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. 

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