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.

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

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

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


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

Abstract:

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

This work was presented at a recent scientific conference:

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

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

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

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

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

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


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

Marissa Edwards

Undergraduate in Biology

Levesque Lab

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

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

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

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


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

Elise Gudde

Master’s Student of Ecology and Environmental Sciences

Levesque Lab

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

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

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


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

Rebecca French

Undergraduate in Animal and Veterinary Sciences

Ishaq Lab

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

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

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


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

Joe Beale

Undergraduate in Animal and Veterinary Sciences

Kamath Lab

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

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

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

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


Yvonne Booker

Undergraduate, Tuskeegee University

Levesque Lab

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

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

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

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

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

Rumening through camel microbes, by Myra Arshad

Written by Myra Arshad

Myra Arshad

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

Allow me to introduce myself. 

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

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

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

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

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

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

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

The Microbes and Social Equity Working Group is delighted to make its published debut, with this collaboratively-written perspective piece introducing ourselves and our goals. You can read about us here.

This piece also debuts the special series we are curating in partnership with the scientific journal mSystems; “Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure“. Over the next few months to a year, we will be adding additional peer-reviewed, cutting edge research, review, concept, and perspective pieces from researchers around the globe on a myriad of topics which center around social inequity and microbial exposures.

Ishaq, S.L., Parada, 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., Pathak, A., Chauhan, 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.A., 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.

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

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

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

Slide from Ishaq et al. Entomology 2020 presentation

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

Slide from Ishaq et al. Entomology 2020 presentation

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

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

Related Presentations

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

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

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

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

Abstract

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

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

A study I contributed to was published!

A study was recently published, led by Dr. Huawei Zeng, USDA Animal Research Station, on gut health, nutrition, and gut microbiota! I contributed analysis and interpretation for the gut community data, and though I appear as last author on this publication, it is truly because I contributed the least and not because I was administrative lead or the lead PI. I have worked with Dr. Zeng for several years, although we have never met in person,

Dr. Zeng’s presentation of this project can be found here: Adequacy of calcium and vitamin D enriches probiotic bacteria and reduces dysbiotic Parasutterela bacteria and inflammation in the colon of C57BL/6 mice fed a Western-style diet


Zeng, H., Safratowich, B.D., Liu, Z., Bukowski, , M.R., Ishaq, S.L. 2021. Adequacy of calcium and vitamin D reduces inflammation, β-catenin signaling, and dysbiotic Parasutterella bacteria in the colon of C57BL/6 mice fed a Western-style diet. Journal of Nutritional Biochemistry. In press.

Abstract

Adoption of an obesogenic diet low in calcium and vitamin D (CaD) leads to increased obesity, colonic inflammation, and cancer. However, the underlying mechanisms remain to be elucidated. We tested the hypothesis that CaD supplementation (from inadequacy to adequacy) may reduce colonic inflammation, oncogenic signaling, and dysbiosis in the colon of C57BL/6 mice fed a Western diet. Male C57/BL6 mice (4-week old) were assigned to 3 dietary groups for 36 weeks: (1) AIN76A as a control diet (AIN); (2) a defined rodent “new Western diet” (NWD); or (3) NWD with CaD supplementation (NWD/CaD). Compared to the AIN, mice receiving the NWD or NWD/CaD exhibited more than 0.2-fold increase in the levels of plasma leptin, tumor necrosis factor α (TNF-α) and body weight. The levels of plasma interleukin 6 (IL-6), inflammatory cell infiltration, and β-catenin/Ki67 protein (oncogenic signaling) were increased more than 0.8-fold in the NWD (but not NWD/CaD) group compared to the AIN group. Consistent with the inflammatory phenotype, colonic secondary bile acid (BA, inflammatory bacterial metabolite) levels increased more than 0.4-fold in the NWD group compared to the NWD/CaD and AIN groups. Furthermore, the abundance of colonic Proteobacteria (e.g., Parasutterela), considered signatures of dysbiosis, was increased more than 4-fold; and the α diversity of colonic bacterial species, indicative of health, was decreased by 30% in the NWD group compared to the AIN and NWD/CaD groups. Collectively, CaD adequacy reduces colonic inflammation, β-catenin oncogenic signaling, secondary BAs, and bacterial dysbiosis in mice fed with a Western diet.


This is part of a multi-year collaboration, with previous publications:

  • Zeng, H., Ishaq, S.L., Liu, Z., Bukowski, M.R. 2017. Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet. Journal of Nutritional Biochemistry 54:18-27. Impact 4.418. Article.
  • Zeng, H., Ishaq, S.L., Zhao, F-Q., Wright, A-D.G. 2016. Colonic inflammation accompanies an increase of b-catenin signaling Lachnospiraceae/Streptococcaceae in the hind-gut of high-fat diet-fed mice. Journal of Nutritional Biochemistry 25:30-36. Impact 4.518. Article

Of mice and many samples

The first mouse study of the Ishaq Lab (in conjunction with the Zhang and Li labs at Husson University) has concluded phase 1, which means that over a few short days, an incredible number of samples needed to be collected, preserved, and processed for further laboratory work (phase 2) which will take through the summer to complete.

Sample collection was made more challenging by the pandemic, because we needed to distance as much as possible, disinfect objects and surfaces, wear masks, and increase the amount of ventilation in a space. Luckily, this type of work lends itself to these types of precautions – not only did we already need to wear a significant amount of protective gear to work with mice or handle their feces, but biosafety work like this requires higher than usual ventilation and frequent sanitation of objects and spaces. Since some of this work could be performed simultaneously in different rooms, we were able to use both Ishaq lab spaces and the ‘mouse house’ to keep people distanced.

During the 40-day mouse study, ‘Team Broccoli’ collected:

  • 640 mouse body weight data measurements
  • 433 fecal samples, which were archived for possible culturing and/or sequencing
  • 400 additional samples collected over two days:
    • 40 blood samples for immune factor identification
    • 360 gut samples
      • Of which, 200 were PMA treated within 12 hours of collection for use in DNA sequencing
      • 160 of which will be cultured to isolate bacteria. This will create 1 ~ 8 isolates per sample that will need to be grown on its own plate, transferred to broth media, and then frozen with glycerol at -80C until they can be revived and studied later this year.

2019 review one of Indoor Air’s top downloaded articles for 2018 – 2019!

A collaborative review article that I was last author on was listed in the top 10% most downloaded papers of 208/2019 in the journal Indoor Air! Even more impressive, this review was published August 20, 2019, and it was still in the top 10% spanning from January 2019 – December 2019!!

This paper stems from my work on the microbiology of the built environment at BioBE, and reviews the interaction between chemistry, microbiology, and health in the built environment. It was co-authored and led by undergraduate students I was mentoring at the time, as well as research associates and PIs from the BioBE lab, and a variety of fabulous collaborators!

From one species to another: A review on the interaction between chemistry and microbiology in relation to cleaning in the built environment

Image of plastic wrapped over soil to inhibit weed growth.

NE IPM funded collaborative proposal!

I’m pleased to announce that a small grant proposal I am part of was just funded by the Northeastern Integrated Pest Management (IPM) Center! The proposal, “A Working Group on Tarping and Soil Solarization”, brings together researchers and food production professionals from across New England to identify the current use of tarping and soil solarization to prevent weed growth without the use of chemcials, as well as identify barriers to adoption of this practice, and develop research proposals to fill any knowledge gaps related to the use of these methods and their effect on crop production, weed suppression, soil microbiota, and the local ecosystem.

Led by Dr. Sonja Birthisel (UM), the working group team is comprised of Dr. Alicyn Smart (UM), myself, Master Nathalie Lounsbury (UNH), and Eva Kinnebrew (UVM). We will be joined by over a dozen other researchers across New England who perform agricultural research, along with dozens of ‘stakeholders’: producers and other food production professionals who have an interest in the group findings and would make use of any knowledge we generate.

Featured Image Credit: Soil Solarization, Wikimedia