Masters of Science in Microbiology student, Marissa Kinney, will be joining the 2023/2024 cohort of graduate students in the Initiative for One Health and the Environment group at UMaine, as she was awarded a fellowship through the group’s NSF NRT funding. She’ll be using this fellowship to cross-train in other research disciplines, and explore the economic and social factors concerning people with Inflammatory Bowel Diseases, alongside One Health co-mentor Dr. Mario Teisl, Director and Professor of the School of Economics.
Marissa joins fellow Ishaq Lab grad student, Lola Holcomb, who was awarded a fellowship by the group and started with the 2022/2023 cohort.
Marissa Kinney
Master of Science student, Microbiology and Animal and Veterinary Sciences
Blurb: Marissa is a Masters student who loves learning and bench microbiology. She completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology. She devoted a large portion of her time in undergrad to research in the laboratories of Dr. Julie Gosse and Dr. Edward Bernard. Since graduating, she worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center, collecting and processing data about violent and drug-related deaths in Maine. While her role at the Center was one she loved dearly, she feels a big pull towards laboratory work and academic research. She recently joined the Ishaq lab and is excited by the new opportunities this position brings.
Marissa was awarded a One Health and the Environment NRT Fellowship 2023 – 2024 at UMaine.
Now, working in my lab, Marissa is focusing on the microbial communities in the gastrointestinal tract, and particularly in the context of broccoli sprouts in the diet and how certain gut bacteria can use them to create an anti-inflammatory compound of interest. She has been developing new protocols for using growth curve analyses and genomic assays (quantitative PCR) to identify bacteria with the capacity to use broccoli sprouts to create anti-inflammatories along different location in the gut, and under difference health or disease states. Over the next few years, she’ll also be learning DNA sequencing library preparation and data analysis, working with human subjects in a diet trial, performing experiments using mice as a model for humans, and a variety of microbiology, genomic, and biochemical laboratory techniques. Marissa’s project is part of a much larger collaborative on the use of dietary broccoli sprouts to resolve symptoms in Inflammatory Bowel Disease patients. As part of that larger collaboration, Marissa will be meeting regularly with the various parts of the project team, including students and researchers at 4 different institutions, and helping on three different projects in the lab to build her skillset. This requires a high degree of organization and coordination, and Marissa immediately stepped into her role.
To expand the lab’s existing work on human gut microbiomes, Marissa will use the NRT training and knowledge base as an opportunity to learn techniques in social sciences and economics. IBD is highly impactful on the wellbeing of people experiencing it acutely or chronically, and there is a large social and economic burden, as well. While any IBD patient could already consume broccoli to potentially receive benefit, nuances in how gut microbes respond to diet, and fears about exacerbating symptoms, preclude this. Being able to understand dietary behaviors, and assess the economic impact of a whole-food palliative strategy, would allow us to better implement our dietary intervention.
Spring 2023; January 18 – May, Wednesdays from 11:00 AM – 12:00 PM EST.
Presented over Zoom.
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
The environment, microbes, and us
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
“Religion, Race and the Microbe: Theological Analysis of Public Health Resistance in the Pandemicine”
May 3, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed, watch the recording here.
Dr. Bradford is a research scholar in NC State’s Public Science Lab for Ecology, Evolution and Biodiversity of Humans and Food where she draws together interdisciplinary engagement of microbes, exploring fermentation, probiotic health and pathogens. Dr. Bradford is also a college Chaplain at Salem Women’s College, and Director of the Center for Contemporary Practice and Wellbeing. Working at the intersections of religion, microbiology, ecology and race, Dr. Bradford’s research investigates the historical entanglement of disease theories, public health strategy, Christian thought, and coloniality to cultivate ecological wisdom, scientific engagement and the pursuit of environmental justice in religious contexts. She asks questions like, how have the historical entanglement of epidemiology, coloniality and Christian teaching contributed to the disease of both body and planet, the disproportionate effects of which are born by black and brown communities? How has demonizing the microbe paved the way for oppression of those deemed sub-human? And how might microbiome science reform Christian thought that often disrupts engagement of science and is complicit in exploitative and exclusionary ways of being?
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Panel Discussion on the Soil and Microbial Conservation
April 26, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed and was not recorded.
This week, we’ll be bringing some speakers back to engage in a panel discussion together on the importance of environmental microbiomes and specifically on soil conservation.
Panel will be hosted byMallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Panel Discussion on the Soil and Microbial Conservation
April 26, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed and was not recorded.
This week, we’ll be bringing some speakers back to engage in a panel discussion together on the importance of environmental microbiomes and specifically on soil conservation.
Panel will be hosted byMallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
A collaborative paper on lobster shell bacteria has just been published in the journal iScience: “Water temperature and disease alters bacterial diversity and cultivability from American Lobster (Homarus americanus) shells.” This paper investigates what happens to bacterial communities on healthy and sick lobsters as they experience different water temperatures for a year.
I joined this project back in the summer of 2020, towards the end of my first year at UMaine, when I was given a large 16S rRNA gene sequence dataset of bacterial communities from the shells of lobsters. I had been asking around for data as a training opportunity for Grace Lee, who at the time was an undergraduate at Bowdoin College participating in the abruptly cancelled summer Research Experience for Undergrads program at UMaine in summer 2020. Instead, Grace joined my lab as a remote research assistant and we worked through the data analysis over the summer and fall. Grace has since graduated with her Bachelor’s of Science in Neuroscience, obtained a Master’s of Science at Bowdoin, and is currently a researcher at Boston Children’s Hospital while she is applying to medical school.
My first point of contact on the project was Jean MacRae, an Associate Professor of Civil and Environmental Engineering at UMaine, who was the one to lend me the data and who had been working on bacterial community sequencing on other projects which I’ve been involved in. Jean has been involved with MSE, and this is our fourth publication together making her the collaborator at UMaine I have co-authored with the most (although it is a tight race 🙂 ).
Jean introduced me to the original research team, including Debbie Bouchard, who is the Director of the Aquaculture Research Institute and was researching epizootic shell disease in lobsters for her PhD dissertation several years ago; Heather Hamlin, Professor and Director of the School of Marine Sciences; Scarlett Tudor (not pictured), the Education and Outreach Coordinator at the ARI; and Sarah Turner (not pictured), Scientific Research Specialist at ARI. The ARI team is involved in a lot of large-scale aquaculture research, education, and outreach to the industry here in Maine, and the collaborative work I have been doing with them has been a new an engaging avenue of scientific study for me.
In 2022, the research team, along with social science Masters student Joelle Kilchenmann, published a perspective/hypothesis piece which explored unanswered questions about how the movement of microbes, lobsters, and climate could affect the spread of epizootic shell disease in lobsters off the coast of Maine. That perspective paper was a fun exercise in hypothesis generation and asking ‘what if’?
This manuscript is more grounded, and features work that was started in 2016. It examines bacterial communities on the shells of lobsters which were captured off the coast of Southern Maine and maintained in aquarium tanks for over a year. The lobsters were split into three treatment groups: those which were kept in water temperatures that mimicked what they would experience in Southern Maine, colder water to simulated what they would experience in Northern Maine, and hotter water to simulate what they would experience in Southern New England over that year. The original project team wanted to know if temperatures would make a different to their health or microbial communities.
Figure S8. Water temperature regimes, related to STAR Methods. A. Temperatures were obtained through the National Oceanographic Data Center (NODC). NODC temperatures reflect those recorded near Eastport, ME (A); Portland, ME (B); and an average of temperatures from Woods Hole, MA (C) and New Haven, CT (D) was used to represent Southern New England. B. Annual temperature cycles used in this project to represent Southern New England (SNE), Southern Maine (SME) and Northern Maine (NME).
The original project team swabbed lobster shells to obtain bacteria to try and grow in the lab, as well as DNA to sequence and identify whole bacterial communities. Grace and I performed the data analysis to identify which taxa were present in those communities, what happened over time or when the water temperature changed, and what bacteria were present or not in lobsters which died during the study.
Figure S11. Lobster carapace sampling using a sterile cotton swab to obtain bacterial communities from the shell surface, related to STAR Methods. The right side of the dorsolateral area of the cephalothorax was sampled for the baseline sampling, the left side for the Time 1, and the right side again for Time 2.
In addition to wanting to know about temperature, we wanted to know specifically how temperature would affect the bacteria if the lobsters had epizootic shell disease. It is not known what causes epizootic shell disease (which is why it is called ‘epizootic’), but it manifests as pitting in the shells of lobsters. Over time, the pitting can weaken shells and make it difficult for the lobster to molt, or make the lobster susceptible to predators or microbial infections. This type of shell disease had been a huge problem in Southern New England over the past few decades, and in Maine we have seen more cases over time.
Figure S10. Examples of lobster shell disease indices, related to STAR Methods. A) 0, no observable signs of disease, B) 1+, shell disease signs on 1-10% of the shell surface, C) 2+, shell disease signs on 11-50% of the shell surface, D) 3+, shell disease signs on > 50% of the shell surface.
The highlights of this project are here, but you can click the link below to read the entire study and what happened to lobster health and lobster microbes over time.
Shell bacteria from healthy lobsters, often overlooked, were included in the study.
Hotter and colder water temperatures affected shell bacterial communities.
Epizootic shell disease reduced bacterial diversity on lobster shells.
Epizootic shell disease could be induced or exacerbated by the loss of commensal bacteria from shells.
Suzanne L. Ishaq1,2,, Sarah M. Turner2,3, Grace Lee4,5,M. Scarlett Tudor2,3, Jean D. MacRae6, Heather Hamlin2,7, Deborah Bouchard2,3
1 School of Food and Agriculture; University of Maine; Orono, Maine, 04469; USA.
2 Aquaculture Research Institute; University of Maine; Orono, Maine, 04469; USA.
3 Cooperative Extension; University of Maine; Orono, Maine, 04469; USA.
4 Department of Neuroscience, Bowdoin College, Brunswick, ME 04011; USA.
5 Boston Children’s Hospital, Boston, MA 02115; USA.
6 Department of Civil and Environmental Engineering; University of Maine; Orono, Maine, 04469; USA.
7 School of Marine Sciences; University of Maine; Orono, Maine, 04469; USA.
Summary
The American lobster, Homarus americanus, is an economically valuable and ecologically important crustacean along the North Atlantic coast of North America. Populations in southern locations have declined in recent decades due to increasing ocean temperatures and disease, and these circumstances are progressing northward. We monitored 57 adult female lobsters, healthy and shell-diseased, under three seasonal temperature cycles for a year, to track shell bacterial communities using culturing and 16S rRNA gene sequencing, progression of ESD using visual assessment, and antimicrobial activity of hemolymph. The richness of bacterial taxa present, evenness of abundance, and community similarity between lobsters was affected by water temperature at the time of sampling, water temperature over time based on seasonal temperature regimes, shell disease severity, and molt stage. Several bacteria were prevalent on healthy lobster shells but missing or less abundant on diseased shells, although some bacteria were found on all shells regardless of health status.
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
The environment, microbes, and us
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
“Soil health – towards a ‘microbial agriculture’?“
Dr. Anna Krzywoszynska, PhD. and Paula Palanco Lopez
April 19, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed, watch the recording here.
Abstract: Soils have long been considered primarily through a physico-chemical lens in agriculture and environmental management. Today, however, we are observing a shift towards ecological perspectives, and a growing interest from managing soil quality to managing soil health. What does it mean, however, to know and manage soils as living microbial ecosystems, and what are the consequences of a ‘soil health’ paradigm for the future of agriculture? In this presentation, Dr Krzywoszynska will reflect on the relevance of microbial knowledges and ethics in the emerging regenerative agriculture movement, and in biodiversity governance, while her PhD student Paula Palanco Lopez will reflect on the importance of understanding ‘soil health’ in its own terms, beyond anthropocentric and utilitarian framings.
Dr. Anna Krzywoszynska is an Associate Professor in Anthropology at the University of Oulu, and a research leader in the Biodiverse Anthropocenes programme (Anna Krzywoszynska | University of Oulu). She is an interdisciplinary environmental social scientist with expertise in agricultural and environmental knowledge, more-than-human research, and public participation in science. Her current research interests include human-soil relations and knowledge systems, the co-production of soil knowledge between science and society, and the role of local food systems in achieving socio-environmental justice.
Paula Palanco is a medical anthropologist with a background in Development Studies and Communication. She has completed an Advanced Masters in Cultural Anthropology and Development Studies in KULeuven (Belgium) and worked for the London School of Hygiene and Tropical Medicine (LSHTM), the University of Oxford, and Imperial College London. Paula has carried out research in different topics such as antimicrobial resistance (AMR), air monitoring and cholera epidemics. Currently, she is a PhD candidate in the University of Oulu (Finland), researching the connection between the loss of soil biodiversity and AMR.
Soils have long been considered primarily through a physico-chemical lens in agriculture and environmental management. Today, however, we are observing a shift towards ecological perspectives, and a growing interest from managing soil quality to managing soil health. What does it mean, however, to know and manage soils as living microbial ecosystems, and what are the consequences of a ‘soil health’ paradigm for the future of agriculture? In this presentation, Dr Krzywoszynska will reflect on the relevance of microbial knowledges and ethics in the emerging regenerative agriculture movement, and in biodiversity governance, while her PhD student Paula Palanco Lopez will reflect on the importance of understanding ‘soil health’ in its own terms, beyond anthropocentric and utilitarian framings.
Panel Discussions on the environment, microbes, and us
These two weeks, we’ll be bringing some of our Theme 3 speakers back to engage in a panel discussion together on the importance of environmental microbiomes and our place in ecosystems, and then will continue talking about soil health. Panel will be hosted byKatherine Daiy, Kieran O’Doherty, Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
The environment, microbes, and us
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
“Soil health – towards a ‘microbial agriculture’?“
Dr. Anna Krzywoszynska, PhD. and Paula Palanco Lopez
April 19, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed, watch the recording here.
Abstract: Soils have long been considered primarily through a physico-chemical lens in agriculture and environmental management. Today, however, we are observing a shift towards ecological perspectives, and a growing interest from managing soil quality to managing soil health. What does it mean, however, to know and manage soils as living microbial ecosystems, and what are the consequences of a ‘soil health’ paradigm for the future of agriculture? In this presentation, Dr Krzywoszynska will reflect on the relevance of microbial knowledges and ethics in the emerging regenerative agriculture movement, and in biodiversity governance, while her PhD student Paula Palanco Lopez will reflect on the importance of understanding ‘soil health’ in its own terms, beyond anthropocentric and utilitarian framings.
Dr. Anna Krzywoszynska is an Associate Professor in Anthropology at the University of Oulu, and a research leader in the Biodiverse Anthropocenes programme (Anna Krzywoszynska | University of Oulu). She is an interdisciplinary environmental social scientist with expertise in agricultural and environmental knowledge, more-than-human research, and public participation in science. Her current research interests include human-soil relations and knowledge systems, the co-production of soil knowledge between science and society, and the role of local food systems in achieving socio-environmental justice.
Paula Palanco is a medical anthropologist with a background in Development Studies and Communication. She has completed an Advanced Masters in Cultural Anthropology and Development Studies in KULeuven (Belgium) and worked for the London School of Hygiene and Tropical Medicine (LSHTM), the University of Oxford, and Imperial College London. Paula has carried out research in different topics such as antimicrobial resistance (AMR), air monitoring and cholera epidemics. Currently, she is a PhD candidate in the University of Oulu (Finland), researching the connection between the loss of soil biodiversity and AMR.
Soils have long been considered primarily through a physico-chemical lens in agriculture and environmental management. Today, however, we are observing a shift towards ecological perspectives, and a growing interest from managing soil quality to managing soil health. What does it mean, however, to know and manage soils as living microbial ecosystems, and what are the consequences of a ‘soil health’ paradigm for the future of agriculture? In this presentation, Dr Krzywoszynska will reflect on the relevance of microbial knowledges and ethics in the emerging regenerative agriculture movement, and in biodiversity governance, while her PhD student Paula Palanco Lopez will reflect on the importance of understanding ‘soil health’ in its own terms, beyond anthropocentric and utilitarian framings.
Panel Discussions on the environment, microbes, and us
These two weeks, we’ll be bringing some of our Theme 3 speakers back to engage in a panel discussion together on the importance of environmental microbiomes and our place in ecosystems, and then will continue talking about soil health. Panel will be hosted byKatherine Daiy, Kieran O’Doherty, Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
The environment, microbes, and us
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
“Anthropology, Microbiomes, and Antimicrobial Resistance”
April 12, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed, watch the recording here.
Dr. Cecil Lewis is a Professor and biological and interdiscplinary scientist based at the University of Oklahoma. His primary research focus is the microbiome and community-engaged research, with current work that investigates ancient and contemporary human metabolomes, pathogen evolution, the impact of colonialism on the microbiome and metabolome, along with progressive community-based partnerships across the Americas and Africa. His work is supported by the NSF and NIH. He is the founder and director of Laboratories of Molecular Anthropology and Microbiome Research (LMAMR).
This week, we’ll be bringing all of our Theme 3 speakers back to engage in a panel discussion together on the importance of environmental microbiomes and our place in ecosystems, and then will continue talking about soil health. Panel will be hosted byKatherine Daiy, Kieran O’Doherty, Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
The UMaine Student Symposium is an annual event featuring research presentations from undergraduate and graduate students, and is a way to share student research on campus and with the Maine public.
All of the abstracts for the full program are available here.
The event is free to attend, and will take place at the Collins Center on the UMaine Orono Campus, Friday April 14, 2023.
Several students from the Ishaq Lab will be presenting their ongoing work:
Keagan Rice, Sydney Shair, Marissa Kinney, Sue Ishaq, Ayodeji Olaniyi, Ryan Wijayanayake, and Lola Holcomb at the 2023 UMaine Student Symposium.
“Early Life Exposure to Broccoli Sprouts Confers Stronger Protection against Enterocolitis Development in an Immunological Mouse Model of Inflammatory Bowel Disease“
Hosting Organizations: MSE and the University of Maine Institute of Medicine.
The environment, microbes, and us
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
“Anthropology, Microbiomes, and Antimicrobial Resistance”
April 12, 2023; Wednesday,11:00 AM – 12:00 PM EST. This event has passed, watch the recording here.
Dr. Cecil Lewis is a Professor and biological and interdiscplinary scientist based at the University of Oklahoma. His primary research focus is the microbiome and community-engaged research, with current work that investigates ancient and contemporary human metabolomes, pathogen evolution, the impact of colonialism on the microbiome and metabolome, along with progressive community-based partnerships across the Americas and Africa. His work is supported by the NSF and NIH. He is the founder and director of Laboratories of Molecular Anthropology and Microbiome Research (LMAMR).
This week, we’ll be bringing all of our Theme 3 speakers back to engage in a panel discussion together on the importance of environmental microbiomes and our place in ecosystems, and then will continue talking about soil health. Panel will be hosted byKatherine Daiy, Kieran O’Doherty, Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
The Ishaq Lab 