during the step of protein extraction from the fecal samples that made sure that the proteins came from the animal’s intestines, not from bacteria. The method allowed the investigators to track changes in expression of more than 3000 host proteins.

The investigators, in collaboration with Justin Sonnenburg also at Stanford, collected feces from mice that were either germ-free or limited to up to five bacterial species. They also used mice that had the human version of the gut microbiome. These mice, with their increasingly complicated gut microbiomes, allowed the investigators to figure out how well their technique worked in distinguishing between bacterial and host proteomes as well as see how the proteomes changes with more complicated microbiomes. The investigators also applied their method to human samples.

The investigators established that as the gut microbiome got more complex, the host proteome responded in kind by becoming more complex in the types of proteins expressed. “Our work demonstrates that host responses can be readily measured, that these responses are correlated with the underlying microbiota, and we can measure them fairly simply with modern proteomics methods,” states Elias. “There are tremendous amounts of resources currently being spent on evaluating the microbes, in isolation or in aggregate, but often without coincident studies on their host’s biology.  We believe our study provides a route towards reconciling the two.”

(Credit for the awesome title goes to Chris Pickett of #melodramaticlabnotebook fame, with a helping hand from Shaila Kotadia)

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