Paper published on “Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice”!

The Ishaq and Li labs at UMaine are delighted to announce that our paper on “Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice” has been published in mSystems!! The complete author list, Abstract, and Ackowledgements/Funders portions of the paper can be found at the end of this post.

This paper is part of a larger Broccoli project, in which we are evaluating the use of broccoli sprouts in the diet to enlist gut microbes to produce anti-inflammatories. You can read about the whole project here, with links to other resources.

The Premise

Broccoli sprouts are very high in a compound called glucoraphanin. When glucoraphanin comes in contact with the myrosinase enzyme, also found in the sprouts, it is transformed into a compound that acts an an anti-inflammatory in people!

If you eat raw sprouts, this conversion happens when you cut or chew the sprouts, and that anti-inflammatory will get absorbed in your stomach. If you steam or cook the sprouts, you can inactivate the enzyme and leave the glucoraphanin compound alone. Some of your gut microbes are able to use the compound, and produce the anti-inflammatory right in your gut! We are trying to understand how and when this works, so we can use it to reduce symptoms of Inflammatory Bowel Disease.

The Mouse work

In the winter of 2020-2021, we ran a 40-day study with 40 mice housed at UMaine. The mice were divided into 4 groups: “control” which ate the mouse chow, “control+DSS” which ate the mouse chow and had colitis induced by adding DSS (a salt laxative) to their drinking water, “broccoli” which ate the mouse chow with steamed broccoli sprouts mixed in, and “broccoli+DSS” which ate the mouse chow/steamed broccoli sprouts diet and had colitis induced by adding DSS (salt laxative) to their drinking water. This work was led by Johanna Holman, who was a master’s student at the time; Lousia Colicci, who was an undergrad at Husson University at the time and is applying to medical schools now; Dorein Baudewyns, who was an undergrad at Husson University at the time and is completing a graduate program in Psychology at UMaine; and Joe Balkan, who was completing his senior year of high school at the time and has since begin an undergrad degree in Biology at Tufts University where he is preparing for medical school.

The mice were weighed regularly and fecal samples assessed for blood (signs of colitis). At the end of the study, the mice were euthanized so we could study the bacteria in parts of the intestines that we can’t access in humans. We used as few mice as possible, and got as much information from this study as possible, to do as much good as we can with their sacrifice.

The Health Benefits

As we’d hoped, the broccoli+DSS mice that were eating the broccoli sprouts that were given colitis did much better than the control+DSS group who ate mouse chow during their colitis. The broccoli+DSS mice were able to keep gaining weight as they grew, had better consistency of their stool, and had lower amounts of proteins and other metabolities in their blood which indicate inflammation (lower cytokines and lipocalin). Those graphs are shown in the paper.

The Gut Microbes

We found a lot of interesting things with the microbial communities that were living in different parts of the intestines, but the most exciting was that broccoli sprouts in the diet helped microbial communities stay alive in their original gut locations even during colitis! Certain microbes like to live in particular places in our intestines based on where different ingredients in our diet get processed, or the local environment (like how acidic the intestinal neighborhood is), and this is called biogeography.

In the graph below, our control group mice (eating chow) or the broccoli group (eating chow plus sprouts), we see that microbial communites in the small intestines clustered away from the microbial communities in the large intestines.

The DSS salt laxative, and ulcerative colitis, wreak havoc on gut microbes because they cause physical damage to the lining of the intestine, which where many microbes that can be useful to us live on or near. When we induced colitis in mice that were eating mouse chow (control+DSS group), the damage to the intestines caused a loss to some of the microbes living in different places. The remaining microbes that could survive these tough conditions were basically the same ones regardless of where we we looked in the intestines.

But, if mice had colitis and were eating broccoli sprouts (broccoli+DSS), the microbes were able to survive in their original locations and preserved biogeography! This is important because where microbes live in the gut may determine if the beneficial things they make can help resolve IBD symptoms in specific locations in the gut.

Image by Johanna Holman, graph from the paper.

The Spatial Location of GLR-digesting-genes

Bejamin and Timothy Hunt are undergraduates in Biology who have been working on bioinformatics in the Ishaq Lab since December 2022 after completing Sue’s DNA Sequencing Data Analysis Class. They joined the DSS project to provide in-depth analysis on some of the sequences which matched bacteria that are known to convert GLR into the anti-inflammatory SFN, as well as analyze data comparing numbers of genes known to be involved in the process.

A cartoon of the intestines with bacteria of interest in the jejunum, ceculm and colon,
Cropped figure from the paper, made by Benjamin and Timothy.
Benjamin Hunt

The study of the bioproduction of SFN and its mucosal and luminal activity benefited from the biogeographical analysis of this study. It was interesting to note the extreme dominance of a Bacteroides species in the broccoli treatments. B. thetaiotaomicron was indicated based on BLASTN analysis and an evaluation of matching species but was not directly suggested by the dada-Silva taxonomy assignment. The indication of B. thetaiotaomicron suggested analyzing the presence of the operon BT2159-BT2156, which was generally minimally present (<100) but at relatively high counts (>100,000) in some samples. Significantly, the operon was found at locations where no Bacteroides were identified. We continue to reflect on the similarities and differences in the biogeography of bacterial abundance and operon presence highlighted in the different treatments of this study.

Benjamin and Timothy Hunt

The Next Steps

As part of this project, we cultured hundreds of bacteria from the intestines of mice to try and isolate some of the ones that turn glucroraphanin into sulforaphane. We have a large team of students and researchers participating on the culturing work, some of whom are pictured here. We’ll be providing plenty of updates on that project as we continue to process the bacteria this fall!

The Paper

Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice.

Johanna M. Holman1, Louisa Colucci2, Dorien Baudewyns3, Joe Balkan4, Timothy Hunt5, Benjamin Hunt5, Marissa Kinney1, Lola Holcomb6, Allesandra Stratigakis7, Grace Chen8, Peter L. Moses9,10, Gary M. Mawe9, Tao Zhang7, Yanyan Li1*, Suzanne L. Ishaq1*

1 School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469 2 Department of Biology, Husson University, Bangor, Maine, USA 04401 3 Department of Psychology, University of Maine, Orono, USA 04469 4 Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA 02155 5 Department of Biology, University of Maine, Orono, Maine, USA 04469 6 Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469 7 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790 8Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109 9Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 0540110 Finch Therapeutics, Somerville, Massachusetts, USA 02143

Abstract: Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, and affordable, for managing symptoms. Glucosinolate compounds are highly concentrated in broccoli sprouts, especially glucoraphanin, and can be metabolized by certain mammalian gut bacteria into anti-inflammatory isothiocyanates, such as sulforaphane. Gut microbiota exhibit biogeographic patterns, but it is unknown if colitis alters these or whether the location of glucoraphanin-metabolizing bacteria affects anti-inflammatory benefits. We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 34-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, lipocalin, serum cytokines, and bacterial communities from the luminal- and mucosa-associated populations in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet with DSS treatment performed better than mice fed the control diet with DSS, including significantly more weight gain, lower Disease Activity Indexes, lower plasma lipocalin and proinflammatory cytokines, and higher bacterial richness in all gut locations. Bacterial communities were assorted by gut location, but were more homogenous across locations in the control diet + DSS mice. Importantly, our results showed that broccoli sprout feeding abrogated the effects of DSS on gut microbiota, as bacterial richness and biogeography were similar between mice receiving broccoli sprouts with and without DSS. Collectively, this supports the protective effect of steamed broccoli sprouts against dysbiosis and colitis induced by DSS.

Importance: Evaluating bacterial communities across different locations in the gut provides a greater insight than fecal samples alone, and provides an additional metric by which to evaluate beneficial host-microbe interactions. Here, we show that 10% steamed broccoli sprouts in the diet protects mice from the negative effects of dextran sodium sulfate induced colitis, that colitis erases biogeographical patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. Mice fed the broccoli sprout diet during colitis performed better than mice fed the control diet while receiving DSS. The identification of accessible dietary components and concentrations that help maintain and correct the gut microbiome may provide universal and equitable approaches to IBD prevention and recovery, and broccoli sprouts represent a promising strategy.

Acknowledgements: All authors have read and approved the final manuscript. The authors thank Jess Majors, University of Maine, for her kind and detailed care of the mice during the trial, and for Ellie Pelletier for her informal review of the manuscript. This project was supported by the USDA National Institute of Food and Agriculture through the Maine Agricultural & Forest Experiment Station: Hatch Project Numbers ME022102 and ME022329 (Ishaq) and ME022303 (Li) which supported Johanna Holman; the USDA-NIFA-AFRI Foundational Program [Li and Chen; USDA/NIFA 2018-67017-27520/2018-67017-36797]; and the National Institute of Health [Li and Ishaq; NIH/NIDDK 1R15DK133826-01] which supported Marissa Kinney, Timothy Hunt, and Benjamin Hunt. Lola Holcomb was supported by US National Science Foundation One Health and the Environment (OG&E): Convergence of Social and Biological Sciences NRT program grant DGE-1922560, and through the UMaine Graduate School of Biomedical Sciences and Engineering. 

Celebrating 50 peer-reviewed publications!

I’ve been a researcher since Juy 2010, when I started graduate school, and my first peer-reviewed journal article was accepted in 2012. This summer, I reached 50 peer-reviewed publications, including research papers and reviews. Since I started publishing, I’ve been in grad school, two one-year postdoc positions, one two-year research assistant professor position, and one four-year-and-counting assistant professor position, and my research areas of focuses have shifted 5 or 6 times since then to keep pace with the job I was in at the time. To capture that diversity, I made a word cloud of my publication list, including authors, titles, and journal names:

Word Cloud

Top keywords:

Unsurprisingly, most of my top keywords include the microbes I’m focusing on (bacterial), the animals I’ve worked with (moose, Alces), the sample types I’ve worked with (rumen, soil), and the methodology I use (seqeuencing).

Top co-authors:

None of this would have been possible without hundreds of researchers that I have worked with over the years. Here are a few of the names that pop up in theat wordcloud because I have published so often with them:

  • Carl Yeoman, Montana State University, who was my post-doc advisor for a year and who I’ve continued to publish with on various projects. We’ve co-authored 11 papers!!
  • Andre Wright, my PhD avisor, who has since moved into non-research roles, also with 11 co-authored papers!!
  • Fabian Menalled, Montana State University, who was my post-doc advisor for a year and who I collaborated with for many years on projects which sprung from that first year. We have 7 co-authoured papers!
  • Jean MacRae, University of Maine, and I have collaborated on a handful of different projects since I joined UMaine and have co-authored 4 papers with another currently in review.

Full list of Research Articles (38) and Reviews (12):

1 undergraduate student I mentored, 2 graduate student I mentored

  1. Ishaq, S.L., Hosler2, S., Dankwa, A., Jekielek, P., Brady, D.C., Grey, E., Haskell, H., Lasley-Rasher, R., Pepperman, K., Perry, J., Beal, B., Bowden, T.J. 2023. Bacterial community trends associated with sea scallop, Placopecten magellanicus, larvae in a hatchery system. Aquaculture Reports 32: 101693.
  2. Holman2, J., L. Colucci, L. Baudewyns, D., Balkan1, J., Hunt1, T., Hunt1, B., Kinney2, M., Holcomb2, L., Stratigakis, A., Chen. G., Moses, P., Mawe, G.M., Zhang, T., Li, Y., Ishaq, S.L. 2023. Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice. mSystems. Accepted
  3. Betiku2, O., Yeoman, C., Gaylord, T.G., Ishaq, S., Duff, G., Sealey, W. 2023. Evidence of a Divided Nutritive Function in The Rainbow Trout (Oncorhynchus mykiss) Mid- and Hind-Gut Microbiomes by Whole Shotgun Metagenomic Approach. Aquaculture Reports 30: 101601.
  4. Ishaq, S.L., Turner, S.M., Lee1, G., Tudor, M.S., MacRae, J.D., Hamlin, H., Bouchard, D. 2023. Water temperature and disease alters bacterial diversity and cultivability from American Lobster (Homarus americanus) shells. iScience 26(5): 106606.
  5. Ouverson2, 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. 911199.
  6. Ishaq, S.L., Wissel2, E.F., Wolf, P.G., Grieneisen, L., Eggleston, E.M., Mhuireach, G., Friedman, M., Lichtenwalner, A., Otero Machuca, J., Weatherford Darling, K., Pearson, A., Wertheim, F.S., Johnson, A.J., Hodges, L., Young, S., Nielsen, C.C., Kozyrskyj, A.L., MacRae, J.D., McKenna Myers, E., Kozik, A.J., Tussing-Humphreys, L.M., Trujillo, M., Daniel, G.A., Kramer, M.R., Donovan, S.M., Arshad 1, M., Balkan1, J., Hosler2, S. 2022. Designing the Microbes and Social Equity Symposium, a novel interdisciplinary virtual research conference based on achieving group-directed outputs. Challenges, 13(2), 30.
  7. Holman2, J., Hurd, M., Moses, P., Mawe, G., Zhang, T., Ishaq, S.L., Li, Y. 2022. Interplay of Broccoli/Broccoli Sprout Bioactives with Gut Microbiota in Reducing Inflammation in Inflammatory Bowel Diseases.The Journal of Nutritional Biochemistry 113:109238. (review)
  8. 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. (review)
  9. Sepiel, T. Ishaq, S.L., Larson, C., Menalled, F. 2022. Weed communities in winter wheat: responses to cropping systems and predicted warmer and drier climate conditions. Sustainability 14(11), 6880.
  10. 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. Invited contribution to special collection: The Role of Dispersal and Transmission in Structuring Microbial Communities
  11. 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.
  12. Ishaq, S.L., Parada, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Pathak, A., Chauhan, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K.A., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4. Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure. (review)
  13. Choi2, 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.
  14. Dankwa2, A.S., U. Humagain2, S.L. Ishaq, C.J. Yeoman, S. Clark , D.C. Beitz, and E. D. Testroet. 2021. Determination of the microbial community in the rumen and fecal matter of lactating dairy cows fed on reduced-fat dried distillers grains with solubles. Animal 15(7):100281.
  15. Ishaq, S.L., A. Hotopp2, S. Silverbrand2, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine.iScience 24(6):102663.
  16. Ouverson2, T., Eberly, J., Seipel, T., Menalled, F., Ishaq, S.L. 2021.Temporal soil bacterial community responses to cropping systems and crop identity in dryland agroecosystems of the Northern Great Plains. Frontiers in Sustainable Food Systems 5:75. Invited submission to Plant Growth-Promoting Microorganisms for Sustainable Agricultural Production special collection.
  17. Zeng, H., Safratowich, B.D., Liu, Z., Bukowski, M.R., Ishaq, S.L. 2021. Adequacy of calcium and vitamin D reduces inflammation, β-catenin signaling, and dysbiotic Parasutterella bacteria in the colon of C57BL/6 mice fed a Western-style diet. Journal of Nutritional Biochemistry 92: 108613. Article.
  18. Horve1, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8:e9580.
  19. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20.
  20. Garcia-Mazcorro, J., Ishaq, S.L., Avila-Jaime, B., Rodriguez-Herrera, M.V., Kawas, J.R., Nagaraja, T.G. 2020. Are there any native Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. Animal 14(1):22-30. (review)
  21. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989.
  22. Ishaq, S.L., Rapp1, M., Byerly1, R., McClellan1, L.S., O’Boyle1, M.R., Nykanen1, A., Fuller1, P.J., Aas1, C., Stone1, J.M., Killpatrick1, S., Uptegrove1, M.M., Vischer1, A., Wolf1, H., Smallman1, F., Eymann1, H., Narode1, S., Stapleton, E., Cioffi, C.C., Tavalire, H. 2019. Framing the discussion of microorganisms as a facet of social equity in human health. PLoS Biology 17(11): e3000536. Microbiomes Across Systems special issue. Article.  (review)
  23. Velazquez1, S., Griffiths1, W., Dietz, L., Horve1, P., Nunez1, S., Hu, J., Shen, J., Fretz, M., Bi, C., Xu, Y., Van Den Wymelenberg, K.G., Hartmann, E.M., Ishaq, S.L.2019. From one species to another: A review on the interaction of chemistry, microbiology, and occupancy in the built environment. Indoor Air 26(6): 875-1049. (review). Top 10% most downloaded papers from 2018 – 2019, and 2019 – 2020.
  24. Velazquez1, S., Bi, C., Kline, J., Nunez1, S., Corsi, R., Xu, Y., Ishaq, S.L. 2019. Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community. PeerJ 7:e8147.
  25. Stenson, J., Ishaq, S., Laguerre, A., Loia, A., MacCrone1, G., Mugabo, I., Northcutt, D., Riggio, M., Barbosa, A., Gall, E., Van Den Wymelenberg, K. 2019. Occupant Experience of a Mass Timber Office Building: Monitored and Perceived. Buildings 9:142.
  26. Seipel, T., Ishaq, S.L., Menalled, F.D. 2019. Agroecosystem resilience is modified by management system via plant–soil feedbacks.Basic and Applied Ecology 39:1-9.
  27. Ishaq, S.L., Lachman2, M.M., Wenner, B.A., Baeza, A., Butler, M., Gates, E., Olivo, S., Buono Geddes, J., Hatfield, P., Yeoman, C.J. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed. PLoS ONE 14(6): e0215797.
  28. Ishaq, S.L., Page, C.M., Yeoman, C.J., Murphy, T.W., Van Emon, M.L., Stewart, W.C. 2019. Zinc-amino-acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not. Journal of Animal Science 97(2):687-697.
  29. Horve1, P.F., Lloyd1, S., Mhuireach, G.A., Dietz, L., Fretz, M., MacCrone1, G., Van Den Wymelenberg, K., Ishaq, S.L.2019. Building Upon Current Knowledge of Indoor Microbiology to Construct the Next Era of Research into Microorganisms, Health, and the Built Environment. Journal of Exposure Science and Environmental Epidemiology 30:219–235. Healthy Buildings special issue.  (review)
  30. Yeoman, C.J. and Ishaq, S.L.*, Bichi, E., Olivo, S.K., Lowe, J., Aldridge, B.M. 2018. Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract. Scientific Reports 8:3197. *authors contributed equally. Article
  31. Seshadri, R., Leahy, S.C., Attwood, G.T., The, K.H., Lambie, S.C., Eloe-Fadrosh, E., Pavlopoulos, G., Hadjithomas, M., Varghese, N., Hungate1000 project collaborators, Perry, R., Henderson, G., Creevey, C.J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N., Henrissat, B., Woyke, T., Ivanova, N., Kelly, W.J. 2018. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology 36:359-367.
  32. Zeng, H., Ishaq, S.L., Liu, Z., Bukowski, M. 2018. Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet. Journal of Nutritional Biochemistry 54:18-27.
  33. Ishaq, S.L., AlZahal, O., Walker, N., McBride, B. 2017. Modulation of sub-acute ruminal acidosis by active-dry yeast supplementation and its effect on rumen fungal and protozoal populations in liquid, solid, and epimural fractions.Frontiers in Microbiology 8:1943.
  34. Ishaq, S.L., Yeoman, C.J, Whitney, T.R. 2017. Effects of ground redberry juniper and urea in DDGS-based supplements on ewe lamb rumen microbial communities. Journal of Animal Science 95(10):4587-4599.
  35. Perea1, K., Perz, K., Olivo, S.K., Ishaq, S.L., Williams, A., Lachman, M., Thompson, J., Yeoman, C.J. 2017. Feed efficiency phenotypes involve changes in ruminal, colonic, and small intestine-located microbiota. Journal of Animal Science 95(6):2585-2592.
  36. Ishaq, S.L., Johnson, S.P., Miller, Z.J., Lehnhoff, E.A., Olivo, S.K., Yeoman, C.J., Menalled, F.D. 2017. A living soil inoculum increases soil microbial diversity, crop and weed growth using soil from organic and conventional farms in northeastern Montana. Microbial Ecology 73: 417.
  37. Ishaq, S.L. 2017. Plant-Bacteria Interactions in Agriculture and the Use of Farming Systems to Improve Diversity and Productivity. AIMS Microbiology 3(2): 335-353. (review)
  38. Feng, W., Minor, D., Liu, M., Li, J., Ishaq, S.L., Yeoman, C., Lei, B. 2016. Null Mutations of Group A Streptococcus Orphan Kinase RocA: Selection in Mouse Infection and Comparison with CovS Mutations in Alteration of in vitro and in vivo Protease SpeB Expression and Virulence. Infection and Immunity 25:30-36.
  39. Zeng, H., Ishaq, S.L., Zhao, F-Q., Wright, A-D.G. 2016. Colonic inflammation accompanies an increase of b-catenin signaling Lachnospiraceae/Streptococcaceae in the hind-gut of high-fat diet-fed mice. Journal of Nutritional Biochemistry 35:30-36. 
  40. Salgado-Flores, A., Hagen, L.H., Pope, P.B., Ishaq, S.L., Wright, A-D.G., Sundset, M.A. 2016. Intake of a lichen-based diet altered the rumen and cecum microbial profiles in Norwegian reindeer (Rangifer tarandus tarandus). PLoS ONE 11(5). 
  41. Ishaq, S.L., Moses, P.L., Wright, A-D.G. 2016. The pathology of methanogenic archaea in human gastrointestinal disease. In: The Gut Microbiome – Implications for Human Disease. Mozsik, G. (ed.). InTech. Pp. 19-37.  (review)
  42. Ishaq, S.L., Kim1, C.J., Reis1, D., Wright, A-D.G. 2015. Fibrolytic bacteria isolated from the rumen of North American moose (Alces alces) and their potential as a probiotic for ruminants. PLoS ONE 10:12.
  43. Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Global Rumen Census Collaborators, Janssen, P.H. 2015. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports 5:14567. 
  44. Ishaq, S.L., Sundset, M.A., Crouse, J., Wright, A-D.G. 2015. High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity. Microbial Genetics 1(4):mgen.0.000034. 
  45. Ishaq, S.L., Wright, A-D.G. 2015. Wild Ruminants. In: Rumen Microbiology – Evolution to Revolution. AK Puniya, R Singh, DN Kamra (eds). Springer India. Pp. 37-45. (review)
  46. Ishaq, S.L., Wright, A-D.G. 2015. Terrestrial Vertebrate Animal Metagenomics, Wild Ruminants. In: Highlander, SK, Rodriguez-Valera, F, White, BA. (Ed.) Encyclopedia of Metagenomics: SpringerReference. Springer-Verlag Berlin Heidelberg. DOI: 10.1007/SpringerReference_303275. (review)
  47. St-Pierre, B., Cersosimo, L.M., Ishaq, S.L., Wright, A-D.G. 2015. Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animals. Frontiers in Microbiology 6:776. (review)
  48. Ishaq, S.L., Wright, A-D.G. 2014. Design and validation of four new primers for next-generation sequencing to target the 18S rRNA gene of gastrointestinal ciliate protozoa. Applied and Environmental Microbiology 80(17):5515-5521.
  49. Ishaq, S.L., Wright, A-D.G. 2014. High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway. Microbial Ecology 68(2):185-195. 
  50. Ishaq, S.L., Wright, A-D.G. 2012. Insight into the bacterial gut microbiome of the North American moose (Alces alces). BMC Microbiology 12:212. 

Summer 2023 wrap up

It feels like the summer semester just began, and here we are, already preparing for fall classes! There has been so much going on in the lab that I wasn’t able to keep up with regular posts, so here are some of the highlights.


I attended four symposia/conferences this summer, starting with the virtual MSE 2023 summer symposium in early June, featuring 4 days of invited talks organized around themes, and a 5th day featuring contributed short talks (something new we tried this year). The whole week was fantastic and sparked thoughtful conversation on the using of microbial communities to reduce disparities in positive and negative health outcomes, living conditions, and more. You can find the recorded content on the symposium event page.

Next, I went to the Microbiome Day at Boston University in early July in Boston, MA, where I gave the keynote talk.

I went to the annual meeting for the American Society for Nutrition in Boston, MA in mid-July, where PhD students Johanna Holman, Lola Holcomb, and master’s student Marissa Kinney all presented posters, and most of the lab was able to make it to a puzzle quest at Boda Borg.

And, I went to the Ecological Society of America annual meeting in Portland, OR in August to present some recent work on scallop larval rearing tanks and the bacterial communities we found there. That included an unexpected effect of coastal water dynamics and the phase of the moon. That work has recently been published.


The lab has been bustling all summer as we work on several projects. Master’s student Ayodeji Olaniyi has been working on a project to identify Vibrio bacteria isolated from the sides of scallop larvae hatchery tanks, as part of a larger project investigating microbial communities in hatcheries.

Marissa and visiting postdoc Gloria Adjapong have been preparing a 16S rRNA sequencing library for hundreds of scallop tank biofilm samples we collected last year, although I don’t have any photos of that.

Johanna has been leading a team of students (Alexis Kirkendall, Lilian Nowak, Aakriti Sharma, and Jaymie Sideaway) on a culturing project to screen hundreds of bacterial isolates that were collected from the gastrointestinal tracts of mice eating borccoli sprouts. We are testing them for their capacity to metabolize different glucosinolates into anti-inflammatory compounds, as well as grow on different media types. In the process, we found that the bacteria we are using as a positive control likes to move from one test well to another when its favorite media is available — but not when glucose is present.

Looking ahead to fall

This fall, the lab will be supporting Ayodeji to write and defend his thesis, as he is currently looking for research/technician jobs. His thesis focuses on Vibrio bacteria in scallop larvae hatcheries.

We’ll also be preparing to welcome Alexis back as a graduate student in January 2024, to continue her work on bacteria isolated from mice eating broccoli sprouts.

I’ll be teaching two classes this fall, AVS 254 Intro to Animal Microbiomes, and AVS 454/554 DNA Sequencing Data Analysis lab, and with 90 students enrolled between them I will luckily be assisted by Ayodeji and Lola, who will be co-grading assignments with me.

Finally, I’ve got more travel coming up soon, as I’ll be giving a talk at the 9th SoCal Microbiome Symposium in September!

The first look at Atlantic deep sea scallop bacterial communities in new publication

Our paper was published in Aquaculture Reports, on identifying the bacteria associated with wild and hatchery-raised Atlantic sea scallop larvae, and the biofilms in larval tanks in a hatchery! For the past few years, I’ve been part of a state-wide collaboration between researchers, industry professionals, and educators all working together to understand and improve Atlantic sea scallop hatchery production. To our knowledge, this is the first study to identify bacteria in Atlantic sea scallops, and even though it was a very small project we hope it will lead to a much larger, mult-year project to investigate this in more detail.

Scallops are a diverse animal group of marine bivalve mollusks (family Pectinidae) with global distribution in coastal waters, and Atlantic deep-sea scallops, Placopecten magellanicus, are found along the eastern coast of the United States and Canada. Scallops’ reproductive potential and industry demand make them a prime target for hatchery- and farm-based production, and this has been successfully achieved in bay scallops, but not in sea scallops. Currently, hatcheries collect wild sea scallop adults, or maintain cultured broodstocks, and spawn them in their facilities with the intention of forming a plentiful population to grow to adulthood, spawn, and sell to create a sustainable production cycle while also reducing disruption to the scallops’ natural habitat.

Unfortunately, in sea scallop hatcheries the last two weeks of the larval maturation phase, the veliger-stage, is plagued by large mortality events, going from 60 million sea scallop larvae down to several thousand individuals in a span of 48 hours. Survival of clutches to maturity remains very low, with an industry-standard rate around 1%. This drastic winnowing of larvae reduces the availability of cultured sea scallop spat for farmers, forcing sea scallop farms to rely almost exclusively on sea scallop spat collected from wild populations for stock and is seen as a bottleneck for growth of the industry and achieving sustainable harvests. Hatchery larval die-off is well-demonstrated not to be caused by inadequate diet, lighting, temperature, or atmospheric pressure in aquaculture facilities compared to wild conditions.

This project wanted to know if there was any clue in the bacteria that associate with larvae, or with the tanks they are in. In particular, hactcheries are worried about certain species of bacteria in the genus Vibrio, as they can cause disease to scallops and/or people, but it is tricky to study them because there are many species which do nothing at all. This project is part of another experiment to examine some of the Vibrio we found in tanks.

We sampled from some wild larvae, hatchery larvae, and from tank biofilms to indentify what was there. There were two styles of tank setup, and we collected from used tanks as well as tanks after they had been cleaned and refilled with filtered seawater.

One of the surprising things we found, was that the bacterial communities in biofilms along the sides of larvae tank were more similar to each other (clustering) when samples were collected during the same phase of the lunar cycle. Bacterial richness and community similarity between tank samples fluctuated over the trial in repeated patterns of rise and fall, which showed some correlation to lunar cycle  where richness is high when the moon is about 50% and richness is low during new and full moon phases. This may be a proxy for the effects of spring tides and trends in seawater bacteria and phages which are propagated into hatchery tanks. The number of days since the full moon was significantly correlated with bacterial community richness in tanks: low during the full moon, peaking ~ 21 days after the full moon, and decreasing again at the next full moon.  

Fig. 7. Constrained ordination of bacterial communities in tank samples. Each point represents the bacterial community from one sample. Similarity between samples was calculated using Distance-based Redundancy Analysis (dbDRA), and significant model factors (anova, p < 0.01) are displayed with arrow lengths relative to their importance in the model (f value). The shape of points indicates whether swabbing was either immediately after filtered seawater has been used to fill the tank (cleaned, refilled) or 48 hours after (dirty, drained). Tank setup indicates if water was static, constantly filtered and recirculated in a flow-through system, or setup information was not available (n/a).

These results along with future work, will inform hatcheries on methods that will increase larval survival in these facilities, for example, implementing additional filtering or avoiding seawater collection during spring tides, to reduce certain bacterial taxa of concern or promoting a more diverse microbial community which would compete against pathogens.

Bacterial community trends associated with sea scallop, Placopecten magellanicus, larvae in a hatchery system.

Authors: Suzanne L. Ishaq1*, Sarah Hosler1, Adwoa Dankwa1, Phoebe Jekielek2, Damian C. Brady3, Erin Grey4,5, Hannah Haskell6, Rachel Lasley-Rasher6, Kyle Pepperman7, Jennifer Perry1, Brian Beal8, Timothy J. Bowden1

Affiliations:1 School of Food & Agriculture, University of Maine, Orono ME 044692 Ecology and Environmental Sciences, University of Maine, Orono ME 044733 School of Marine Sciences, Darling Marine Center, University of Maine, Walpole ME 045734 School of Biology and Ecology, University of Maine, Orono ME 044695 Maine Center for Genetics in the Environment, University of Maine, Orono ME 044696 Department of Biological Sciences, University of Southern Maine, Portland ME 041037 Downeast Institute, Beals, ME 046118 Division of Environmental & Biological Sciences, University of Maine at Machias, Machias, ME 04654


Atlantic sea scallops, Placopecten magellanicus, are the most economically important marine bivalves along the northeastern coast of North America. Wild harvest landings generate hundreds of millions of dollars, and wild-caught adults and juvenile spat are increasingly being cultured in aquaculture facilities and coastal farms. However, the last two weeks of the larval maturation phase in hatcheries are often plagued by large mortality events. Research into other scallop- and aquacultured-species point to bacterial infections or altered functionality of microbial communities which associate with the host. Despite intense filtering and sterilization of seawater, and changing tank water every 48 hours, harmful microbes can still persist in biofilms and mortality is still high. There are no previous studies of the bacterial communities associated with the biofilms growing in scallop hatchery tanks, nor studies with wild or hatchery sea scallops. We characterized the bacterial communities in veliger-stage wild or hatchery larvae, and tank biofilms using the 16S rDNA gene V3-V4 region sequenced on the Illumina MiSeq platform. Hatchery larvae had lower bacterial richness (number of bacteria taxa present) than the wild larvae and tank biofilms, and hatchery larvae had a similar bacterial community (which taxa were present) to both wild larvae and tank biofilms. Bacterial richness and community similarity between tank samples fluctuated over the trial in repeated patterns of rise and fall, which showed some correlation to lunar cycle that may be a proxy for the effects of spring tides and trends in seawater bacteria and phages which are propagated into hatchery tanks. These results along with future work, will inform hatcheries on methods that will increase larval survival in these facilities, for example, implementing additional filtering or avoiding seawater collection during spring tides, to reduce bacterial taxa of concern or promote a more diverse microbial community which would compete against pathogens.


The authors would like to thank the staff at the Downeast Institute for supporting the development and implementation of this project, as well as for financially supporting the DNA sequencing; Meredith White of Mook Sea Farm for sharing her expertise and collecting biofilm samples; the Darling Marine Center for sharing their expertise and collecting biofilm samples; and the Sea Scallop Hatchery Implementation (Hit) Team for their expertise, review of this work, and funding support, who are financially supported by the Atlantic States Marine Fisheries Commission and Michael & Alison Bonney. The authors thank Lilian Nowak for assistance with related lab work to this project, and the Map Top Scholars Program for related financial support. The authors also thank Nate Perry for helping us collect wild scallop larvae. All authors have read and approved the final manuscript. This project was supported by the USDA National Institute of Food and Agriculture through the Maine Agricultural & Forest Experiment Station, Hatch Project Numbers: ME0-22102 (Ishaq), ME0-22309 (Bowden), and ME0-21915 (Perry); as well through NSF #OIA-1849227 to Maine EPSCoR at the University of Maine (Grey). This project was supported by an Integrated Research and Extension Grant from the Maine Food and Agriculture Center, with funding from the Maine Economic Improvement Fund.

Johanna’s review published on how gut microbes can make anti-inflammatory compounds when you eat broccoli

A massive literature review led by Johanna Holman, and featuring our collaborative team of broccoli sprout and microbes researchers, was accepted for publication!

As part of her master’s of science thesis, Johanna Holman reviewed hundreds of journal articles on anti-inflammatory, health-promoting dietary compounds in broccoli and other vegetables or fruits, and how microbes in the digestive tract can transform inactive precursors from foods into those beneficial compounds. This is part of a broader research collaboration on how glucoraphanin in broccoli sprouts can be made into sulforaphane, which acts as an anti-inflammatory in humans. Humans are unable to convert glucoraphanin to sulforaphane, and a small amount of this occurs naturally thanks to enzymes in the broccoli sprouts. But, certain gut microbes can make the conversion and this has helped resolve colitis and other symptoms in mice in laboratory trials (manuscripts in preparation).

A diagram with two panels, and a cartoon mouse in the middle.  The cartoon mouse is eating broccoli, and a cartoon of the digestive tract is overlaid on the mouse's abdomen. Lines emanating from the broccoli point to the left panel, and show the compound glucoraphanin being converted into sulforaphane by the myrosinase enzyme. Lines emanating from the colon of the mouse point to the panel on the right, showing the same biochemical conversion by gut microbes.
Artwork by Johanna Holman.

If you aren’t familiar with broccoli sprouts, a lovely review on their history, current food culture, and safe production was just published by some of our colleagues: Sprout microbial safety: A reappraisal after a quarter-century.

Check out the review

Holman, J., Hurd, M., Moses, P.,  Mawe, G.,  Zhang, T., Ishaq, S.L., Li, Y. 2022. Interplay of Broccoli/Broccoli Sprout Bioactives with Gut Microbiota in Reducing Inflammation in Inflammatory Bowel Diseases. Journal of Nutritional Biochemistry, in press.


Inflammatory Bowel Diseases (IBD) are chronic, reoccurring, and debilitating conditions characterized by inflammation in the gastrointestinal tract, some of which can lead to more systemic complications and can include autoimmune dysfunction, a change in the taxonomic and functional structure of microbial communities in the gut, and complicated burdens in a person’s daily life. Like many diseases based in chronic inflammation, research on IBD has pointed towards a multifactorial origin involving factors of the host’s lifestyle, immune system, associated microbial communities, and environmental conditions. Treatment currently exists only as palliative care, and seeks to disrupt the feedback loop of symptoms by reducing inflammation and allowing as much of a return to homeostasis as possible. Various anti-inflammatory options have been explored, and this review focuses on the use of diet as an alternative means of improving gut health. Specifically, we highlight the connection between the role of sulforaphane from cruciferous vegetables in regulating inflammation and in modifying microbial communities, and to break down the role they play in IBD.

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.


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.


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; Special Issue “Sustainable Weed Control in the Agroecosystems


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