MSE seminar this Wednesday: Dr. Katie Amato, “The Human Microbiome and Health Inequities”

This Wednesday there is another installment in the spring 2022 Microbes and Social Equity speaker series! Each week, we’ll hear from a researcher who will share their work and perspective on how microbes are involved in all aspects of our lives, and how those microbes can affect individuals, communities, and ecosystems.

This series will run from Jan 19 – Apr 27, Wednesdays at 12:00 – 13:00 EST. These are presented over Zoom, and open to researchers, practitioners, students, and the public. Registration is free, and required for each individual seminar you would like to attend. You can find the full speaker list, details, and registration links for each seminar in the series here.

“The Human Microbiome and Health Inequities”

Dr. Katherine (Katie) Amato, PhD

January 26, 2022, 12:00 – 13:00 EST. Register for this free talk.

Dr. Katie Amato. Photo borrowed from Northwestern University.

About the speaker: Dr. Katherine (Katie) Amato is an Assistant Professor of Anthropology at Northwestern University. From her faculty profile page: “Katie Amato is a biological anthropologist studying the gut microbiota in the broad context of host ecology and evolution. She is particularly interested in understanding how changes in the gut microbiota impact human nutrition and health in populations around the world, especially those with limited access to nutritional resources.”

Faculty profile page.

Talk summary: The talk explores how the microbiome is likely to be a mediating pathway that translates disparities in people’s environments to disparities in health outcomes. It outlines the current state of the literature in this area and broadly suggests ways to move forward. Dr. Amato’s recent publication on this topic can be found here.

MSE seminar today: Dr. Sue Ishaq, “Microbes at the nexus of environmental, biological, and social research”

Today kicks off the spring 2022 Microbes and Social Equity speaker series! Each week, we’ll hear from a researcher who will share their work and perspective on how microbes are involved in all aspects of our lives, and how those microbes can affect individuals, communities, and ecosystems.

This series will run from Jan 19 – Apr 27, Wednesdays at 12:00 – 13:00 EST. These are presented over Zoom, and open to researchers, practitioners, students, and the public. Registration is free, and required for each individual seminar you would like to attend. You can find the full speaker list, details, and registration links for each seminar in the series here.


“Microbes at the nexus of environmental, biological, and social research”

Dr. Sue Ishaq, PhD

January 19, 2022, 12:00 – 13:00 EST. Register for this free talk

About the speaker: Dr. Sue Ishaq is an Assistant Professor of Animal and Veterinary Science at the University of Maine, in the School of Food and Agriculture. She received her doctorate in Animal, Nutrition and Food Science from the University of Vermont in 2015 where her graduate study focused on the rumen microbiology of the moose.  She held post-doctoral positions at Montana State University, and a research faculty position at the University of Oregon.  Since 2019, her lab in Maine focuses on host-associated microbial communities in animals and humans, and in particular, how host and microbes interact in the gut. In addition to her research on gut microbes, Dr. Ishaq is the founder of the Microbes and Social Equity working group.  This group formed to examine, publicize and promote a research program on the reciprocal impact of social inequality and microbiomes, both human and environmental.

MSE seminar this Wednesday: Dr. Sue Ishaq, “Microbes at the nexus of environmental, biological, and social research”

This Wednesday kicks off the spring 2022 Microbes and Social Equity speaker series! Each week, we’ll hear from a researcher who will share their work and perspective on how microbes are involved in all aspects of our lives, and how those microbes can affect individuals, communities, and ecosystems.

This series will run from Jan 19 – Apr 27, Wednesdays at 12:00 – 13:00 EST. These are presented over Zoom, and open to researchers, practitioners, students, and the public. Registration is free, and required for each individual seminar you would like to attend. You can find the full speaker list, details, and registration links for each seminar in the series here.


“Microbes at the nexus of environmental, biological, and social research”

Dr. Sue Ishaq, PhD

January 19, 2022, 12:00 – 13:00 EST. Register for this free talk

About the speaker: Dr. Sue Ishaq is an Assistant Professor of Animal and Veterinary Science at the University of Maine, in the School of Food and Agriculture. She received her doctorate in Animal, Nutrition and Food Science from the University of Vermont in 2015 where her graduate study focused on the rumen microbiology of the moose.  She held post-doctoral positions at Montana State University, and a research faculty position at the University of Oregon.  Since 2019, her lab in Maine focuses on host-associated microbial communities in animals and humans, and in particular, how host and microbes interact in the gut. In addition to her research on gut microbes, Dr. Ishaq is the founder of the Microbes and Social Equity working group.  This group formed to examine, publicize and promote a research program on the reciprocal impact of social inequality and microbiomes, both human and environmental.

Registration open for Microbes and Social Equity speaker series, Jan 19 – April 27

Registration is now open for the Microbes and Social Equity speaker series, which is in its second year this spring. Hurry, the first seminar is on Wednesday, Jan 19th!

The seminars are free and open for anyone to attend, but require registration to Zoom for each of the talks. You can find the full speaker list and registration links to all the talks on the 2022 series page, which will update as we confirm additional speakers.

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.   

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. This speaker series explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field. 

“The Microbes and Social Equity Speaker Series 2022”

Spring 2022; Jan 19 – Apr 27, Wednesdays at 12:00 – 13:00 EST

Presented over Zoom. Registration is free, and required for each seminar.

Hosting Organization: MSE and the University of Maine Institute of Medicine


“Microbes at the nexus of environmental, biological, and social research”

Dr. Sue Ishaq, PhD

January 19, 2022, 12:00 – 13:00 EST. Register for this free talk

Sue Ishaq, photo courtesy of Patrick Wine, 2021.

About the speaker: Dr. Sue Ishaq is an Assistant Professor of Animal and Veterinary Science at the University of Maine, in the School of Food and Agriculture. She received her doctorate in Animal, Nutrition and Food Science from the University of Vermont in 2015 where her graduate study focused on the rumen microbiology of the moose.  She held post-doctoral positions at Montana State University, and a research faculty position at the University of Oregon.  Since 2019, her lab in Maine focuses on host-associated microbial communities in animals and humans, and in particular, how host and microbes interact in the gut. In addition to her research on gut microbes, Dr. Ishaq is the founder of the Microbes and Social Equity working group.  This group formed to examine, publicize and promote a research program on the reciprocal impact of social inequality and microbiomes, both human and environmental.


“The Human Microbiome and Health Inequities”

Dr. Katherine (Katie) Amato, PhD

January 26, 2022, 12:00 – 13:00 EST. Register for this free talk.

Dr. Katie Amato. Photo borrowed from Northwestern University.
Dr. Katie Amato. Photo borrowed from Northwestern University

About the speaker: Dr. Katherine (Katie) Amato is an Assistant Professor of Anthropology at Northwestern University. From her faculty profile page: “Katie Amato is a biological anthropologist studying the gut microbiota in the broad context of host ecology and evolution. She is particularly interested in understanding how changes in the gut microbiota impact human nutrition and health in populations around the world, especially those with limited access to nutritional resources.”

Faculty profile page.

Talk summary: The talk explores how the microbiome is likely to be a mediating pathway that translates disparities in people’s environments to disparities in health outcomes. It outlines the current state of the literature in this area and broadly suggests ways to move forward. Dr. Amato’s recent publication on this topic can be found here.


Title TBD

Dr. Liat Shenhav, PhD

February 16, 2022, 12:00 – 13:00 EST. Register for this free talk.

Dr. Liat Shenhav. Photo borrowed from Twitter page.
Dr. Liat Shenhav. Photo borrowed from Twitter page.

About the speaker: Dr. Liat Shenhav is an Independent Research Fellow at The Rockefeller University

Institutional profile page.


“20 important questions in microbial exposure and social equity + recent work on urban greenspace microbiomes”

Dr. Jake Robinson, PhD

Feb 23rd, 2022, 12:00 – 13:00 EST. Register for this free talk.

A black and white portrait of Dr. Jake Robinson, who is wearing a black shirt and light sportscoat over it. Jake is outside in front of some bushes.
Dr. Jake Robinson

About the speaker: Dr. Jake Robinson is an ecologist and researcher. He recently completed a PhD at the University of Sheffield, UK. His academic interests lie at the intersection of microbial ecology, ecosystem restoration and social research. He will soon be publishing a book called Invisible Friends, which is all about our extraordinary relationship with microbes, and how they shape our lives and the world around us. 

Professional page.


Title TBD

Dr. Douglas Call, PhD

March 30, 2022, 12:00 – 13:00 EST. Register for this free talk.

About the speaker: Dr. Douglas Call is a Regents Professor at the Paul G. Allen School for Global Health, in Molecular Epidemiology, and the Associate Director for Research and Graduate Education, at Washington State University.

Faculty profile page.


“Decomposition as Life Politics” 

Dr. Kristina Lyons, PhD

April 6, 2022, 12:00 – 13:00 EST. Register for this free talk.

Dr. Kristina Lyons. Photo reused from the University of Pennsylvania faculty page.
Dr. Kristina Lyons. Photo reused from the University of Pennsylvania faculty page.

About the speaker: Dr. Kristina Lyons is an Assistant Professor of Anthropology and with the Penn Program in Environmental Humanities at the University of Pennsylvania. She also holds affiliations with the Center for Experimental Ethnography and the Center for Latin American and Latinx Studies. Kristina’s current research is situated at the interfaces of socio-ecological conflicts, science, and legal studies in Colombia and Latin America. Her manuscript, Vital Decomposition: Soil Practitioners and Life Politics (Duke 2020), was awarded honorable mention by the Bryce Wood Book Award committee from the Latin American Studies Association. She has also collaborated on the creation of soundscapes, street performances, photographic essays, graphic novels, popular education audiovisual projects, community radio programs, digital storytelling platforms, and various forms of literary writing.

Professional page.

Talk summary: How does attention to and stewardship of soils point to alternative frameworks for living and dying? Dr. Lyons explores the way life strives to flourish in the face of violence, criminalization, and poisoning produced by militarized, growth-oriented development in the midst of the U.S.-Colombia war on drugs.


Title TBD

Dr. Travis J. De Wolfe, PhD

Date TBD, 2022, 12:00 – 13:00 EST.

About the speaker: Dr. Travis J. De Wolfe, Ph.D. is a Postdoctoral Research Fellow in the Department of Pediatrics at the University of British Columbia.

Institutional profile page.


Title TBD

Dr. Maya Hey, PhD

Date TBD, 2022, 12:00 – 13:00 EST.

About the speaker: Dr. Maya Hey is a postdoctoral researcher with the Future Organisms project as part of an international trans-disciplinary team investigating Responsible Research and Innovation (RRI). She brings a humanities and social science perspective to the life sciences, calling upon feminist, intersectional, and multispecies approaches to map out human response-ability in a more-than-human world. She is vested in questions related to fermentation, particularly as they relate to discourses of health, the rhetoric of microbiomes, and how we come to know microbial life.”

Professional page.



Logo designed by Alex Guillen

MSE special session at ASM Microbe 2022 conference

The Microbes and Social Equity working group is putting together a special session at the American Society for Microbiology’s annual Microbe meeting, which will be held in Washington, D.C. from June 9 – 13, 2022.

CTS16 (PPS). Microbes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice

June 11, 2022, 1:45 PM – 3:45 PM

Room 206

DESCRIPTION

Microorganisms are critical to many aspects of biological life, including human health. 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. 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. This special session explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field.

5 Presentations

1:45 PM – 3:45 PMMicrobes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice
Suzanne Ishaq; Univ. of Maine, Orono, ME
1:45 PM – 2:15 PMInvited Speaker
Monica Trujillo; Queensborough Community Coll., New York, NY
2:15 PM – 2:45 PMInvited Speaker
Ariangela Kozik; Univ. of Michigan, Ann Arbor, MI
2:45 PM – 3:15 PMInvited Speaker
Carla Bonilla; Gonzaga Univ., Spokane, WA
3:15 PM – 3:45 PMPanel Discussion

Upon completion of this Cross-Track Symposium, the participant should be able to:

  • Recognize the connections that microbiomes have to social equity. This will be demonstrated with examples/case studies presented by speakers.
  • Discuss relevant issues in microbiomes and their connection to social equity and identify issues which could be explored further.
  • Appraise your own work for these connections between microbiomes and social equity, to designate places for professional growth and applying equitable design.

Track(s)/Subtrack(s)Host Microbe Biology

The Microbes and Social Equity working group is turning 2!

It doesn’t seem that long ago that we were just an assorted group of interested researchers having a chat, but here we are two years later gaining international support and interest.  We greatly appreciate your interest in this group, and are pleased to share some of our recent updates.

We currently have 115 members of the Microbes and Social Equity working group, and another 33 people signed up just for the newsletter. In 2021, we ran a very successful speaker series, virtual symposium, and collectively had quite a few publications, presentations, and developments! We are excited to continue that momentum in 2022, and are planning another speaker series and virtual symposium, finalizing our journal special collection with mSystems, and furthering the collaborative projects we have begun. We will also be adding additional leadership roles for the group, to better accommodate our group and give more attention to our growing activities and initiatives.

Publications


mSystems Special Collections:

We are making great progress adding to our special collection with mSystem, with 3 papers published and several more currently in review! We will continue adding contributions through 2022. 

  1. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice | mSystems 
  2. Teaching with Microbes: Lessons from Fermentation during a Pandemic | mSystems
  3. Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome | mSystems  


Upcoming

  • Francisco Parada’s postdoc, Dr. Ismael Palacios-García finished collecting his probiotic/lifestyle randomized trial, collecting cognitive electrophysiology (EEG+EGG), microbial (DNA from fecal samples), and phenomenological data (questionnaires) over 4+ months. They hope they will be publishing some of these results soon!  
  • Jake Robinson is working on “Invisible Friends”, a popular science book anticipated for release in 2022. From Jake’s page: “Invisible Friends is about our extraordinary relationship with microbes, and how they shape our lives, our health, and the world around us. The book aims to challenge the prevailing negative perception of microorganisms, by highlighting the weird, wonderful, and indispensable roles they play in our health, behaviour, society, and ecosystems!”

Presentations

Upcoming: 

The Microbes and Social Equity speaker series 2022 is under development! We hope to invite speakers for a virtual series running January through April, Wednesdays from 12:00 – 13:00 EST. Registration is required but the series is free to attend.

inVIVO Planetary Health, virtual conference, Dec 1-7, 2021. Register here. Several MSE group members will be giving talks there, such as:

  • Sue Ishaq, “Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice”
  • Ari Kozik, “The human microbiome and health disparities: restoring dysbiosis as a matter of social justice”
  • Jake Robinson, “Microbiome-inspired green infrastructure (MIGI): a bioscience roadmap for urban ecosystem health”

2nd Rhode Island Microbiome Symposium, in person conference, University of Rhode Island Kingston, RI, January 14, 2022. Register here.

  • Sue Ishaq, ​”Microbes at the nexus of environmental, biological, and social research”

American Society for Microbiology (ASM) Microbe 2022, in person conference, Washington, DC (USA), June 9-13, 2022.

  • ‘Field Work & DEI Part 1: Fostering Equitable Partnerships with the Communities in Your Field Work Location’. The session’s date is June 11, 2022 (11:45AM – 12:30PM).
    • Ishaq,”Microbes and Social Equity: what is it and how do we do it?”
  • MSE special session, “Microbes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice”. The session’s date is June 11, 2022 (1:45PM – 3:45PM), and the event is under development.
    • Featuring panelists Monica Trujillo, Ari Kozik, and Carla Bonilla

Past

Mike Friedman hosted a very successful MSE Special Session (together with the Microbial Ecology section) at this year’s virtual Ecological Society of America meeting. Naupaka Zimmerman, Justin Stewart, Monica Trujillo and Sue Ishaq gave short presentations on social justice and various aspects of environmental and human microbiota. But the bulk of the session was taken up by audience discussion of issues in environmental justice and microbes, practical and suggested policies and education.

Ishaq Lab presentations and live discussions at Ecological Society of America virtual meeting

Next week kicks off the live events, including with question + answer, discussions, and special sessions being held in real time, for the Ecological Society of America’s annual conference, which is being held virtually this year. Prerecorded presentations are already available on demand.

Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?

Session 1-PS7: Vital Connections in Ecology: Breakthroughs in Understanding Species Interactions

Poster and narration available on demand.

Live discussion: Monday, August 2, 2021, 9:30 AM – 10:30 AM Pacific Time

Abstract:

Background/Question/Methods
The invasive European fire ant (Myrmica rubra) threatens native ant species and human health along the coast of Maine, United States. M. rubra mortality has been associated with infection by Pristionchus entomophagus, a necromenic nematode that is hypothesized to transfer pathogenic bacteria acquired from the environment to ant colonies. To investigate this hypothesis, we conducted a series of experiments on nematode-infected ants collected from Mount Desert Island. First, we isolated bacteria cultured from nematodes emerging from M. rubra cadavers and assessed the ability of the nematodes to acquire and transfer environmental bacteria to Galleria mellonella waxworm larvae. Second, we identified bacteria which were potentially transferred from nematodes to infected ant nests on MDI using bacterial community similarity and sequence tracking methods.

Results/Conclusions
Multiple bacterial species, including Paenibacillus spp., were found in the nematodes’ digestive tract. Serratia marcescens, Serratia nematodiphila, and Pseudomonas fluorescens were collected from the hemolymph of nematode-infected G. mellonella larvae. Variability was observed in insect virulence in relation to the site origin of the nematodes. In vitro assays confirmed uptake of red fluorescence protein (RFP)-labeled Pseudomonas aeruginosa strain PA14 by nematodes. Bacteria were highly concentrated in the digestive tract of adult nematodes, some bacteria were observed in the digestive tract of juveniles with a more significant amount on their cuticle, and none on the cuticle of adults. RFP-labeled P. aeruginosa were not observed in hemolymph of G. mellonella larvae, indicating an apparent lack of bacterial transfer from juvenile nematodes to the insects despite larval mortality.

Host species was the primary factor affecting bacterial community profiles. Spiroplasma sp. and Serratia marcescens sequences were shared across ants, nematodes, and nematode-exposed G. mellonella larvae. Alternative to the idea of transferring bacteria from environment to host, we considered whether nematode-exposure might disorder or depauperate the endobiotic community of an insect host. While total bacterial diversity was not statistically lower in nematode-exposed G. mellonella larvae when compared to controls, 16 bacterial sequence variants were less abundant in nematode-exposed larvae, while three were increased, including Serratia, Pseudomonas, and Proteus.
This study suggests that transfer of bacteria from nematodes to ants is feasible, although largely serendipitous, and may contribute to ant mortality in Maine. Hypothetically, the use of an engineered biological control, such as nematodes carrying specifically-seeded bacterial species, may be effective, especially if the pathogenic bacteria are naturally found in soil ecosystems and represent a low risk for biosafety control.

Poster Citation: Hotopp*, A., Silverbrand, S., Ishaq, S.L., Dumont, J., Michaud, A.,  MacRae, J.,  Stock, S.P.,  Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Ecological Society of America 2021. (virtual). Aug 2-6, 2021. (poster)

Recent Press and Publications:

Bacteria from nematodes could be used to kill fire ants, UMaine research reveals”, Marcus Wolf, University of Maine news, July 27, 2021.

Ishaq, S.L., A. Hotopp2, S. Silverbrand2, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Assessment of pathogenic bacteria transfer from Pristionchus entomophagus (Nematoda: Diplogasteridae) to the invasive fire ant (Myrmica rubra) and its potential role in  colony mortality in coastal Maine. iScience 24(6):102663. Article.


Talk #93066, “The effect of simulated warming ocean temperatures on the bacterial communities on the shells of healthy and epizootic shell diseased American Lobster (Homarus americanus)”

COS 87: Climate Change: Communities 1
Recorded talk available on demand.

Live discussion: Wednesday, August 4, 2021, 12:00 PM – 1:00 PM Pacific Time
The presentation will be available on demand starting on July 26th, and requires registration to the ESA conference.

Abstract

Background, question, and methods

The American lobster, Homarus americanus, is a vital species for the fishing industry along the North Atlantic coast of North America. However, populations in Southern New England have declined, most likely due to increasing ocean temperatures and prevalence of emerging disease. Our previous work suggested that temperature may not be the sole cause for epizootic shell disease (ESD). Here, we examined the shell bacterial communities and progression of ESD in non-shell diseased and diseased adult female lobsters under three simulated seasonal temperature cycles for a year.

Fifty-seven female lobsters were wild-caught from Maine’s management zones F and G, and were assessed for shell disease progression on a scale of 0 (no observable signs) to 3 (visible disease on >50% of the shell surface). ESD-negative lobsters (apparently healthy) and ESD-positive (diseased) lobsters were randomly dispersed into 3 systems, and within each system, healthy and diseased lobsters were placed into separate tanks. These systems were maintained at three temperature ranges comparable to the average seasonal ocean temperatures for Southern New England (SNE), Southern Maine (SME), and Northern Maine (NME) regions. Samples were collected at three timepoints, a baseline “summer” temperature where all tanks were the same temperature, a winter temperature four months later, and a summer temperature 10 months after that.

A total of 131 experimental samples, plus 10 controls, passed PCR amplification, amplicon quantification and purification, Illumina MiSeq ver. 4 sequencing, and quality-control filtering.  Sequences were processed using the R software platform, using DADA2, phyloseq, vegan, and assorted other packages.

Results and conclusions

The bacterial richness on lobster shells at the baseline timepoint, when lobsters were wild-caught, was higher than the winter time point, 4 months later, or the summer time point, 10 months later, for the same lobsters after having been kept in tanks, regardless of their temperature or shell disease status.  Similarly, the bacterial community membership (unweighted Jaccard similarity) was similar for all samples at baseline, but diverged for later time points.

Tank temperature significantly affected microbial community membership (unweighted Jaccard similarity), as well as the abundance of those community members (weighted Bray-Curtis dissimilarity).

Contrary to our expectations, ESD shell disease index did not progress over time or in warmer conditions, and we hypothesized that frequent tank water changes and shell moltings may have reduced the microbial load. Preliminary results indicate that shell stage and shell disease index were positively associated with increased bacterial richness on lobster shells.

Citation: Ishaq*, S.L., Lee, G., MacRae, J., Hamlin, H., Bouchard, D. “The effect of simulated warming ocean temperatures on the bacterial communities on the shells of healthy and epizootic shell diseased American Lobster (Homarus americanus).” Ecological Society of America 2021. (virtual). Aug 2-6, 2021. (accepted talk)


For some reason the ESA meeting site kept my Montana affiliation from 2017 for all 3 of my submissions.

SS 17: “Microbiomes and Social Equity” (19205)

Prerecorded content available on demand.

Live discussion: Thursday, August 5th, 2021, 9:30 AM – 10:30 AM Pacific Time

Microbiomes — environmental, human and other organismal symbionts — are increasingly seen as critical physiological, developmental and ecological mediators within and among living things, and between the latter and our abiotic environments. Therefore, it is no surprise that microbial communities may be altered, depleted or disrupted by social and economic determinants. Social inequality entails concrete alterations and differentiation of microbial communities among social groups, by way of such factors as nutritional access, environmental pollutants or green space availability, often to the detriment of human and ecosystem health. This special session will be organized as a panel discussion with break-out groups in order to provide participants the opportunity to discuss the ways in which social inequity interacts with microbiomes, and how we might intervene as scientists and communities to promote favorable microbiomes while advancing social equality. We hope to generate research questions and actionable items.

Panel speakers: Michael Friedman, Naupaka Zimmerman, Justin Stewart, Monica Trujillo, Sue Ishaq, Sierra Jech, Jennifer Bhatnagar, and Ariangela Kozik

ESA meeting program
: https://www.esa.org/longbeach/

Citation: The Microbes and Social Equity Working group, “Special Session 17: “Microbiomes and Social Equity” (19205).”, Ecological Society of America 2021. (virtual). Aug 5, 2021.

Recent Publication:

Ishaq, S.L., Parada Flores, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Chauhan, A., Pathak, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4.

A close-up picture of petri dishes containing a light yellow film of microbes.

2020 Year In Review

As has become a New Year’s Eve tradition, here is the Ishaq Lab’s Year in Review for 2020! In previous years, I remarked on difficult and delightful times alike, but 2020 has been a year full of intense loss for so many, and some have unfairly borne more of that heavy weight. In reflecting on whether to go ahead with the post for this year, I chose to do so and to include a tone of optimism and hope because, for the first time in the Ishaq Lab, I am not writing the story of me, I am writing the story of we. Even though we couldn’t all be together this year, the Ishaq Lab has tried to do our best to stay connected, and I have had the pleasure of watching my new lab team work together and grow as scientists. I am proud of how they have handled this year, and I wanted to share their triumphs.

Research

2020 was the year for launching the first official projects of the Ishaq Lab, including a field project, a mouse project, and a handful of data analysis or microbial community projects.

A screenshot from a virtual lab meeting, featuring 5 women.

Early in the year, students began joining the lab, and we had our very first lab meeting, featuring Adwoa Dankwa (UM Perry lab), Alex Fahey (in the office with me), Tindall Ouverson (MSU, Menalled/Seipel lab), and Johanna Holman. Ironically, we had our first lab meeting over Zoom to facilitate students in multiple geographic areas, not suspecting we would only have virtual lab meetings this year.

The first field project was a literal one – a soil project! Because of the pandemic response in the spring and early summer, laboratory work was reduced until we could do so safely in enclosed spaces. But, we were able to launch a field project because the samples could be collected and processed by one person alone over the summer. Undergrad Nick Hershbine, who is majoring in Ecology and Environmental Sciences, has been investigating the microbial community in blueberry soil from farms around Maine. This is part of a larger project led by Dr. Lily Calderwood, and is supported by the  Wild Blueberry Commission of Maine (“Exploration of Soil Microbiota in Wild Blueberry Soils“). Nick is in the process of data analysis and interpretation, and we hope to write up the preliminary results over the winter.


The Ishaq Lab also launched its first mouse project! This is my first time managing mice, and luckily I have expert collaborators at Husson University and a stellar grad student taking the lead on those portions. I’ll be overseeing the microbial ecology aspects, done by master’s student Johanna Holman for her graduate work. Joe Balkan, a Biology undergrad at Tufts University, has been reviewing previous literature for culturing protocols, and will be joining us for two weeks over break to help with some bacterial work. Undergrad Evan Warburton, who started in the fall semester, will pick up that microbiology work from Joe at the beginning of the spring semester.

The Ishaq Lab also had its first student presentation this year, by master’s student Sarah Hosler giving a graduate seminar on her proposed research for her degree, which involves host-microbial interactions in ruminants. The first portion of laboratory work for her project will take place starting in winter break. We’re not ready to share any details, but first we will be trying out some new methodology, as well as recreating some older methodology which has fallen out of fashion.

As part of that first step, Sarah will be assisting with the Capstone project of undergrad Emily Pierce, who was awarded a UMaine CUGR undergrad fellowship to fund her work this spring. Emily will be investigating host-microbe interactions during Cryptosporidium parvum infections, something which routinely devastates newborn livestock. We had anticipated running this experiment last summer, but postponed it for safety. Emily and master’s of professional studies Alex Fahey have made good use of that delay, however, and have been spending the time reading scientific manuscripts, assembling experimental protocols, and designing their project. Alex does not need to complete a thesis for her degree, it’s more about assembling a variety of skills, so she has participated in a number of supportive activities this year.

Undergrad Jade Chin has been working on her Honor’s Thesis project, the scope of which has had to nimbly pivot over the past year as we weren’t sure what we would be able to accomplish during the pandemic. For example, we spent two months waiting for DNA extraction kits to arrive due to supply shortages and the federal disruption of the postal service. Those kits are critical to the very first step of the experimental procedures and one we could not skip. Jade will defend her Honors thesis in spring 2021, including a written thesis, an oral presentation, and even a short interview with her thesis committee, although it will be less formal and less strenuous than a graduate-level defense.

Grace Lee, an undergrad at Bowdoin College, has been working on data analysis of microbial communities associated with lobster in aquaculture, which is part of a larger project by Drs. Debbie Bouchard, Jean MacRae, and Heather Hamlin. The dataset is a large and complicated one, though with an elegant experimental design. We anticipate writing up the results beginning this winter and continuing through the spring. Grace will be joined by an undergrad who I have been mentoring in my AVS 401 Capstone class, who will be contributing a literature review for the manuscript.


Three papers were published this year, which were all part of previous projects at former positions. This included the culmination of my post-doc work in the Menalled Lab from back in 2016, and one of the small projects I participated in while at BioBE from 2017 to mid 2019.

  1. Horve, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8: e9580. Article.
  2. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20. Article.
  3. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989. Article. This was accepted in 2019 but not officially published till 2020.

It’s very common to have a slump in publications when starting a new position, and particularly when that involves moving to a new institution and establishing a new lab group. Research can take awhile to gain momentum, especially when you need to recruit and train new lab members. Or, when those lab members have to pause their lab work for global public health reasons. The Ishaq lab isn’t worried, we’ll make up for it in 2021. With all the ongoing projects, we anticipate a handful of other papers being developed next year. I’ve also got four manuscripts that have been in review for months, a process which has also been (understandably) delayed because of the pandemic.

Five stickers advertising the Ishaq Lab, with different photos of lab equipment, bacterial culture plates, and sheep.
We tried out some designs for Ishaq Lab stickers!

Teaching

I taught three new classes this year; one that was new to me and two that I developed myself. In spring 2020, I taught a special topics version of my DNA sequencing data analysis class, which means that I got provisional approval to teach it as a one-off while I completed the full course approval. Because the data analysis class is cross-listed for undergraduate seniors and for graduate students, it needed to go through two different curricula approval processes, and curricula must be approved a certain amount of time before the first instance of the class. That class has now been formally approved as AVS 454/554. From the spring version, two scientific manuscripts are in review, and a third is in preparation while more data are added. We managed to achieve a lot in the spring class, considering halfway through the semester we switched to remote instruction only as the early throes of the pandemic descended.

The other two new classes I taught this fall, including the first part of the Animal and Veterinary Sciences Capstone Experience, AVS 401, which instructs students on writing and presenting research proposals and matches students with a research mentor to try and complete the project. It was particularly challenging to do that this fall, when many researchers still had their work on pause because of the pandemic. I’ll be continuing this class in the spring as AVS 402, in which students present what they’ve done. While only a few AVS students will pursue research as a career, they will all need to implement the scientific method and the ethos of research into their lives no matter where they end up. Being able to find, assess, and critique information are all critical skills which this Capstone Experience helps them to develop.

I taught AVS 254, Introduction to Animal Microbiomes. I’ve previously taught some of this material, but to very different student audiences, which required a lot of course development on the fly over the semester. Even with the previous material, I still needed to revise all my previous lectures to adapt to a new lecture length, add new ones to make up about half the semester, and, as our understanding of host-associated microbiomes evolves over time, the course materials needed to be updated (annually) to present up-to-date knowledge. The last lecture of the semester was a compiled video of ‘science journeys‘, featuring researchers in host-associated microbiology sharing what they work on and how they got here. You can watch the video, too!

I also spent a lot of time this fall curating the Teaching Statement portion of my tenure packet, some of which I shared as a series of posts this fall. Next spring I will have my third-year review, which will be the first official hurdle and where I get more substantive feedback from my peer committee about the trajectory of my teaching, research, and outreach as I develop my packet to apply for tenure in ~ year 5. In 2021, I have a planned blog post describing the history and process of tenure, and I will likely share other portions of my tenure packet, such as my research statement.

Presentations from my couch

As I recently posted, 2020 has been The Year of The Virtual Conference. Many conference in spring and summer of 2020 were outright cancelled, but some managed to revise their format and be held virtually later in the year. This was achieved with a combination of live-streaming and pre-recorded content, all of which became on-demand during the conference. Viewers could ask questions through a chat function, or by posting questions directly to the presentation page. While early attempts to host large virtual meetings with researchers in multiple time zones faced a steep learning curve, overall, I think many people realized the potential provided by a virtual platform. For example, without travel costs, more students and early career researchers could afford to attend, and researchers with family care, health, or other constraints could participate on their own time.

Seven of the eight planned scientific presentations of my work took place in 2020, listed here with some links to video content.

Outreach

Screenshot from an online seminar. The video of the speaker is in the upper right corner, and the title slide is the rest of the image. The seminar is "A crash course in the gut microbiome" by Sue Ishaq at the University of Maine.

Similarly, seven of the eight planned public presentations took place, with some links to video content in the list below:

  1. University of Maine Medicine seminar series (virtual), “A crash course in the gut microbiome” , Nov 6, 2020. pdf of slides with annotated comments: ishaq-ummed-gut-crash-course-20201106
  2. Genomes to Phenomes (G2P) group, University of Maine. Co-hosted a session with grad student Alice Hotopp, on gut microbes and survival of reintroduced animals. Oct 30, 2020.
  3. University of Maine Cooperative Extension Oxford County 4-H Teen Science Cafe (virtual), “Gut microbes on the farm”, Oct 15, 2020. 
  4. BioME (Bioscience Association of Maine) Virtual Coffee Hour, “What is a microbiome and where can I get one?” Oct 14, 2020. I introduced myself and my research to 65 participants, who are biomedical professionals and state representatives in Maine. 
  5. University of Maine Cooperative Extension Oxford County 4-H Jamboree (virtual), “Gut microbes on the farm”, Aug 13, 2020. Video.
  6. Invited to lead Journal Club with the Fogler Library, August 4, 2020. led a 1 hour discussion on gut microbes and survival of reintroduced animals.
  7. Albright College Science Research Institute summer program 2020, which engages grades 5-12 in research.  “A crash course in the gut microbiome”, virtual presentation, Aug 4, 2020.

I’ve also been endeavoring to promote the AVS Capstone Experience projects, in part by sharing student-written project summaries on social media and UMaine news outlets. I will do something similar at the end of the spring 2021 semester when projects are complete. And, the online conferences have gotten me thinking about how to create an on-demand virtual symposium that is open to the public…

Blog

I published 45 posts this year, including this one, and was much chattier this year with over 26,000 words total. The most popular post this year was What is academic Outreach/Extension, a sleeper post from 2017 which finally ended the popularity reign of Work-Life Balance: What Do Professors Do?. A number of posts were tied for the least popular this year with one view each, but at the bottom of that possibly-arbitrary list, was A collaborative project got published on the biogeography of the calf digestive tract!, a publication announcement from 2018.

My site had its most popular year, with just over 5,000 visitors taking >8,250 views from 112 countries, as shown in the image below. This November had a record number of visitors, with >1,100! In total, my site has had >15,200 visitors and just under 24,000 views since January 2016, more than I had imagined possible when I began. The website visitors are joined by 64 wordpress followers, 100 on Instagram, 113 on Facebook, nearly 1200 on Twitter, and 0 on Tumblr, which I set up because wordpress will auto-reblog to there, just in case anyone still uses Tumblr.

Life

I picked up a new hobby this year – axe throwing! I tried it at an axe bar last winter and instantly took a shine to it. We made wood targets at home and bought a few throwing axes, and while I haven’t become the maverick I had hoped, it is a lot of fun. I’ve also picked up an arguably more useful skill, basic electrical work to change outlets and light switches! We’ve been slowly updating and renovating our house, and I’m looking forward to learning drywalling and flooring next near.

Looking Ahead

2021 is anticipated to be an exciting year, and will be a combination of wrapping up current projects so some of my students can graduate, as well as progressing the graduate work of Johanna and Sarah. In my “free time”, I’ll continue to fine-tune my curricula, and it’ll be back to the writing table as I revise the research proposals that I submitted this year which were not awarded funding. Of the twelve proposals I submitted in 2020, two were awarded, one is already revised and back in review, at least two will be revised and resubmitted, and at least two new ones are planned.

I’ll be part of my first graduate thesis defense as part of the committee, as Tindall Ouverson is expected to defend her master’s in 2021 from Montana State University. Tindall’s first paper on soil bacteria in agricultural fields is currently in review, and the data analysis for two more (one of which is not on soil microbes) is underway.

I’ll also be leading the committee for Jade’s Honors thesis defense in March. Alex won’t be giving a defense to finish her degree, but she’ll still be informally meeting her committee to reflect on her academic journey and if she’s prepared for a professional career. Johanna and Sarah will soon be inviting faculty to their committees, and next year I will be chairing those meetings.

I’ll be teaching the AVS 402 Capstone class for the first time, but as I already spent the fall semester with AVS seniors in AVS 401, it shouldn’t be any trouble. Just a LOT of revising papers and giving feedback. I’ll be teaching my DNA analysis class again, and will spend the next few weeks updating the materials from last spring when I taught the special topics version. I’ll also be compiling datasets for my students to work on, and hopefully, to turn into scientific manuscripts by the end of the semester.

A number of events developed by the Microbes and Social Equity working group will come to fruition in 2021, and I will finally be able to tell you about them in detail! Stay tuned for information on a speaker series running from February through April, a hybrid (virtual and in person) symposium in June, and a public announcement of a scientific journal special collection.

I’m also pleased to say that one of my cousins will be joining the website behind-the-scenes in 2021, to add alternative text to my website images to make them more inclusive. This and other work will serve as part of the requirement for science/service hours for membership to the Science National Honor Society! I’ll leave it to my cousin to make a formal introduction in a blog post on science accessibility, but welcome to the team!


See you next year!

Title slide of a presentation on "Framing the discussion of microorganisms as a facet of social equity in human health" by Dr. Suzanne (Sue) Ishaq for the inVIVO Planetary Health 2020 conference.

The year of the virtual conferences

2020 has been an interesting year for scientific conferences and meetings, which typically bring dozens to thousands of researchers and professionals together to share their work. Some of the bigger meetings, or those occurring early on in the pandemic, elected to cancel their events because there was no time to adjust the logistics for hosting a massive meeting online.

As the year progressed with no sign of the pandemic abating, more conferences opted for a modified event online. This included live-stream and/or recorded content, spacing the event over a longer period to reduce “zoom fatigue”, and making network events smaller virtual versions. It certainly would have been more rewarding to be able to have these in person, but I am pleased that conference organizers chose safety as their priority.

In some ways, having virtual content made the material more accessible. recordings meant you could watch content at your convenience, more organizations provided or required subtitles for presentations, and those who would otherwise not be able to attend, because of cost, childcare, or travel constraints, were able to participate.

The Ishaq Lab presentations for 2020 is below, with presenters denoted with an asterisk (*).

  1. Ishaq*, S.L.”Framing the discussion of microorganisms as a facet of social equity in human health”, inVIVO Planetary Health 2020 meeting. (revised to virtual) Amsterdam, Netherlands. Dec 2020.
  2. Yeoman*, C., Lachman, M., Ishaq, S., Olivo, S., Swartz, J., Herrygers, M., Berarddinelli, J.  “Development of Climactic Oral and Rectal Microbiomes Corresponds to Peak Immunoglobin Titers in Lambs.”  Conference of Research Workers in Animal Diseases (CRWAD) 2020. (revised to virtual) Dec 5, 2020.
  3. 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. (revised to virtual). Nov 15-25, 2020.
  4. Ouverson*, L..,  DuPre, M.E., Ishaq, S.L.,  Bourgault, M., Boss, D., Menalled, F., Seipel, T. “Soil microbial community response to cover crop mixtures, termination methods, and climate in the Northern Great Plains.” Ecological Society of America (ESA) 2020. (revised to virtual) Salt Lake City, UT. Aug 2020.
  5. Menalled*, F.D., Seipel, T., Ishaq, S.L. “Agroecosystem resilience is modified by management system via plant–soil feedbacks.” Ecological Society of America (ESA) 2020. (revised to virtual) Salt Lake City, UT. Aug 2020.
  6. [meeting cancelled] Horve*, P.F., Dietz, L., Ishaq, S.L., Fretz, M., Van Den Wymelenberg, K. “Characterization of Viable Microbial Communities on Healthcare Associated Window Components.” American Society for Microbiology Microbe 2020, Chicago, IL. Jun 2020.
  7. [meeting cancelled] Horve*, P.F., Dietz, L., Ishaq, S.L., Fretz, M., Van Den Wymelenberg, K. “Characterization of Viable Microbial Communities on Healthcare Associated Window Components.” 2020 Microbiology of the Built Environment (MoBE) Gordon Research Conference, Andover, NH. Jun 2020.
  8. Ishaq*, S.L. “Framing the discussion of microorganisms as a facet of social equity in human health”. 3rd annual  Institute for Health in the Built Environment Build Health 2020. (revised to virtual) Portland, OR. May 2020. (invited). Video.
  9. Zeng*, H., Safratowich, B.D., Liu, Z., Bukowski, M.R., Ishaq, S.L. “Supplementation of calcium and vitamin D reduces colonic inflammation and beta-catenin signaling in C57BL/6 mice fed a western diet.” American Society for Nutrition 2020. (revised to virtual) Seattle, WA. June 2020.
Screenshot from an online seminar. The video of the speaker is in the upper right corner, and the title slide is the rest of the image. The seminar is "A crash course in the gut microbiome" by Sue Ishaq at the University of Maine.

UMaine Institute of Medicine seminar available online

Last Friday, I gave a seminar on “A crash course in the gut microbiome” to the University of Maine Institute of Medicine as part of their fall seminar series. You can find the previous seminars in that series here.

I was delighted to have the opportunity to share my science to researchers around Maine, and to have so many engaging questions!

You can find my seminar recording here, and a pdf of the slides with my presenter notes as annotated comments can be found here: