Dr. Scott Chimileski

Assistant Professor of Microbiology

Department: Natural Science
Programs: Biology, Human Health and the Environment


I am a microbial scientist interested in the endless biodiversity of microbial organisms, including bacteria, archaea, fungi, slime molds and microscopic animals. I write “endless” because studies have estimated that there may be one trillion unique microbial species on this planet!

My research specialty is the social or multicellular aspect of microbial science. Biologists once thought of bacteria and other “unicellular” organisms as solitary creatures, however now we appreciate that they are highly interactive organisms that live in multicellular communities, communicate with one another, cooperate, compete, and coordinate to engage in collective behaviors. For example, most bacteria live in nature within a type of microbial community called a biofilm, where they are encased in a self-produced extracellular matrix. Biofilms are just one of these many interrelated “emergent properties” of microbes.

I also have a background and continued interest in archaea. Just a few decades ago, scientists did not even know that archaea existed, because they are microscopic organisms that appear visually similar to bacteria. But starting in the 1970s, genetic studies revealed that the domain Archaea is one of the three major evolutionary divisions of life on Earth, together with Bacteria and Eukarya. Many archaea are considered “extremophiles” because they live in environments that would kill almost any other life form. I studied horizontal gene transfer and biofilm formation in halophilic, or salt-loving, haloarchaea during my doctoral research.

Beyond my research areas, I often think and write about “big picture” connections between microbial organisms and the biosphere. A major goal of my teaching, writing and photography is to highlight the beauty and biology of microbes far and wide, and the ways that they interconnect with larger organisms. This includes the diverse microbiome that we all have on and within our own bodies. (About half of “you” is microbial by cell count, believe it or not, and we are even more microbial in terms of the genetic information that the microbiome contains.) Microbes were the first organisms at the origin of life and they conditioned the early planet, making it possible for plants and animals to arise. And microbial life continues to be the support system for the biosphere, mediating global biogeochemical cycles and forming the foundation of the entire food web.

Courses Taught

🍃 BIO 101 Intro Biology I
🧬 BIO 102 Intro Biology II
🔬 BIO 199 Exploring Biology
🦠 BIO 376 Environmental Microbiology
🌎 BIO 499 Bioremediation

Academic Background

2015–2019 | Harvard Medical School | Postdoctoral Fellow in Microbiology, Kolter Lab
2015 | University of Connecticut | PhD in Genetics and Genomics
2008 | University of Connecticut | BA in Biological Sciences, Minors in English and Molecular Cell Biology

Interests and Activities

🦠 Photography and microscopy. My portfolio and catalog of microbial science photography can be found on my website: http://microbephotography.com/
🦠 I am a Guest Curator at the Harvard Museum of Natural History (HMNH). From 2015-2018, my postdoctoral advisor Roberto Kolter and I spearheaded and developed the Microbial Life exhibition there, which remains open through March 2020. We also created a photography exhibition originally launched at the HMNH in 2017 called World in a Drop: Photographic Explorations of Microbial Life, which continues to travel to major venues in the UK, Denmark, Uruguay, Colombia, China and several other sites in the United States. World in a Drop is now also seen in Freer Science Hall!
🦠 I am a Review Editor for Biology of Archaea at the Journal Frontiers in Microbiology.
🦠 I am an Associate Blogger at the microbiology blog, Small Things Considered.
🦠 Exploration! I have explored for photography expeditions and other field work, many parts of British Columbia, Yellowstone National Park in Wyoming, Glacier National Park in Montana, and Capitol Reef National Park in Utah. I’ve also traveled to the village of Delft in the Netherlands where microbes were first discovered, and to the UK, Colombia, Italy, China, Switzerland and Greece.



Peer-reviewed articles

  • Kolter R, Chimileski S (2018) The end of microbiology. Environmental Microbiology 20:6
  • Chimileski S, Franklin MJ, Papke RT (2014) Biofilms formed by the archaeon Haloferax volcanii exhibit social motility and cellular differentiation, and facilitate horizontal gene transfer. BMC Biology 12:65
  • Chimileski S, Dolas K, Naor A, Gophna U, Papke RT (2014) Extracellular DNA metabolism in Haloferax volcanii. Front. Microbiol. 5:57
  • Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J (2014) DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival. PLOS ONE 9(4)
  • Ouellette M, Jackson L, Chimileski S, Papke RT (2015) Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. Front. Microbiol. 6:251
  • Chimileski S, Papke RT (2015) Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions. Front. Microbiol. 6:362

3D model

Scientific animation/script writing

Doctoral thesis

  • Chimileski S (2015) Social features of an archaeon: biofilm formation, social motility, eDNA metabolism and gene transfer in Haloferax volcanii. University of Connecticut Doctoral Dissertations. 847.
Book chapter
  • Papke RT, Chimileski S (2012) Gene transfer mechanisms, population genetics and the evolution of haloarchaea, in Advances in Understanding the Biology of Halophilic Microorganisms. Vreeland R (ed.)


  • 2018 | PROSE Award in Biological Sciences for Life at the Edge of Sight
  • 2018 | British Medical Association (BMA) Award for Life at the Edge of Sight
  • 2016 & 2017 | BioArt Award, Federation of Societies for Experimental Biology (FASEB)
  • 2016 | Passion in Science Award for Arts and Creativity, New England Biolabs
  • 2014 | Antonio H. and Marjorie J. Romano Graduate Fellowship in Microbiology
  • 2014 | Nature writing competition winner; invited contributor at blogs.nature.com



Contact »

Freer Science Hall, Room 119