Hartmann lab at the Microbiome Center Symposium

On April 16th, the Hartmann lab group took a day trip down to the University of Chicago for the 2019 Microbiome Symposium.

Hartmann lab members Erica Hartmann, Jiaxian Shen, Alex McFarland, Clayton Johnson, and Ryan Blaustein at the 2019 Microbiome Research Symposium.

We listened to some lovely talks from researchers in various fields, but all of the talks highlighted emerging methods in microbiome research. The day served as a great opportunity to network with scientists from around the Chicagoland area. Three of our members (Ryan Blaustein, Alex McFarland, and Jiaxian Shen) used the symposium as an opportunity to share their research in poster form.

Antimicrobial paints have a blind spot

Spore-forming bacteria survive on surfaces coated with antimicrobial, latex paints

  • Antimicrobial paints kill most bacteria within 24 hours, but some survive
  • Such products are typically tested on pathogens but not common bacteria like Bacillus
  • Antimicrobial paints could favor antibiotic resistance — making harmless bacteria like Bacillus harmful

SEM image of Bacillus timonensis spores with vegetative cells in the background. Image credit: Jinglin Hu

EVANSTON, Ill. — Antimicrobial paints offer the promise of extra protection against bacteria. But Northwestern University researchers caution that these paints might be doing more harm than good.

In a new study, the researchers tested bacteria commonly found inside homes on samples of drywall coated with antimicrobial, synthetic latex paints. Within 24 hours, all bacteria died except for Bacillus timonensis, a spore-forming bacterium. Most bacilli are commonly found in soil, and many are also found in indoor environments.

“If you attack bacteria with antimicrobial chemicals, then they will mount a defense,” said Northwestern’s Erica Hartmann, who led the study. “Bacillus is typically innocuous, but by attacking it, you might prompt it to develop more antibiotic resistance.”

Bacteria thrive in warm, moist environments, so most die on indoor surfaces, which are dry and cold, anyway. This makes Hartmann question the need to use antimicrobial paints, which may only be causing bacteria to become stronger.

A painted surface that we perceive as smooth is actually quite mountainous on the micro-scale. Image credit: Daniela Ruiz

Spore-forming bacteria, such as Bacillus, protect themselves by falling dormant for a period of time. While dormant, they are highly resistant to even the harshest conditions. After those conditions improve, they reactivate.

“When it’s in spore form, you can hit it with everything you’ve got, and it’s still going to survive,” said Hartmann, assistant professor of civil and environmental engineering in Northwestern’s McCormick School of Engineering. “We should be judicious in our use of antimicrobial products to make sure that we’re not exposing the more harmless bacteria to something that could make them harmful.”

The study was published online on April 13 in the journal Indoor Air.

One problem with antimicrobial products — such as these paints — is that they are not tested against more common bacteria. Manufacturers test how well more pathogenic bacteria, such as E. coli or Staphylococcus, survive but largely ignore the bacteria that people would more plausibly encounter.

E. coli is like the ‘lab rat’ of the microbial world,” Hartmann said. “It is way less abundant in the environment than people think. We wanted to see how the authentic indoor bacteria would respond to antimicrobial surfaces because they don’t behave the same way as E. coli.”

The study, “Impacts of indoor surface finishes on bacterial viability,” was supported by the Alfred P. Sloan Foundation (award number G-2016-7291) and the Searle Leadership Fund.

This story was originally published by Northwestern University.

What we can learn from ISS microbes

PhD student Alex McFarland and postdoc Ryan Blaustein review data comparing ISS and Earth-based microbes

Our latest publication, led by postdoc Ryan Blaustein, is an Editor’s pick in the journal mSystems! He used pangenomics to see if there was anything special about microbes in a very special built environment: the International Space Station. Luckily for astronauts, while there are some particular features of ISS microbes, they don’t look like they’re going to do humans any harm. Peruse some of the popular media pieces covering this work below.

Good news: space bacteria (probably) aren’t evolving to destroy us in Popular Science

Study on Microbes Found on International Space Station Is “Quite a Relief” on inverse.com

New paper on antimicrobials and antibiotic resistance out

Dust with higher levels of triclosan, represented by orange triangles, contain more antibiotic-resistant bacteria. Graphic by Vlad Tchompalov.

Our latest work, in collaboration with the Biology and the Built Environment Center, is out in mSystems! Read it for yourself, and check then out some of the media coverage:

Your dust bunnies are alive but fighting them with antibacterials is a bad idea on CBC Radio’s Quirks & Quarks

Your gym mats may be breeding antibiotic-resistant germs in PBS NewsHour

Microbes that live at the gym are pumped up on antibiotic resistance in CBC News

Civil & Environmental Engineering shines at the French Science Fair

Hartmann lab members Sarah Ben Maamar, Ryan Blaustein, and Adam Glawe, along with friends from the Gaillard (Marco Alsina) and Cusatis (Madura Partridge) labs, shared an interactive hands-on experience to illustrate how UV light causes damage to DNA at the Science L.A.B.²: Learning and Building Bridges day. This event is organized by the Embassy of France in the US and the Consulate of France in Chicago. In the demo students exposed blue-colored bacteria to UV light. While some bacteria die when exposed to UV, others mutate and turn white. This experiment gave students an opportunity to explore effects of UV light and UV protection on bacterial survival and mutation rate. Take-home message: wear sunscreen!

Ryan, Sarah, Adam, and Marco pose next to their demo

Sarah walks students through the demo

Postdoc Ryan Blaustein Receives NIH Fellowship

Hartmann Lab Postdoc Ryan Blaustein recently received a TL1 Fellowship supported by the National Institutes of Health-National Center for Advancing Translational Science (NIH-NCATS). The award provides multidisciplinary training to clinician scientists and engineers to conduct translational research to improve care of children and adolescents.

Ryan’s proposed project aims to determine the impacts of chemotherapy and antibiotics on the intestinal microbiome (i.e., community of bacteria living in the gut) in children using experimental systems. This research is important because pediatric patients receiving intensive cancer treatments are at an increased risk for developing microbiome-associated health complications, such as diabetes, asthma, obesity, and antibiotic-resistant infections.

To advance potential cancer treatment strategies that may mitigate such risks, we will use multi-omic methods to test the hypotheses that (1) chemotherapeutics and antibiotics have distinct and overlapping effects on the microbiome and (2) certain therapeutic combinations have synergistic impacts on microbiome metabolic functioning during and after treatment. These studies will provide a strong foundation for future translational research on microbiome dynamics in pediatric oncology.

Ryan’s program will be co-mentored by Dr. Patrick Seed at the NU Feinberg School of Medicine and Lurie Children’s Hospital, kicking off a new, exciting collaboration for the Hartmann Lab!

Hartmann lab welcomes Marshall Plan Scholarship Fellow

We are thrilled to host a visiting master’s student, Lisa Michelitsch, starting next month. Lisa’s visit is sponsored by a generous scholarship from the Marshall Plan Foundation. Here’s why she’s excited to come to Chicagoland:


During my bachelor´s degree program in Molecular Biology, I had the honor of doing two research internships abroad within Europe as well as working in multiple laboratories in Graz. This was a meaningful addition for my young academic education and simultaneously opened new scientific doors for me. Working in different laboratories with different people from all over the world showed me how important it is to create mutual understanding of different people’s views and opinions. In my mind, this is essential for exchanging knowledge between people with different cultures or backgrounds. From this constructive experience, I knew that I want to do my master thesis abroad to further broaden my scientific and personal horizon.

In addition, a well built network will give me the opportunity to keep up-to-date on new discoveries and ideas, which would be good for me to constantly develop myself in an area I love. Furthermore I get the chance to connect with people, which is another passion of mine. Following this idea (and big thanks to my supervisor, Alex Mahnert at the Department of Environmental Biotechnology in Graz), I had the chance to get in touch with Erica Marie Hartmann in person at her exciting presentation about the dust microbiome in July 2017. I was impressed by her work and the engagement of sharing knowledge with the public, which I think is one of the most important things in today´s science.

And thanks to the Marshall Plan Foundation, I now have the financial support to do my master thesis in the Hartmann Lab at Northwestern. The Foundation established an academic exchange program to fund scholarships for academic exchange between Austria and the U.S. with a special focus on Universities of Applied Sciences and Technical Universities. They support students, helping them in their career development and opening doors for transnational mobility. A key element of the scholarship is the freedom of the fellows to choose a research topic and the appropriate University fitting their individual needs.

The opportunity to choose the topic on my own was not only given by the scholarship but also by Erica, which really means a lot to me. I have decided to work on a new microbiome project centered on toothbrushes, which I´m very curious about. I can´t wait to join Erica’s group because I´m really motivated and eager to learn new methods and share ideas with all lab members.

I am convinced that this experience not only helps me in giving my master´s program the perfect closure but also provides a specific boost for a promising scientific career in the future.

Besides the amazing scientific opportunities that I get at Northwestern, I am also looking forward to going to the U.S. for the first time and to living in Chicago for an extended period of time.

NU Bioscientist Huseyin Demir on working in the Hartmann lab

We were fortunate to have several wonderful undergrads, in addition to David, in the lab over the summer. Rising sophomore Huseyin Demir is part of the NU Bioscientist program, which funded his summer research experience. Here’s what he had to say about it:

As a part of the NU Bioscientist program here at Northwestern, I was able to get a summer research grant that aims to introduce and expose freshmen to research in a field of their choice. I had very little lab experience prior to joining the Hartmann Lab, but this grant made it possible for me to do research as a full-time job.

I looked into utilizing a relatively new technique called PMA-qPCR, which uses a DNA binding agent called Propidium Monoazide and qPCR in order to differentiate between the viable and non-viable bacteria in a given sample. I first tested the technique on practice samples to develop a reliable method and then used it to supplement and provide a comparison to PhD student Jinglin Hu’s data in assessing viability of bacteria on surfaces with different paints.

My work in the lab was guided by our technician, Adam Glawe, who familiarized me with the lab techniques I needed to perform this project and provided constant feedback on the data collection and analysis.

I now feel much more comfortable doing research in a lab setting, and I look forward to working with the Hartmann Lab on many more projects during my undergraduate career.

Undergrad David Park reflects on his summer research project

David Park, who is a junior at Northwestern, is wrapping up his summer research project, funded by a Summer Undergraduate Research Grant. This is what he has to say:

David Park, setting up samples for PCR.

Last April, I received the Summer Undergraduate Research Grant from the Office of Undergraduate Research. The grant was for a new project that compares the genetic composition of dust-borne Staphylococcus aureus and its other strains in clinical settings. Immediately after hearing the news about the grant award, I began screening for S. aureus in the collection of bacterial samples that had been generated by the laboratory’s cultivation team. The methods included agar plate streaking, DNA extraction, and polymerase chain reaction (PCR), which together made up the biggest part of my time in lab.

Laboratory guidance and assistance from Alex McFarland, our graduate student who recently joined the lab, and other lab members was very valuable; the weeks of screening went smoothly with their help. It was interesting to find a clinically common bacterial species in indoor dust, especially those that are potentially hazardous due to antibiotic resistance. During the process, I learned more about microbiology and microbiological research, and feel more comfortable performing lab techniques, which I am glad about.

The goal of the screening so far was to have dust-borne S. aureus samples ready for sequencing. Sequencing is the next step of the project, which I hope to get into after my month-long shadowing program in South Korea.