Upcoming talk at the 9th Southern California Microbiome Symposium in September!

I’m ecstatic to be heading back to southern California this September to present at the 9th annual Southern California Microbiome Symposium. I’ll be sharing my work on microbes and social equity, especially as pertains to food systems and sustainability. Registration is free, and can be found here.

Happening today: MSE symposium session “Reconsidering ‘One Health’ Through Microbes”

The Microbes and Social Equity working group, and The University of Maine Institute of Medicine present a virtual symposium on:

“Living in a Microbial World”

June 5 – 9th, 2023.

Format: virtual meeting, Zoom platform.

The full program is here.

Session 1: Reconsidering ‘One Health’ Through Microbes

Monday, June 5th, 11 am – 2:30 pm EST. This event has passed, watch the recorded talks.

Microbes and Social Equity concepts are based on the idea that microbes connect individuals, societies, and ecosystems. One Health & the Environment concepts are based on similar ideas of connectivity. This session will explore the connections between MSE and One Health, how microbiome research connects to One Health, and how we can broaden our own research to include other disciplines. The primary goals for this session are 1) to convene researchers in multiple disciplines and envision ways to work together, and 2) to collaboratively generate definitions of One Health & the Environment with respect to microbiomes.

Hosts and organizers:

Dr. Tiff Mak (they/she), PhD, Postdoctoral Research Fellow at the Novo Nordisk Foundation Center for Biosustainability at DTU. They work at the intersection of Microbial Ecology, Fermentation and Integrated Food Systems, and are interested in community interaction dynamics and relationality, from the scale of the microbial to the planetary.

Dr. Sue Ishaq, PhD, Assistant Professor of Animal and Veterinary Science, School of Food and Agriculture, University of Maine. Animal microbiomes, diet and gut, microbes and social equity.

Speakers, 11~12:00 EDT:

Rob Beiko, PhD

Dr. Rob Beiko, PhD., is a Professor and Head of the Algorithms and Bioinformatics research cluster in the Faculty of Computer Science at Dalhousie University. His research aims to understand microbial diversity and evolution using machine learning, phylogenetics, time-series algorithms, and visualization techniques. His group is developing software tools and pipelines to comprehensively survey genes and mobile genetic elements in bacterial genomes, and understand how these genomes have been shaped by vertical inheritance, recombination, and lateral gene transfer. He is also a co-founder of Dartmouth Ocean Techonlogies, Inc., a developer of environmental DNA sampling devices.

Marta Scaglioni

Dr. Marta Scaglioni, PhD. is a Cultural Anthropologist and holds a PostDoc position at Cà Foscari University of Venice (Italy) within the frame of the ERC Project HealthXCross. She is interested in how microbiome research operates in the African continent and how microbial data, knowledge, and funding travel across national boundaries and across a Global North/Global South axis.

Dr. Lucilla Barchetta, PhD., is a Cultural Anthropologist and PhD in Urban Studies. She currently works as Postdoctoral Fellow within the ERC project Health X Cross based at the University Ca’ Foscari of Venice, where she studies One Health epistemologies and open data governance in multidisciplinary data-centric science and collaboration.

Break, ~12:05 – 12:20 EDT

Panel Discussion, 12:20~13:00 EDT:

  • Need for interdisciplinarity and collaboration, with collection and ontological credit
  • Narrative on One Health, and thinking about other definitions of health

Break, 3:00 – 13:15 EDT

Breakout room discussions, 13:15 ~ 14:30 EDT:

  1. Microbes in One Health research
  1. Defining One Health/Conservation
  1. Teaching microbes + One Health

Related to this session, here are recorded talks from previous MSE events:

Recording available from my recent talk on broccoli sprouts, microbes, and social equity

I was recently in Boston, MA to present some of my collaborative research on broccoli sprouts, gut microbes, and social equity, to the Harvard Chan Medical School NIEHS Center for Environmental Health. You can watch the recording of that presentation, as well as their full speaker series, here.

A cartoon of brightly colored, smiling bacteria.

Ishaq, S. “Microbes and Social Equity: what is it and how do we do it?” Harvard Chan-NIEHS Center for Environmental Health’s “Environmental Health in Action” colloquium series. Boston, MA, May 10, 2023. (invited)

A logo that says "The Broccoli Project"
Designed by Johanna Holman.

If you’d like more info on this ongoing research, you can check out:

Lola passes her comprehensive exam!

Congratulations to Lola Holcomb, for passing the graduate comprehensive exam!! She now goes from being a PhD student to a PhD candidate, and for the next few years will focus on developing her own research designs and writing her thesis.

The exam was set by her PhD program in the Graduate School of Biomedical Sciences and Engineering, and involved writing a 6-page research proposal over the past two months, and on the day of, giving a 1-hour presentation and answering questions from her committee for up to two hours. The focus of the proposal and the presentation are a hypothetical experiment she designs on a topic that is similar to her existing research but not directly related. In that way, you can test a student’s ability to translate their existing knowledge and fact-finding skills to a totally new area and see how well they can reason through a new problem. The committee will ask students to explain their thought process, methods, and how they will assess the progress on the hypothetical project. It’s a long and arduous process, but Lola’s depth of knowledge and ability to problem-solve helped her pass with ease!

Paper by former colleagues published on rainbow Trout (Oncorhynchus mykiss) midgut and hindgut microbiomes using whole shotgun metagenomics

As a postdoc at Montana State University in 2015/2016 with Carl Yeoman’s lab, I consulted on a project led by then-PhD student Lola Betiku on a metagenomics dataset from two locations from the digestive tract of trout. Lola is now an Assistant Professor at Florida A&M University, and has been kind enough to continue working on this project to get it published. It was just accepted in the journal Aquaculture Reports!

Citation

Betiku, O., Yeoman, C., Gaylord, T.G., Ishaq, S., Duff, G., Sealey, W. 2023. Evidence of a Divided Nutritive Function in The Rainbow Trout (Oncorhynchus mykiss) Mid- and Hind-Gut Microbiomes by Whole Shotgun Metagenomic Approach. Aquaculture Reports 30: 101601.

Highlights

  • •Animal and plant protein diets were fed to rainbow trout in a commercial setting.
  • •Shotgun metagenomic analysis of the mid-GIT and hind-GIT was carried out.
  • •Diets influenced microbial compositions in the two GIT sections.
  • •Animal protein-based diet provided metabolites for microbial protein fermentation.
  • •Plant-based diet enhanced amino acid catabolism in the mid-GIT section.

Abstract

The nutritive role and ecology of gut-dwelling microbes in rainbow trout remain enigmatic. To improve our understanding of the rainbow trout gastrointestinal tract (GIT) microbiome, we performed whole shotgun metagenomic analyses on the assembled contigs from luminal contents from both mid- and hind-GIT regions for taxonomic and functional classifications of fish-fed animal and plant protein dietary sources. Our study revealed that trout respond well to the two diets containing animal and plant protein sources when supplemented with essential amino acids to meet the requirements of the fish. Microbes present were predominantly bacteria (89.9%) and mainly of the phyla Tenericutes, Firmicutes, Fusobacteria, and Proteobacteria. Eukaryotic (8.8%) microbes were mainly from phyla Ascomycota and Basidiomycota, while Archaea (<1%) were also present and predominantly from the phylum Euryarchaeota. Comparisons of genus-level classifications and functional profiles revealed compositional differences in these GIT locations that appear modulated by differences in the dietary treatments. The functional analysis provided evidence of amino acid biosynthesis/catabolism and methane production in the mid-GIT, while in the hind-GIT, proteolytic hydrolysis and butyrate metabolism were expressed in the trout fed with plant protein diet. The animal protein-based diet provided metabolites for microbial protein fermentation in the hind-GIT. Our report highlights and identifies the potential nutritive contributions of GIT microbes to trout and a potentially crucial functional division along the GIT. Finally, the plant-based diet enhanced amino acid catabolism in the midgut section, while the hindgut section supports evidence of methanogen fermentation.

Upcoming presentations at the American Society for Nutrition conference

The Ishaq Lab will be presenting at a few research conferences this summer, with a few more in the works for the fall.

Broccoli sprouts in a tray

American Society for Nutrition meeting, July 22-25, 2023, Boston, Massachusetts

Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis.

Poster, abstract P20-022-23, July 23

Authors: Johanna M. Holman*1, Lola Holcomb2, Louisa Colucci3, Dorien Baudewyns4, Joe Balkan5, Grace Chen6, Peter L. Moses7,8, Gary M. Mawe7, Tao Zhang9, Yanyan Li1, Suzanne L. Ishaq1

Affiliations: 1 School of Food and Agriculture, University of Maine, 2 Graduate School of Biomedical Sciences and Engineering, University of Maine, 3 Department of Biology, Husson University, 5 Department of Chemical and Biological Engineering, Tufts University, 6 Department of Internal Medicine, University of Michigan Medical School, 7 Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, 8 Finch Therapeutics, 9 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University.

Objectives: Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, affordable, and safe for managing symptoms. Ongoing research has identified inactive compounds in broccoli sprouts, like glucoraphanin, and that mammalian gut microbiota play a role in metabolizing it to the anti-inflammatory sulforaphane. The objectives were to identify biogeographic location of participating microbiota and correlate that to health outcomes. 

Methods: We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 40-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, fecal lipocalin, and sequenced bacterial communities from the contents and mucosa in the jejunum, cecum, and colon. 

Results: Mice fed the broccoli sprout diet while receiving DSS performed better than mice fed the control diet while receiving DSS for all disease parameters, including significantly more weight gain (2-way ANOVA, p < 0.05), lower Disease Activity Index scores (2-way ANOVA, p < 0.001), and higher bacterial richness in all gut locations (linear regression model, p < 0.01 for all locations measured). Bacterial communities were assorted by gut location except in the mice receiving the control diet and DSS treatment (Beta-diversity, ANOVA, p < 0.05 for each). Importantly, our results suggested that broccoli sprout feeding completely abrogated the effects of DSS on gut microbiota, as bacterial communities were similar between mice receiving broccoli sprouts with and without DSS. 

Conclusions: Spatially resolved microbial communities provide greater insight when investigating host-microbe interactions. Here, we show that a 10% broccoli sprout diet protects mice from the negative effects of dextran sodium sulfate induced colitis, that colitis erases biogeographical patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. 

Funding Sources: This work was funded by the NIH, USDA, NSF NRT, and UMaine GSBSE.

 

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease.

Poster, abstract P20-021-23, July 23

Authors: Lola Holcomb*1, Johanna Holman2, Molly Hurd3, Brigitte Lavoie3, Louisa Colucci4, Gary M. Mawe3, Peter L. Moses3,5, Emma Perry6, Allesandra Stratigakis7, Tao Zhang7, Grace Chen8, Suzanne L. Ishaq1, Yanyan Li1

1 Graduate School of Biomedical Sciences and Engineering, University of Maine, 2 School of Food and Agriculture, University of Maine, 3 Larner College of Medicine, University of Vermont, 4 Department of Biology, Husson University, 5 Finch Therapeutics, 6 Electron Microscopy Laboratory, University of Maine, 7 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, 8 Department of Internal Medicine, University of Michigan Medical School.

Objectives: Inflammatory Bowel Diseases (IBD) are chronic conditions characterized by inflammation of the gastrointestinal (GI) tract that burden daily life, result in complications, and disrupt the gut microbiome. Many studies on diet and IBD in mice use an ulcerative colitis model, despite the availability of an immune-modulated Crohn’s Disease model. The objective of this study was to establish IL-10 deficient mice as a model for studying the role of dietary broccoli and broccoli bioactives in reducing inflammation, modifying the immune response, and supporting GI tract microbial systems. 

Methods: Interleukin-10-knockout (IL-10-ko) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed either a control diet or one containing 10% raw broccoli sprouts. Diets began 7 days prior to inoculation with Helicobacter hepaticus, which triggers Crohn’s-like symptoms in these immune-impaired mice, and ran for 2 additional weeks. 

Results: Broccoli sprouts decreased (p < 0.05), fecal lipocalin (LCN2), a biomarker for intestinal inflammation, and fecal blood, diarrhea, and overall Disease Activity Index. Sprouts increased gut microbiota richness, especially in younger mice (p < 0.004), and recruited different communities in the gut (B-diversity, ANOVA, p < 0.001), especially in the colon (B-diversity, ANOVA, p = 0.03). The control group had greater prevalence and abundance of otherwise commensal bacteria which trigger inflammation in the IL-10-ko mice. Helicobacter was within the top-5 most prevalent core genera for the control group, but was not within the top-5 for the broccoli group. Disease parameters and microbiota changes were more significant in younger mice receiving broccoli.

Conclusions : A diet containing 10% raw broccoli sprouts may be protective against negative disease characteristics of Helicobacter-induced enterocolitis in IL-10-ko mice, and younger age is the most significant factor (relative to diet and anatomical location) in driving gut bacterial community richness and similarity. The broccoli diet contributes to prevalence and abundance of bacterial genera that potentially metabolize dietary compounds to anti-inflammatory metabolites in the gut, are bacteriostatic against pathogens, and may ease disease severity.

Funding Sources: This work was funded by the NIH, USDA, NSF NRT, and UMaine GSBSE.

Establishing Growth Curve Assays for Bacterial Glucosinolate Metabolism: A Study Protocol

Poster, abstract P22-030-23, July 23

Marissa Kinney*1, Ryan Wijayanayake1, Johanna Holman1, Timothy Hunt2, Benjamin Hunt 2, Tao Zhang3, Grace Chen4, Yanyan Li1 , Suzanne L. Ishaq1

1School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469; 2 School of Biology and Ecology, University of Maine, Orono, Maine, USA 04469; 3 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790; 4 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109 

Objective: Inflammatory bowel diseases (IBD) cause dysfunction of the gastrointestinal (GI) tract and can result in hospitalization, suffering and disruption to overall health. Recent work has demonstrated the anti-inflammatory capacity of a broccoli sprout-diet in artificially-induced GI inflammation in pathogen free C57BL/6 mice. Microbiota samples obtained from the GI tract of these mice will be used to study the presence and activity of broccoli glucosinolate hydrolysis to create microbial-sourced bioactives, to further understand the relationship between broccoli-diets and inflammation reduction. It is imperative to validate or replicate qPCR protocols which have been established for glucosinolate metabolism in Bacteroides thetaiotaomicron (B. theta), in other bacterial species. Additionally, this project will focus on developing new growth curve assays for glucosinolate metabolism, as these methods are lacking in published literature. 

Methods: Pathogen free C57BL/6 mice were given dextran sodium sulfate (DSS) into their drinking water to create a disease profile similar in development and morphology to human ulcerative colitis (UC), a type of IBD. DSS and a steamed broccoli sprout diet were administered. Samples were taken from the digesta, jejunum, cecum, and colon of mice fed broccoli diets. About 806 bacterial isolates will be grown up/cultured anaerobically on minimal/selective media containing glucosinolate-related compounds (glucoraphanin, sinigrin) to determine hydrolysis activity via spectroscopy to measure optical density of growth in competent isolates. Successful isolates will be further analyzed with LC/MS to confirm production of bioactive products, and with qPCR using the B. theta positive control genome to help identify gene targets (α-1,6-mannanase, glycosyl hydrolase, nicotinamide-dependent oxidoreductase, and transcriptional regulator protein) for glucosinolate conversion in isolates. 

Results  N/A

Conclusions: In the initial study from which these samples are sourced, mice fed a broccoli diet had less inflammation than those fed a control diet and DSS, and had higher bacterial diversity in their gut. We expect that bacteria isolated from the GI of broccoli-fed mice will contain more glucosinolate-metabolizing genes.

Funding: NIH (Li and Ishaq) and USDA (Li). 

Broadening Perspectives by Situating Nutrition Education in Broader Social Contexts: A Study Protocol

Poster, abstract number 1490287, July 23

Authors: Ashley Toney*1, Patricia Wolf*2, Sue Ishaq*3

Affiliations: 1Dept. of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, 2 Department of Nutrition Science, Purdue University, 3 School of Food and Agriculture, University of Maine

Objectives: The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Given the complexity and nuance of evidence-based nutrition delivery, MSE sought to provide a conceptual structure. The goals are 1) convene diverse researchers, educators, learners, and practitioners, 2) publish and present evidence-based information within socio-cultural contexts, and 3) teach audiences to define ways for integrating equity into their work.

Methods: MSE hosted a 14-week speaker series in 2021, 2022, and 2023, with researchers from various disciplines (e.g., nutrition, gut microbes, food security). The series lead into a 5-day symposium of speakers and guided discussions to generate co-written documents identifying research needs and resources. We use targeted and non-targeted event promotion to attract audiences, and reach/impact is evaluated through registration, attendance, social media views, or attendee feedback. The series provides learning sessions that build concepts over time, guiding attendees past the conceptual roadblock of being new to interdisciplinary research and grappling with grand challenges. This extended period to learn stimulates participation in activity-based collaboration during symposia, even from new members or students. 2023 symposium attendees will be surveyed on their impressions on the event, how it impacted their perspective on experimental design, whether attendees started with the series and followed up with the symposium, and whether having the preface of the series aided in being able to create actionable outputs in a guided co-working session.

Results: n/a

Conclusions: Benefits include nuanced knowledge/perspective sharing, establishing and nurturing interdisciplinary collaboration, and sparking conversations on critical topics in policy, sustainability, host and microbial metabolism, etc. In the last 3 years, MSE published 4 papers together, with ~ 50 independent papers from members. Event recordings are used as curriculum in nutrition, microbiology, and pre-med biology.

Funding Sources: NIH/NIDDK, Allen Foundation (Ishaq); National Dairy Council (Toney)

2023 MSE speaker series is wrapped for the season!

Thank you to our speakers, attendees, and organizers for our most popular MSE speaker series yet! We had ~600 attendees and nearly 3,000 registrations!!

You can catch up on the entire 2023 series, the event page has links to the recordings.

Similarly, you can find recordings from our 2022 series, our 2021 series, and from our 2022 symposium, by checking out our Past Events pages.

If you’d like to continue these conversations, MSE is hosting its 2023 symposium, “Living in a Microbial World” virtually on June 5-9. It’s free and all are welcome to attend.

Marissa Kinney awarded an NSF NRT graduate fellowship from the UMaine Initiative for One Health and the Environment!

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

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.

An American lobster on a countertop next to a ruler.

Lobster shell microbes, epizootic shell disease, and climate change manuscript is published!

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.

You can read the paper here.

Woman sitting outside.

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 🙂 ).

Four professors wearing full regalia, as well as face masks, posing for a photo in a hallway.

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’?

A steamed lobster on a plate.

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.

Four panels of lobsters showing the progression of a healthy lobster to ones with more and more pitting in their shells.
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.

“Water temperature and disease alters bacterial diversity and cultivability from American Lobster (Homarus americanus) 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.

Lola standing in front of her poster which displays the results of her research on gut microbes.

Upcoming presentations at the UMaine Student Symposium

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:

Members of the Ishaq Lab posing together for a photo outside.
Keagan Rice, Sydney Shair, Marissa Kinney, Sue Ishaq, Ayodeji Olaniyi, Ryan Wijayanayake, and Lola Holcomb at the 2023 UMaine Student Symposium.

Portrait of Lola Holcomb, wearing a block sweater on a beach at sunset

“Early Life Exposure to Broccoli Sprouts Confers Stronger Protection against Enterocolitis Development in an Immunological Mouse Model of Inflammatory Bowel Disease“

Student Name(s): Lola Holcomb

Other authors: Johanna Holman

Abstract Number: 1035

Presentation is based on work that is in review.

“Establishing Growth Curve Assays for Bacterial Glucosinolate Metabolism“

Student Name(s): Marissa Kinney

Other authors: Ryan Wijayanayake, Johanna Holman

Abstract Number: 909

Presentation is based on work that is in progress.

“The Veterinary Immersion Plan: An Innovative Solution to Address Non Predictive Barriers to Entering the Field of Veterinary Medicine”

Student Names: Zach Inniss, Kurt Janscy

Abstract number: 911

Presentation is based on work created and driven by Zach Inniss.

“Investigating The Activity of Bacteria Isolated from Tank Biofilms in a Hatchery System for Sea Scallop, Placopecten magellanicus Larvae”

Student Name(s): Ayodeji Olaniyi

Abstract Number: 419

Presentation is based on work that is in progress.

Ayodeji won a graduate student research award for this poster!

“Assessing the Small Animal Veterinary Needs of Rural Maine and Implementing an Effective Management Plan”

Student Name(s): Marielle Pelletier

Abstract Number: 835

Presentation created and driven by Ellie Pelletier and Tegwin Taylor.

“Assessment of the Association of Sea Scallop Larvae Mortality and Vibrio spp. in Hatchery Systems”

Student Names: Sydney Shair, Keagan Rice

Abstract number: 844

Presentation based on collaborative work in this and the Perry labs.

“Utilizing Sulfloraphane from Broccoli to Treat IBD“

Student Name(s): Ryan Wijayanayake

Abstract Number: 1055