1. Changes to the gut microbiome resulting from acarbose treatment are associated with increased longevity in mice

   New preprint posted to the bioRxiv

   I'm excited to announce that we've posted a preprint of our latest manuscript to the bioRxiv, as well as submitted it for peer review to the open access journal Microbiome. I'll update this note if and when it gets accepted.

   Edit 2019-06-20: Our submission to Microbiome was tranferred to BMC Microbiology, and was finally accepted (more than a full year in review!). Check it out in print.

   These days it seems like the only research more over-hyped than "microbiome" is longevity-enhancement. It is therefore with some trepidation that I have released into this world of buzz the first chapter of my dissertation, titled: "Changes in the gut microbiota and fermentation products associated with enhanced longevity in acarbose-treated mice."

   Previous work (done by my co-authors on this paper as well as others) has conclusively demonstrated that treatment with the anti-diabetic drug acarbose substantially increases lifespan in mice (also). The magnitude of …

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2. Not all carbs are bad

   Getting enough fiber might do more than keep you regular.

   This brief post was written as a popular science article for a class on science communication. My own research is currently focused on exactly this topic: describing microbial community dynamics associated with acarbose treatment and the production of butyrate.

   A quick internet search search for “low-carb diets” comes back filled with promises to make you sleek, spry, and slim just by cutting out this entire category of foods. The popularity of these diets shouldn't surprise you. Recent research has implicated overconsumption of sugars, the simplest form of carbohydrates, and starchy foods, which can quickly be broken down into sugars, in the increased risk of heart disease, obesity, even some forms of dementia. Americans have responded quickly, with 50% trying to limit their intake of sugars and carbohydrates according to a 2014 survey. That same survey found only 74% of respondents believe that a healthy diet can include moderate amounts of …

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3. Do bacterial species exist?

   Any of my friends or colleagues who have had the "pleasure" of talking about science with me for more than a few hours know that I am prepared, at the drop of a hat, to rant extensively about several standing debates in biology which I consider merely semantic. For instance:

   Q: Are viruses alive?

   A: Who CARES!? Viruses do what they do. Cellular organisms do something else. What difference does it make if we decide to allow our middle-schoolers to draw little dotted lines around animals, bacteria, and viruses? And I don't even want to hear the word "prion".

   I have a similar level of disdain for people who try to decide on a single definition for "species". Ultimately I am a pluralist: the definition should be tailored to the scientific question. Paleontologists, you have your morphological species concept, because what else do stony fossils allow? Are you studying speciation …

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4. Even pathogens hate a cheater

   I would like to apologize for the long delay since my last post. The excuse (I keep telling myself) is that, having already written too many computational articles, it was time to prove that I could write about biology too. Unfortunately I'm not nearly as good at reading the literature as I should be. Anyway, it's done. You can stop complaining now.

   One barrier to engineering bacteria for biofuel production or any other human endeavor is that evolutionary rates are scaled by population sizes and growth rates. For an organism with massive population sizes (trillions of individuals or more) and doubling times on the order of hours, evolution can occur quite quickly. Genetic variants within the population which are capable of growing faster will quickly take over. For an organism which is, for example, wasting a huge fraction of its energy producing your future gasoline, you can bet this months …

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