Author: Kat Milligan-Myhre

New Kat MM lab members!

I am very excited to announce that we have several new members of the Milligan-Myhre lab. In alphabetical order:

Katie D’Amelio, research technician, completed her M.S. at Drexel University in Philadelphia, PA where she studied the gut microbiome of army ants. Her research focused on identifying how different factors such as host genetics, transmission mode, and host natural history may shape the diversity of microbes found within the army ant gut. She has switched from insects to vertebrates and now studies the gut microbiota of stickleback fish in the Kat Lab.  She will focus on sequencing bacterial communities of stickleback guts and creating whole genomes of bacterial isolates.

Lucas J. Kirschman, postdoc, is a physiological ecologist who studies how life history trade-offs affect animal development, immune function and how these interactions can scale up to ecosystem level processes. He recently received his Ph.D. from Southern Illinois University Carbondale where he studied the pleiotropic effects of neuroendocrine stress on during a critical window of development in larval amphibians. Dr. Kirschman will initially focus on host selection and shaping of gut microbial communities, including both developmental tradeoffs and immune response genes.

Amber R. Nashoba, postdoc and research professional, is interested in the application of evolutionary theory to understand and address environmental change. Her dissertation research studied population-level adaptation, natural selection, and the response to selection of a native prairie legume (Chamaecrista fasciculata). This project focused on the empirical application of Fisher’s Fundamental Theorem of Natural Selection and among-year environmental variation in the form of trait relationships, adaptive capacity, and fitness landscapes. She recently completed a Future Faculty Fellowship at the Northeastern University; during this time, she examined allele frequency change in drought and salinity associated genes in newly restored Spartina alterniflora in a Rhode Island salt marsh. In our lab, Dr. Nashoba will focus on phenotypic changes in a population of stickleback that is undergoing rapid selection and adaption to a novel microbial environment. Dr. Nashoba has been a member of the American Indian Science and Engineering Society since 2011.

Kat O’Brien, fish technician, previously worked at Northeastern University modeling Atlantic cod (Gadus morhua) Essential Fish Habitat (EFH) in the Gulf of Maine. With the rising ocean temperature and cod stocks declining, EFH is a good indicator where the few remaining cod could be. This information enables researchers and managers to make cogent decisions on fishing area designations. O’Brien now works as a husbandry technician at UAA, working in both the vivarium and in the Milligan-Myhre labs. She will focus on creating a vivarium for our recently funded stickleback stock center. O’Brien enjoys fly fishing, beach combing for sea glass, walking her dog, and SCUBA diving (not in Alaska).

I’m very excited about our newest members!  Now, back to the science.


Pros and cons of traveling as an assistant professor

I (Dr. Kat) have had an incredibly busy summer in terms of traveling. I have been trying to determine whether this amount of travel was appropriate/worthwhile for an assistant professor ending the 2nd year on the tenure track. Rather than just turn it over in my tiny brain, I thought I would write a post on it, to give others insight as well. Time permitting (ha!) I’d like to write a blog post for each of the work-related trips to summarize what I learned from each.

My Summer Travel:

ASM Microbe 2017 meeting in New Orleans May 31-June 5

Field work various days

Fish Microbiota workshop in Trondheim Norway June 17-25

SING workshop in Tucson Arizona July 9-15

Talkeetna trapping trip a weekend in July

Family trip end of August for two weeks

Wedding for close friends a weekend in August

Camping mid-week for two nights


Other obligations:

Teaching ANSEP high school students Microbiology 3 afternoons per week for two weeks

Hiring research tech/post docs

Committees (students and departmental)



Networking. I met several people in person that I follow on twitter/studied their work/used their assays/etc. I’ve gained a new perspective on their work, received great advice for how to proceed down the tenure track, and received valuable advice for my work/TT path/balancing work-life/becoming a better mentor/giving back to my tribe. There are a couple of possible collaborations that may come from meeting various folks, including a chat with a person I sat next to on the plane who happens to work in my field. That networking is much harder to do over email/twitter/phone calls/skyping.

Visiting new places to gain a bigger perspective of the world. This is true in terms of place, people, research, mentoring, and insight into how I can become a better contributor to both my scientific and personal networks.

Exposure for my lab. This overlaps with networking quite a bit. Although I didn’t get much traffic at my poster at ASM, I was able to talk to quite a few people about the work our lab is doing and get feedback during one-on-one meetings. My students/postdoc also presented at Evolution and came back with some great ideas for their own projects. I gave a talk at the Fish Microbiota workshop that was well received, and may result in some collaborations.

Insight into what others are doing in my field. As a PI, I have almost no time during the day to catch up on the latest in publications. While I read abstracts/peruse papers from links via twitter, or take a quick look through the latest titles/abstracts that come to my email from pubmed and google scholar updates, listening to a talk provides more information in a short period of time. At meetings I also tend to learn more about things happening outside my field, or studies that are only tangentially related to my studies but that could have a big impact in the way we proceed. Not to mention the papers online are summaries of work that was done years ago, and typically don’t include the negative data or failed assays that are presented at posters/talks/gleamed from talking to people at a meeting.



Time away from my family. This was especially hard as I have two daughters who are asking questions like “Do you love your work more than you love me?” (seriously folks, this was asked between trips 2 and 3.)

Time away from mentoring. While I feel like my lab handled my time away from the lab OK, this summer I didn’t feel like I was being a good mentor. In my mind, that includes weekly meetings, having time in the lab to help trouble shoot assays, handling my own project, etc. I obviously wasn’t in the lab or field as much this summer, and my disconnect from my mentees reflects that.

Time away from data collecting/processing. I need to publish papers from my own lab, and yet I collected very little data myself this summer. Since I teach during the spring and fall semester, this means I won’t have as much data for the year as I would like. This is weighing heavily on my mind as I enter my third year on the tenure track.

Time away from teaching prep. My teaching load is heavier than some and lighter than others. Theoretically I don’t need much teaching prep time, but I still would like more time to process the feedback I got back from my students last year, and to develop new classes.

Less time for subsistence and no time in Kotzebue. Summer is prime time in Alaska for fishing and berry collecting. Due to my travels this year I made the hard decision to not go home to Kotzebue to help my dad with fishing or my folks with berry picking and hunting. My parents are getting older, and my chances to camp/fish/hunt/pick with them is getting smaller with each season. One of the reasons I moved to Alaska was to be closer to my folks and home so that I could regain a connection with my family. The professional travel and decision to use vacation time in the Lower ’48 is stripping away my chances to do so.

I am so so so so far behind in administrative duties. As in my inbox is overflowing, and a student is waiting for me to finish my IRB training so that he can proceed with his work. (which also means it’s time to wrap up this post)



While the networking and perspectives gained this summer were valuable, next summer I am going to prioritize time in Kotzebue, writing, and in the lab. I will send more of my students/mentees to conferences rather than attending myself. As a new PI, this summer was a good time to travel in that I was able to make valuable connections and get exposure to our work just as we’re prepping manuscripts. Strategically, although it was time well spent overall professionally, I think I could have shortened a couple of the trips and still gotten as much out of the conferences. I arrived a day early for each trip (traveling from Alaska means that most of my trips took an entire day for flights) and left either the last or next day for each trip. I will shorten that for future trips and lose a day or two on either end.

I am going to push to have my family join me on more of my trips next year to minimize my time away from them. This will cut back dramatically on my networking (many of the connections I made were over drinks, meals, or hikes).  I will also likely only attend a few days of a conference, rather than spend a week away at a time.

One final thought: There are pros and cons to attending big general meetings (ASM microbe) vs small meetings (Fish microbiota and SING). I was able to get a broader look into research that is only tangentially related to my work at ASM microbe and I met some great potential collaborators at ASM who didn’t attend the smaller meetings. However, the connections I made at the Fish Microbiota and SING meetings were deeper because we spent so much more time together (hiking trips, several dinners, social hours) and single sessions (as opposed to the multiples sessions in different rooms in large buildings at ASM) meant that I gave my full attention to each talk at the smaller meetings. I like the balance of a large meeting and a small meeting. Because the work in our lab is so interdisciplinary (microbiology, immunology, ecology, evolution), I think I will send my mentees to more meetings next year and only attend one small and one large meeting myself next summer.

One more final-final thought: I have some personal travel time at the end of the summer. This is the first real vacation with my entire family in three years. While it comes at a tricky time (just before classes start!) due to a family event, I am hoping it provides a desperately needed break just before I dive into year three. I also hope to incorporate real vacations in future summers.

May 2017: Awards and travel

Both Kelly Ireland and Kenneth Sparks were awarded the OURS-INBRE undergraduate research award! Congratulations to both. This funding will allow Kenneth to create a Stickleback mock community from bacteria isolated from stickleback guts in Oregon and two Alaskan populations, and allow Kelly to use the qRT-PCR assay she has been developing to determine the immune response to microbes in several different stickleback populations. Well done to both students.

Curious about what we do? Chat with one of us at the following meetings!

May 18/19 – Fairbanks, Alaska – Research technician and soon-to-be graduate student Ruth Isenberg will present a poster at the University of Alaska Biomedical Research Conference: “The Effect of a Host’s Environment on the Composition of Their Gut Microbiota”

June 1-5 – New Orleans, LA – Dr. Kat will present a poster and give a poster talk at the ASM Microbe meeting: “Fishing for Contributions of Host Genetic Background to Host-Microbe Interactions”
Poster talk:  6/2/2017 1:45:00 PM – 6/2/2017 2:35:00 PM
Poster: Poster Presentation Date/Time: Sunday Jun 4, 2017 12:15 PM – 2:15 PM
(For a meeting of this size, we are not able to consider special scheduling concerns)
Poster Board Number: SUNDAY – 887

June 19-23 – Trondheim, Norway – Dr. Kat will present a talk at the Fish Microbiota Workshop titled: Gene-by-environment interactions drive microbiota variation and response to antibiotics

June 23-27 – Portland, OR – Postdoctoral fellow Emily Lescak will give a talk titled: Gene-By-Environment Interactions Drive Developmental Responses to Antibiotic Exposure in Threespine Stickleback Fish

Other recent presentations:

Emily Lescak gave a talk at the Pacific Northwest regional Chapter of the Society of Environmental Toxicology and Chemistry meeting in Anchorage Alaska in April 2017 titled: Gene-By-Environment Interactions Drive Developmental Responses to Environmentally Relevant Levels of Antibiotic Exposure in Threespine Stickleback Fish

Graduate student Ryan Lucas presented a poster at the American Fisheries Society Alaska meeting in March 2017 in Fairbanks titled: Effects of tetracycline on somatic development in threespine stickleback fish

Postdoctoral Fellowship in Microbiology and/or Immunology

Update: We have hired a postdoctoral fellow. More details will follow in an updated post.

We are hiring! A postdoctoral position is available immediately at the University of Alaska Anchorage Biological Sciences Department in the laboratory of Dr. Kat Milligan-Myhre. We are interested in someone who has strengths in microbiology and/or immunology, and who is interested in using threespine stickleback fish as a model to study host-microbe interactions. You will study the contribution of the host genetic background on the interactions between the host and the microbiota, with a focus on the ability of the host to resist developmental delays due to the disruption of the microbiota and/or immune system.


  • PhD in Biological Sciences, with an emphasis in microbiology, immunology or evolution preferred
  • Enthusiasm to learn new techniques; good organizational skills; detailed oriented record keeping; ability to work well with others
  • Willingness to move to Anchorage, Alaska


  • Grant-writing experience
  • Mentor undergraduate/graduate students
  • Outreach opportunities throughout the year
  • Teaching opportunities available, but not required
  • Experiment with freezing and recovering fish sperm and eggs
  • Play with (I mean experiment with) microbes in our collection
  • Learn lab management skills through duties shared among lab members (fish husbandry, microbe stock maintenance, ordering supplies, etc)

Other details:

Full-time position

Funding for position through Dec 2018, possibly through Dec 2019

How to apply:

Equal opportunity employer. We encourage women and minorities to apply.

Please send Dr. Kat Milligan-Myhre ( at alaska dot edu) your cover letter, CV, three references, a statement of research interests and career goals (not restricted to academia), and favorite winter activity.

Research Technician wanted!

Update: We have hired a research technician. Updated post will follow soon. Thank you to everyone who applied!

We are hiring! Our research technician will be heading off to grad school mid-summer 2017. We need a new research technician to start in June 2017.

Your duties (among other things):

Help lab mates (undergraduates, graduate students, postdoc; see “People” to learn who you will work with) with their projects, including microbiome studies, immunology studies, field studies, etc (see the “About” section for a full description of what our lab works on)

Maintain fish in the lab

Experiment with freezing and recovering fish sperm and eggs

Maintain and expand microbe stocks

Play with (I mean experiment with) microbes in our collection

Order supplies/help keep things orderly

Opportunities to do outreach in the STEM fields throughout the year


Bachelor’s degree, preferably in Biology-related field

0-4 years experience

Enthusiasm to learn new techniques, organizational skills, detailed oriented, record keeping, ability to work well with others required

Willingness to move to Anchorage, Alaska

Other details:

40 hours/week

Research Tech level 2-3

Funding for position through Dec 2018, possibly through Dec 2019

How to apply:

The position is listed as temporary. For UAA, this means 18 months, after which you will need to take 120 days off.  We may be able to extend that, depending on funding.

Please send Kat an email (see “Contact us”) with your CV, 3 references, and a cover letter, and apply to the link below.

Equal opportunity employer. We encourage women and minorities to apply.


Mid summer accomplishments

I like to take a moment once in a while and think about what we’ve accomplished. It’s important to do that, because the day to day grind of doing science often involved lots of small jobs that don’t seem to contribute to the overall picture. Today’s thoughts:

It’s been almost a year since I started at the University of Alaska Anchorage. I started with a completely empty space to house my fish, and an almost completely empty bench. I was very fortunate to hire my postdoc, Dr. Emily Lescak, who started shortly after I did. Together we stuffed my bench with everything we would need to look at microbes, measure the development and isolate DNA from fish, and analyze the host immune responses to microbes.  Our very first undergraduate student, Brianna Triplett from my hometown (hopefully I’ll be able to talk about what it means to me to be able to have students from Alaska work with me), helped us clean, organize, and collect our first bits of data while taking a challenging course load.

In addition to building up a lab, we built a working fish facility from scratch. We were extremely lucky to be able to use a pre-fab rack from a generous PI at UAA, Dr. Tim Hinterberger, for raising fish from embryos through the juvenile stage; however, we needed larger tanks for adults. We haggled with makers of fish racks until we realized there was no way we were going to be able to afford to purchase enough racks for two rooms and decided to build our own. This wouldn’t have been possible without the help of Mark Currey, who works with Dr. Bill Cresko at the University of Oregon, and the countless phone calls and emails that he answered and photos he shared. We were also fortunate to have a tech in the vivarium, Joyce, who had experience putting together pipes and working with fish. Soon-to-be graduate student, Ryan Lucas, and patient and hard-working undergraduates, Koral Campbell, Kenneth Sparks, and Kelly Ireland, worked with Joyce, myself and Emily to put the shelves together, design piping and filtration systems, and glue and cut countless pipes. We are almost done with 4 racks, and are starting to work on our second fish facility room. Our large tanks for recirculating water just arrived today and are awaiting cleaning and assembly in the facility.

Spring brought our first germ free fish experiments in the lab, which is very important for a lab that studies host-microbe interactions! It was our first big experiment that was done almost completely in our lab (huge thanks to Mark and Bill for sharing their fish!). Our undergraduate student Keagan Whitcomb has been diligently taking measurements from various images we have from the fish, and we hope to present that data soon.


Making our first germ free fish!

In Alaska, spring and summer are prime times for harvesting food to last through the winter. In the lab this year, spring and early summer were prime times for collecting the data and materials we will analyze through the rest of the summer, fall and winter. We were able to collect fish and water samples from 4 different populations, and produce eggs for experiments from three different populations. Our collaborator, Dr. Brandon Briggs from UAA, will help us isolate DNA and characterize the microbes in the water, which we can then compare to the microbes in the guts of our stickleback. So many comparisons ahead!

IMAG3121 Gary and Koral take notes and pictures as Emily collects fishIMAG3436

A busy day in the lab! From left to right, Ryan examines colonies isolated on plates, Koral puts away new plates she poured, high school Hutton awardee Gary characterizes colonies from stickleback guts, and Kenneth examines microbial colonies under the microscope. (BTW, I put together that microscope!)


From top to bottom: Gary, Koral, Ryan and Emily isolate microbes from water and gut samples on a packed bench

In June we sadly watched Dr. Frank von Hippel pack his lab and ship it to it’s new home at Northern Arizona University. Dr. von Hippel has been an important mentor my first year here, as he was the only other stickleback researcher on campus and one of the few researchers in the state of Alaska to have a highly coveted RO1 grant from NIH. He was also a wonderful graduate mentor to Emily and undergraduate mentor to Ryan. He was very kind to introduce me to several stickleback researchers from other universities, as my lab will be the new Alaska contact for several researchers who study Alaskan stickleback populations. We started a collaborative research project with Dr. von Hippel before he left. We hope will turn into a productive and interesting project in the years to come.

It’s been a productive and busy year. A huge thank you to all everyone in our lab for their hard work, our collaborators at UAA and UO, and future collaborators who have been helping me put together ideas!

May 2016: Funding and summer plans

We are excited to have been chosen as mentors for the American Fisheries Society’s Hutton Program. An Anchorage high school student will be working with us this summer on metagenomic data analysis.

Masters student Ryan Lucas has received an Alaska INBRE graduate student fellowship to study the effects of clinical levels of antibiotics on microbial community composition and immune response in stickleback. Ryan started working in the lab mid-May, and is hard at work developing new assays for the lab.

Postdoc Emily Lescak has received an NSF Broadening Participation postdoctoral fellowship to study the effects of environmentally-relevant levels of antibiotics on microbial community composition and development in stickleback.

Lab Members on the Road!

Kat gave a talk to the University of Alaska Biomedical Research Conference (UABRC) in Fairbanks Alaska in May 2016, and will be giving a talk at the Evolution Meeting in Austin Texas in June.

Emily will be attending ECOGEO‘s Training Workshop for early career researchers in ‘omics in Honolulu in July. This two day workshop will help Emily apply bioinformatic methods and tools to environmental ‘omics data experimental design and processing.

High school volunteer Foster was accepted into the Research Institute at MIT this summer. Foster will work on biostats heavy projects with MIT researchers for several weeks.

Stickleback as a model to study host-microbe interactions

Gut doodle 2015

Welcome to our lab!  Our lab is interested how the genetic background of the host influences the relationship between microbes and the hosts with which they interact.

We adapted the heterogenetic threespine stickleback (Gasterosteus aculeatus) fish for host-microbe studies. Threespine stickleback exhibit genetic variability both within and between populations that inhabit diverse environments, making them appropriate model organisms for studying how environment and genetic variation shape host-microbe interactions. This species is a well-established model for understanding evolution, ecosystem dynamics, development, and the impact of environmental contaminants on physiology.   

We developed a gnotobiotic stickleback model to manipulate the microbial environment in which the fish develop, and discovered that the genetic background of the host contributes to the intensity of the innate immune response to microbiota. Our lab now focuses on determining the mechanisms underling these differences, and identifying other phenotypes that are influenced by gene by environment interactions.