Only 1 week remaining to submit your poster abstract for the Northern New England Microbiome Symposium at UMaine on June 11!

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

9:00 – 9:15 Welcome and Opening Remarks

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.

A headshot of Dr. Sue Ishaq, PhD in which she is wearing a black and white houndstooth pattern waistcoat and a white button up shirt. Graphics have been added to show a strand of DNA and the words "love your microbes"

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.

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.

Genetic and Microbiome Control of Addiction-like Behaviors in Mice”, Dr. Jason Bubier, Ph.D., Senior Research Scientist, Center for Addiction Biology, The Jackson Laboratory

Jason A. Bubier, Ph.D., is a Senior Research Scientist at The Jackson Laboratory, where he leads research at the intersection of genetics, behavior, and addiction biology. His work focuses on uncovering the genetic and physiological factors that shape vulnerability to addictive substances, with current projects examining the microbiome’s influence on behavior, the genetic architecture of opioid‑induced respiratory depression, and systems‑level pathways involved in addiction.

Dr. Bubier has spent more than two decades at The Jackson Laboratory, advancing through multiple research roles and contributing to major initiatives in functional genomics and behavioral genetics. He has authored more than 80 scientific publications, and his work is widely cited across fields including immunology, bioinformatics, and addiction science.

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.

Gut Anthro“, Dr. Amber Benezra, Assistant Professor of Science and Technology Studies at Stevens Institute of Technology

Dr. Benezra is a sociocultural anthropologist researching how studies of the human microbiome intersect with biomedical ethics, public health/technological infrastructures, and care. In partnership with human microbial ecologists, she has been developing an “anthropology of microbes” to address global health problems across disciplines. Her book, Gut Anthro (published by University of Minnesota Press in 2023) is the first ethnography of the microbiome.

“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. 

Heather Richard

Genomic Strategies for Discovering Microbial Dark Matter using Metagenomics“ Scott Tighe, M.S., Senior Research Associate, Environmental Microbiome Engineering Research Group, Dept of Civil Engineering, University of Vermont.
Scott Tighe is currently Senior Research Associate in the Environmental Microbiome Engineering Research Group in the Dept of Civil Engineering at the University of Vermont and past technical director of the UVM Genomics Facility. He has expertise in all areas of genomics, microbiology, and mycology with a specific focus on advancing the methods used for microbiome and metagenomic analysis. He specializes performing metagenomic analysis in global extreme sites such Greenland, Antarctica, Romania, Saudi Arabia, Crete, Tahiti, and the International Space Station to name a few and is currently the science lead of the Extreme Microbiome Project (XMP). Short Abstract: The ability to perform advanced genomic techniques on samples collected from extreme environments demands high performance reagents and techniques not commonly used in most labs today. For the past15 years, our projects have developed novel sampling and DNA sequencing protocols for profiling a variety of environments, including snow, glaciers, Antarctic lakes, Romanian caves, thermophilic ecosystems, halophilic, acidic, alkaline lakes, anaerobic digestors as well as organisms from bioaerosols and the International Space Station. Technical approaches include novel liquid concentrating devices, sample disruptors, biopulverizers, and field use of the Oxford Nanopore DNA sequencer. Whole Genome sequencing results indicate that for many unique sights, 5-30% of all organisms are not classified beyond Genus with a large number being new species.

A Sample-to-results Workflow for Sequencing from Wastewater“, Dr. Siva Chavadi, PhD. Senior FAS, NEBNext Products, NEB

Speaker Bio: Siva Chavadi (he/him) is a Senior FAS (NEBNext NGS sample prep reagents) at New England Biolabs, working with academic and core facilities as well as industrial collaborators to implement scalable NGS workflows. Previously at GENEWIZ/Azenta, he supported NGS service operations and customer applications. He holds a PhD in Animal Sciences from University of Hyderabad, India with research focused on TB diagnostics and vaccine development using functional genomics tools.

Antibiotic-Free Liquid Surface Coatings for the Tunable Control of Protein and Microorganism Adhesion: The rise of antibiotic resistance is one of the greatest global public health challenges of our time”, Dr. Caitlin Howell, PhD, Associate Professor of Bioengineering, Department of Chemical and Biomedical Engineering, University of Maine

Caitlin Howell is an Associate Professor of Bioengineering in the Department of Chemical and Biomedical Engineering at the University of Maine. She received her MS in Biology from UMaine, her PhD in Physical Chemistry from the University of Heidelberg in Germany, then completed a postdoc at the Wyss Institute for Bioinspired Engineering at Harvard University before returning to UMaine to found the Biointerface Engineering Lab in 2016. Her research group is focused on designing surfaces to leverage the power of living systems to address human problems.

Caitlin Howell

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.

From Bugs to Breakthroughs: Sequence the Invisible Majority with QIAseq.”, Dr. Kevin W. Joseph, PhD, Genomics Field Application Scientist

Kevin graduated from University of Maine in 2012 with a BS in Microbiology and later acquired his PhD in Infectious Disease and Microbiology from the University of Pittsburgh. During his graduate work, he focused on HIV-1 single genome sequencing and integration site analysis of clonally-expanded, replication competent, HIV-1 proviruses in patients with long-term viral suppression. He developed the Individual Proviral Sequencing Assay (IPSA) to study these rare targets, which enables sequencing of full-length HIV-1 single-genome proviruses and their integration sites with high sequencing efficiency. Kevin has brought his knowledge and expertise to QIAGEN where he assists researchers with NGS, PCR assay and oligonucleotide design, and in-lab training/support.

Illumina innovation roadmap“, Jennifer Mosher, Senior Sequencing Specialist, Illumina

Jennifer Mosher is a Senior Sequencing Specialist at Illumina, with deep expertise spanning field applications, marketing, and NGS-based proteomics. With over a decade in academia, she previously led operations for NGS at the Cornell Genomics Core before transitioning to industry, where she partners with both academic and commercial leaders to drive adoption of advanced sequencing technologies and assays.

This workshop broadly includes combining microbiome data with other data types, combining qualitative and quantitative data, learning to evaluate microbiome data using demographic data, dealing with unbalanced groups especially in human microbiomes, and how to choose statistical tests for microbiome projects.

8:00 – 9:00 am   Breakfast, provided

9 – 10- ish am            Case Study Presentations, 20 min each, hosted by Sue Ishaq 

“Human data pitfalls TBD” Kevin Roberge, PhD. UMaine: Lecturer, Mathematics and Adjunct Professor, Women’s, Gender & Sexuality Studies.

Statstical decisions TBDLaura Jackson, Ph.D., UMaine: Bioinformatics Program Coordinator & Graduate FacultyGraduate School of Biomedical Science & Engineering, Bioinformatician – CORE Strategic Operational Services.

“A case study in human microbiomes TBD”, Lola Holcomb, PhD, University of New England, Bioinformatics Postdoc

10 – 10:15  Break, snacks and coffee provided

10:15 – 11 Panel discussion, symposium speakers are welcome to join

11 – 12 Open working time for data wrangling advice and analysis workflow storyboarding as a group

  • Kevin Roberge, can help with analysis storyboarding, identifying assumptions, math
  • Laura Jackson, can help with coding, statistics and deciding which to use, RNAseq data, 16S data, meta-analyses
  • Lola Holcomb, can help with coding, metagenomics data, 16S data, meta-analyses
  • Sue Ishaq, can help with some 16S, but will be helping to coordinate the workshop

12 – 1:30 lunch, provided

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!

Celebrating student achievements in 2026

As the academic year draws to a close (for the students), a flurry of awards ceremonies recognize their dedication and ingenuity. This year, as every year, the Ishaq Lab is grateful for all we have to celebrate! Only about a third of the lab was able to make it to our end of the semester good-bye party, but I look forward to their celebrating their continued successess in the lab and beyond.

Alexandra Ruff, Bella Murphy, Aaron Williams, Ashleys Reynolds, and Sue

Doctors

Johanna Holman, PhD., was recognized as an Outstanding Graduating Student for 2026 by the UMaine Graduate Student Government, and received her doctorate in Microbiology! This was actually her FOURTH award during her graduate studies. Johanna wasn’t able to have her doctoral hood bestowed at the UMaine graduate student graduation, as she just flew to Birmingham, England to start a postdoc position in the lab of Dr. Lindsay Hall, who focuses on early life microbial exposure and health.

Future Doctors

Aaron Williams, B.S. Zoology, was awarded Honors for his thesis! Aaron started in the lab for a bit his first year, and came back in his last two years to complete his Honors research thesis on bacterial metabolism of glucoraphanin as a means of surviving acidic conditions, as well as effect on the byproducts produced. Here we are posing with the spectrophotometer that played a critical role in generating very large spreadsheets of data. Aaron is heading to Tufts Veterinary College in the fall!

Mia Poirier, B.S. Biology (Pre-Med Concentration) and Madison Ringuette, B.S. Animal and Veterinary Science (Pre-Vet Concentration), and Miri Talalay, B.S. Zoology and Veterinary Studies, are also graduating. Mia and Madison are both taking a year to gain medical and research experience before diving back into college for medical and veterinary programs, respectively. Over the last semester, Mia and Madison helped with two mouse trials investigating the effect of broccoli sprout diets on the gut microbiome, which can use the diet to make anti-inflammatories to reduce symptoms. The first was a pilot project testing our two of our bacterial cultures as probiotics, which is part of Alexis Kirkendall’s work, and the second was a project investigating the efficacy of broccoli sprout diets for resolving gut and neuroinflammation in young adult mice, which is part of Ashley Reynold’s work. Mis was awarded funding for her work in the lab: 2025/2026 Undergraduate Research Award from the UMaine Center for Undergraduate Research and the UMaine Institute of Medicine. Miri had been working us since her first year at UMaine! Miri worked on a variety of projects, helping provide key technical support on some of our years-long culturing projects. This included the screening of hundreds of bacterial cultures for their ability to metabolize glucoraphanin, and whether they would be able to use glucoraphanin and its byproducts to survive in acidic conditions (which Aaron also focused on).

All four Future Doctors will be featured as authors and contributors on our manuscript in development, led by Johanna, which will present the culturing work we’ve done over the last four years! We hope to get that submitted for peer review this summer.

Today’s second Microbiome Workshop at UMaine showcases comparative sequencing technologies and continues skill building!

Today was a blast at the Microbiome Workshop on Long-Read Amplicon Library Generation, the second in a series of hands-on workshops this spring that I have been coorganizing with Alex Sacco, Genomics Facility Manager at UMaine! This one was led by Alex, who is a genius at sorting out the complex math and coordination to combine multiple projcts with multiple targets onto one Oxford Nanopore Technology flow cell!!

Today we used materials generously provided by New England Biolabs, whos sponsorship provided the opportunity for 11 students to learn how to prepare their samples for sequencing. We are grateful to Siva Chavadi and Heidi Iuvino from NEB for their time, expertise, and support! NEB will be joining us on campus in June, too, for the Microbiome Symposium at UMaine.

We are also grateful to UMaine CORE, for helping to organize these workshops and ensure that students had access to specialized equipment and supplies.

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 which had been amplified with PCR, students learned how to ligate barcodes and combine samples into a pool for using the Oxford Nanopore MinION Nanopore Sequencing Student Workshop Protocol.

By amplifying and sequencing these variable regions, students generated data that can be used to compare microbial community composition across different sample types. Students who were at both workshops will also be able to compare the two sequencing strategies we have focusd on, which use different technology and provide unique perspectives during data analysis and interpretation.

MSE virtual seminar today: “Microbial Communities in the Leaves Around Us”

The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

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.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine, and the Applied Microbiology International via the 2025 Dororthy Jones Diversity and Inclusion Acheivement Award.

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. 

You can find recordings from previous series here.


“Microbial Communities in the Leaves Around Us”

Dr. Naupaka Zimmerman, Ph.D. (he/him/his)

Apr 29, 2026 11:00 – 13:00 EDT. The recording will be available online here after the event.

Dr Naupaka Zimmerman is an Assistant Professor in the Environmental Studies Program at the University of Kansas (KU). He was previously an Associate Professor of Biology and Director of the MS Biology Program at the University of San Francisco. His research explores microbial ecology, with a focus on the communities of fungi that live inside plant leaves without causing disease, known as endophytes. His work investigates how environmental conditions, host species, and geography influence the diversity and function of these microbes.

Born and raised on the Big Island of Hawaiʻi, Dr Zimmerman has studied the microbial ecology of native Hawaiian plants, particularly Metrosideros polymorpha. At USF, his lab worked on plant–microbe interactions in urban environments and sustainable agricultural systems, including research across San Francisco and at Star Route Farms in Marin County. He plans to extend that work to agricultural and grassland systems in the midwest in his new role at KU. His team uses fieldwork, microscopy, DNA sequencing, and bioinformatics to understand how plant-associated microbes contribute to ecosystem processes such as decomposition, plant health, and resilience to pathogens. His lab website is here.


Logo designed by Alex Guillen

Only 3 weeks remaining to submit your poster abstract for the Northern New England Microbiome Symposium at UMaine on June 11!

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

9:00 – 9:15 Welcome and Opening Remarks

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.

A headshot of Dr. Sue Ishaq, PhD in which she is wearing a black and white houndstooth pattern waistcoat and a white button up shirt. Graphics have been added to show a strand of DNA and the words "love your microbes"

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.

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.

Genetic and Microbiome Control of Addiction-like Behaviors in Mice”, Dr. Jason Bubier, Ph.D., Senior Research Scientist, Center for Addiction Biology, The Jackson Laboratory

Jason A. Bubier, Ph.D., is a Senior Research Scientist at The Jackson Laboratory, where he leads research at the intersection of genetics, behavior, and addiction biology. His work focuses on uncovering the genetic and physiological factors that shape vulnerability to addictive substances, with current projects examining the microbiome’s influence on behavior, the genetic architecture of opioid‑induced respiratory depression, and systems‑level pathways involved in addiction.

Dr. Bubier has spent more than two decades at The Jackson Laboratory, advancing through multiple research roles and contributing to major initiatives in functional genomics and behavioral genetics. He has authored more than 80 scientific publications, and his work is widely cited across fields including immunology, bioinformatics, and addiction science.

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.

Gut Anthro“, Dr. Amber Benezra, Assistant Professor of Science and Technology Studies at Stevens Institute of Technology

Dr. Benezra is a sociocultural anthropologist researching how studies of the human microbiome intersect with biomedical ethics, public health/technological infrastructures, and care. In partnership with human microbial ecologists, she has been developing an “anthropology of microbes” to address global health problems across disciplines. Her book, Gut Anthro (published by University of Minnesota Press in 2023) is the first ethnography of the microbiome.

“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. 

Heather Richard

Genomic Strategies for Discovering Microbial Dark Matter using Metagenomics“ Scott Tighe, M.S., Senior Research Associate, Environmental Microbiome Engineering Research Group, Dept of Civil Engineering, University of Vermont.
Scott Tighe is currently Senior Research Associate in the Environmental Microbiome Engineering Research Group in the Dept of Civil Engineering at the University of Vermont and past technical director of the UVM Genomics Facility. He has expertise in all areas of genomics, microbiology, and mycology with a specific focus on advancing the methods used for microbiome and metagenomic analysis. He specializes performing metagenomic analysis in global extreme sites such Greenland, Antarctica, Romania, Saudi Arabia, Crete, Tahiti, and the International Space Station to name a few and is currently the science lead of the Extreme Microbiome Project (XMP). Short Abstract: The ability to perform advanced genomic techniques on samples collected from extreme environments demands high performance reagents and techniques not commonly used in most labs today. For the past15 years, our projects have developed novel sampling and DNA sequencing protocols for profiling a variety of environments, including snow, glaciers, Antarctic lakes, Romanian caves, thermophilic ecosystems, halophilic, acidic, alkaline lakes, anaerobic digestors as well as organisms from bioaerosols and the International Space Station. Technical approaches include novel liquid concentrating devices, sample disruptors, biopulverizers, and field use of the Oxford Nanopore DNA sequencer. Whole Genome sequencing results indicate that for many unique sights, 5-30% of all organisms are not classified beyond Genus with a large number being new species.

A Sample-to-results Workflow for Sequencing from Wastewater“, Dr. Siva Chavadi, PhD. Senior FAS, NEBNext Products, NEB

Speaker Bio: Siva Chavadi (he/him) is a Senior FAS (NEBNext NGS sample prep reagents) at New England Biolabs, working with academic and core facilities as well as industrial collaborators to implement scalable NGS workflows. Previously at GENEWIZ/Azenta, he supported NGS service operations and customer applications. He holds a PhD in Animal Sciences from University of Hyderabad, India with research focused on TB diagnostics and vaccine development using functional genomics tools.

Antibiotic-Free Liquid Surface Coatings for the Tunable Control of Protein and Microorganism Adhesion: The rise of antibiotic resistance is one of the greatest global public health challenges of our time”, Dr. Caitlin Howell, PhD, Associate Professor of Bioengineering, Department of Chemical and Biomedical Engineering, University of Maine

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.

From Bugs to Breakthroughs: Sequence the Invisible Majority with QIAseq.”, Dr. Kevin W. Joseph, PhD, Genomics Field Application Scientist

Kevin graduated from University of Maine in 2012 with a BS in Microbiology and later acquired his PhD in Infectious Disease and Microbiology from the University of Pittsburgh. During his graduate work, he focused on HIV-1 single genome sequencing and integration site analysis of clonally-expanded, replication competent, HIV-1 proviruses in patients with long-term viral suppression. He developed the Individual Proviral Sequencing Assay (IPSA) to study these rare targets, which enables sequencing of full-length HIV-1 single-genome proviruses and their integration sites with high sequencing efficiency. Kevin has brought his knowledge and expertise to QIAGEN where he assists researchers with NGS, PCR assay and oligonucleotide design, and in-lab training/support.

Illumina innovation roadmap“, Jennifer Mosher, Senior Sequencing Specialist, Illumina

Jennifer Mosher is a Senior Sequencing Specialist at Illumina, with deep expertise spanning field applications, marketing, and NGS-based proteomics. With over a decade in academia, she previously led operations for NGS at the Cornell Genomics Core before transitioning to industry, where she partners with both academic and commercial leaders to drive adoption of advanced sequencing technologies and assays.

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.

Lola Holcomb, PhD, University of New England, Bioinformatics Postdoc

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!

MSE virtual seminar Apr 29: “Microbial Communities in the Leaves Around Us”

The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

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.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine, and the Applied Microbiology International via the 2025 Dororthy Jones Diversity and Inclusion Acheivement Award.

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. 

You can find recordings from previous series here.


“Microbial Communities in the Leaves Around Us”

Dr. Naupaka Zimmerman, Ph.D. (he/him/his)

Apr 29, 2026 11:00 – 13:00 EDT. The recording will be available online here after the event.

Dr Naupaka Zimmerman is an Assistant Professor in the Environmental Studies Program at the University of Kansas (KU). He was previously an Associate Professor of Biology and Director of the MS Biology Program at the University of San Francisco. His research explores microbial ecology, with a focus on the communities of fungi that live inside plant leaves without causing disease, known as endophytes. His work investigates how environmental conditions, host species, and geography influence the diversity and function of these microbes.

Born and raised on the Big Island of Hawaiʻi, Dr Zimmerman has studied the microbial ecology of native Hawaiian plants, particularly Metrosideros polymorpha. At USF, his lab worked on plant–microbe interactions in urban environments and sustainable agricultural systems, including research across San Francisco and at Star Route Farms in Marin County. He plans to extend that work to agricultural and grassland systems in the midwest in his new role at KU. His team uses fieldwork, microscopy, DNA sequencing, and bioinformatics to understand how plant-associated microbes contribute to ecosystem processes such as decomposition, plant health, and resilience to pathogens. His lab website is here.


Logo designed by Alex Guillen

From DNA to data: students experience microbial community sequencing firsthand in today’s workshop at UMaine

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!

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.

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.

The 2nd Northern New England Microbiome Symposium will be held at UMaine on June 11!

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

9:00 – 9:15 Welcome and Opening Remarks

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.

A headshot of Dr. Sue Ishaq, PhD in which she is wearing a black and white houndstooth pattern waistcoat and a white button up shirt. Graphics have been added to show a strand of DNA and the words "love your microbes"

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.

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.

Genetic and Microbiome Control of Addiction-like Behaviors in Mice”, Dr. Jason Bubier, Ph.D., Senior Research Scientist, Center for Addiction Biology, The Jackson Laboratory

Jason A. Bubier, Ph.D., is a Senior Research Scientist at The Jackson Laboratory, where he leads research at the intersection of genetics, behavior, and addiction biology. His work focuses on uncovering the genetic and physiological factors that shape vulnerability to addictive substances, with current projects examining the microbiome’s influence on behavior, the genetic architecture of opioid‑induced respiratory depression, and systems‑level pathways involved in addiction.

Dr. Bubier has spent more than two decades at The Jackson Laboratory, advancing through multiple research roles and contributing to major initiatives in functional genomics and behavioral genetics. He has authored more than 80 scientific publications, and his work is widely cited across fields including immunology, bioinformatics, and addiction science.

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.

Gut Anthro“, Dr. Amber Benezra, Assistant Professor of Science and Technology Studies at Stevens Institute of Technology

Dr. Benezra is a sociocultural anthropologist researching how studies of the human microbiome intersect with biomedical ethics, public health/technological infrastructures, and care. In partnership with human microbial ecologists, she has been developing an “anthropology of microbes” to address global health problems across disciplines. Her book, Gut Anthro (published by University of Minnesota Press in 2023) is the first ethnography of the microbiome.

“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. 

Heather Richard

Genomic Strategies for Discovering Microbial Dark Matter using Metagenomics“ Scott Tighe, M.S., Senior Research Associate, Environmental Microbiome Engineering Research Group, Dept of Civil Engineering, University of Vermont.
Scott Tighe is currently Senior Research Associate in the Environmental Microbiome Engineering Research Group in the Dept of Civil Engineering at the University of Vermont and past technical director of the UVM Genomics Facility. He has expertise in all areas of genomics, microbiology, and mycology with a specific focus on advancing the methods used for microbiome and metagenomic analysis. He specializes performing metagenomic analysis in global extreme sites such Greenland, Antarctica, Romania, Saudi Arabia, Crete, Tahiti, and the International Space Station to name a few and is currently the science lead of the Extreme Microbiome Project (XMP). Short Abstract: The ability to perform advanced genomic techniques on samples collected from extreme environments demands high performance reagents and techniques not commonly used in most labs today. For the past15 years, our projects have developed novel sampling and DNA sequencing protocols for profiling a variety of environments, including snow, glaciers, Antarctic lakes, Romanian caves, thermophilic ecosystems, halophilic, acidic, alkaline lakes, anaerobic digestors as well as organisms from bioaerosols and the International Space Station. Technical approaches include novel liquid concentrating devices, sample disruptors, biopulverizers, and field use of the Oxford Nanopore DNA sequencer. Whole Genome sequencing results indicate that for many unique sights, 5-30% of all organisms are not classified beyond Genus with a large number being new species.

A Sample-to-results Workflow for Sequencing from Wastewater“, Dr. Siva Chavadi, PhD. Senior FAS, NEBNext Products, NEB

Speaker Bio: Siva Chavadi (he/him) is a Senior FAS (NEBNext NGS sample prep reagents) at New England Biolabs, working with academic and core facilities as well as industrial collaborators to implement scalable NGS workflows. Previously at GENEWIZ/Azenta, he supported NGS service operations and customer applications. He holds a PhD in Animal Sciences from University of Hyderabad, India with research focused on TB diagnostics and vaccine development using functional genomics tools.

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.

From Bugs to Breakthroughs: Sequence the Invisible Majority with QIAseq.”, Dr. Kevin W. Joseph, PhD, Genomics Field Application Scientist

Kevin graduated from University of Maine in 2012 with a BS in Microbiology and later acquired his PhD in Infectious Disease and Microbiology from the University of Pittsburgh. During his graduate work, he focused on HIV-1 single genome sequencing and integration site analysis of clonally-expanded, replication competent, HIV-1 proviruses in patients with long-term viral suppression. He developed the Individual Proviral Sequencing Assay (IPSA) to study these rare targets, which enables sequencing of full-length HIV-1 single-genome proviruses and their integration sites with high sequencing efficiency. Kevin has brought his knowledge and expertise to QIAGEN where he assists researchers with NGS, PCR assay and oligonucleotide design, and in-lab training/support.

Illumina innovation roadmap“, Jennifer Mosher, Senior Sequencing Specialist, Illumina

Jennifer Mosher is a Senior Sequencing Specialist at Illumina, with deep expertise spanning field applications, marketing, and NGS-based proteomics. With over a decade in academia, she previously led operations for NGS at the Cornell Genomics Core before transitioning to industry, where she partners with both academic and commercial leaders to drive adoption of advanced sequencing technologies and assays.

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.

Lola Holcomb, PhD, University of New England, Bioinformatics Postdoc

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!

If you would like to help sponsor this event, please contact sue.ishaq@maine.edu.

Spring 2026 conferences and workshops

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.

A recipe for health: a bit of diet, a dash of microbes, and plenty of social equity

  • Presented by: Sue Ishaq, University of Maine
  • When: 21-05-2026 from 16:00 to 17:30
  • 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 Venice, Italy, to speak at a workshop titled: “Integrating Qualitative and Quantitative Data in Microbiome Research and Postgenomics: Toward an Interdisciplinary Dialogue”. The talks and discussion will focus on combining qualitative and quantitative data.

The University sits in the heart of Venice! 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.

Photo By Freddo213 – Own work, CC BY-SA 4.0.

By Freddo213 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=128410869

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.

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.

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

MSE virtual seminar today: “Unravelling Periprosthetic Joint Infection”

The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

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.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine, and the Applied Microbiology International via the 2025 Dororthy Jones Diversity and Inclusion Acheivement Award.

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. 

You can find recordings from previous series here.


“Unravelling Periprosthetic Joint Infection”

Dr. Robin Patel, M.D.

Mar 25, 2026, 11:00 – 13:00 ET. The recording will be available online here after the event.

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.