CV

Research Assistant Professor of Microbial Ecology

University of Oregon
College of Design
Biology and the Built Environment
5231 University of Oregon
103 Pacific Hall
Eugene, OR 97403-5231

sueishaq@uoregon.edu  |  sueishaqlab@gmail.com

Google Scholar | LinkedIn | Mendeley | ORCID | Research Gate  |  NCBI | GitHub


EDUCATION

Ph.D. Animal, Nutrition and Food Science, University of Vermont, Burlington, VT
2010 – 2015
Advisor: Dr. André-Denis G. Wright
Dissertation | Seminar

B.Sc. Animal Science, University of Vermont, Burlington, VT
2003 – 2007
Minor in Nutrition and Food Science

PROFESSIONAL EXPERIENCE

Research Assistant Professor of Microbial Ecology,
Biology and the Built Environment Center, University of Oregon, Eugene OR
June 2017 – present

Post Doctoral Research Associate,
Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT
May 2016 – May 2017
Dr. Fabian D. Menalled

Post Doctoral Research Associate,
Department of Animal and Range Sciences, Montana State University, Bozeman MT
April 2015 – April 2016
Dr. Carl J. Yeoman

Graduate Student,
Department of Animal Science, University of Vermont, Burlington, VT
July 2010 – March 2015

Anaerobic Culturing Apprenticeship,
University of Tromsø, Tromsø, Norway
January, 2012
Dr. Monica A. Sunset

TEACHING EXPERIENCE

  • 2018, HC 209H: Introduction to mammalian microbiomes, University of Oregon, Clark Honors College, developed course
  • 2016, BIOM 405: Host-associated microbiomes, Montana State University; developed and taught lab section and team-taught class lecture
  • 2015, BIOM 405: Host-associated microbiomes, Montana State University; developed and taught lab section
  • 2010 – 2012, ASCI 141: Anatomy and physiology of domestic species, University of Vermont; graduate teaching assistant for lab section
  • 2012, ASCI 110: Animal nutrition, metabolism and feeding, University of Vermont; graduate teaching assistant for lab section

ADMINISTRATIVE EXPERIENCE

  • 2018 – , Academic Editor, PLoS ONE
  • 2018 – , Pod-Coordinator, 500 Women Scientists Eugene
  • 2017 – 2018, Implicit Bias Working Group, University of Oregon
  • 2017 – , Search committee member; University of Oregon, BioBE Center
  • 2017,  Grant review; USDA

RESEARCH SUPORT

Current
2018 – 2019, UO-OHSU Collaborative Seed Grant, $50,000
Martindale (PI), Van Den Wymelenberg (PI), Bohannan, Fahimipour, Ishaq, Kiraly.  Predicting healthcare-associated Clostridioides difficile infection probabilities in inpatient units. Key personnel, co-wrote

2018 – 2021, USDA AFRI NIFA Agricultural Production Systems, $500,000 ($19,153 subaward PI)
Menalled (PI), Trowbridge, Weaver,  Seipel, Bourgault, Yeoman.   Diversifying cropping systems through cover crops and targeted grazing: impacts on plant-microbe-insect interactions, yield and economic returns.

2017 – 2019,  Alfred P. Sloan Foundation Non-Research Grant, $125,000
Van Den Wymelenberg, Green. Biology and Built Environment (BioBE) Center.  Key personnel, co-wrote
Completed
2013 – 2015, USDA AFRI NIFA Pre-doctoral Fellowship Grant, $79,000 (PI).  
Investigating the rumen bacteria of the North American moose (Alces alces) for the potential for improving efficiency of feed digestion in livestock.


PROFESSIONAL MEMBERSHIPS

  • 2017 – , 500 Women Scientists
  • 2016 – , American Association for the Advancement of Science
  • 2011 – 2016, American Society of Animal Science (ASAS)
  • 2012 – , American Society for Microbiology (ASM)
  • 2017 – , Ecological Society of America (ESA)
  • 2016 – , Green Mountain Chapter of Alpha Zeta, University of Vermont
  • 2018 – , International Society of Indoor Air Quality and Climate

HONORS AND AWARDS

  • 2014, American Society of Animal Science President’s’ Pick Poster, Kansas City
  • 2007, Justin Morrill Honors Scholar, University of Vermont
  • 2005, 2006, Dean’s List, University of Vermont
  • 2003 – 2007, Presidential Scholarship, University of Vermont
  • 2003 – 2007, University of Vermont Scholarship

SERVICE

  • 2015 – , Citizen Science volunteer, Adventure Scientists: Gallatin Microplastics Initiative, 2015-2017; Timber Tracking Project, 2018
  • 2015 – 2017, Child Advancement Project mentor, Thrive, Bozeman, MT
  • 2015 – , Owner and Chief Editor of “Give Me the Short Version”, a Facebook page dedicated to presenting scientific articles to the general public in a short and easy to understand format. https://www.facebook.com/givemetheshortversion/
  • Ad hoc, Ongoing science communication, outreach, and education: www.sueishaqlab.org, https://biobe.uoregon.edu/, https://sites.google.com/view/500ws-eugene/
  • Ad hoc, Mentoring: As research faculty: 8 undergraduates (current), 1 post-bac (previous); As a post-doc: 1 technician, 1 graduate student; As a graduate student: 5 graduate students, 15 undergraduate (including 9 in one semester)
  • Ad hoc, Manuscript review; https://publons.com/author/480672/suzanne-ishaq#profile
  • Ad hoc, Conference Presentation review:
    • Poster abstracts (by invitation) for the Annual Biomedical Research Conference for Minority Students, November 2016 in Tampa Bay, FL.
    • Oral presentations for the Ecological Society of America’s Buell and Brawn Awards, August 2017 in Portland, OR.

 PUBLICATIONS

Yeoman, C.J., Ishaq, S.L., Bichi , E., Olivo, S., 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. Impact 4.259. Article.

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. A reference genome set for the ruminant microbiome. Nature Biotechnology 36:359-367.  Impact Factor 41.667Article.

Zeng, H., Ishaq, S.L., Liu, Z., Bukowski, M.R. 2017. 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.  Impact 4.418. Article.

Ishaq, S.L., AlZahal, O., Walker, N., McBride, B. 2017. An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced sub-acute ruminal acidosis conditions, with or without active dry yeast supplementation.  Frontiers in Microbiology 8:1943. Impact 4.076. Article.

Ishaq, S.L., Yeoman, C.J., Whitney, T.R. 2017. Ground Juniperus pinchotii and urea in supplements fed to Rambouillet ewe lambs. Part 2: Ewe lamb rumen microbial communities. Journal of Animal Science Oct; 95(10):4587-4599. Impact 2.014. Article.

Companion paper: Whitney 2017 JAS

Perea, K., Perz, K., Olivo, S., Williams, A., Lachman, M., Ishaq, S.L.,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. Impact 2.014. Article.

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(2): 417-434. Impact 3.630. Article.

Companion paper: Johnson et al. 2017 Weed Science

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: in press. Impact 3.731. Article.

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 25:30-36. Impact 4.518. Article

Salgado-Flores, A., Hagen, L.H., Pope, P.B., Ishaq, 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). Impact 3.234. Article

Ishaq, S.L., Kim, C.J., Reis, 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): e0144804. Impact 3.23. Article

Henderson, G, F. Cox, S. Ganesh, A Jonker, W Young, L. Abecia, E. Angarita, P. Aravena, G.N. Arenas, C. Ariza, G.T. Attwood, J.M. Avila, J. Avila-Stagno, A. Bannink, R. Barahona, M. Batistotti, M.F. Bertelsen, A. Brown-Kav, A.M. Carvajal, L. Cersosimo, A.V. Chaves, J. Church, N. Clipson, M.A. Cobos-Peralta, A.L. Cookson, S. Cravero, O.C. Carballo, K. Crosley, G. Cruz, M.C. Cucchi, R. de la Barra, A.B. De Menezes, E. Detmann, K. Dieho, J. Dijkstra, W.L.S. dos Reis, M.E.R. Dugan, S.H. Ebrahimi, E. Eythórsdóttir, F.N. Fon, M. Fraga, F. Franco, C. Friedeman, N. Fukuma, D. Gagić, I. Gangnat, D.J. Grilli, L.L. Guan, V.H. Miri, E. Hernandez-Sanabria, A.X.I Gomez, O.A. Isah, S. Ishaq, E. Jami, J. Jelincic, J. Kantanen, W.J. Kelly, S.-H. Kim, A. Klieve, Y. Kobayashi, S. Koike, J. Kopecny, T.N. Kristensen, S.J. Krizsan, H. Lachance, M. Lachman, W.R. Lamberson, S. Lambie, J. Lassen, S.C. Leahy, S.-S. Lee, F. Leiber, E. Lewis, B. Lin, R. Lira, P. Lund, E. Macipe, L.L. Mamuad, H.C. Mantovani, G.A. Marcoppido, C. Marquez, C. Martin, G. Martinez, M.E. Martinez, O.L. Mayorga, T.A. McAllister, C. McSweeney, L. Mestre, E. Minnee, M. Mitsumori, I. Mizrahi, I. Molina, A. Muenger, C. Muñoz, B. Murovec, J. Newbold, V. Nsereko, M. O’Donovan, S. Okunade, B. O’Neill, S. Ospina, D. Ouwerkerk, D. Parra, L.G.R. Pereira, C. Pinares-Patiño, M. Poulsen, M. Rodehutscord, T. Rodriguez, K. Saito, F. Sales, C. Sauer, K. Shingfield, N. Shoji, J. Simunek, Z. Stojanović-Radić, B. Stres, X. Sun, J. Swartz, Z.L. Tan, I. Tapio, T.M. Taxis, N. Tomkins, E. Ungerfeld, R. Valizadeh, P. van Adrichem, J. van Hamme, W. van Hoven, G. Waghorn, R.J. Wallace, M. Wang, S.M. Waters, M. Witzig, A.D.G. Wright, H. Yamano, T. Yan, D.R Yañez-Ruiz, C.J. Yeoman, R. Zambrano, J. Zeitz, M. Zhou, H.W. Zhou, C.X. Zou, P. Zunino, & P.H. Janssen. 2015. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Nature Scientific Reports 5:14567. Impact 5.58Article

Ishaq, S.L., Sundset, M.A., Crouse, J., Wright, A-D.G. 2015. High-throughput DNA sequencing of the moose rumen from different geographical location reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity. Microbial Genetics, 2015(1). No Impact Factor yet. Article

Pellegrini, Suzanne Ishaq, “A Comparative Analysis Of The Moose Rumen Microbiota And The Pursuit Of Improving Fibrolytic Systems.” (2015). Graduate College Dissertations and Theses. Paper 365. Dissertation

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. Impact 3.67. Article

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. Impact 2.97. Article

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. Impact 2.73. Article

INVITED REVIEWS/BOOK CHAPTERS

Ishaq, S.L. 2017. Plant-Bacteria Interactions in Agriculture and the Use of Farming Systems to Improve Diversity and Productivity. In Plant probiotic bacteria: solutions to feed the World, AIMS Microbiology 3(2): 335-353. Article.

Ishaq S.L., Wright A-D.G., Moses, P.L. (2016). Ch 2: The pathology of methanogenic archaea in human gastrointestinal disease. In: The Gut Microbiome – Implications for Human Disease. Mozsik, G. (ed.). InTech. Pp. 19-37. Article.

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. Article.

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. Article.

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. Article.

INVITED PRESENTATIONS

“The Microbiome of the Digestive Tract” Oregon Museum of Science and Industry (OMSI) After Dark event: “It’s Alive! (Mind and Body)”, Portland, OR, Apr 25, 2018. Post. Ishaq OMSI After Dark 20180425

“Geographical differences in the moose microbiome.” 500 Women Scientists Eugene Science Salon, “Gut Stuff: the battle of nature versus nurture in the microbiome”. First National Taphouse, Eugene, OR, Mar 11, 218.

“A crash course in the gut microbiome.” OMSI Science Pub, Whirled Pies, Eugene, OR, Feb 8, 2018. PostIshaq OMNISci 20180208

“From host-associated microbiomes to ‘house-associated’ microbiomes.” Institute for Ecology and Evolution, University of Oregon, Eugene, OR, Oct 21, 2017.

“Mapping the Microbial Development of the Dairy Calf Digestive Tract.” Center for Biofilm Engineering, Montana State University, Bozeman, MT, Feb 16, 2017.

“A comparative analysis of the moose rumen microbiota and the pursuit of improving fibrolytic systems.” The Department of Animal Science, University of Vermont, Burlington, VT. Mar 19, 2015. The Department of Animal And Range Sciences, Montana State University, Bozeman, MT, Aug 25, 2015.

“Metagenomics and identification of cellulolytic bacteria in the rumen of moose.” The Department of Arctic Biology, University of Tromsø, Tromsø, Norway. Jan 13, 2012

“Metagenomics and identification of cellulolytic bacteria in the rumen of moose.” The Department of Animal Science, University of Vermont, Burlington, VT. Dec 10, 2010, Dec 2, 2011, Nov 9, 2012, Oct 18, 2013.

CONFERENCE PROCEEDINGS

Ishaq*, S.L., Vandegrift, R, Kline, J., Fahimipour, A., Stenson, J., Cil, G., Crowley, R., Wilson, H., Northcutt, D., Hartmann, E., Johnson-Shelton, D., Brown, G.Z., Green, J., Van Den Wymelenberg, K. Poster: “The microbial ecotone of the built environment and the interplay of microbial sources of indoor air bacteria in single-family homes in Oregon.” 17th meeting of the International Society for Microbial Ecology. Leipzig, Germany. August 2018.

Ishaq*, S.L., R. Vandegrift, J. Kline, A. Fahimipour, J. Stenson, R. Crowley, H. Wilson, D. Northcutt, E. Hartmann, D. Johnson-Shelton, G.Z. Brown, J. Green, K. Van Den Wymelenberg. “Microscopic roommates: The biological sources of indoor air bacteria of single-family homes in Portland, Oregon.”  15th Conference of the International Society of Indoor Air Quality and Climate (ISIAQ). Philadelphia, PA. July 2018. (accepted talk)

Vandegrift*, R., S.L. Ishaq, J. Kline, A. Fahimipour, J. Stenson, R. Crowley, H. Wilson, D. Northcutt, E. Hartmann, D. Johnson-Shelton, G.Z. Brown, J. Green, K. Van Den Wymelenberg.  “Shut the front door: seasonal patterns in window operation drive fungal and bacterial community dissimilarity between indoor and outdoor air.” 15th Conference of the International Society of Indoor Air Quality and Climate (ISIAQ). Philadelphia, PA. July 2018. (accepted talk)

Vandegrift*, R., S.L. Ishaq, J. Kline, A. Fahimipour, J. Stenson, R. Crowley, H. Wilson, D. Northcutt, E. Hartmann, D. Johnson-Shelton, G.Z. Brown, J. Green, K. Van Den Wymelenberg. Poster: “Shut the front door: seasonal patterns in window operation drive fungal and bacterial community dissimilarity between indoor and outdoor air.” 11th International Mycological Congress. San Juan, Puerto Rico.  July 2018.

Ishaq, S.L., R. Vandegrift, J. Kline, A. Fahimipour, J. Stenson, G. Cil, R. Crowley, H. Wilson, D. Northcutt, E. Hartmann, D. Johnson-Shelton, G.Z. Brown, J. Green, K. Van Den Wymelenberg. “The Role of Plants Indoors.”  2nd annual Institute of Health and the Built Environment Consortium meeting. Portland, OR. May 2018. (invited talk)

Ishaq*, S.L., Seipel, T., Thornton, A.M., Olivo, S., Yeoman, C.J., Menalled, F. D. Poster: Soil bacterial diversity in response to stress from farming system, climate change, weed diversity, and wheat streak virus.  Ecological Society of America (ESA), Portland, OR, August 2017.

Ishaq, S.L.*, O. AlZahal, N. Walker, B. McBride. 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.  Congress on Gastrointestinal Function, Chicago, IL, April 2017. (accepted talk).

Perea, K.,  K. Perz, S. Olivo, A. Williams, M. Lachman, S. Ishaq*, J. Thomson, and C. Yeoman. Poster: Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small intestine-located microbiota. Congress on Gastrointestinal Function, Chicago, IL, April 2017.

Ishaq*, S.L., Bichi, E., Olivo, S.K., Lowe, J., Yeoman, C.J., Aldridge, B.M. Influence of colostrum on the microbiological diversity of the developing bovine intestinal tract. Joint Annual Meeting, Salt Lake City, Utah, July 2016. (accepted talk)

Ishaq*, S.L., Yeoman, C.J., Whitney, T.R. Ground redberry juniper and urea in DDGS-based supplements do not adversely affect ewe lamb rumen microbial communities. Joint Annual Meeting, Salt Lake City, Utah, July 2016. (accepted talk)

Travis Whitney’s companion presentation can be found here.

Ishaq*, S.L., Johnson, S.P., Miller, Z.J., Lehnhoff, E.A., Olivo, S.K., Yeoman, C.J., Menalled, F.D. Poster: Farming Systems Modify The Impact Of Inoculum On Soil Microbial Diversity. American Society for Microbiology (ASM), Boston, MA, June 2016.

Lachman*, M.M., Ishaq, S.L., Swartz, J., Olivo, S.K., Herrygers, M.R., Berardinelli, J.G., Voyich, J.M., Yeoman, C.J. The Intertwined Successional Development of Lamb Gut Microbiota and Immune System. Montana Academy of Sciences annual meeting, Butte, MT, April 2016.

Zeng*, H., Ishaq, S., Zhao, F.Q., Wright, A.D. Colonic inflammation and enhanced-beta-catenin signaling accompany an increase of the Lachnospiraceae/Streptococcaceae in the hind gut of high-fat diet-fed mice.  Federation of American Societies for Experimental Biology Conference, April, 2016.

Doyle*, J., Eggers*, M.J., Geddes, J.B., Klassen, J., Ishaq, S.L., Bends, A.L., Eggers, J.A., Not Afraid, A., Old Elk, J., Three Irons, E., Ewing*, S.A. Investigating sources of water to Chief Plenty Coups Spring: Water chemistry and microbial communities suggest seasonably variable contamination American Water Resources Association conference, Missoula, MT, October 2015.

Moses, P.L., Ishaq, S.L., Gupta, K., Maurer, S.M., Wright*, A-D.G. Biodiversity of human gut methanogens varies with concentration of exhaled breath methane. ACG 2015 Annual Scientific Meeting, Honolulu, HI, Oct 2015.

Duff*, G.C., Ishaq, S.L., Lachman, M., Yeoman, C.J. Morphological, microbiological, and biochemical development of the ruminant gastrointestinal tract. Joint Annual Meeting, Orlando, FL, Jul 2015.

AlZahal*, O., Ishaq, S.L., St-Pierre, B., Wright, A-D.G., McBride, B.W. Poster: Investigating the impact of dietary changes on rumen microbial community during the transition period in Holstein dairy cows using high-throughput sequencing. J Dairy Sci. 98 (Suppl. 2):735. Joint Annual Meeting, Orlando, FL, Jul 2015.

Ishaq*, S.L., Kim, C.J., Wright, A-D.G. Poster: The effects of administering a fibrolytic probiotic made from moose rumen bacteria to neonatal lambs. Joint Annual Meeting, Orlando, FL, Jul 2015.

AlZahal*, O., Ishaq, L., Wright, A-D.G., McBride, B.W. Poster: Investigating the impact of dietary changes on rumen microbial community during the transition period in Holstein dairy cows. Symposium on Gut Health in production of Food Animals. St. Louis, MO, Nov 2014.

Ishaq*, S.L., Wright, A-D.G. Poster: Fibrolytic bacteria isolated from the rumen of North American moose (Alces alces).” Joint Annual Meeting, Kansas City, MO, Jul 2014. Invited to present poster at the American Society of Animal Science (ASAS) Presidents’ Pick Poster Session during the ASAS Awards Ceremony.

Ishaq*, S.L., Reis, D., Lachance, H.M., Wright, A-D.G. Poster: Streptococcus gallolyticus isolates from the rumen of moose (Alces alces) in Vermont. American Society for Microbiology (ASM), Boston, MA, May 2014.

Ishaq*, S.L., Wright, A-D.G. Poster: Investigating the microbiome of the rumen of the moose (Alces alces). FEMS, Leipzig, Germany, Jul 2013.