In science there are experiments that try to construct simple, tractable models of complex phenomena, with the goal of developing insights that will be relevant to the more complicated systems. Alternatively, there are experiments that try to infer insights amid a flurry of coexisting factors. Each of these approaches has its merits and flaws. I … Continue reading How to build a gut microbiome in 119 easy steps
About a recent paper from my lab: Deepika Sundarraman, T. Jarrod Smith, Jade V. Z. Kast, Karen Guillemin, and Raghuveer Parthasarathy, “Disaggregation as an interaction mechanism among intestinal bacteria,” Biophysical Journal (2022). Some bacteria stick together; others do not. We have seen these variations among bacteria inside the zebrafish gut, and it’s probably the case … Continue reading Things Fall Apart; The Bacterial Cluster Cannot Hold
Our microbial ecology journal club, in addition to being fun and educational, is a limitless source of data presentation examples both wonderful and terrible. Here’s a recent example that drives me up the wall. It’s from a study [1] on correlations between pre-term births and various chemicals that may or may not be associated with … Continue reading When Should You Make a Plot of p-values? Never.
About a recent paper from my lab: B. H. Schlomann and R. Parthasarathy, “Gut bacterial aggregates as living gels,” eLife, 10: e71105 (2021). DOI: 10.7554/eLife.71105. What do gut bacterial colonies look like? My group has been exploring this question for years, and ever since our first forays peering inside larval zebrafish it has been evident … Continue reading Living Gels
About a paper from my lab [1] on competition and cooperation among gut microbes. Is the whole more than the sum of its parts? This question arises throughout the sciences, as one wonders whether understanding the constituents of some system suffices to understand the system as a whole. Sometimes the answer is “yes.” Electromagnetic fields, … Continue reading Tossing Starfish from the Tidepools — Gut Microbiome Edition
About a new paper from my lab [1] on why gut bacteria swim, and whether their host cares. Many bacteria swim. It’s a great way to explore one’s surroundings, run away from toxins, or move toward regions with more food. Over the past several years, as we’ve used 3D microscopy to peer inside zebrafish to … Continue reading Putting the brakes on gut bacteria
Synopsis: In a recent paper from my lab [1], we report on watching gut bacteria get pummeled by low doses of antibiotics. The antibiotics induce changes in the spatial organization of the microbes, with major consequences for their ability to persist in the gut. Motivations At high enough doses, antibiotic drugs will kill bacteria, or at … Continue reading An intestinal amplifier for antibiotics
I decided to make a version of the abstract for my upcoming presentation at the March Meeting of the American Physical Society that (i) has a movie, and (ii) is revised slightly from the version I submitted a few months ago. My talk is one of two invited talks at a pair of focus sessions … Continue reading Bacterial behaviors and the physical landscape of the zebrafish gut [APS talk abstract]
Are there general laws governing the gut microbiome? This is an important question if we’re to make sense of how the microbial ecosystem inside each of us influences health and disease, without being overwhelmed by its diversity and complexity. It’s also the question that, almost verbatim, starts off a recent paper from my lab, … Continue reading Kepler, Newton, and Gut Microbes
Synopsis: A blurb about a recent paper from my lab [1], on our discovery that the bacterium that causes cholera can manipulate the mechanical environment of an animal gut to expel resident bacteria. Introduction: cholera’s tools, and ours Cholera killed more people in the 19th century than any other epidemic disease, and it continues to … Continue reading New Tricks from an Old Bacterium
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The Eighteenth Elephant 