First first-authorship paper accepted for Olivia Choi from the Kamath Lab!

Olivia Choi, a doctoral candidate in the Kamath lab at the University of Maine, has had her first scientific paper accepted for which she is the first author – a position indicative of the amount of work and organization that she put into developing this work and wrangling the large research team involved. Olivia’s graduate work is winding down as she concentrates on writing up papers and her dissertation, and she is planning on defending her PhD and looking for a postdoc in 2022 in wild animal microbiomes and ecology.

Olivia brought this 16S rRNA dataset to use in my AVS590 data analysis class back in spring 2020, of bacterial communities in different locations on birds of different species, which had been sampled as part of her dissertation work on bird migration and range changes, microbial carriage, and risk of transmission of microbes to other animals. I mentored her through analysis and preliminary manuscript writing as part of that course. The research team generously invited me to join the author team, and I continued to provide mentorship as Olivia worked through the complex task of melding various types of microbiology data.


Choi, O., Corl, A., Lublin, A., Ishaq, S.L., Charter, M., Pekarsky, S., Thie, N., Tsalyuk, M., Turmejan, S., Wolfenden, A., Bowie, R.C.K., Nathan, R., Getz, W.M., Kamath, P.L. 2021. High-throughput sequencing for examining Salmonella prevalence and pathogen – microbiota relationships in barn swallows. Frontiers in Ecology and Evolution 9:681.

Abstract:

Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pathogenesis. Little is known about the effects of potential pathogens, such as Salmonella, on the microbiome in wildlife, which are known to play an important role in disease transmission. Recent studies have expanded the traditional use of 16S rRNA gene amplicon data from high-level characterization of host-associated microbial communities (i.e., the microbiome) to detection of specific bacteria. Few studies, however, have evaluated the ability of high-throughput 16S rRNA gene sequencing data to detect potential bacterial pathogens in comparison with laboratory culture-based methods. To address this knowledge gap, we evaluated the utility of 16S rRNA gene sequencing for potential pathogen detection and explored the relationship between potential pathogens and microbiota. First, we compared the detection of Salmonella spp. in barn swallows (Hirundo rustica) using 16S rRNA data with standard culture techniques. Second, we examined the prevalence of Salmonella using 16S rRNA data and examined the relationship between Salmonella presence or absence and individual host factors. Lastly, we evaluated host-associated bacterial diversity and community composition in Salmonella present versus absent birds. Out of 108 samples, we detected Salmonella in 6 (5.6%), 25 (23.1%), and 3 (2.8%) samples based on culture, unrarefied 16S rRNA gene sequencing data, and both techniques, respectively. In addition, we found that Salmonella presence and absence differed between birds based on migratory status and weight and that bacterial community composition and diversity differed between Salmonella present versus absent birds, with eleven bacterial taxa differentially abundant between the two groups. The results of this study highlight the value of high-throughput 16S rRNA gene sequencing data for bacterial pathogen detection and for examining relationships between potential pathogens and host-associated microbial communities. Further, this study emphasizes an approach using 16S rRNA gene sequencing data for simultaneously monitoring multiple pathogens in wild avian reservoirs, which is important for prediction and mitigation of disease spillover into livestock and humans. 

This work was presented at a recent scientific conference:

Choi*, O.N., Corl, A., Wolfenden, A., Lublin, A., Ishaq, S.L., Turjeman, S., Getz, W.M., Nathan, R., Bowie, R.C.K., Kamath, P.L. “High-throughput sequencing for examining Salmonella prevalence and pathogen -microbiota relationships in barn swallows.”  69th Annual – 14th Biennial Joint Conference of the Wildlife Disease Association & European Wildlife Disease Association. (virtual). Aug 31 – Sept 2, 2021.

Welcome new Ishaq Lab members!

It’s a new school year, and that means new members have joined the Ishaq Lab team – primarily undergraduates in Animal and Veterinary Sciences who are participating in research in fulfillment of their Capstone Experience senior projects. Over the next few months, we’ll be sharing more details about our new team members and their projects.

While UMaine is back on campus, not all of our students are local, so we had a hybrid meeting of in-person and Zoom attendees. We have members at Husson University in Bangor, Maine; Tufts University in Medford, Massachusetts; and Stony Brook University in Stony Brook, New York!

We use collaborative file sharing such as Google Drive, virtual meeting spaces like Zoom, and messaging platforms such as Slack for a few projects to facilitate our research and keep track of information. To help us connect more easily, and especially to help get everyone in my office on screen together, we’ll be adding more virtual conferencing equipment, too.

Most of the Ishaq Lab Fall 2021 team were able to make it to a Welcome Meeting recently.

Student point of view on researching microbes, flying squirrels, and mice around farms in Maine

Five women taking a photo together at a farm.  They are standing a few feet apart from each other, and standing in front of a cow feedlot with two cows eating.

This summer, a collaborative project was launched by the Ishaq Lab, Danielle Levesque, and Pauline Kamath at UMaine Orono and Jason Johnston at UMaine Presque Isle; “Climate Change Effects on Wild Mammal Ranges and Infectious Disease Exposure Risk at Maine Farms.”

Funded by the University of Maine Rural Health and Wellbeing Grand Challenge Grant Program, this project assesses pathogen carriage by mice and flying squirrels on or near farms in several locations in Maine. We live-capture mice and flying squirrels in traps, collect the poop they’ve left in the trap, and conduct a few other health screening tests in the field before releasing them. To maximize the information we collect while minimizing stress and interference to the animals, information is being collected for other projects in the Levesque Lab at the same time. We will be collecting samples for another few weeks, and then working on the samples we collected in the lab over the fall and winter.

One of the major goals of the funding program, and this project, is to engage students in research. After a few months on the project, some of our students describe their role and their experiences so far…


A close-up of a deer mouse sitting in a live capture trap in the forest.  In the background is one of the researchers kneeling on the ground.

Marissa Edwards

Undergraduate in Biology

Levesque Lab

Hi! My name is Marissa Edwards and I am an undergraduate research assistant with Danielle Levesque. This summer, my role has been to set traps, handle small mammals, and collect fecal and tissue samples from deer mice.

A pine marten sitting in a live capture trap in a forest.

One of the skills I’ve learned this summer is how to properly ear tag a mouse. To catch mice, we set traps across UMaine’s campus as well as other parts of Maine, including Moosehead Lake, Flagstaff Lake, and Presque Isle.

During our trip to Moosehead Lake, I saw a marten for the first time (it was in one of our traps). I did not know martens existed and initially thought it was a fisher cat. It was both a cool and terrifying experience!


Northern flying squirrel sitting on a net with a forest in the background.

Elise Gudde

Master’s Student of Ecology and Environmental Sciences

Levesque Lab

Hello, my name is Elise Gudde, and I am currently a master’s student at the University of Maine in the Ecology and Environmental Sciences program. I work in Dr. Danielle Levesque’s lab studying small mammal physiology in Maine.

Northern flying squirrel sitting on a net with a forest in the background.

This summer, as a part of the squirrel project, I work to trap small mammal species in Maine, such as white footed mice, deer mice, and flying squirrels in order to determine which species have shifted their range distributions as a result of climate change. Being a part of the research team, this summer has brought me all over Maine! I have been able to travel to Orono, Greenville, New Portland, and Aroostook County to study many interesting mammals. I even got to handle an Eastern chipmunk for the first time! As a member of the animal-handling side of the research team, I also collect fecal and tissue samples from the animals. These samples are then handed off for other members of the team to research in the lab!


Rebecca French wearing a white laboratory coat, a fabric face mask, and beige latex gloves while using a yellow plastic loop tool to spread bactrial cultures on fresh agar media plates to look for growth.  Rebecca is sitting at a biosafety cabinet with the glass window slide down between her and what she is working on.  Assorted scientific materials can be seen in the background.

Rebecca French

Undergraduate in Animal and Veterinary Sciences

Ishaq Lab

In the beginning of this project, I had no idea what I was getting myself into when I began researching flying squirrels and mice. I came into it with almost no in-person lab experience, so I had a lot to learn.

So far, I have been focusing on making media on petri dishes for culturing bacterial growth and after plating fecal bacteria on said plates; discerning what that growth can be identified as.

We are using media with specific nutrients, and colored dyes, and certain bacteria we are interested in will be able to survive or produce a color change. I have also been performing fecal flotations and viewing possible eggs and parasites under a microscope. What I’ve found most fun about this project is putting into practice what I have learned only in a classroom setting thus far. It is also very satisfying to be a part of every step of the project; from catching mice, to making media, to using that media to yield results and then to be able to have a large cache of information to turn it all into a full fledged project.


Joe Beale, posing for a photo in an open office space.

Joe Beale

Undergraduate in Animal and Veterinary Sciences

Kamath Lab

Hello! My name is Joseph Beale, and I am an undergraduate at the University of Maine working on the squirrel project as a part of my capstone requirement for graduation. My primary responsibility in this project is the molecular testing of samples obtained from the field. Primarily I will be working with ear punch samples taken from flying squirrels and field mice. DNA extracts from these field samples will be run via qPCR. The results of this qPCR will tell us if these squirrels are carrying any pathogens. 

The pathogens we will be testing for are those found in Ixodes ticks. The qPCR panel which we will be running the extracted DNA from the ear punches on tests for Borrelia burgdorferi, the causative agent of Lyme disease, Anaplasma phagocytophilum, the causative agent of anaplasmosis, and Babesia microti, the causative agent of Babesiosis. These pathogens and respective diseases discussed are all transmitted through Ixodes ticks. Deer ticks are the most common and famous of the Ixodes genus. The Ixodes genus encapsulates hard-bodied ticks. Along with deer ticks, Ixodes ticks found in Maine include: woodchuck ticks, squirrel ticks, mouse ticks, seabird ticks, and more. Mice and squirrel are ideal hosts for these Ixodes ticks, therefore becoming prime reservoirs for these diseases. In our research, we are interested in determining the prevalence of these diseases in squirrels and mice as these hosts can spread these diseases to humans and other animals in high tick areas. 

qPCR, quantitative polymerase chain reaction, allows for the quantification of amplified DNA in samples.  This will help tell us if these pathogens are present in samples and in what capacity. In qPCR provided DNA strands are added to the reaction. These strands match with the genome of the intended pathogens. If the pathogens are present in our samples, the provided DNA strands will bind to the present pathogen DNA. PCR will then work to manufacture billions of copies of this present pathogen DNA. 

When not working on this project, I also work in the University of Maine Cooperative Extension Diagnostic Research Laboratory as a part of the Tick Lab. In this position I have honed the molecular biology skills that I will in turn use for the squirrel project. 


Yvonne Booker

Undergraduate, Tuskeegee University

Levesque Lab

Microbes and the Mammalian Mystery“, reblogged from the University of Maine REU program.

Hello everyone! My name is Yvonne Booker and I am a rising senior, animal and poultry science major at Tuskegee University in Tuskegee, Alabama. I am interested in animal health research, with a particular focus in veterinary medicine. I’ve always wanted to be a veterinarian, but as I progressed throughout  college, I became interested in learning more about animal health and how I might help animals on a much larger and impactful scale–which led me to the REU ANEW program. Currently climate change is causing an increase in global temperatures, putting pressure on animals’ ability to interact and survive within their environment. Consequently, scientists are now attempting to understand not just how to prevent climate change, but how these creatures are adapting to this emerging challenge.

My research experience this summer is geared toward addressing this global issue. I am currently working in Dr. Danielle Levesque’s Lab, which aims to study the evolutionary and ecological physiology of mammals in relation to climate. My project involves conducting a literature review of the microbiome of mammals, to learn more about how their microbial community plays a role in how they adapt in a heat-stressed environment.

Our knowledge of vertebrate-microbe interactions derives partly from research on ectotherms. While this research paves the path for a better understanding of how organisms react to temperature changes, fewer studies have focused on how mammals deal with these extreme temperature shifts—specifically, the abrupt surge in climate change. The ability of endotherms to  thermoregulate alters our knowledge of (1) how mammals create heat tolerance against these environmental challenges and (2) how this internal process alters mammals’ adaptability and physiology over time. We suggest that the microbiome plays an essential part in understanding mammals’ heat tolerance and that this microbial community can help researchers further understand the various processes that allow mammals to survive extreme temperatures.

As a student of the REU ANEW program my goal was to go out of my comfort zone and study animals in an applied fashion that would impact animal health on an environmental and ecological scale; and this program was just that! My mentor, Dr. Levesque was wonderful in guiding me through conducting this research, while giving me the independence to create my own voice. The program directors, Dr. Anne Lichtenwalner and Dr. Kristina Cammen, have also  been extremely supportive throughout this entire program equipping students with the tools they need to succeed as researchers. Although research was my primary focus this summer, some of my favorite memories involved building community with the students and the staff. From weekly check-ins on zoom to virtual game nights of complete smiles and laughter, this program has been one for the books! The One Health and the Environment approach to this Research Experience for Undergraduate students has encouraged me to build on my curiosity within the field of science, and I’m looking forward to applying what I’ve learned to my career in the future.

Rumening through camel microbes, by Myra Arshad

Written by Myra Arshad

Myra Arshad

Did you know that camels have three stomach chambers or that they have to throw up their own food in order to digest their food properly? Have you felt excluded from science spaces before? Then this blog post is for you!

Allow me to introduce myself. 

My name is Myra, and I am a rising senior at SUNY Stony Brook University, where my major is Ecosystems and Human Impact, with a biology minor. In a nutshell, my major is interdisciplinary with a focus on conservation and ecology within human societies. 

If I were to describe my college experience in one word I’d pick “surprises”. I never actually saw myself being a scientist in my middle and high school years. I found it hard to care about abstract concepts or theories that felt so far removed from humanity, particularly minority communities. But, during college I found myself falling in love with environmental studies, and along with it, the beautiful complexities that come with being human in our increasingly anthropogenic world. 

At UMaine, we focus on the One Health Initiative, which views the health of humans, animals, and the environment as interconnected. When COVID-19 caused everyone to go into lockdown, I was fortunate to find this farm was looking for crew members, with a focus on food security. While certainly not how I planned to spend the summer of 2020, farming for underserved communities is where I saw how impactful One Health was. Organic farmers commonly use plastic mulch as a popular alternative to pesticides for weed suppression. At my home institution, I lead a project on the impacts of microplastics on earthworm health, an Ecotoxicology lab (students of the lab affectionately gave it the nickname “the Worm lab”).  We use earthworm health as an indicator of soil health, which in turn is crucial for crop flourishment. The Worm Lab and farming emboldened me to pursue science and, ergo, look for this REU! 

At UMaine, I am a member of the Ishaq Lab where I work on the camel metagenome project. Basically, scientists in Egypt raised camels on different diets, then used samples from their feces to sequence their microbial genome. These microbes live in the camel rumen (part of the camel stomach), and help the camel digest their food. What I do with Dr. Ishaq’s lab is, I perform data analysis on these sequences to see how the microbial gene profile changes with different diets. Camels are essential for transportation and food for the communities that rely on them, so finding the most efficient feed for them is important. Camels also release methane depending on their diet so it’s possible humans could control methane production of camels through their diet. 

Being a part of the REU ANEW program for 2021 definitely has been an interesting experience, since it is the first time this program has been conducted virtually. Even though I would have loved to have seen everyone in person and spent time in lovely Orono, Maine, I’m glad for the research opportunity as it has further solidified my love of research and the One Health initiative.

Myra’s poster for the REU Research Symposium, virtual, Aug 13, 2021.

Interview with WeTalkScience: animal microbiome

A few weeks ago, I sat down with Sheba A-J, one of the producers of the WeTalkScience podcast, to talk about one of my recent publications in the research journal iScience, at which Sheba is also an editor. Listen to find out how lobsters are like humans, how I got involved on a project working with ants and nematodes, and how you can help make science a more welcoming place.

The full publication is:

Ishaq, S.L., A. Hotopp, S. Silverbrand, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine. iScience 24(6):102663. Article.

Pilot project funded to study Vibrio bacteria in scallop farming

A collaborative pilot project was funded by the Maine Food and Agriculture Center (MFAC) to investigate Vibrio bacteria in scallop hatcheries in Maine! This will support some ongoing work by a collaborative research team at UMaine and the Downeast Institute, as we develop a long-term, larger-scale project investigating scallop health and survival in hatcheries, something which will be critical to supporting sustainable and economically viable aquaculture productions.

“Investigating microbial biofilms in Maine hatchery production of sea scallop, Placopecten magellanicus.”

Principal Investigator: Sue Ishaq

Co-Investigators:

  • Dr. Tim Bowden, Associate Professor of Aquaculture, University of Maine
  • Dr. Jennifer Perry, Assistant Professor of Food Microbiology, University of Maine
  • Dr. Brian Beal, Professor of Marine Ecology, University of Maine at Machias; and Research Director/Professor, Downeast Institute
  • Dr. Erin Grey, Assistant Professor of Aquatic Genetics, University of Maine

Project Summary: Atlantic deep-sea scallops, Placopecten magellanicus, are an economically important species, generating up to $9 million in Maine alone. Despite their potential to the aquaculture industry, hatchery-based sea scallop production cannot rely on the generation of larvae to produce animals for harvest. In hatcheries, the last two weeks of the larval maturation phase is plagued by massive animal death, going from 60 million scallop larvae down to a handful of individuals in a span of 48 hours. This forces farmed scallop productions to rely on collection of wild scallop spat (juveniles), but wild population crashes, habitat quality, harvesting intensity, and warmer water temperatures threaten the sustainability and economic viability of this industry. The reasons for sea scallop larvae death remain unknown, but other cultured scallop species are known to suffer animal loss from bacterial infections, including from several bacterial species of  Vibrio and Aeromonas. At the Downeast Institute in Beals, Maine, biofilms appear on tank surfaces within 24 hours. Routine screening for the presence of Vibrio sp. in tanks at DEI reveals no obvious signs of colonies in scallop tanks. Preliminary culturing and genetic identification from these biofilms suggests a species of Pseudoalteromonas, known biofilm formers which outcompete or inhibit other microorganisms. Our goal is to investigate the dynamics of tank surface biofilms in bivalve aquaculture facilities. Our long-term goals are to understand microbial community assembly and animal health during scallop hatchery production, and to standardize management practices to enhance the success of cultured scallop production.  

Experimental design schematic for this project. Our objectives are to 1) Identify the microbial community members involved in tank biofilms, and if it is a repeated or novel community assembly, and 2) Test for biofilm antagonism in vitro, using competing microorganisms, chemical treatments, and environmental conditions. 

“Healthcare and the microbiome” at the Microbes and Social Equity virtual symposium, June 18, 2021

The Microbes and Social Equity working group and The University of Maine Institute of Medicine present an inaugural symposium on:

“Microbes, Social Equity, and Rural Health”

June 14 – 18th, 2021

Format: virtual meeting, Zoom platform.

Day 1 of the Microbes and Social Equity virtual symposium

Session 5: “Access to healthcare and the microbiome”

Friday, June 18th, 13:00 ~ 16:30 EST. Registration for this session is closed.

Section leader: Emily Wissel

Access to healthcare, including treatment and preventative care, is critical to moderate beneficial host-microbe interactions and mitigate host-pathogen interactions, yet healthcare is inequitably distributed and often curbed by social policy. For instance, maternity care is well-demonstrated to improve health outcomes and facilitate the transfer of beneficial maternal microbes to newborns. Policies which support breastfeeding likewise promote this transfer of maternal microbes. Similarly, newborns and infants with access to care in their first five years of life have better outcomes overall than those with limited access. This difference in care during early life can impact lifelong differences in outcomes, reinforcing inequalities present at birth. This session will cover topics from the vaginal microbiome during pregnancy to the infant gut microbiome after birth, with perspectives from a clinician, public health researchers, and a biological scientist.

Program and Registration

Registration, a full speaker list and program, and details of each day can be found here.

Registration will occur for each (day) section individually, so participants can select which topics to participate in, or all of them. 

Registration is free and open to the public.

Summary

Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic, medical, or political constraints that restrict available choices that may impact our health.   

Many human clinical conditions or diseases have been established as being related  to the state of the human microbiome.  It is known that collective social inequity can drive the prevalence, morbidity, and mortality of some of these diseases or conditions. When access to a nutritious  diet and healthcare are impeded by social inequity, these disparities can also affect the human microbiome; this can further contribute to reduced or poorly functioning microbiomes. 

Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. The emergence of the SARS-CoV2 (COVID-19) pandemic has dramatically altered our daily lives and the availability and ability to access essential resources, which has been worsened by pre-existing social inequity. Yet, the pandemic has also highlighted the inherent social disparity among those more likely to be exposed to infectious diseases.  

This meeting highlights recent investigations into beneficial and detrimental instances of microbial exposure, in the context of how social policy may mediate or deepen disparities between and within populations. In addition to invited presentations on thematic sections, each section will involve a discussion session using smaller breakout groups, to facilitate conversations and brainstorming between attendees.  These groups will be arranged around smaller themes or research questions, and group members will identify knowledge gaps for future research, as well as list actionable steps that can be taken using existing research to promote equitable social policy.  Ideally, meeting attendees will gain knowledge, collaborators and connections, and a path forward for turning their research into evidence-based policy to support public health.

Meeting dynamics

Unlike traditional symposium formats, this meeting will present some plenary-style talks by experts in the field, including biological scientists, social scientists, practitioners or policy makers, as well as facilitate discussion among participants. Each thematic section will feature 90 minutes of talks, which will be recorded and made publicly available after the live session.  After each plenary session, there will be 90 minutes of discussion in groups led by speakers and MSE group members, and assisted by notetakers, with ~10 participants per breakout room. Participants will be encouraged to “problem solve” a suggested topic or one of their own choosing.  The goal is to create action items that are meaningful for group participants, such as ideas for curricula development, identifying research needs or best practices, suggestions for engaging research in policy, and more.

“Stress and the microbiome” at the Microbes and Social Equity virtual symposium, June 17, 2021

The Microbes and Social Equity working group and The University of Maine Institute of Medicine present an inaugural symposium on:

“Microbes, Social Equity, and Rural Health”

June 14 – 18th, 2021

Format: virtual meeting, Zoom platform.

Day 1 of the Microbes and Social Equity virtual symposium

Session 4: “Social and Environmental Stress”

Thursday, June 17th, 13:00 ~ 16:30 EST.   Registration for this session is closed.

Section leader: Patricia Wolf

While it has been established that human behavior may impact microbiome structure, it has become evident that this is only part of the story. Historically racist housing policies may lead to inequitable exposure of those living in segregated neighborhoods to environmental pollutants. Additionally, life-long exposure to social and environmental stress faced by minority groups within the US may increase risk to disease through the alteration of host and bacterial metabolites. These inequities were compounded during the COVID-19 pandemic, during which neighborhood structural environments led to differing access to healthcare and treatment for the disease. Notably, those with the least access often were subject to higher exposure to the disease due to having “essential” employment. This session will explore the social and environmental factors that can impact human microbiomes, and will discuss measures that investigators should incorporate into research in order to fully understand microbial mechanisms of disease.

Program and Registration

Registration, a full speaker list and program, and details of each day can be found here.

Registration will occur for each (day) section individually, so participants can select which topics to participate in, or all of them. 

Registration is free and open to the public.

Summary

Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic, medical, or political constraints that restrict available choices that may impact our health.   

Many human clinical conditions or diseases have been established as being related  to the state of the human microbiome.  It is known that collective social inequity can drive the prevalence, morbidity, and mortality of some of these diseases or conditions. When access to a nutritious  diet and healthcare are impeded by social inequity, these disparities can also affect the human microbiome; this can further contribute to reduced or poorly functioning microbiomes. 

Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. The emergence of the SARS-CoV2 (COVID-19) pandemic has dramatically altered our daily lives and the availability and ability to access essential resources, which has been worsened by pre-existing social inequity. Yet, the pandemic has also highlighted the inherent social disparity among those more likely to be exposed to infectious diseases.  

This meeting highlights recent investigations into beneficial and detrimental instances of microbial exposure, in the context of how social policy may mediate or deepen disparities between and within populations. In addition to invited presentations on thematic sections, each section will involve a discussion session using smaller breakout groups, to facilitate conversations and brainstorming between attendees.  These groups will be arranged around smaller themes or research questions, and group members will identify knowledge gaps for future research, as well as list actionable steps that can be taken using existing research to promote equitable social policy.  Ideally, meeting attendees will gain knowledge, collaborators and connections, and a path forward for turning their research into evidence-based policy to support public health.

Meeting dynamics

Unlike traditional symposium formats, this meeting will present some plenary-style talks by experts in the field, including biological scientists, social scientists, practitioners or policy makers, as well as facilitate discussion among participants. Each thematic section will feature 90 minutes of talks, which will be recorded and made publicly available after the live session.  After each plenary session, there will be 90 minutes of discussion in groups led by speakers and MSE group members, and assisted by notetakers, with ~10 participants per breakout room. Participants will be encouraged to “problem solve” a suggested topic or one of their own choosing.  The goal is to create action items that are meaningful for group participants, such as ideas for curricula development, identifying research needs or best practices, suggestions for engaging research in policy, and more.

Illustrated image of a cross section of the ground. A light brown ant is pictured in the ground along with a microbe. Text to the left of the image reads, "Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?". The names of six professors are listed below the text and image at the bottom left. In the bottom right corner, text reads, "The University of Maine" with "The University of Arizona" below it.

Paper published on bacterial transfer in insects and possible ecological impacts.

A collaborative paper on bacterial transfer in insects and the possible ecological impacts of that in the wild has been published in iScience! This work began a decade ago in the labs of Dr. Ellie Groden, recently retired Professor of Entomology in the School of Biology and Ecology at the University of Maine, and later Dr. Patricia Stock, a Professor in the School of Animal and Comparative Biomedical Sciences at the University of Arizona, who were investigating colony collapse of European fire ants (Myrmica rubra) which are invasive to Maine. The ants have a nasty bite, and can dramatically disturb the local plant and insect wildlife in coastal Maine.

Slide from Ishaq et al. Entomology 2020 presentation

When these invasive ant colonies collapsed, Drs. Groden and Stock wanted to find out why, as a possible means of developing a biological control strategy. It was thought that particular nematodes would ingest soil bacteria, and transfer it to ants once the worms invaded ant tissues to complete parts of their life cycle. This particular worm infection doesn’t kill the ants, but perhaps the soil bacteria were. Ants were collected from different colony sites, and investigations on the nematode worms inhabiting the ants were conducted.

Slide from Ishaq et al. Entomology 2020 presentation

Most of the work for this project was completed several years ago, with the exception of DNA sequencing data from a bacterial transfer experiment. I was added to the project by my collaborator at UMaine, Dr. Jean MacRae, an Associate Professor in the Department of Civil and Environmental Engineering who introduced me to the research team and shared the 16S rRNA dataset to use in my AVS 590 data analysis class in spring 2020. That semester was when the pandemic hit, and forced the course to move to remote-only instruction in March. UMaine graduate students Alice Hotopp and Sam Silverbrand were taking the class and learning 16S analysis on this dataset, and I mentored them through the analysis all the way to manuscript writing despite the incredible challenges that spring threw our way.

At the completion of the course, we shared the draft manuscript with the rest of the research team, who mentioned that several undergraduate honor’s theses had been written about the earlier experiment, but never published in a scientific journal. The team spent summer 2020 combining the three papers into one massive draft. The pandemic slowed down manuscript review, understandably, but I’m pleased to say that it was accepted for publication! In addition, this collaboration has led to further collaborations in the Ishaq Lab, several presentations (listed below), and is Sam’s first scientific publication, congrats Sam!!

Related Presentations

Alice Hotopp, A., Samantha Silverbrand, Suzanne L. Ishaq, Jean MacRae, S. Patricia Stock, Eleanor Groden. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?Ecological Society of America 2021 (virtual). Aug 2-6, 2021 (accepted poster).

Ishaq*, S.L., Hotopp, A., Silverbrand, S.,   MacRae, J.,  Stock, S.P.,  Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Entomological Society of America 2020 (virtual). Nov 15-25, 2020. (invited talk)

Illustrated image of a cross section of the ground. A light brown ant is pictured in the ground along with a microbe. Text to the left of the image reads, "Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?". The names of six professors are listed below the text and image at the bottom left. In the bottom right corner, text reads, "The University of Maine" with "The University of Arizona" below it.

IshaqS.L., A. Hotopp2, S. Silverbrand2, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal MaineiScience. In press. Impact 5.08.

Abstract

The necromenic nematode Pristionchus entomophagus has been frequently found in nests of the invasive European ant Myrmica rubra in coastal Maine, United States, and may contribute to ant mortality and collapse of colonies by transferring environmental bacteria. Paenibacillus and several other bacterial species were found in the digestive tracts of nematodes harvested from collapsed ant colonies. Serratia marcescens, Serratia nematodiphila, and Pseudomonas fluorescens were collected from the hemolymph of nematode-infected wax moth (Galleria mellonella) larvae.

Virulence against waxworms varied by site of origin of the nematodes. In adult nematodes, bacteria were highly concentrated in the digestive tract with none observed on the cuticle. In contrast juveniles had more on the cuticle than in the digestive tract. .  Host species was the primary factor affecting bacterial community profiles, but Spiroplasma sp. and Serratia marcescens sequences were shared across ants, nematodes, and nematode-exposed G. mellonella larvae. 

“Natural resources and the microbiome” at the Microbes and Social Equity virtual symposium, June 16, 2021

The Microbes and Social Equity working group and The University of Maine Institute of Medicine present an inaugural symposium on:

“Microbes, Social Equity, and Rural Health”

June 14 – 18th, 2021

Format: virtual meeting, Zoom platform.

Day 1 of the Microbes and Social Equity virtual symposium

Session 3: “Natural resources and access to environmental microbes”

Wednesday, June 16th, 13:00 ~ 16:00 EST.  Registration for this session is closed.

Section leader: Gwynne Mhuireach

The relationship between health and greenspace is well-established. There is also a recognized association between social equity and distribution of greenspace in many cities—parks are often larger, higher quality, and more prevalent in higher-income, upper-class neighborhoods; private yards and gardens are a luxury sometimes inaccessible to lower-income households; even street trees tend to be older, larger, and more numerous in higher income neighborhoods. New evidence shows that exposure to microbial diversity may be an important ecosystem service provided by urban greenspace, as exposure to greater microbial diversity early in life is related to lower prevalence of autoimmune disorders, such as allergies and asthma. This session will explore how environmental justice can be used to resolve health, microbial, and land access disparities.

Program and Registration

Registration, a full speaker list and program, and details of each day can be found here.

Registration will occur for each (day) section individually, so participants can select which topics to participate in, or all of them. 

Registration is free and open to the public.

Summary

Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic, medical, or political constraints that restrict available choices that may impact our health.   

Many human clinical conditions or diseases have been established as being related  to the state of the human microbiome.  It is known that collective social inequity can drive the prevalence, morbidity, and mortality of some of these diseases or conditions. When access to a nutritious  diet and healthcare are impeded by social inequity, these disparities can also affect the human microbiome; this can further contribute to reduced or poorly functioning microbiomes. 

Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. The emergence of the SARS-CoV2 (COVID-19) pandemic has dramatically altered our daily lives and the availability and ability to access essential resources, which has been worsened by pre-existing social inequity. Yet, the pandemic has also highlighted the inherent social disparity among those more likely to be exposed to infectious diseases.  

This meeting highlights recent investigations into beneficial and detrimental instances of microbial exposure, in the context of how social policy may mediate or deepen disparities between and within populations. In addition to invited presentations on thematic sections, each section will involve a discussion session using smaller breakout groups, to facilitate conversations and brainstorming between attendees.  These groups will be arranged around smaller themes or research questions, and group members will identify knowledge gaps for future research, as well as list actionable steps that can be taken using existing research to promote equitable social policy.  Ideally, meeting attendees will gain knowledge, collaborators and connections, and a path forward for turning their research into evidence-based policy to support public health.

Meeting dynamics

Unlike traditional symposium formats, this meeting will present some plenary-style talks by experts in the field, including biological scientists, social scientists, practitioners or policy makers, as well as facilitate discussion among participants. Each thematic section will feature 90 minutes of talks, which will be recorded and made publicly available after the live session.  After each plenary session, there will be 90 minutes of discussion in groups led by speakers and MSE group members, and assisted by notetakers, with ~10 participants per breakout room. Participants will be encouraged to “problem solve” a suggested topic or one of their own choosing.  The goal is to create action items that are meaningful for group participants, such as ideas for curricula development, identifying research needs or best practices, suggestions for engaging research in policy, and more.