Author: sueishaqlab

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.

MSE virtual seminar today: “The nuts and bolts of microbiome stewardship: what are we trying to protect?”

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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.

Registration is required but free. Click here to register!

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.

“The nuts and bolts of microbiome stewardship: what are we trying to protect?”

Dr. Rob Beiko, PhD and Dr. Zhongzhi Sun

Sept 30, 2026, 11:00 – 13:00 EDT. The recording will be available online here after the event.

Dr. Robert Beiko is a Professor in the Faculty of Computer Science at Dalhousie University who specializes in the analysis of DNA and protein sequences to better understand biodiversity, evolution, and ecology. He is also Director of Data at Dartmouth Ocean Technologies, Inc. His lab is currently developing software tools and algorithms to better understand the evolution and transmission of antimicrobial-resistance genes, and new computational methods to identify species and infer their ecological roles using environmental DNA. His lab website is here.

Dr. Zhongzhi Sun is a postdoctoral fellow in the Faculty of Computer Science at Dalhousie University, where he works in Dr. Robert Beiko’s lab. He completed his PhD at the University of Ottawa under the supervision of Dr. Daniel Figeys, focusing on peptide-centric analyses in human gut metaproteomics. Prior to his PhD, he completed his undergraduate studies and his MSc in microbiology at Shandong University in China. Building on his background in genomics, metagenomics, and metaproteomics, he currently applies multi-omics methods to study interactions between microbiomes and human hosts, as well as between microbiomes and their environments, including soil ecosystems. He is also a member of the Microbiome Stewardship research team, which aims to define the policies and collective actions needed to maintain microbiome diversity and functioning in support of human and ecosystem health.

Congratulations to Heather Richard for starting a job in environmental conservation in Maine!

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Congratulations to Heather Richard on starting her post-graduate career in conservation with Scarborough Land Trust as Marsh Project Director! Heather has been a grad student working with me, mycologist Pete Avis, ecologists Andy Rominger and Brian McGill, engineer Jean MacRae, and geochemist Tomoko Komada, for the past few years to study Maine coastal salt marshes.

Long before she joined my lab to work on microbial communities in some of Maine’s coastal salt marshes, Heather was an ecologist, educator, and bioinformatician. Over her career, she’s used hands-on experiences in nature (a.k.a. living labs or nature’s classroom) to inspire a love of the natural world while teaching the process of scientific inquiry to students of all ages. Her enthusiasm for environmental science similarly helped her unite people during public outreach and policy work towards common goals of information sharing and evidence-based conservation strategies to benefit communities and the ecosystems around them. And, her unwavering fascination with nature and her dedication to understanding (i.e. science) led her along a path of scientific inquiry to solve problems. In fact, her PhD program was just one leg of her lifelong journey in conservation. As she is coming to the end of her PhD project and looking for her next opportunity, Heather landed a position at Scarborough Land Trust where she will oversee the management and coordination of various restoration and science projects with multiple interest groups starting this fall, as she wraps up her dissertation and resulting scientific manuscripts.

Heather’s focus at UMaine has been to catalogue the microbiomes associated with coastal salt marsh ecosystems in Maine. There are approximately 800 locations in Maine where roads and bridges cross tidal creeks, which requires culverts or other infrastructure to direct the flow of water, and 90% of these structures are considered undersized. These restrictive crossings impound freshwater upstream of the restriction site, keeping it flooded and lowering salinity. This disrupts the native vegetation and soil microbes adapted to salty conditions, making the marshes highly vulnerable to invasive plants. Healthy salt marshes act as blue carbon ecosystems by trapping and storing large amounts of atmospheric carbon in their soils. However, tidal restrictions disrupt this process and can turn these areas into major hotbeds for potent greenhouse gas production. Understanding how microbes react to restrictions in marshes, and whether they can still sequester carbon instead of losing chemical resources from the marsh, can help us learn how to more effectively use infrastructure that does not negatively impact water flow, native plants, or microbes. Microbial communities can be viewed as an integrated response to environmental conditions over time, whereas variables such as salinity and carbon flux are instantaneous measurements that capture only a snapshot of a dynamic system. That means these methods can potentially be very useful and informative for those who protect, monitor and restore salt marsh habitats.

Heather studied soil/sediment as these areas host a high diversity of microbes, which are responsible for a majority of the chemical processing that happens there, such as breaking down the plant, animal, or chemical waste into simpler compounds or elements which can be sequestered into the soil, taken up by the plants, or fuel more microbial activity. The bacteria, archaea, and fungi that live in the sediment of marshes are somewhat specific to the plants, animals, chemicals, environment, and humans around the marsh, thus each marsh must be “microbially mapped” to know which microbes are present and where specifically, and what they are doing. This is important for knowing how microbes are affected by change: will they sequester carbon or release methane if the community is changed by a storm, or by the installation of a culvert? What will the microbes do if the marsh dries out or gets flooded?

To answer some of these questions, Heather has explored whether bacterial, archaeal, and fungal communities would have different members present and/or would make different products if they were located up- or downstream from a restriction site, like a culvert under a roadway placed in the waterway of the marsh. The marshes she chose to study because of their level of restriction, including marshes that had natural water flow and no infrastructure/restrictions, some which has been restored to their natural water flow by the removal of infrastructure/restrictions, and some which had their waterflow altered such as by too-small culverts which affected the tidal flow of seawater and caused the marsh to be too dry or too flooded.

Heather has been analyzing the data for a few years, including hundreds of marsh sediment samples with information on microbial communities, each of which contains hundreds of bacteria, archaea, and fungi, as well as data on the chemical composition of those hundreds of samples, and environmental characteristics of each site.

Heather discovered too much to name here, but here are some highlights: The microbiomes found in the regularly flooded marsh adjacent to tidal channels at depths within the rhizosphere (plant roots) are likely to be particularly sensitive to hydrology alterations because of the low elevation in these areas and close proximity to tidal creeks. Hydrologic restrictions that increase water residence time can prolong anoxic conditions and reduce tidal flushing, promoting environments that favor methanogenic and other anaerobic microorganisms while suppressing aerobic processes. These changes may also reduce the capacity of the marsh plant Spartina alterniflora to oxygenate the rhizosphere under highly reduced conditions and, where sulfide accumulates, may further reinforce redox-driven shifts in microbial community composition. The presence of natural marsh microbial communities at some restricted sites should not be interpreted as evidence that these tidal restrictions have no ecological impact: restrictions at sites with less freshwater influence that reduce tidal inundation upstream without impounding freshwater may have similar oxygen and salinity conditions as the natural sites in the lower/downstream part of marshes while increasing aerobic carbon mineralization at deeper depths and increasing salinity stress in the higher/upstream part of the marshes.

Now that she’s wrapping up, Heather will condense what she learned and how she did it into a dissertation, the chapters of which will be formed into several manuscripts. This will include one with the information about the microbial communities present and which environmental conditions were associated with certain taxa or biochemical pathways, one on a particular marsh before and after it was restored, and one on the process of setting up a collaborative marsh-conservation network across multiple states and institutions to facilitate evidence-based restoration strategies.

These papers exemplify what Heather’s new job will entail, and this position is a wonderful embodiment of what she wants to use her degree to accomplish. The Ishaq Lab wishes Heather the best of luck, and is excited to see how she’ll help Maine communities in her new position!

MSE virtual seminar Sept 30: “The nuts and bolts of microbiome stewardship: what are we trying to protect?”

sueishaqlabLeave a comment
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.

Registration is required but free. Click here to register!

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.

“The nuts and bolts of microbiome stewardship: what are we trying to protect?”

Dr. Rob Beiko, PhD and Dr. Zhongzhi Sun

Sept 30, 2026, 11:00 – 13:00 EDT. The recording will be available online here after the event.

Dr. Robert Beiko is a Professor in the Faculty of Computer Science at Dalhousie University who specializes in the analysis of DNA and protein sequences to better understand biodiversity, evolution, and ecology. He is also Director of Data at Dartmouth Ocean Technologies, Inc. His lab is currently developing software tools and algorithms to better understand the evolution and transmission of antimicrobial-resistance genes, and new computational methods to identify species and infer their ecological roles using environmental DNA. His lab website is here.

Dr. Zhongzhi Sun is a postdoctoral fellow in the Faculty of Computer Science at Dalhousie University, where he works in Dr. Robert Beiko’s lab. He completed his PhD at the University of Ottawa under the supervision of Dr. Daniel Figeys, focusing on peptide-centric analyses in human gut metaproteomics. Prior to his PhD, he completed his undergraduate studies and his MSc in microbiology at Shandong University in China. Building on his background in genomics, metagenomics, and metaproteomics, he currently applies multi-omics methods to study interactions between microbiomes and human hosts, as well as between microbiomes and their environments, including soil ecosystems. He is also a member of the Microbiome Stewardship research team, which aims to define the policies and collective actions needed to maintain microbiome diversity and functioning in support of human and ecosystem health.

Fall conferences

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This fall, I will be attending three conferences/workshops to present my lab’s research, as well as to learn from others.

Maine Public Health Association 2026 Annual Conference

Thursday, October 1, 2026 @ 8:00 am – 4:30 pm, at the Augusta Civic Center, 76 Community Drive, Augusta, Maine

This will be my first time attending MPHA’s annual conference, to present research on our broccoli sprout diet intervention.

A cartoon of a woman eating broccoli, with the digestive tract shown on her shirt, and smiling microbes in the background.

NOVA Scholars Meeting

Oct 19-20, 2026, at the headquesters for the NOVA Institute for Health. Held annually in Baltimore, I attended in 2023 and 2024 to learn from other researchers and practitioners working on community based improvements through science.

The Puerto Rico Center for Microbiome Sciences (COBRE) 2nd Microbiome Symposium

Dec 1, 2026, in San Juan, Puerto Rico.

This will be my first trip to Puerto Rico, and I’m thrilled to be able to speak about my work on broccoli sprouts, microbiome stewardship, and microbes and social equity.

MSE virtual seminar today: “The Secret World Within: How the Microbiome Provides Insight into Gynecologic Health”

sueishaqlabLeave a comment
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.

Registration is required but free. Click here to register!

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.

“The Secret World Within: How the Microbiome Provides Insight into Gynecologic Health”

Dr. Nicole Jimenez, PhD

Aug 26, 2026, 11:00 – 13:00 EDT.

Nicole Jimenez, PhD

Dr. Nicole Jimenez is a postdoctoral fellow at the University of Arizona College of Medicine-Phoenix, specializing in gynecologic health research. Raised in Arizona, she was inspired by mentors in programs such as the Si Se Puede Foundation and ASU’s Los Diablos, and by her innate curiosity, to pursue a career as a scientist. She completed her doctoral degree in 2021 from Virginia Commonwealth University as part of the Vaginal Microbiome Consortium, studying the microbiome in the context of bacterial vaginosis, trichomoniasis, and pregnancy. Currently, her postdoctoral research, conducted in Dr. Melissa Herbst-Kralovetz’s lab, focuses on conditions such as chronic pelvic pain, endometriosis, adenomyosis, cervical and endometrial cancer, utilizing multi-omic pipelines, microbial culturomics, and 3D epithelial cell models. Dr. Jimenez has demonstrated a strong commitment to academic excellence, evidenced by recently securing the American Cancer Society postdoctoral fellowship, publishing manuscripts in microbiology and clinically focused journals, and receiving the 2025 University of Arizona Outstanding Postdoctoral Scholar Award. Driven by her passions for science, advocacy, and mentorship—having guided 22 students across various levels—she is actively preparing for a transition to an independent faculty position to continue her translational work on understudied gynecologic conditions through the lens of the microbiome. A recent article can be found here.

There is nothing like being in a gorgeous ecosystem for inspiring conservation to protect it

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As far as auspicious beginnings go, listening to dozens of tropical birds share news in a blooming city park while watching the rising sun peek out of the clouds leftover from a pre-dawn rain, the city traffic a distant hum under the nearby laughter of morning walkers watching their dogs frolic, is a heck of a way to begin a week-long conference on microbes and global health. Microbes feed the planet by interfacing between geological processes and biological ones: single-celled microbes take basic elements up to complex chemical compounds and back down again to the basics, all of which allows more complex forms of life to access the chemicals they need. Microbes help provide critical nutrients to the plants in this park, they help the parrots digest their food, they can even act as the physical seeds around which molecules of water gather into drops to create rain.

The International Society of Microbial Ecology hosts their major scientific conference every two years in rotating locations around the world, this year in Auckland, New Zealand. While every flavor of microbiology can be found here at the conference, there are always themes of building a collective and reducing the negative impacts of human activities while amplifying the positive ones. For example, there were presentations about the detriment of clearcutting for mono-cropping of commodities, as well as presentations on how migratory grazing of domesticated livestock creates biodiversity hotspots in grasslands due to manure and urine nutrients as well as turnover of plants (grazing allows for competition from other plants but also germinates seeds that need to pass through a digestive tract). In short, the way we live our lives and interact with the planet affects the microbes we interact with and the ones we leave behind, and when we do this intentionally and with mutual benefit in mind, everything can flourish.

Yet, deciding on that course of action is not necessarily without logistical burdens: what should we change, and what will be the outcome? Do the benefits outweigh the problems that will occur? How do we prioritize land use decisions when some people think the destruction of air, water, soil, plants, animals, and people caused by data centers is worth it to support mass surveillance of the public? Thus, the process of making policy decisions or design choices which intentionally support microbial communities for the benefit of environments, organisms, and renewing natural resources can be arduous: between sparse information about remote microbes, to getting people to agree on the value of nature, to enacting change across borders, it is understandable that the pace of innovation crawls in comparison to the swiftness of changes to our world and the urgency to save ourselves while we can (microbes and other life on this planet will survive the consequences our actions even if we don’t). Worthwhile endeavors are neither quick nor cheap, and if we can focus for decades on making space travel and inhabitation viable, then surely the collective intelligence of humanity can figure out how to terraform without destroying the very ground beneath our feet.

My goals were triple-fold at the ISME conference: to learn about cutting-edge research, to widen and strengthen my network of colleagues, and to make progress on spreading awareness of and setting priorities for the Ethics, Conservation and Management Planning Working Group of the new Microbial Conservation Specialist Group of the IUCN Species Survival Commission (IUCN SSC MCSG ECMP). Some of the leadership team of that group was in Auckland, and we took the opportunity to meet about setting priorities over the next year.

Gabriele Berg, Raquel Peixoto, Sue, Jack Gilbert chatting about ISME and microbial conservation.
Some of the IUCN team at ISME20: Jack Gilbert, Gabriele Berg, Chris Greening, Lucy Harper, Sue, Raquel Peixoto

Additionally,, I initiated conversations about the group to invite researchers who are already working in this conceptual space, which was incredibly easy at the ISME conference because everyone here has some connection to sustainability, conservation, stewardship, equitable collaborations, and sharing of research outcomes. In particular, the session on “Indigenous Knowledge – solutions for global environmental changes” featured speakers who were all focused on protecting microbial communities and the unique ecosystems that host them, as well as trying to prevent the bioprospecting from and exclusion of local (and especially Indigenous, see most of recorded modern history for examples) peoples that occurred during the ‘gold rush’ early years of microbial ecology, ecology, conservation, anthropology – actually pretty much most fields were used as an excuse to pillage. One audience member of that session told the story of how, after the first papers describing novel microbes in delicate and uncatalogued ecosystems in Argentina were published, researchers from other countries flooded to the area to study and collect them, often actively destroying ecosystems in the process by driving on the very microbial mats they had come to study.

With a complicated legacy to remediate and learn from, conservation must be united with ethics, and thus the ECMP subgroup is tasked with learning from history, promoting equitable practices already being used around the globe, and trying to enact these best practices into education and policy to move us into a better way of treating each other and planet.

Learn more about the Ethics Subgroup and the Microbial Special Group

Please visit the MCSG website for more information, and if you are at ISME20, reach visit the Applied Microbiology International publications display table to learn more and join an information session.

Gilbert, J., Scholz, A., Dominguez-Bello, M.G., Korsten, L., Berg, G., Singh, B., Boetius, A., Wang, F., Greening, C., Wrighton, K., Bordenstein, S., Jansson, J., Lennon, J., Souza, V., Allard, S.M., Thomas, T., Cowan, D., Crowther, T., Nguyen, N., Harper, L., Haraoui, L-P., Ishaq, S., McFall-Ngai, M., Redford, K.H., Peixoto, R. 2025. Safeguarding Microbial Biodiversity: Microbial Conservation Specialist Group (MCSG) within the Species Survival Commission of the International Union for Conservation of Nature (IUCN). Editorial Published in multiple journals simultaneously, including mSystems, Sustainable Microbiology, the ISME Journal, and FEMS Microbial Ecology.

Gilbert, J., Peixoto, R., Scholz, A., Dominguez-Bello, M.G., Korsten, L., Berg, G., Singh, B., Boetius, A., Wang, F., Greening, C., Wrighton, K., Bordenstein, S., Jansson, J., Lennon, J., Souza, V., Thomas, T., Cowan, D., Crowther, T., Nguyen, N., Harper, L., Haraoui, L-P., Ishaq, S., Redford, K. 2025. Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity. Nature Microbiology 10:2359–2360. (correspondence)

MSE virtual seminar Aug 26: “The Secret World Within: How the Microbiome Provides Insight into Gynecologic Health”

sueishaqlabLeave a comment
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.

Registration is required but free. Click here to register!

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.

“The Secret World Within: How the Microbiome Provides Insight into Gynecologic Health”

Dr. Nicole Jimenez, PhD

Aug 26, 2026, 11:00 – 13:00 EDT. The recording will be available online here after the event.

Nicole Jimenez, PhD

Dr. Nicole Jimenez is a postdoctoral fellow at the University of Arizona College of Medicine-Phoenix, specializing in gynecologic health research. Raised in Arizona, she was inspired by mentors in programs such as the Si Se Puede Foundation and ASU’s Los Diablos, and by her innate curiosity, to pursue a career as a scientist. She completed her doctoral degree in 2021 from Virginia Commonwealth University as part of the Vaginal Microbiome Consortium, studying the microbiome in the context of bacterial vaginosis, trichomoniasis, and pregnancy. Currently, her postdoctoral research, conducted in Dr. Melissa Herbst-Kralovetz’s lab, focuses on conditions such as chronic pelvic pain, endometriosis, adenomyosis, cervical and endometrial cancer, utilizing multi-omic pipelines, microbial culturomics, and 3D epithelial cell models. Dr. Jimenez has demonstrated a strong commitment to academic excellence, evidenced by recently securing the American Cancer Society postdoctoral fellowship, publishing manuscripts in microbiology and clinically focused journals, and receiving the 2025 University of Arizona Outstanding Postdoctoral Scholar Award. Driven by her passions for science, advocacy, and mentorship—having guided 22 students across various levels—she is actively preparing for a transition to an independent faculty position to continue her translational work on understudied gynecologic conditions through the lens of the microbiome. A recent article can be found here.

The Microbiome Stewardship special collection is open at Sustainable Microbiology!

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The Stewardship of Microbiomes in Human and Environmental Systems special collection is open at Sustainable Microbiology!

The collection is led by senior editor, and principal investigator of the Microbiome Stewardship group, Dr. Kieran O’Doherty, and will feature invited contributions. Starting with the foundational framework paper, the collection establishes clear guiding principles, premises, core responsibilities, and case studies for preserving microbial biodiversity across diverse habitats. The featured research will span multiple disciplines, to address how the deterioration of microbiomes in many environments leads to adverse health outcomes for humans, animals, plants, and entire ecosystems. Importantly, the open-access articles call for unified sociopolitical action and policy-driven governance to integrate microbiome conservation into global public health and environmental protection standards.

You can read the full open-access collection at Sustainable Microbiology, a journal published by Applied Microbiology International, one of the organizations that supports the Microbes and Social Equity working group, as well as the Microbiome Stewardship group.

MSE virtual seminar today: “Searching for missing gut microbes in the Amazon”

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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.

Registration is required but free. Click here to register!

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.

“Searching for missing gut microbes in the Amazon”

Dr. Emma Allen-Vercoe, PhD

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

Dr. Emma Allen-Vercoe obtained her BSc (Hons) in Biochemistry from the University of London, and her PhD in Molecular Microbiology through an industrial partnership with Public Health England. Emma started her faculty career at the University of Calgary in 2005, with a Fellow-to-Faculty transition award through CAG/AstraZeneca and CIHR, to study the normal microbes of the human gut. In particular, she was among the few that focused on trying to culture these ‘unculturable’ microbes in order to better understand their biology. To do this, she developed a model gut system to emulate the conditions of human and other animal guts and allow communities of microbes to grow together, as they do naturally. Emma moved her lab to the University of Guelph in late 2007, and has been a recipient of several awards (through the Canada Foundation for Innovation) that have allowed her to develop her specialist anaerobic fermentation laboratory further. Emma is a Tier 1 Canada Research Chair, and her lab studies many microbial ecosystems, including those of Indigenous people of the Amazon, people in the industrialized world suffering from chronic disease, and those of honey bees and native pollinator insect species of Canada. Her faculty page is here.

The IUCN Microbe Specialist Group will be convening at the International Society for Microbial Ecology meeting in Auckland in August!

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Sometimes dreams do come true – I am finally getting a chance to visit New Zealand, thanks to my new role as co-Vice-Chair of the Ethics, Conservation and Management Planning Working Group (other Co-Vice Chair is Louis-Patrick Haraoui) of the new Microbial Conservation Specialist Group of the IUCN Species Survival Commission (IUCN SSC MCSG ECMP). While the number of words in that group’s formal name implies that it’s going to take a long time to accomplish anything, the new MCSG group is actually a nimble collaboration of researchers and policy makers who are working on conserving the microbial communities that allow us to thrive on this planet.

Created in 2025 and led by Drs. Jack Gilbert and Raquel Peixoto, the MCSG is the first IUCN body dedicated to protecting all microbial ecosystems, including those which are at risk or already losing microbial diversity because of degradation and human activities, and those ecosystems where human activities have not yell fully changed the microbial communities.  The group is working to integrate microbial biodiversity into mainstream conservation frameworks by developing new tools for assessment, advancing policy inclusion, coordinating action across ecosystems, and developing strategies to bring attention to the need to consider microbes in the health of organisms and ecosystems.

This August, the global microbial ecology community is converging on Auckland, New Zealand, for the International Society for Microbial Ecology (ISME) conference. You might remember my last visit two years ago to the ISME conference in Cape Town, South Africa, when I was fortunate enough to have the federal funding to bring much of my lab group. New Zealand hosts stunning landscapes, and not just because of the geography: New Zealand is one of the global leaders in environmental, animal, and plant conservation thanks to its deeply rooted Indigenous conservation practices. Auckland will provide the perfect backdrop for discussing the microscopic worlds that keep our planet alive. Attending ISME is always a highlight for me, and I’m excited to hear about wild animal microbiomes, and generally about the effects of environments on host microbiomes while I’m there.

Beyond the main conference sessions, the highlight of this trip will be participating in the meetings of the Microbial Conservation Specialist Group. While historic conservation efforts were constrained by resources and public attention to focus on visible and adorable wildlife like mammals and birds, protecting microbial diversity is just as critical for maintaining ecosystem stability and resilience. Engaging with this specialist group offers a vital platform to advocate for the inclusion of fungi, bacteria, and archaea in global conservation policies and frameworks. This journey promises to be a powerful blend of cutting-edge science and meaningful advocacy, and I cannot wait to bring these insights back to the research collaborations I have developed over the past few years on Microbiome Stewardship, how to go about it, and the practicality of protecting microbes at different scales.

Opportunities to learn more about the MCSG at ISME

  1. Please visit the MCSG website for more information, and if you are at ISME20, reach visit the Applied Microbiology International publications display table to learn more and join an information session.
  2. Subscribe to the MCSG newsletter here.
  3. If you will be attending ISME20 and would like to meet with me for coffee to learn more about the MCSG group, please email me at sue.ishaq@maine.edu!

Opportunities to learn more about the Microbes and Social Equity working group ISME

Of course, I will also be representing the MSE group at ISME. While I did not have time to prepare a formal event there, if you are part of MSE and would like to meet for coffee, or if you are curious about the group and would like to learn more (also while drinking coffee), please let me know at sue.ishaq@maine.edu!

IUCN Microbe Specialist Group’s recent publications

Gilbert, J., Scholz, A., Dominguez-Bello, M.G., Korsten, L., Berg, G., Singh, B., Boetius, A., Wang, F., Greening, C., Wrighton, K., Bordenstein, S., Jansson, J., Lennon, J., Souza, V., Allard, S.M., Thomas, T., Cowan, D., Crowther, T., Nguyen, N., Harper, L., Haraoui, L-P., Ishaq, S., McFall-Ngai, M., Redford, K.H., Peixoto, R. 2025. Safeguarding Microbial Biodiversity: Microbial Conservation Specialist Group (MCSG) within the Species Survival Commission of the International Union for Conservation of Nature (IUCN). Editorial Published in multiple journals simultaneously, including mSystems, Sustainable Microbiology, the ISME Journal, and FEMS Microbial Ecology.

Gilbert, J., Peixoto, R., Scholz, A., Dominguez-Bello, M.G., Korsten, L., Berg, G., Singh, B., Boetius, A., Wang, F., Greening, C., Wrighton, K., Bordenstein, S., Jansson, J., Lennon, J., Souza, V., Thomas, T., Cowan, D., Crowther, T., Nguyen, N., Harper, L., Haraoui, L-P., Ishaq, S., Redford, K. 2025. Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity. Nature Microbiology 10:2359–2360. (correspondence)