I'm an assistant professor of animal and veterinary studies at the University of Maine, Orono, studying how animals get their microbes. I am also the Founder and Lead of the Microbes and Social Equity working group.
Today was a blast at the Microbiome Workshop on Amplicon Library Generation, which was generously sponsored by QIAGEN!!! Their sponsorship provided the opportunity for 7 students to learn how to prepare their samples for sequencing.
We are grateful to Kevin Joseph, Chao Jie Zhen, and Karen Rodland from QIAGEN for their time, expertise, and support!
Brigit Humphreys, Fernanda Amaral Della Rosa, and Chao Jie ZhenKevin Josepg, Miranda Seixas and Alexandra Ruff
We are also grateful to Alex Sacco, Genomics Facility Manager at UMaine, as well as UMaine CORE, for helping to organize the workshop and ensure that students had access to specialized equipment and supplies. Alex and I have been co-organizing a series of workshops, and we hope to make these a regular part of genomics education at UMaine.
Miranda Seixas and Alexandra Ruff
Miranda Seixas and Alexandra Ruff
Brigit Humphreys and Fernanda Amaral Della Rosa
Carly Coughlin
Brigit Humphreys, Chao Jie Zhen, and Georgia Hynes
Brigit Humphreys, Chao Jie Zhen, Lydia Teng
During today’s workshop, students investigated the diversity of microbial communities by preparing sequencing libraries targeting bacterial, archaeal, and fungal marker genes. Using extracted microbial DNA, students amplified regions of the bacterial and archaeal 16S rRNA gene as well as the fungal ITS region, which are widely used for taxonomic classification of microbial species.
Students used the QIAseq 16S/ITS Pro Screening Panel, which targets multiple variable regions of the 16S gene and the fungal ITS region across three primer pools. Students learned how to use the DNA from their samples to generate copies of the gene they are interested in using PCR. Unlike other kits, this one calls for three reactions for each sample sample for different regions of the genes. These are combined later, allowing for screening of the full 16S gene and the ITS region rather than a fragment that might only be 1/4 to 1/3 of the whole gene (some sequncing is limited to certain lengths of DNA).
Following targeted amplification, students performed bead‑based cleanup steps and completed a second PCR to add unique sample indices and Illumina sequencing adapters. The resulting libraries were purified, quality‑controlled using fragment analysis concepts discussed during the workshop, and prepared for downstream sequencing on Illumina platforms.
By amplifying and sequencing these variable regions, students generated data that can be used to compare microbial community composition across different sample types. QIAGEN will be joining us on campus in June, too, for the Microbiome Symposium at UMaine. We will be hosting a data workshop there, and I also teach a class on data analysis in the fall.
Whether we are interested in the way coastal wetlands sequester carbon, how diet affects us differently, or how public and environmental health are inextricably linked – research on the microbiome can reveal how systems connect. Join us for two days to learn about how microbial communities impact ecosystems, food production, health, and more; to hear from experts researching these issues in New England and beyond; and discuss the technology and data analysis which can boost your own research.
UMaine Buchanan Alumni House, 160 College Ave, Orono, ME 04473
Dr. Sue Ishaq, PhD, Associate Professor of Microbiomes, Associate Director of Special Projects in the School of Food and Agriculture at the UMaine; member of the Board of Directors at ASM; Founder and Lead of the Microbes and Social Equity working group.
9:15 – 10:15 Plenary Presentation
“The second messenger c-di-GMP in Bordetella”
Dr. Federico Sisti, Ph.D., Investigator, Institute of Biotechnology and Molecular Biology (IBBM) of the National Scientific and Technical Research Council (CONICET). Dr. Sisti is incoming President-Elect at the American Society of Microbiology, and the first ASM President representing its global membership.
10:15 – 10:30 Break
10:30 – 12:00 Session 1: Microbial mayhem or tiny partners in health?
“Leveraging organ-on-chip technology to study gut microbiome effects on human health and disease“, Dr. Dani Brassino, PhD, Assistant Professor of Gut Microbiome and Cancer Interactions, The University of Vermont College of Medicine.
Following a B.S. in Nutrition Science and at the University of Texas, Dani Brasino acquired a PhD in Chemical Engineering at the University of Colorado. At CU, she developed synthetic phospholipids as part of an artificial cell project and acquired experience in microfluidics fabrication. Combining these experiences, she led development of a novel polycarbonate-based organ-on-chip platform as a postdoc at Oregon Health and Science University. Now her lab, the μMicrobiome Lab, aims to further develop and apply gut microbiome-on-chips to study the relationship between the human gut microbiome, distal disease progression, and therapeutic efficacy.
“Addiction and the microbiome”, Dr. Jason Bubier, Ph.D., Senior Research Scientist, Center for Addiction Biology, The Jackson Laboratory
“Food insecurity, gut microbiome, health”, Dr. Maria Carlota Dao, Ph.D., Assistant Professor of Human Nutrition, University of New Hampshire.
Dr. Maria Carlota Dao is an Assistant Professor of Human Nutrition in the Department of Agriculture, Nutrition, and Food Systems at the University of New Hampshire. As an interdisciplinary scientist focused on obesity research, she investigates the interplay of cardiometabolic risks, dietary and psychosocial factors, and the gut microbiota. Through this work she seeks to address obesity in health disparity populations. Prior to becoming a faculty member at UNH, Dr. Dao worked as a scientist at the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University. Her training includes a postdoctoral fellowship at the Sorbonne University and INSERM (Institute of Cardiometabolism and Nutrition) in France, and a PhD in Biochemical and Molecular Nutrition from the Friedman School of Nutrition Science and Policy at Tufts University.
12:00 – 1:15 Lunch, provided
1:15 – 2:45 Session 2: Biochemical geniuses: microbes from soil to sea
“How to build a microbiome to “breed” better plant-inoculants.” Dr. Anna O’Brien, PhD., Assistant Professor of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire.
She is originally from the Pacific Northwest. She received her B.S. in Plant Biology from the University of Washington, her PhD from the University of California Davis, where she worked with Jeffrey Ross-Ibarra and Sharon Strauss on the impacts of rhizosphere biota on trait divergence and adaptation in the wild relatives of maize. Anna Post-doc’ed at the University of Toronto, primarily with Megan Frederickson, but also with Chelsea Rochman, David Sinton and unofficially, Stephen Wright, in everything to do with duckweeds and duckweed microbiomes (from mutualisms, to ecotoxicology, to engineering better tools, and experimental “evolution” and epigenetics).
“Salt marsh microbiomes are impacted by waterway restrictions in coastal Maine.” Heather Richard, M.S., PhD. Candidate in Ecology and Environmental Sciences, UMaine.
Heather joined the University of Maine in 2021 as a PhD student with the Maine eDNA program and studies the impacts of bridges and roads on microbial communities in salt marsh habitats. Her background in Ecology led her to pursue a career in informal environmental education for several years before getting a Master’s degree in Marine Biology from San Francisco State University studying biofilms on microplastics pollution. Upon returning to Maine in 2016 she led local research for a coastal non-profit organization and has since been dedicated to studying coastal environmental issues relevant to Maine. She has found a true passion in bioinformatic analysis and is eager to learn new tools for data analysis of all kinds.
“Extreme microbiomes“, Scott Tighe, M.S., Senior Research Associate, Environmental Microbiome Engineering Research Group (EMERG Laboratory), University of Vermont, led the UVM Genomics CORE for 20 years.
2:45 – 3:00 Break
3:00 – 4:00 Session 3: Practical Applications
“Beverage safety”, Sam White, M.S., Quality Control Collaboratory (QC2), University of Southern Maine
Samantha White is a dedicated researcher and educator with extensive experience in analytical chemistry and the craft beverage industry. Sam manages the Quality Control Collaboratory at USM where she leads lab operations, quality control initiatives, research projects, and industry outreach programs.
“Title TBD” Dr. Sivaiva (Siva) Chavadi, PhD. Sr. Field Application Scientist NGS US-EAST, New England Biolabs
Several more talks are being arranged, details to follow!
4:00 – 5:00 pm Posters and networking
Agenda for June 12, 2026
Data analysis workshop in development!
8:00 – 9:00 am Breakfast, provided
9 – 12:00 pm Presentations, discussion, and demos in R on dealing with challenging datasets.
This includes combining microbiome data with other data types, combining qualitative and quantitative data, learning to evaluate microbiome data using demographic data, dealing with unba;anced groups especially in human microbiomes, and how to choose statistical tests for microbiome projects.
Workshop led by:
Sue Ishaq, PhD.
Laura Jackson, Ph.D., UMaine: Bioinformatics Program Coordinator & Graduate FacultyGraduate School of Biomedical Science & Engineering, Bioinformatician – CORE Strategic Operational Services.
Kevin Roberge, PhD. UMaine: Lecturer, Mathematics and Adjunct Professor, Women’s, Gender & Sexuality Studies.
We are grateful to our financial supporters, who helped make this symposium possible and accessible!
Future Microbiome Researcher Sponsors
These incredible sponsors not only helped support this symposium, but their generous donation helped to create several hands-on laboratory workshops to support training in microbiome technology!
Gold Sponsors
Silver Sponsors
If you would like to help sponsor this event, please contact sue.ishaq@maine.edu.
I’ll be on the road and in the air frequently this spring, as I was graciously invited on two international trips, I am participating in an international conference here in the US, and I am fostering microbiome events in Maine!
Ghent, Beligum
In May, I’ll be visiting Belgium for my first time, as I present my research at a seminar at Ghent University, and meet with health researchers and students!
Ghent is brimming with art, history, and science, and I’m looking forward to being steeped in these as I tour the canals a bit.
Where: MS Teams and Auditorium A – Campus Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent
Language: English
Organizer: The Interdisciplinary Medical and Health Seminar of May 2026 is co-organized by the Department of Public Health and Primary Care and the Department of Internal Medicine and Pediatrics.
Immediately after my trip to Ghent, I’ll travel to Trento, Italy, to speak at a microbiome workshop focused on combining qualitative and quantitative data.
Nestled in the Alps in northern Italy, Trento is likewise a hub for art, history, and science, and I can’t wait to learn from my colleagues while reveling in this view. I’ll finally get to spend time with Dr. Roberta Rafetta in person, as we’ve been colleagues for several years through MSE but only online.
Scope of the workshop: While always challenging to combine data with very different types, scopes, and timeframes, being able to combine complex (and often qualitative) social science data with quantitative microbial data is key to understanding the human microbiome. The workshop is led by my colleague Roberta, as well as the Segata Lab, who are leading a collaboration on the microbiome of people living in Antarctica.
“Reconciling time-averaged diet history, time-specific microbiome data, and time-independent feelings about diet and health.”
Presented by: Sue Ishaq, University of Maine
Abstract: Cruciferous vegetables, and the microbial metabolites that they stimulate in the gut, are sources of antioxidants and anti-inflammatories. For example, broccoli sprouts contain inactive glucosinolates (GSL), especially glucoraphanin (GLR), which some bacteria convert into bioactive sulforaphane (SFN) (i.e., GSL conversion). Broccoli sprout diets robustly reduce gut inflammation and other symptoms in mouse models of colitis, and GSL conversion is achieved in people using diet or GLR supplementation, with some evidence that regular consumption trains bacteria for GSL conversion over time. However, conversion efficiency is variable and unpredictable in people, and little is known about the specific bacteria, genes, or metabolic pathways responsible for GSL conversion. This study evaluated the impact of a 4- week steamed broccoli sprout dietary intervention, which is rich in GLR, on gut microbiome entrainment for GLR conversion (qPCR, metagenomics), gut microbial community structure or function (16S rRNA and metagenomics), gut metabolites (LC/MS-MS metabolite and untargeted metabolomics), and how diet made people feel (open-ended survey), as well as the correlation of GLR conversion and gut microbiota with self-reported diet (survey) and healthy eating index via the 2023 daily guidelines for Americans (diet history). While each data set provides results, the combination of datasets should yield information on why we saw these results. This presentation will focus on the conceptual and statistical challenges of combining radically distinct types of data to understand objective and subjective health information.
Washington, DC
In June, I’ll be heading back to D.C. for the ASM Microbe conference, to present my work as well as to engage in strategic planning and science advocacy as part of responsibilities as a member of the board.
“Making Microbial Anti-Inflammatories from Plant Secondary Compounds in Broccoli Sprouts, from Culture to Gut“
Authors: S. Ishaq, J. Holman, A. Kirkendall, L. Holcomb, A. Reynolds; University of Maine, Orono, ME, United States.
Inactive glucoraphanin (GLR) is found in broccoli, broccoli sprouts, and supplements, and specific gut bacteria are critical to biosynthesizing it into antioxidant and anti-inflammatory sulforaphane (SFN) in the colon, where it directly resolves colitis. GLR conversion in people is highly variable, and certain people lack some/all high-performing GLR-converting bacteria. Little is known about which gut bacteria/gene pathways are competent; if conversion can be induced/increased by introducing a probiotic; and if a probiotic would persist and remain active during acute gut inflammation when many taxa perish.
We previously identified that different preparations of broccoli sprouts fine-tunes the dispersal of dietary and microbially mediated metabolites in the gut, and induces gut-location-specific changes in bacterial communities. Using different parts of the intestines in broccoli sprout-fed mice, we isolated ~330 bacterial strains from 9 distinct morphologies using selective media and anaerobic culturing. We identified 16 bacterial candidates which grew better with GLR and metabolized it (confirmed with LC-MS/MS), which included pure-strain isolates, especially Enterobacter asburiae, and multi-species communities, especially Enterobacter asburiae, Bacillus sp., Paenibacillus sp., Clostridium farciminis, Enterococcus faecalis, that were stable across a dozen culturing passages.
While our isolated bacteria and our mixed colony strains all possess glycoside hydrolases CAZyme families which are implicated in GLR-conversion, only some strains used them. We performed RNA transcriptomics analysis on our probiotics with and without GLR in nutritious broth. In the mixed bacterial culture samples grown with GLR, all strains are active, but Clostridium and Bacillus dominate. But, with GLR, the Enterobacter asburiae in the mixed community dominates the transcriptome at the 12-hour and 24-hour time point when literature confirms that similar species have peak GLR-metabolizing activity. This matches our growth trial data, in which our GLR-metabolizing bacteria show a second bump in growth at 12 or 16 hours when cultured with GLR compared to media alone.
Finally, we piloted the use of our isolated strain, Enterobacter asburiae, and our mixed community as probiotics, with or without a 10% steamed broccoli sprout diet, as a means of abrogating the effects of chemically induced ulcerative colitis in a mouse model.
Funder: This work was supported by the NIH NIDDK, Biomedical Association of Maine, and the University of Maine Small Animal Research Facility.
Orono, Maine
Scattered across April, May, and June, are several workshops and a symposium at the University of Maine that I am co-organizing.
Sequencing Workshops for UMaine students and postdocs
Alex Sacco, CORE Genetics Facility Manager, and Sue Ishaq, Assoc. Prof. of Microbiomes, are organizing a series of hands-on workshops for graduate and undergraduate students to learn how to generate sequencing libraries for microbial communities or host genomes!
Microbiome Workshop 1: 16S and ITS Amplicon Library Generation with QIAGEN, April 15, 2026. Students will prepare amplicon sequencing libraries using QIAGEN kits for the 16S rRNA gene from bacteria and archaea, and the ITS region of fungi. This includes attaching barcodes/indexes and sequencing adapters, and quality control checks. Then, students will set up a sequencing run using Illumina chemistry. The sequencing reagents, and lunch, are generously provided by Qiagen, one of our Future Microbiome Researcher Sponsors for the Northen New England Microbiome Symposium.
Microbiome Workshop 2: Long-read amplicon analysis with New England Biolabs and Oxford Nanopore, May 1. Students will prepare amplicon sequencing libraries using NEB for whole-length 16S rRNA gene from bacteria and archaea, and the ITS region of fungi. This includes attaching barcodes/indexes and sequencing adapters, and quality control checks. Then, students will set up a sequencing run using Oxford nanopore chemistry. The sequencing reagents, and lunch, are generously provided by New England Biolabs, one of our Future Microbiome Researcher Sponsors for the Northen New England Microbiome Symposium.
Microbiome Workshop 3: RNA-Seq with Illumina, May 11-15, 2026. Students will prepare RNA sequencing libraries (for microbial or host RNA) using Illumina kits and workflows. This includes attaching barcodes/indexes and sequencing adapters, and quality control checks. Student will also set up a sequencing run using samples from the group using Illumina chemistry. The sequencing reagents, and lunch, are generously provided by Illumina, one of our Future Microbiome Researcher Sponsors for the Northen New England Microbiome Symposium.
The 2nd Northern New England Microbiome Symposium
Whether we are interested in the way coastal wetlands sequester carbon, how diet affects us differently, or how public and environmental health are inextricably linked – research on the microbiome can reveal how systems connect. Join us for two days to learn about how microbial communities impact ecosystems, food production, health, and more; to hear from experts researching these issues in New England and beyond; and discuss the technology and data analysis which can boost your own research.
UMaine Buchanan Alumni House, 160 College Ave, Orono, ME 04473
Events will be hosted January – December in 2026, on the last Wednesday of every month, 11:00 – 13:00 pm ET. Presented over Zoom.
After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.
New this year: the live session will be available free, but the on-demand video-recording will only be available to MSE members for the first year (and available to the public afterwards).
Summary:
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 we, 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.
Dr. Robin Patel is the Elizabeth P. and Robert E. Allen Professor of Individualized Medicine, Director of the Infectious Diseases Research Laboratory, Co-Director of the Clinical Bacteriology Laboratory, Vice Chair of Education in the Department of Laboratory Medicine and Pathology, and former Chair of the Division of Clinical Microbiology, at the Mayo Clinic. Professor Patel’s research focuses on understanding the inherent biology of periprosthetic infection. She has over 635 peer-reviewed publications, is supported by the National Institutes of Health and the Centers for Disease Control and Prevention, is the Director of the Laboratory Center of the Antibacterial Resistance Leadership Group of the National Institutes of Health, and is the Past President of the American Society for Microbiology. Her faculty page is here.
Events will be hosted January – December in 2026, on the last Wednesday of every month, 11:00 – 13:00 pm ET. Presented over Zoom.
After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.
New this year: the live session will be available free, but the on-demand video-recording will only be available to MSE members for the first year (and available to the public afterwards).
Summary:
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 we, 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.
Dr. Robin Patel is the Elizabeth P. and Robert E. Allen Professor of Individualized Medicine, Director of the Infectious Diseases Research Laboratory, Co-Director of the Clinical Bacteriology Laboratory, Vice Chair of Education in the Department of Laboratory Medicine and Pathology, and former Chair of the Division of Clinical Microbiology, at the Mayo Clinic. Professor Patel’s research focuses on understanding the inherent biology of periprosthetic infection. She has over 635 peer-reviewed publications, is supported by the National Institutes of Health and the Centers for Disease Control and Prevention, is the Director of the Laboratory Center of the Antibacterial Resistance Leadership Group of the National Institutes of Health, and is the Past President of the American Society for Microbiology. Her faculty page is here.
This paper was a collaborative effort by several members of the Microbiome Stewardship team, Panuya Athithan (grad student working with Emma), Kieran O’Doherty (fearless leader of the MiSt group), Emma Allen-Vercoe (maven of the human microbiome), and myself. Panuya and I led the paper, weaving our favorite stories of microbial symbioses together with existing studies that support the need for stewardship. Panuya is currently a PhD student working with Emma on a variety of projects, including a gut microbiome and early life project she was interviewed about here. She’s also a Young Director at the non-profit Fora: Network for Change, and was previously an undergraduate researcher while at the University of Waterloo.
A little over a year ago, the author team was discussing the need for papers which outline examples of critical host-microbial or ecosystem-microbial partnerships which are irreplaceable (unless you have several million years of free time to wait for evolution), as a means of supporting calls for taking action now to preserve life and ecosystems on what is currently the only planet we call home.
Over a series of conversations with the MiSt group, as well as during the first public meeting to create the IUCN Microbe Specialist Group, our author team honed our paper to address the concerns of researchers over the ability and practicality of stewardship microbes.
Left to right in the photo are some of the MiSt group; front: Zhongzhi (Michael) Sun, Emma Allen-Vercoe, Sue Ishaq; middle: Mikaela Beijbom, Mallory Choudoir, Sarah Elton, Kieran O’Doherty, Panuya Athithan; back: Grace Gabber, Andreas Heyland, Rob Beiko.
This paper is one of the first in a forthcoming special issue (announcement coming soon!), which will feature several invited papers from my microbiome stewardship colleagues (both original team and expansion pack researchers). These papers will expand upon the concept of what it means to share microbes between individuals, communities, and ecosystems; what it would mean to consider microbes as shared natural resources to which everyone had an innate right to; and how it would look for public and planetary health to reduce the harm of human industry and consumerism to live more sustainably and regain all the benefits that the microbial world can provide us.
Microbes first into the life rafts: preserving microbiomes to secure health in degrading ecosystems
Authors: Panuya Athithan 1,2*, Suzanne L. Ishaq 2,3,4*, Emma Allen-Vercoe 1,2 Kieran C. O’Doherty 2,4,5
1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1
2 The Microbiome Stewardship research group
3 School of Food and Agriculture, University of Maine, Orono, Maine, 04469
4 The Microbes and Social Equity working group, Orono, Maine, 04469
5 Department of Psychology, University of Guelph, Guelph, Ontario, N1G 2W1
Abstract
All organisms on the planet intrinsically rely on microbial ecosystems, and there are increasing calls from research communities to consider microbiota when administering personal or public health, ecosystem health, and the use of microbiota in personal or environmental health remediation, such as reducing the impacts of climate change, or protecting at-risk habitats which host rare microbiota. Through our collective work on the integral nature of microbiomes to host and environmental health, on health policy, and on the development of research and policy agendas, we have previously developed the concept of ‘microbiome stewardship’ and guidelines to promote consideration of microbial communities broadly or in specific scenarios. The practicality of stewarding one versus many microbiota is highly contextual, and will require different strategies for different scales of conservation. Here, we provide scientific arguments for the need for microbial stewardship, examples of possible solutions scaled to different ecological challenges or conservation goals, discourse on the logistical challenges which have been cited by research communities, and opportunities to use cutting-edge microbiome concepts and technology to implement large-scale interventions.
Sustainability Statement
Microorganisms are responsible for environmental and organismal health, and the stewardship of microbiota has applications for human, plant, animal, and environmental health on local and global scales. The concepts described here are pertinent, in particular, to the United Nations’ Sustainable Development Goal 3) good health and wellbeing. Additionally, our paper is relevant to goals 6) clean water and sanitation, 9) industry, innovation, and infrastructure, 11) sustainable cities and communities, 12) responsible consumption and production, 13) climate action, 14) life below water, 15) life on land, and 17) partnerships for the goals.
Graphical abstract: The concept of microbiome stewardship can be applied at multiple scales to provide guidance on both specific or general microbial interactions. Graphic made in Biorender under licence.
I was on a team led by Senior Federal Affairs Officer Nicole Zimmerman from the ASM Policy Team, along with incoming ASM President-Elect Dr. Federico Sisti, and current ASM President Dr. Alexander McAdam.
ASM is always looking for members who would like to learn how to advocate for science, share their stories with lawmakers, and help shape the future of science policy. You can find out more about recent advocacy from the ASM Policy Action Center, and specifically hear about ways to get involved iin the Action Network. Earlier in my career, I never thought I would be interested in getting involved in policy, or confident enough to advocate on behalf of 38,000 microbiologists, but the ASM Policy Training made it really easy for me to identify needs or concerns from my colleagues and students, collect data to demonstrate the impact of policies on our industry, and specify steps that legislators could take to seize opportunities or provide resolutions. With the global social, political, and economic turmoil we have all been facing for years– to put it mildly – having the opportunity to be a small part of building the future has been a meaningful part of my career. I highly recommend it!
Offering expertise and building trust
One of the messages that we were keen to share with US (and all) policymakers, articulated by incoming ASM President-Elect Dr. Federico Sisti, is that ASM members around the world have an incredible breadth and depth of expertise in all topics related to microbiology, and that we are here to help. ASM has always had a strong initiative for providing scientific information and policy support, including ASM policy staff and our thousands of members.
But, to create the collaborations between scientists and policy makers requires time to build trust and establish regular communication. Here, I had an advantage in that 3 of my meetings were with Maine lawmakers (Senators Angus King and Susan Collins, and Representative Jared Golden), and being a voting constituent lends weight to my voice as I spoke about how reduction in funding for education, and disruptions to research funding which also impacted student research opportunities, impacted students and communities in Maine.
From the classroom to Congress
Serendipitously, I know one of the staff members in Senator Susan Collins’ office, and it was a delightful surprise to run into Michael DeLorge, co-Valedictorian at UMaine in 2024 and student in my Intro to Animal Microbiomes class. My microbiomes class talks about the need for science in policymaking, as well as the need for diverse and far-reaching collaborations in order to solve global challenges, such as those set out by the United Nations Sustainable Development Goals.
I got even further into the connection between research and public policy, as well as federal funding, in my Capstone In Animal Science course, nicknamed “How To Be A Researcher”. I have a whole lecture about the federal funding process in the US, historic funding levels, and how agencies had been trying to improve equity in the distribution of funds (including to rural areas, primarily undergraduate institutions, and other universities which had received less research and education funding).
I also teach my students about designing impactful research by identifying problems to solve and the relevant impacted communities (humans, animals, plants, other organisms, ecosystems). Over the semester, students design research projects and detail them in funding proposals, but we write them backwards by first identifying who/what the students want to help, then identifying the problem or what they could help with, and then outlining the strategy for finding information so we could make a positive change.
And, I’m sure my Capstone students will be happy to hear that I put into practice what I make them do in the classroom: all of my meetings on Capitol Hill were essentially “Elevator Speeches”, short pitches which identify a problem and a possible solution in a succinct format that allows the listener to engage in a discussion with you. I’m happy to report that I kept all my speeches under the meeting time limit 😊
The views expressed in this post and in my meetings were my own and did not represent the institutions I am affiliated with.
The Lab is delighted to finally announce the publication of a study on the efficacy of a glucoraphanin supplement in converting to sulforaphane, and of the effect on or participation of gut microbes! The article can be found online here.
The study was run back in 2021 at Appalachian State University by Dr. Giuseppe Valacchi, Alessandra Pecorelli, and colleagues, when participants were given one dose of a glucoraphanin supplement combined with the plant enzyme myrosinase (which converts the GLR into the anti-inflammatory sulforaphane by the time the supplement gets to your small intestines), or one dose of the glucoraphanin supplement alone (in the absence of the plant enzyme, this requires gut microbes to convert GLR to SFN).
Yanyan and I were introduced to Dr. Jed Fahey when he joined the UMaine Institute of Medicine faculty network in 2022. We talked to Jed about his recent work Brassica Protection Products, a company he founded back in 1997 with Dr. Paul Talalay, and Yanyan and I were invited as collaborators in 2023 by Antony Talalay, CEO and Co-Founder, and Paul’s son.
As part of their dissertations, Marissa Kinney performed qPCR to quantify microbial genes during her master’s, and Lola Holcomb performed 16S rRNA bacterial community sequencing during her PhD. We submitted the manuscript for peer review in Dec 2024. After a slow review process, the paper was finally released in Feb 2026, and we’ve begun brainstorming the next step in our research. While Jed, Tony, and the BPP team are, of course, interested in how their supplement can be used to improve health, the Ishaq Lab is also interested in teasing apart why some people’s gut microbiome is very responsive to GLR supplementation and will produce a fair amount of sulforaphane, while other’s people’s gut won’t react to glucoraphanin at all.
Even more intriguing were the participants in the study who had very little glucoraphanin conversion even when the myrosinase enzyme that can do the conversion was provided in the supplement. In fact, there was a lot of variability in how effective the enzyme was depending on the person- implying there are other biological or environmental factors at play which may be impeding the conversion of glucoraphanin into an anti-inflammatory.
Angela Mastaloudis, Lola Holcomb, Jed W. Fahey, Camila Olson, David C. Nieman, Colin Kay, Robert O’Donnell, Alessandra Pecorelli, Marissa Kinney, Yanyan Li, Suzanne L. Ishaq & Giuseppe Valacchi. Scientific Reports, In Press. (2026)
Abstract: Inactive glucoraphanin (GR) in broccoli is converted to the antioxidant, anti-inflammatory, and anti-bacterial sulforaphane (SF) by cruciferous vegetable enzyme myrosinase (Myr), or similar enzymes from specific gut bacteria; both sources have variable efficiency. The effects of exogenous Myr on the conversion efficiency of GR to SF was compared to gut microbial Myr-like activity. In a randomized, double-blind, crossover study, sixteen subjects (9 F: 7 M) received a single oral dose of GR in broccoli seed extract with Myr-containing mustard seed powder, or broccoli seed extract alone, both with ascorbic acid. GR + Myr, on average, doubled the bioavailability of SF (39.8 ± 3.1%) compared to GR alone (18.6 ± 3.1%), and increased the conversion rate in the first 8 h (25.4% ± 2.7%) compared to GR alone (8.0% ± 2.7) based on measurement of urinary metabolites. There were no differences in fecal bacterial communities after the single dose; however, four bacterial GR-converting genes significantly correlated with GR conversion (p < 0.0155). To our knowledge, this is the first human study to simultaneously investigate (1) a well-defined Myr source, (2) broccoli seeds as source of GR, (3) prediction of gut microbial responsiveness to GR.
Events will be hosted January – December in 2026, on the last Wednesday of every month, 11:00 – 13:00 pm ET. Presented over Zoom.
After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.
Registration to the seminar and social hour is free, but required. New this year: the live session will be available free, but the on-demand video-recording will only be available to MSE members for the first year (and available to the public afterwards).
Summary:
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 we, 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.
Dr. Ashley Shade, PhD. is a Director of Research with the French National Center for Scientific Research at the University of Lyon, France. She studies microbial community ecology, biodiversity, and microbial responses to disturbances such as climate change. In 2024, she received the U.S. Presidential Early Career Award for Scientists and Engineers from President Biden for her work on microbial community resilience. As of 2025, she is the Editor in Chief of the scientific journal mSystems.
The Ishaq Lab is testing out some probiotics in mice this spring, as we look towards the next phase of our broccoli sprouts and gut microbiome work: generating solutions. It has been five years since our last mouse experiments, in part, because we have been busy digging into samples, data, and ideas from those studies.
We gained valuable insight into which and how gut bacteria might metabolize the inactive glucosinolates from broccoli sprouts – glucoraphanin being the one we focus on – and produce byproducts like sulforaphane which our gut cells can use to reduce the chemical and physical damage caused by inflammation or oxidation.
This process is easy in the lab and tricky in the real world – not everyone has the bacteria in their gut which can do it, some have the bacteria but they are not active, and some have the bacteria but they are making a different version of the byproduct which we cannot use.
For the past three years, we have been screening >300 gut bacteria to identify and select ones with the ability to grow in the presence of GLR and metabolize it into the byproducts SFN or SFN-nitrile (which can be antimicrobial towards some bacteria).
In culture, the byproducts more-or-less all help the bacteria to survive by providing sulfur, glucose, or other chemicals it needs, but also by acting as an antioxidant compound that binds to a free oxygen (reactive oxygen species) so it doesn’t try to bond with chemicals on the surface of cells and cause them damage (oxidation damage). The byproducts also appear to help the bacteria thrive in acidic culture media which they otherwise can’t survive. When cultured with colon cells and GLR, some of those bacteria and their byproducts reduce inflammation.
The culmination of the past few years of work was to choose two bacterial cultures to try out our idea: that probiotics plus the broccoli sprout diet would help individuals who were not responsive to the diet. Because the gut microbiome, health, and the way that an individual and their microbes respond to diet are all very complicated processes that are specific to each person, it’s easier to test some of these concepts first in the lab or, which we did in early January, in animal models that mimic disease conditions in humans.
We ran a short trial in mice to find out if our two bacterial cultures that were so successful in the lab would also be effective when put back into the chaotic and competitive ecosystem of the gut. To further challenge our bacteria, we tested their ability to survive and reduce inflammation during a flare up of ulcerative colitis.
Every day for almost two weeks, we weighed each mouse (shown below) to make sure the colitis did not cause too much weight loss. Sue, Alexis, Johanna, and Ashley were all approved to handle the mice, so we were in charge of picking them up to weigh them. This was no easy task – mice are agile!
Each day, we also collected feces from the cages to check for diarrhea, or for blood, which are two symptoms of colitis. Our undergrads Madison and Brian worked tirelessly to tweeze feces into collection tubes, and to use the FOBT cards to check for blood.
We used custom made gelatin cubes filled with probiotic to deliver our treatments. The gelatin stuck to the side of the cages which allowed us to easily see that our mice were consuming their probiotic.
It will take us months to process some of the samples we collected which are the most cost-effective to run, and the rest will have to wait in the freezer until we receive more funding (which could take months or years as the changes to the federal funding system have doubled the time it takes for proposals to be reviewed and the ~5-20% of accepted projects to receive funding). We collected >500 fecal samples (each with 5 – 10 pellets/sample), 200 gut samples, 100 intestinal tissue samples, and 50 blood samples! To help maximize the benefits of this experiment and use all parts of these mice we also collected samples for a course at UMaine which teaches pre-medical, pre-veterinary, nursing, biology, and other health-focused students how to make and read tissue slides, to better understand anatomy, physiology, developmental biology, and health.
Still, we gained valuable data already, and the experiment provided a unique opportunity for students to receive hands-on-training for evaluating disease intensity using fecal samples, using tissues to make slides for histology, evaluating intestinal damage to tissues, collecting samples using aseptic technique to prevent contaminating them, working safely with microbes, and collaboratively working as a team to advance knowledge of health. Myself and our grad team (Johanna, Alexis, and Ashley) managed the project, and our undergrad team (Madison, Brian, Aaron, and Alexandra) were there to help us label ~1000 tubes for sample collection, and collect hundreds of fecal pellets out of the used bedding so we could track mouse microbes. Undergrads were also able to learn some general mouse care and research facility care from the ‘mouse house’ technician at UMaine, Alexis R. A former UMaine undergrad in the AVS program, Alexis R. manages and cares for a wide variety of animal species and she was instrumental in helping us manage our intensive sample collection schedule.
Johanna, Ashley, Alexis, and Sue put in long hours during the mouse trial to collect samples each day.
This project was made possible by the help of many. Again, we are grateful to Alexis and the UMaine CORE staff who not only support research at specialized facilities but helped us to afford to run our pilot project, to Emma who runs the UMaine Electron Microscopy Lab for teaching students histology and microscopy, to all the undergraduate and graduate students who worked tirelessly to help each other on this project, and to the funding agencies which supporting the lab work that helped us get to this project: the Biomedical Association of Maine (graduate awards), the Crohn’s and Colitis Foundation (graduate awards), the NIH NIDDK, and the USDA.
The Ishaq Lab 