Collaborative paper published on winter wheat, farming practices, and climate!

The second paper from Tindall’s master’s work at Montana State University in the Menalled Lab has been accepted for publication! Tindall defended her master’s in August 2021, and has been working at a plant production company in Bozeman since then.

Ouverson, T., Boss, D., Eberly, J., Seipel, T.,  Menalled, F.D., Ishaq, S.L. 2022. Soil  bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system. Frontiers in Sustainable Food Systems.

Abstract

Soil microbial communities are integral to highly complex soil environments, responding to changes in aboveground plant biodiversity, influencing physical soil structure, driving nutrient cycling, and promoting both plant growth and disease suppression. Cover crops can improve soil health, but little is known about their effects on soil microbial community composition in semiarid cropping systems, which are rapidly becoming warmer and drier due to climate change. This study focused on a wheat-cover crop rotation near Havre, Montana that tested two cover crop mixtures (five species planted early season and seven species planted mid-season) with three different termination methods (chemical, grazed, or hayed and baled) against a fallow control under ambient or induced warmer/drier conditions. Soil samples from the 2018 and 2019 cover crop/fallow phases were collected for bacterial community 16S rRNA gene sequencing. The presence and composition of cover crops affected evenness and community composition. Bacterial communities in the 2018 ambient mid-season cover crops, warmer/drier mid-season cover crops, and ambient early season cover crops had greater richness and diversity than those in the warmer/drier early season cover crops. Soil microbial communities from mid-season cover crops were distinct from the early season cover crops and fallow. No treatments affected bacterial alpha or beta diversity in 2019, which could be attributed to high rainfall. Results indicate that cover crop mixtures including species tolerant to warmer and drier conditions can foster diverse soil bacterial communities compared to fallow soils.

Figure 1, showing a schematic of the fields and experimental design.

Related works from that research group include:

Paper published on the 2021 MSE symposium!

I am delighted to announce that a collaborative paper on the 2021 Microbes and Social Equity Symposium was just published! I was invited by the Challenges journal’s editor-in-chief to submit a contribution about the group’s activities, and the together the session organizers, speakers, student assistants, and I wrote about our experiences putting this together. The journal is dedicated to published highly interdisciplinary research which looks things from multiple perspectives and which contributes to Planetary Health.

We learned that, much like microbes, audiences don’t always act the way you expect them to. Even better: we learned that by providing collaborative working time after listening to speaker sessions, which could be used to get our thoughts down on paper, we could capture the magic and inspiration of the conversations we had post-talks and revisit those later as research and outreach resources.

You can check out the full article here.

And, if you are interested by what you read about last year’s event, check out this year’s symposium, happening next week!

Designing the Microbes and Social Equity Symposium, a Novel Interdisciplinary Virtual Research Conference Based on Achieving Group-Directed Outputs

Suzanne L. Ishaq 1,2,*, Emily F. Wissel 3, Patricia G. Wolf 4,5, Laura Grieneisen 6, Erin M. Eggleston 7, Gwynne Mhuireach 8, Michael Friedman 9, Anne Lichtenwalner 1,10, Jessica Otero Machuca 11, Katherine Weatherford Darling 12,13, Amber L. Pearson 14, Frank S. Wertheim 15, Abigail J. Johnson 16, Leslie Hodges 17, Sabrina K. Young 18, Charlene C. Nielsen 19, Anita L. Kozyrskyj 20, Jean D. MacRae 21, Elise McKenna Myers 22, Ariangela J. Kozik 23, Lisa Marie Tussing-Humphreys 24, Monica Trujillo 25, Gaea A. Daniel 26, Michael R. Kramer 27, Sharon M. Donovan 28, Myra Arshad 29, Joe Balkan 30 and Sarah Hosler 31

Abstract: The Microbes and Social Equity working group was formed in 2020 to foster conversations on research, education, and policy related to how microorganisms connect to personal, societal, and environmental health, and to provide space and guidance for action. In 2021, we designed our first virtual Symposium to convene researchers already working in these areas for more guided discussions. The Symposium organizing team had never planned a research event of this scale or style, and this perspective piece details that process and our reflections. The goals were to 1) convene interdisciplinary audiences around topics involving microbiomes and health, 2) stimulate conversation around a selected list of paramount research topics, and 3) leverage the disciplinary and professional diversity of the group to create meaningful agendas and actionable items for attendees to continue to engage with after the meeting. Sixteen co-written documents were created during the Symposium which contained ideas and resources, or identified barriers and solutions to creating equity in ways which would promote beneficial microbial interactions. The most remarked-upon aspect was the working time in the breakout rooms built into the schedule. MSE members agreed that in future symposia, providing interactive workshops, training, or collaborative working time would provide useful content, a novel conference activity, and allow attendees to accomplish other work-oriented goals simultaneously.

Affiliations:

1    School of Food and Agriculture, University of Maine, Orono, Maine 04469, USA; 2    Institute of Medicine, University of Maine, Orono, Maine 04469, USA; 3    School of Nursing, Emory University, Atlanta, Georgia 30322; 4    Department of Nutrition Science, Purdue University, West-Lafayette, Indiana, USA, 47907; 5    Department of Animal Sciences, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA; 6    Department of Genetics, Cell, & Development, University of Minnesota, Minneapolis, Minnesota 55108, USA; 7    Department of Biology, Middlebury College, Middlebury, Vermont 05753, USA; 8    Department of Architecture, University of Oregon, Eugene, Oregon 97403 USA; 9    Department of Science and Mathematics, Pratt Institute, Brooklyn, New York 11205, USA; 10   Cooperative Extension, University of Maine, Orono, Maine 04469, USA; 11   Mayo Clinic, Orlando, Florida 32837, USA; 12   Social Science Program University of Maine at Augusta Bangor, Maine 04401, USA; 13   Graduate School of Biomedical Science & Engineering, University of Maine, Orono, Maine 04469, USA; 14   Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, Michigan 48824, USA; 15   Cooperative Extension, University of Maine, Springvale, Maine 04083, USA; 16   Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA; 17   Economic Research Service, United States Department of Agriculture, USA; 18   Economic Research Service, United States Department of Agriculture, USA; 19   School of Public Health, University of Alberta, Edmonton, Alberta, Canada; 20   Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada; 21   Department of Civil and Environmental Engineering, University of Maine, 5711 Boardman Hall, Orono, Maine 04469, USA; 22   Boston Consulting Group, Bethesda, Maryland 20814, USA; 23   Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan. Ann Arbor, Michigan 48109, USA; 24   Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois 60612, USA; 25   Department of Biology, Queensborough Community College, Queens, New York 11364, USA; 26   Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia 30322, USA; 27   Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA; 28   Department of Food Science and Human Nutrition, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 USA; 29   Department of Biology, Stoney Brook University, Stony Brook, New York 11794, USA; 30   Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA; 31   School of Food and Agriculture, University of Maine, Orono, Maine 04469, USA;

Collaborative paper accepted on winter wheat, weeds, and climate.

The last paper to be generated from the large-scale, multi-year, collaborative research I participated in as a postdoc at Montana State University in the Menalled Lab in 2016 has finally been accepted for publication! At the time, I was working on the soil bacteria associated with winter wheat crops under different simulated climate change scenarios, and with added stressors like weed competition and different farming strategies. I was part of a large team of researchers looking at various aspects of agricultural stressors on long-term food production, including several agroecologists who led the development of this paper.

Weed communities in winter wheat: responses to cropping systems and predicted warmer and drier climate conditions.

Tim Seipel, Suzanne L. Ishaq, Christian Larson, Fabian D. Menalled. Sustainability 202214(11), 6880; https://doi.org/10.3390/su14116880. Special Issue “Sustainable Weed Control in the Agroecosystems

Abstract

Understanding the impact of biological and environmental stressors on cropping systems is essential to secure the long-term sustainability of agricultural production in the face of unprecedented climatic conditions. This study evaluated the effect of increased soil temperature and reduced moisture across three contrasting cropping systems: a no-till chemically managed system, a tilled organic system, and an organic system that used grazing to reduce tillage intensity. Results showed that while cropping system characteristics represent a major driver in structuring weed communities, the short-term impact of changes in temperature and moisture conditions appear to be more subtle. Weed community responses to temperature and moisture manipulations differed across variables: while biomass, species richness, and Simpson’s diversity estimates were not affected by temperature and moisture conditions, we observed a minor but significant shift in weed community composition. Higher weed biomass was recorded in the grazed/reduced-till organic system compared with the tilled-organic and no-till chemically managed systems. Weed communities in the two organic systems were more diverse than in the no-till conventional system, but an increased abundance in perennial species such as Cirsium arvense and Taraxacum officinale in the grazed/reduced-till organic system could hinder the adoption of integrated crop-livestock production tactics. Species composition of the no-till conventional weed communities showed low species richness and diversity, and was encompassed in the grazed/reduced-till organic communities. The weed communities of the no-till conventional and grazed/reduced-till organic systems were distinct from the tilled organic community, underscoring the effect that tillage has on the assembly of weed communities. Results highlight the importance of understanding the ecological mechanisms structuring weed communities, and integrating multiple tactics to reduce off-farm inputs while managing weeds.

The related works from that project include:

Similar work has been done by that group, including:

New perspective paper published on microbial transmission and lobsters.

A cookie in the shape of a lobster with icing to make it look like a pirate.

A collaborative perspective article was just published in Frontiers in Microbiology, which discusses epizootic shell disease in American lobsters, the role of microbes, and the movement of microbes in an aquatic environment. Because this is a perspective article, it is more of a thought exercise than my other publications, which either report findings or review other published literature, but it was intriguing to think about animal health in the context of rapidly-changing environmental conditions and microbial communities.

I previously presented some of the microbial community data related to the larger project from which this perspective piece came about, and this research team will continue to work on analyzing data from several experiments to develop into a research article later this year.

A steamed lobster on a plate.

This larger, collaborative project on lobster shell disease and warming ocean waters was begun by researchers at the Aquaculture Research Institute: Debbie Bouchard, Heather Hamlin, Jean MacRae, Scarlett Tudor, and later Sarah Turner as a grad student. I was invited to participate in the data analysis aspect two years ago.

At the time, Grace Lee was a rising senior at Bowdoin College, and accepted to my lab for the UMaine REU summer 2020 session, which was canceled. Instead, I hired Grace to perform DNA sequence analysis remotely, by independently learning data analysis following the teaching materials I had generated for my sequencing class.  I invited Joelle Kilchenmann to this piece after a series of conversations about microbes and social equity, because her graduate work in Joshua Stoll’s lab focuses on lobster fishing communities in Maine and understanding the challenges they face.


Ishaq, S.L., Turner, S.M., Tudor, M.S.,  MacRae, J.D., Hamlin, H., Kilchenmann, J., Lee1, G., Bouchard, D. 2022. Many questions remain unanswered about the role of microbial transmission in epizootic shell disease in American lobsters (Homarus americanus). Frontiers in Microbiology 13: 824950.

This was an invited contribution to a special collection: The Role of Dispersal and Transmission in Structuring Microbial Communities

Abstract: Despite decades of research on lobster species’ biology, ecology, and microbiology, there are still unresolved questions about the microbial communities which associate in or on lobsters under healthy or diseased states, microbial acquisition, as well as microbial transmission between lobsters and between lobsters and their environment. There is an untapped opportunity for metagenomics, metatranscriptomics, and metabolomics to be added to the existing wealth of knowledge to more precisely track disease transmission, etiology, and host-microbe dynamics. Moreover, we need to gain this knowledge of wild lobster microbiomes before climate change alters environmental and host-microbial communities more than it likely already has, throwing a socioeconomically critical industry into disarray. As with so many animal species, the effects of climate change often manifests as changes in movement, and in this perspective piece, we consider the movement of the American lobster (Homarus americanus), Atlantic ocean currents, and the microorganisms associated with either.

Microbes and Social Equity journal collection up to 6 published contributions!

The Microbes and Social Equity working group has been working with the scientific journal mSystems for the past year to develop a special collection of articles which highlight the connections between microbiomes, microbial exposures, social structures, and political contexts, as well as ways in which social, political, or economic changes could improve the way we interact with microbes to induce positive effects on our health and our planet.

The sixth contribution has just been published, and we have a handful more currently in the peer-review process! We plan to collect 25 invited contributions by the end of this year. You can check out the entire collection as it grows using the link below.

For more real-time discussions about microbes and social equity, check out our speaker series which is currently running until May 4th. You can also check out recordings from past talks.

mSystems Special Series: Social Equity and Disparities in Microbial Exposure

New publication on rumen microbes which may have uses in biofuel production

A scientific article led by my colleague Dr. Alaa Rabee at the Desert Research Center in Egypt was just published online and is now available! Dr. Rabee and I have been collaborating remotely on projects related to the bacteria in the rumen of camels, sheep, and cows, as Dr. Rabee’s work focuses on the isolation of bacteria which can degrade plant materials efficiently and could be used to produce biofuels. He will be spending 6 months working in my lab as a visiting scholar, which was delayed until this year because of the pandemic.


Rabee, A.E., Sayed Alahl, A.A., Lamara, M., Ishaq, S.L. 2022. Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production. PLoS ONE 17(1): e0262304. Article.

Abstract

Lignocellulosic biomass such as barley straw is a renewable and sustainable alternative to traditional feeds and could be used as bioenergy sources; however, low hydrolysis rate reduces the fermentation efficiency. Understanding the degradation and colonization of barley straw by rumen bacteria is the key step to improve the utilization of barley straw in animal feeding or biofuel production. This study evaluated the hydrolysis of barley straw as a result of the inoculation by rumen fluid of camel and sheep. Ground barley straw was incubated anaerobically with rumen inocula from three fistulated camels (FC) and three fistulated sheep (FR) for a period of 72 h. The source of rumen inoculum did not affect the disappearance of dry matter (DMD), neutral detergent fiber (NDFD). Group FR showed higher production of glucose, xylose, and gas; while higher ethanol production was associated with cellulosic hydrolysates obtained from FC group. The diversity and structure of bacterial communities attached to barley straw was investigated by Illumina Mi-Seq sequencing of V4-V5 region of 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes and Bacteroidetes. The dominant genera were RC9_gut_group, RuminococcusSaccharofermentansButyrivibrioSucciniclasticumSelenomonas, and Streptococcus, indicating the important role of these genera in lignocellulose fermentation in the rumen. Group FR showed higher RC9_gut_group and group FC revealed higher RuminococcusSaccharofermentans, and Butyrivibrio. Higher enzymes activities (cellulase and xylanase) were associated with group FC. Thus, bacterial communities in camel and sheep have a great potential to improve the utilization lignocellulosic material in animal feeding and the production of biofuel and enzymes.

MSE paper published on “Twenty important research questions in microbial exposure and social equity”

The Microbes and Social Equity working group has published its second collaborative paper together, led by Dr. Jake Robinson and featuring 25 other MSE group researchers in various fields related to microbiomes, social equity, and ecosystems. In developing this paper, we had many conversations about what had been accomplished in research related to microbial exposure, as well as what had yet to be done. We provide some background information as context, and spend the majority of the paper outlining twenty of the most poignant research directions. There are so many questions yet to be answered about the way the microbial communities interact with human lives, and how our lives impact them back. In our enthusiasm for the topics, we could have endlessly chatted about research, such that we decided to limit ourselves to twenty questions. We hope that this piece becomes a source for inspiration for others who continue this conversation and future research in these areas.

You can find a link below to read the full article, and links to the authors’ twitter feeds if you’d like to check them out on social media. You’ll be able to hear more about this publication in an upcoming seminar from Jake, as part of the 2022 MSE speaker series, which is open to all and free to attend over zoom.


Robinson, J.M., Redvers, N., Camargo, A., Bosch, C.A., Breed, M.F., Brenner, L.A., Carney, M.A., Chauhan, A., Dasari, M., Dietz, L.G., Friedman, M., Grieneisen, L., Hoisington, A.J., Horve, P.F., Hunter, A., Jech, S., Jorgensen, A., Lowry, C.A., Man, I., Mhuireach, G., Navarro-Pérez, E., Ritchie, E.G., Stewart, J.D., Watkins, H., Weinstein, P., and Ishaq, S.L. 2022. Twenty important research questions in microbial exposure and social equity. mSystems 7(1): e01240-21. Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure

ABSTRACT

Social and political policy, human activities, and environmental change affect the ways in which microbial communities assemble and interact with people. These factors determine how different social groups are exposed to beneficial and/or harmful microorganisms, meaning microbial exposure has an important socioecological justice context. Therefore, greater consideration of microbial exposure and social equity in research, planning, and policy is imperative. Here, we identify 20 research questions considered fundamentally important to promoting equitable exposure to beneficial microorganisms, along with safeguarding resilient societies and ecosystems. The 20 research questions we identified span seven broad themes, including the following: (i) sociocultural interactions; (ii) Indigenous community health and well-being; (iii) humans, urban ecosystems, and environmental processes; (iv) human psychology and mental health; (v) microbiomes and infectious diseases; (vi) human health and food security; and (vii) microbiome-related planning, policy, and outreach. Our goal was to summarize this growing field and to stimulate impactful research avenues while providing focus for funders and policymakers.

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

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

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

The Microbes and Social Equity working group is turning 2!

It doesn’t seem that long ago that we were just an assorted group of interested researchers having a chat, but here we are two years later gaining international support and interest.  We greatly appreciate your interest in this group, and are pleased to share some of our recent updates.

We currently have 115 members of the Microbes and Social Equity working group, and another 33 people signed up just for the newsletter. In 2021, we ran a very successful speaker series, virtual symposium, and collectively had quite a few publications, presentations, and developments! We are excited to continue that momentum in 2022, and are planning another speaker series and virtual symposium, finalizing our journal special collection with mSystems, and furthering the collaborative projects we have begun. We will also be adding additional leadership roles for the group, to better accommodate our group and give more attention to our growing activities and initiatives.

Publications


mSystems Special Collections:

We are making great progress adding to our special collection with mSystem, with 3 papers published and several more currently in review! We will continue adding contributions through 2022. 

  1. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice | mSystems 
  2. Teaching with Microbes: Lessons from Fermentation during a Pandemic | mSystems
  3. Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome | mSystems  


Upcoming

  • Francisco Parada’s postdoc, Dr. Ismael Palacios-García finished collecting his probiotic/lifestyle randomized trial, collecting cognitive electrophysiology (EEG+EGG), microbial (DNA from fecal samples), and phenomenological data (questionnaires) over 4+ months. They hope they will be publishing some of these results soon!  
  • Jake Robinson is working on “Invisible Friends”, a popular science book anticipated for release in 2022. From Jake’s page: “Invisible Friends is about our extraordinary relationship with microbes, and how they shape our lives, our health, and the world around us. The book aims to challenge the prevailing negative perception of microorganisms, by highlighting the weird, wonderful, and indispensable roles they play in our health, behaviour, society, and ecosystems!”

Presentations

Upcoming: 

The Microbes and Social Equity speaker series 2022 is under development! We hope to invite speakers for a virtual series running January through April, Wednesdays from 12:00 – 13:00 EST. Registration is required but the series is free to attend.

inVIVO Planetary Health, virtual conference, Dec 1-7, 2021. Register here. Several MSE group members will be giving talks there, such as:

  • Sue Ishaq, “Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice”
  • Ari Kozik, “The human microbiome and health disparities: restoring dysbiosis as a matter of social justice”
  • Jake Robinson, “Microbiome-inspired green infrastructure (MIGI): a bioscience roadmap for urban ecosystem health”

2nd Rhode Island Microbiome Symposium, in person conference, University of Rhode Island Kingston, RI, January 14, 2022. Register here.

  • Sue Ishaq, ​”Microbes at the nexus of environmental, biological, and social research”

American Society for Microbiology (ASM) Microbe 2022, in person conference, Washington, DC (USA), June 9-13, 2022.

  • ‘Field Work & DEI Part 1: Fostering Equitable Partnerships with the Communities in Your Field Work Location’. The session’s date is June 11, 2022 (11:45AM – 12:30PM).
    • Ishaq,”Microbes and Social Equity: what is it and how do we do it?”
  • MSE special session, “Microbes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice”. The session’s date is June 11, 2022 (1:45PM – 3:45PM), and the event is under development.
    • Featuring panelists Monica Trujillo, Ari Kozik, and Carla Bonilla

Past

Mike Friedman hosted a very successful MSE Special Session (together with the Microbial Ecology section) at this year’s virtual Ecological Society of America meeting. Naupaka Zimmerman, Justin Stewart, Monica Trujillo and Sue Ishaq gave short presentations on social justice and various aspects of environmental and human microbiota. But the bulk of the session was taken up by audience discussion of issues in environmental justice and microbes, practical and suggested policies and education.

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

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

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


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

Abstract:

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

This work was presented at a recent scientific conference:

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