Tag: Updates

iScience Backstory on our collaborative work on ants, nematodes, and bacterial transfer

sueishaqlabLeave a comment

Over the summer, an article was published which featured a handful of researchers from across the US and research spanning a decade on the bacterial communities associated with invasive ants and nematodes in Maine. At the time, we were invited to also contribute a “Backstory” article to the scientific journal iScience which described the journey and the ideas.

That story authored by myself and Ellie Groden (senior researcher on the journal article) has just been published, and can be found here. I’d like to thank Dr. Sheba Agarwal, who was the editor on the paper, helped us develop our Backstory, and also spoke to me about this and other work as a guest on the WeTalkScience podcast.

Introducing the new MSE Directors Team!

ewisselLeave a comment

As the Microbes and Social Equity group (MSE) has grown and dramatically gained members (~120 members and many more subscribed to our newsletter) in 2021, it has become time to add leadership roles in charge of different aspects of running the group! The current list of Directors are self nominated MSE group members, who have generously volunteered their time in 2022 to support the initiatives and development of this international collaboration alongside Sue Ishaq.

The MSE group logo, microbes being weighed on the scale of justice!

MSE Director of Professional Development

Dr. Srinivasan Mahalingam, PhD, searching for post-doc position

This position will focus on finding existing professional development opportunities, as well as working with MSE members to develop new professional development opportunities which may be used for existing MSE members or the general scientific community.

Srinivasan is pictured from the shoulders up, wearing a light blue and red plaid button-up collared shirt, against a beige background.

Srinivasan Mahalingam: Srinivasan is a Ph.D. student in Animal Science at Bharathidasan University (India), working under the guidance of Professor Govindaraju Archunan. His PhD research focuses on the impact of cervicovaginal mucus microbiota (bacterial diversity, volatile fatty acids, and secretory proteins) on buffalo estrus. His is particularly interested in learning more about role of microbiota and their biomolecules (bacterial generated fatty acids and proteins/peptides) on the reproductive tract and intestine. He is currently seeking post-doctoral training to advance my professional research career. The opportunities and resources are immense. People in working societies are tremendously helpful and encouraging, and networking with other scientists has led to a wealth of opportunities. As he wishes to continue his contribution towards science and humanity, he feels MSE can provide ample opportunity to extend group members research professional in an adequate way.

MSE Director of Fundraising

Dr. Ashish Pathak, J.D., LL.M, Ph.D., Adjunct Professor/Research Scientist, Florida Agricultural and Mechanical University

This position will focus on finding funding for current and future MSE initiatives, such as events, travel to conferences, professional development, and salary compensation for MSE Director or assistant roles.

Ashish Pathak standing in front of calm ocean water on an overcast day, wearing a yellow collared polo shirt.

Ashish Pathak: Ashish’s academic background includes a BS in Biology followed by an MS and PhD in Environmental Sciences from FAMU, Tallahassee. Prior to graduate school at SOE, Ashish completed a law degree (akin to JD in the US) followed by an LLM degree (Master’s in Legal Law). During the MS program in law, he researched the nexus between impoverished communities and decline in human health due to complete lack of environmental equity and related environmental justice issues. Having held post-doctoral and now a research scientist position at FAMU’ SOE, he continues to conduct research at the intersection of sustainability sciences, the nexus between Food-Energy and Water, especially surrounding racial disparities and inequity with populations of color, and accomplish 14 out of the 17 sustainability development goals adopted by the United Nations in 2016

Social Media Management Team

This team will focus on connecting our members to our social media accounts and vice versa, to streamlining our social media content, and to assist in communications within the group and to the general scientific community. This position will also help improve existing webpages and consider additional functionality (e.g. online reading lists, a group-facing or public-facing member directory)

MSE Director of Social Media

Sarah Ishak, M.S. student, Université de Sherbrooke

arah is pictured here in front of a large body of water along a green trail. She is holding up two peace signs with her hands and is wearing a blue top and grey pants with a purple jacket tied around her waist.

Sarah Ishak: Hailing from the Land Down Under (Australia), Sarah is now a Master’s student at Université de Sherbrooke in Québec, Canada. She graduated from the University of Adelaide with a Bachelor of Science (Advanced) degree, and a Bachelor of Science (Honours) degree in Ecology and Environmental Science. Her current research project is looking at the microbiome of boreal mosses from the Eeyou-Istchee region of Québec. She joined the MSE working group in the hopes of helping to provide under-represented communities the space to share their research. In conjunction with Emily Wissel and Dr. Katherine Maki, we hope to share stories and keep you updated on what the MSE Working Group has in store! You can find Sarah on twitter @microbluvrsarahvrsarah

Social Media Curator

Emily Wissel, PhD candidate, Emory University
Bio below!

Social Media Curator

Dr. Katherine Maki, PhD., Post Doc at NIH

Katherine Maki is pictures here in front of a field in a flowery blouse and a black blazer.

Katherine Maki: Katherine Maki is a postdoctoral fellow at the National Institutes of Health, Clinical Center, in the Translational Biobehavioral and Health Disparities Branch, and she is transitioning to an Assistant Clinical Investigator Position in the same department early 2022. Dr. Maki is a nurse practitioner and received her PhD from the University of Illinois at Chicago, College of Nursing. Her dissertation research examined the effects of chronic sleep disruption on the microbiome and cardiovascular system in rats. As a postdoctoral fellow, Dr. Maki worked on an interdisciplinary team on several intramural and extramural research protocols focusing on the human microbiome. She combines oral and gut microbiome analyses with biosignal and neuroimaging technology to study the gut-brain axis, and how it relates to health and disease. Dr. Maki is particularly interested in the relationship between environmental factors such as poor sleep and alcohol abuse with cardiovascular risk through microbial and metabolite mechanisms in humans.

MSE Director of Resource Dissemination

Emily Wissel, PhD candidate, Emory University

This position will work closely with Social Media and Resource Archiving Teams, and will focus on gathering information and resources to share within the group (e.g. new publications, funding opportunities). This position will facilitate resource gathering from members, and curate in-group emails to disseminate to interested members only to avoid excessively emailing group members.

Emily Wissel on a sandy beach, with a view of the ocean and a mountainside in the background. She has glasses and is wearing a long sleeve green jacket.

Emily Wissel: Emily Wissel is a PhD candidate and NSF Graduate Research Fellow at Emory University. Her dissertation work explores how the gut and vaginal microbiome change during pregnancy and how factors like antibiotics impact that shift. Emily explores how our understanding of the microbiome can meaningfully inform health interventions and help us better understand mental health and cognition. You can find Emily on Twitter @emily_wissel

MSE Director of Resource Archiving

Patrick Horve, PhD student, University of Oregon

This position will focus on the long-term archiving of group documents, media, and other materials, including making them readily available to members, and revising working documents into a more professional draft before archiving.

Patrick is pictured here in a navy blue suit and tie against a red brick

Patrick Horve: Patrick is currently a PhD student at the University of Oregon in Eugene, Oregon in the Institute of Molecular Biology. He is broadly interested in the interactions between microorganisms and the world around them, including the environment, other microorganisms, animals, and humans. These interactions can be both detrimental and beneficial for all of the individuals involved, making both positive and negative engagement with beneficial microbiomes through access to public resources, nutritious food, clean water and air, safe shelter, social interactions, and effective medicine a potentially (and often) inequitable process. By working with MSE, he hopes to encourage the combining of microbiology and social equity work and the promotion of evidence-based and equitable public policy. You can find him on twitter at @PatrickHorve

UMaine REU ANEW program applications for undergraduates are open for summer 2022!

sueishaqlabLeave a comment

The University of Maine Research Experience for Undergraduates (REU) ANEW 2022 program is now open and accepting applications!  The REU program is intended to engage undergraduates in research, including those who have no or very little research experience.

Applications are currently being accepted for the REU ANEW summer 2022 program which is planned to be run in person from June 6 to August 12, 2022. Applications must be received by February 15, 2022 for full consideration. 

The website is updated with information for next year’s program and a new application form, or you can check out the attached poster:

reu-anew-flyer-2022Download

The Microbes and Social Equity working group is turning 2!

sueishaqlabLeave a comment

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.

Speaking in The Wildlife Society Nutritional Ecology seminar series!

sueishaqlabLeave a comment

I was invited to present a seminar in to the spring to The Wildlife Society Nutritional Ecology seminar series, and I’m honored to be part of an all-star line-up!! The talks being given from November through March, and you can find more info the TWS’ seminar announcement, which I have quoted below:

Please join The Wildlife Society’s Nutritional Ecology Working Group for our winter webinar series (https://wildlife.org/newg/webinar-series/). We will host virtual webinars at Noon (Mt Standard Time) on the second Wednesday of every month from 10 November 2021 – 9 March 2022. 

This year’s webinar theme is “The digestive biome and the influence of these organisms on nutrition and condition of wildlife.”  Our list of speakers this year are very diverse across many taxa!

Nutrition is vitally important for every life process of every living creature—from optimizing growth and reproduction to decreasing susceptibility to disease, predation, and death.  The science of nutritional ecology links food resources available to an animal with individual- and population-level performance, as well as to habitat- and landscape-level dynamics.  With data collected on nutritional requirements, food availability and quality, foraging and life history strategies under different environmental conditions, and body mass and condition, managers can predict how changes in one will impact the other. This provides a clear path for managing food resources in a way that optimizes population performance, or alternatively, for managing animal populations to optimize the health of ecosystems.  As global issues such as climate change, loss of habitat, and the spread of disease and parasites increasingly impact wildlife populations, the need for understanding the degree to which populations are limited by nutrition, and how we can best manage for nutrition, increases as well.

All webinars will be held at 12:00 pm Mountain Standard Time.  A flyer with zoom link will be sent out ahead of each webinar.

November 10th, 2021 – Jennifer Forbey – Boise State University. “Manipulating metabolites & microbes to manage wild herbivores”

 December 8th, 2021 – Kevin Kohl – University of Pittsburgh. “Who’s in charge here?: Microbial contributions to animal physiology, ecology, and evolution”

 January 12th, 2022 – Denise Dearing – University of Utah “Metabolic enabling and detoxification by gut microbes”

 February 9th, 2022 – Candace Williams – San Diego Zoo Wildlife Alliance. “Gut microbiota and their role in rhinoceros infertility”

 March 9th, 2022 – Sue Ishaq – University of Maine. “Moose rumen microbes and you”

For additional questions on the Nutritional Ecology Working Group, please visit our website (https://wildlife.org/newg/) or send us an email (tws.nutritional.ecology@gmail.com).  

The Wildlife Society

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

sueishaqlabLeave a comment

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

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

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

Abstract:

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

This work was presented at a recent scientific conference:

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

Invited presentation about microbes and social equity this winter

sueishaqlabLeave a comment

Mark your calendars – I have been invited to give two presentations on microbes and social equity in general, and the MSE group in particular, this winter! Both events require prior registration.

You can also catch up with our recent publication as well as the other awesome work in the mSystems Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure.

 10th annual conference of inVIVO Planetary Health 

This year’s theme is “Project Earthrise: From Healing to Flourishing for People, Places and Planet”

1-7 December 2021. Virtual conference, with on-demand and live-stream content. Registration is required.

From the event site: “The meeting will bring together a tremendous network of like-minded people from diverse fields whose interests span from planetary/population/ environmental health to microbial ecology/ systems biology and the deep biological mechanisms—all aiming to work in a more integrated systems framework as we seek to improve personal, environmental, economicand societal health alike. As always, our emphasis on meaningful collaborations and productive friendships as on the data and opportunities we generate.”

My talk title is pending.

2nd Rhode Island Microbiome Symposium at URI College of Pharmacy

14 January, 2022. In person. Registration is required.

From the event site: “The goal of this symposium is to promote microbiome and microbial research in Rhode Island and the Northeast by bringing together researchers from state universities and hospitals who currently work on microbiome research or who are interested in starting microbiome research.  We hope this symposium will stimulate networking and result in new collaborations, grant proposals and manuscripts.  While the scope is broad to encourage participation, the general focus will be on microbiome research relevant to the State of Rhode Island such as ocean health, aquaculture and precision medicine initiatives.”

Dr. Suzanne Ishaq
University of Maine
School of Food and Agriculture

Title: Microbes at the Nexus of Environmental, Biological, and Social Research

Invited Keynote Speaker

Dr. Ishaq 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, 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. Membership is free and open to all.

Photo credit: Patrick Wine, University of Maine

Accepted into the first cohort of the UMaine EMPOWER Mentoring Program!

sueishaqlabLeave a comment

I’m pleased to announce that I was accepted into the first cohort of researchers for the new Enhanced Mentoring Program with Opportunities for Ways to Excel in Research (EMPOWER) at the University of Maine! We had our program launch yesterday, during which the 28 early-career researchers and their established-career mentors met to discuss the program goals, namely, to gain professional development in funding proposal writing and increase our success rate in an increasing-competitive research funding system.

Dr. Anne Lichtenwalner graciously accepted my request to act as my mentor for the program, which formalizes the mentorship and guidance she has voluntarily offered me without hesitation in my first two years at UMaine. Anne and I have also co-mentored four undergraduate students through their senior Capstone Experience research project in Animal and Veterinary Science. Over the next year, we will meet regularly to discuss and develop my research proposals related to animal health and microbiomes.

Welcome new Ishaq Lab members!

sueishaqlabLeave a comment

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

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

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

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

Listen to your microbes

sueishaqlabLeave a comment

Microbes are found everywhere, including on our skin or in our digestive tract, and the ones that hang out with us are called “host-associated”. Microbes interact with us in many different of ways, for better or for worse. To describe some common host-microbe interactions, the AVS254 Intro to Animal Microbiomes students collaborated on some playlists! Check them out on Spotify, and please note some songs are rated E for ‘explicit’ language. 

Pathobiont: Ever had a microbe that you thought loved you only to have it turn on you? This playlist takes you from besties to bacteriosis.

Symbiont: Sometimes you just can’t live without your microbes. Welcome to your happily ever after, even if it is a tiny one.

Exogenous: Sometimes hosts and microbes are like ships passing in the night. This playlist tells you about the microbe that got away.