Samodha C. Fernando

Photo of Samodha Fernando
Areas of Expertise
Ruminant Nutrition
Associate Professor
Nutritional Biochemistry

Experience

Associate Professor, Nutritional Biochemistry, July 2017 – present; University of Nebraska, Lincoln, NE
Assistant Professor, Nutritional Biochemistry, April 2011 – June 2017; University of Nebraska, Lincoln, NE
Courtesy appointments in School of Biological Sciences (Jan 2013 – present) and in Food
Science and Technology (July 2011 – present); University of Nebraska, Lincoln, NE
Associate Member, Nebraska Center for Virology and Nebrasks Food for Health Center

EDUCATION

2008 – 2011 - Postdoctoral Associate, Massachusetts Institute of Technology, Cambridge, MA Host microbe interactions

Ph.D. 2008 - Oklahoma State University, Stillwater, OK: Animal Nutrition/Microbial Genomics,

M.S. 2004 - Oklahoma State University, Stillwater, OK: Animal Science/ Reproductive Physiology,

B.S. 2002 – University of Kelaniya, Sri Lanka: Major Microbiology

Professional memberships

American Society of Animal Science
American Society of Microbiology
Gamma Sigma Delta, Honor Society of Agriculture

Awards

  • IANR's Junior Faculty for Excellence in Research Award (2015)
  • IANR Dinsdale Family Faculty Award (2015)
  • American Society of Animal Science Early Career Achievement Award (2015) – Awarded at the American Association of Animal Science National Meeting in Orlando, FL.
  • Oklahoma State University Research Excellence Award for outstanding research contribution in Biological Sciences (2008) - Awarded at Graduate Commencement
  • Phoenix Award for exemplary achievement in leadership, scholarship, professional involvement and university and community service at Oklahoma State University, Runner-up (2008)
  • Outstanding Ph.D. Student in the Department of Animal Science (2008)
  • Outstanding Research in Biological Sciences, First Prize, Oral Presentation. Biochemistry and Molecular Biology Graduate Student Association (2007)
  • Joe V. Whiteman Award for Outstanding graduate student scientific paper in Animal Science (2007)
  • Sitlington Graduate Fellowship Award (2005-2007)
  • Best Poster in Biological Science, Oklahoma State University Research Symposium (2006)
  • Outstanding Research in Biological Sciences, First Prize, Poster Presentation. Biochemistry and Molecular Biology Graduate Student Association (2005)
  • Williams Outstanding Thesis Award, College of Agricultural Sciences and Natural Resources, Oklahoma State University (2005)
  • Outstanding Research in Biological Sciences, First Prize, Oral Presentation. Biochemistry and Molecular Biology Graduate Student Association (2004)

Graduate Training

Supervised Masters students; 2 completed (3 current)
Supervised Ph. D students; 2 completed (5 current)
Served committees besides supervisory; M.S. 13 completed; Ph. D 20 completed
Supervised Postdoctoral Associates; 2 completed (1 current)
Supervised Undergraduate Researchers; 12 completed (4 current)
Supervised High School Researchers; 3 completed

Patents

  • Novel probiotic bacterial strains each with the ability to inhibit growth of Streptococcus bovis and Fusobacterium necrophorum in cattle that are linked to acidosis and liver abscesses. – Currently pending
  • GRAS approved probiotic bacterial strain with the ability to inhibit growth of Streptococcus bovis and Fusobacterium necrophorum in cattle that are linked to acidosis and liver abscesses. – Currently pending

Refereed Journal Articles

  1. Klein, C., D. Gonzalez, C. Kahesa, J. Mwaiselage, N. Aluthge, S. Fernando, J. T. West, C. Wood, and P. C. Angeletti. The Relationship Between the Cervical Microbiome, HIV Status, and Pre-Cancerous Lesions 2019. Journal mBio, Vol 10; 1 e02785 – 18. DOI: 10.1128/mBio.02785-18.
  2. JV Judy, GC Bachman, TM Brown-Brandl, SC Fernando, KE Hales, KJ Harvatine, PS Miller, PJ Kononoff. Increasing the concentration of linolenic acid in diets fed to Jersey cows in late lactation does not affect methane production (2019). J Dairy Sci. 2019 Jan 3;. https://doi.org/10.3168/jds.2018-14608.
  3. JV Judy, GC Bachman, TM Brown-Brandl, SC Fernando, KE Hales, PS Miller, RR Stowell, PJ Kononoff. Reducing methane production with corn oil and calcium sulfate: Responses on whole-animal energy and nitrogen balance in dairy cattle (2018). J Dairy Sci. 2019 Jan 3; https://doi.org/10.3168/jds.2018-14567.
  4. JV Judy, GC Bachman, TM Brown-Brandl, SC Fernando, KE Hales, PS Miller, RR Stowell, PJ Kononoff. Energy balance and diurnal variation in methane production as affected by feeding frequency in Jersey cows in late lactation (2018). J Dairy Sci. 2018 Dec;101(9):10899-10910. https://doi.org/10.3168/jds.2018-14596.
  5. Erin M Duffy, Shauna M Tietze, Allison L Knoell, Nirosh D Aluthge, Samodha C Fernando, Ty S Schmidt, Dustin T Yates, Jessica L Petersen. Rumen bacterial composition in lambs is affected by β-adrenergic agonist supplementation and heat stress at the phylum level (2018). Translational Animal Science, Volume 2, Issue suppl_1, 27 September 2018, Pages S145–S148, https://doi.org/10.1093/tas/txy052
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  6. Williams HE, Cochrane RA, Woodworth JC, DeRouchey JM, Dritz SS, Tokach MD, Jones CK, Fernando SC, Burkey TE, Li YS, Goodband RD, Amachawadi RG. Effects of dietary supplementation of formaldehyde and crystalline amino acids on gut microbial composition of nursery pigs (2018). Scientific Reports, 25; 8(1) :8164 doi: 10.1038/s41598-018-26540-z.
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  7. Niederwerder MC, Constance LA, Rowland RRR, Abbas W, Fernando SC, Potter ML, Sheahan MA, Burkey TE, Hesse RA, Cino-Ozuna AG. Fecal Microbiota Transplantation Is Associated With Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease (2018). Frontiers in Microbiology, 23; 9; 1631. doi: 10.3389/fmicb.2018.01631.
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  8. Drehmel OR, Brown-Brandl TM, Judy JV, Fernando SC, Miller PS, Hales KE, Kononoff PJ. The influence of fat and hemicellulose on methane production and energy utilization in lactating Jersey cattle (2018). J Dairy Sci. 2018 Sep;101(9):7892-7906. doi: 10.3168/jds.2017-13822.
    Role: Helped with methane sampling and was the lead for sequencing and bioinformatics analysis of the rumen microbiome
  9. Morota, G., Ventura R.V., Silva, F.F., Koyama, M., Fernando S.C. Machine learning and data mining advance predictive big data analysis in precision animal agriculture (2018). Journal of Animal Science, 96; 4, 1540-1550, https://doi.org/10.1093/jas/sky014
    Role: Wrote the microbiome modeling section of this review
  10. Henry A. Paz, Kristin E. Hales, James E. Wells, Larry A. Kuehn, Harvey C. Freetly, Elaine D. Berry, Michael D. Flythe, Matthew L. Spangler, and Samodha C. Fernando. Rumen bacterial community structure impacts feed efficiency in beef cattle (2018). Journal of Animal Science, 96; 3, 1045-1058. https://doi.org/10.1093/jas/skx081
    Role: Corresponding Author
  11. Chad G. Bower, Regan E. Stanley, Samodha C. Fernando, and Gary A. Sullivan. The effect of salt reduction on the microbial community composition and quality characteristics of sliced roast beef and turkey breast (2018). Journal LWT-Food Science and Technology, 90: 583-591
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  12. Huyen Tran, Christopher L. Anderson, Justin W. Bundy, Samodha C. Fernando, Phillip S. Miller, Thomas E. Burkey. Effects of spray-dried porcine plasma on fecal microbiota in nursery pigs (2018). 2018 Jan 27. doi: 10.1093/jas/skx034. [Epub ahead of print]
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  13. Christopher L. Anderson, Matthew B. Sullivan, and Samodha C. Fernando. Digestible energy content drives the dynamic response of bovine rumen viral communities (2017). Microbiome, 5:155 https://doi.org/10.1186/s40168-017-0374-3
    Role: Corresponding Author
  14. Castillo-Lopez, E., Moats, J., Aluthge, N.D., Ramierez Ramirez, H., Christensen, D., Mutsvangwa, T., Greg, P., and Fernando, S.C. (2017). Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows. Journal of Applied Microbiology. November 7 doi: 10.1111/jam.13630. [Epub ahead of print]
    Role: Corresponding Author
  15. Castillo-Lopez, E., Jenkins, C.J.R., Aluthge, N.D., Tom, W., Kononoff, P.J. and Fernando, S.C. (2017). The effect of regular or reduced-fat distillers grains with solubles on rumen methanogenesis and the rumen bacterial community. Journal of Applied Microbiology. Sep. 11. doi: 10.1111/jam.13583. [Epub ahead of print]
    Role: Corresponding Author
  16. Rebbeca Duar, Steven Frese, Samodha Fernando, Thomas Burkey, Guergana Tasseva, Daniel Peterson, Jochen Blom, Cory Wenzel, Christine Szymanski, and Jens Walter. 2017. Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Applied Environmental Microbiology June 2017 vol. 83 no. 12 e00132-17
    Role: Performed the gnotobiotic pig infection studies
  17. Mary E. Walter, Alicia Ortiz, Casey Sondgeroth, Nathan M. Sindt, Nikolas Duszenko, Jennie L. Catlett, You Zhou, Shah Valloppilly, Christopher Anderson*, Samodha Fernando#, Nicole R. Buan. 2016. High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea. Journal of Microbiological Methods. 131: 113-121 http://www.sciencedirect.com/science/article/pii/S0167701216302974
    Role: Was the lead for sequencing and bioinformatics analysis for mutation detection
  18. Paz, HA*, Anderson, CL*, Muller, MJ*, Kononoff, PJ, and Fernando SC#. 2016. Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method. Frontiers in Microbiology, 7; 1206. http://dx.doi.org/10.3389/fmicb.2016.01206
    Role: Corresponding Author
  19. Fang Xie, Christopher L. Anderson*, Kelsey R. Timme, Scott G. Kurz, Samodha C. Fernando#, and Jennifer R. Wood. 2016. Obesity-Dependent Increases in Oocyte mRNAs are associated with Increases in Pro-Inflammatory Signaling and Gut Microbial Abundance of Lachnospiraceae in Female Mice. Endocrinology. 157 (4): 1630-43 doi: 10.1210/en.2015-1851.
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  20. Sambeek, D.M., Tran, H., Fernando S.C., Ciobanu, D.C., Miller, P.S., and Burkey, T.E., 2015. Alteration of the pig intestinal microbiome when vaccinated against or inoculated with porcine circovirus 2 using a multivariate analysis model. Journal of Animal Science doi: 10.2527/jas.2015-9861
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  21. Christopher L. Anderson*, Galen E. Erickson, Jim C. MacDonald, and Samodha C. Fernando#. 2016. Rumen bacterial communities can be adapted faster to high concentrate diets than currently implemented feedlot programs. Journal of Applied Microbiology. 120 (3): 588-599 doi: 10.1111/jam.13039
    Role: Corresponding Author
  22. Ramirez-Ramirez, Hugo; Harvatine, Kevin; Castillo Lopez, E; Fernando, SC#; Aluthge, N*; Jenkins, Chad; Anderson, Christopher*; Kononoff, Paul. 2016. Reduced fat dried distillers grains with solubles reduces the risk for milk fat depression and supports milk production and ruminal fermentation in dairy cows. Journal of Dairy Science. 99 (3): 1912-1928
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  23. Boyd, B. M., A. Jones, L. Franzen-Castle, K. Jenkins, R. Rasby, M. Luebbe, R. Stowell, S. C. Fernando, and G. E. Erickson. 2015. Producer concerns and perceptions regarding the effect of methane on cattle production and the environment: A survey of Nebraska producers. Professional Animal Scientist. 31 :601-607 doi:10.15232/pas.2015-01425
    Role: Was the project leader and was involved in data collection and design
  24. Har JY, Helbig T, Lim JY, Fernando SC, Penn K, Reitzel AM, Thompson JR: Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression (2015) Frontiers in Microbiology 6: 818 doi: 10.3389/fmicb.2015.00818
    Role: Performed community analysis, FISH analysis and all expression analysis of the project
  25. Fernando SC#, Wang J, Sparling K, Garcia GD, Francini-Filho RB, de Moura RL, Paranhos R, Thompson FL, Thompson JR: Microbiota of the Major South Atlantic Reef Building Coral Mussismilia (2014) Microbial Ecology. DOI 10.1007/s00248-014-0474-6
    Role: Performed all experiments, analysis and wrote the manuscript
  26. Lo Sasso G, Ryu D, Mouchiroud L, Fernando SC, Anderson CL*, Katsyuba E, Piersigilli A, Hottiger MO, Schoonjans K, Auwerx J: Loss of Sirt1 function improves intestinal anti-bacterial defense and protects from colitis-induced colorectal cancer. Plos One 2014, 9(7):e102495.
    Role: Was the lead for sequencing and bioinformatics analysis of the microbiome
  27. Paz HA, Klopfenstein TJ, Hostetler D, Fernando SC, Castillo-Lopez E, Kononoff PJ: Ruminal degradation and intestinal digestibility of protein and amino acids in high-protein feedstuffs commonly used in dairy diets (2014). Journal of dairy science.
    Role: Performed Real-time PCR analysis
  28. Penn, K., Wang, J., Fernando, S.C., Thompson, J.R. (2014). Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacterial bloom. The ISME Journal, open access, 1-13.
    Role: Performed all experiments and analysis
  29. Castillo-Lopez E, Ramirez Ramirez HA, Klopfenstein TJ, Hostetler D, Karges K, Fernando SC, Kononoff PJ. (2014). Ration formulations containing reduced-fat dried distillers grains with solubles and their effect on lactation performance, rumen fermentation, and intestinal flow of microbial nitrogen in Holstein cows. Journal of Dairy Science, 97, (3):1578-1593
    Role: Performed Real-time PCR analysis
  30. Castillo-Lopez, E., Ramirez Ramirez, H., Klopfenstein, T., Anderson C.L.*, Aluthge, N.D.*, Fernando, S.C., Jenkins, T., Kononoff, P.J. (2014). Effect of feeding dried distillers grains with solubles on ruminal biohydrogenation, intestinal fatty acid profile, and gut microbial diversity evaluated through DNA pyro-sequencing. Journal of Animal Science, 92, (2):733:743
    Role: Was the lead for bioinformatics analysis of the microbiome
  31. Castillo-Lopez, E., Klopfenstein, T., Fernando, S.C., Kononoff, P. (2013). In vivo determination of rumen undegradable protein of dried distillers grains with solubles and evaluation of duodenal microbial crude protein flow. Journal of Animal Science, 91(2):924-34.
    Role: Performed Real-time PCR analysis
  32. Ramirez Ramirez, H., Nestor, K., Tedeschi, L. O., Callaway, T. R., Dowd, S. E., Fernando, S.C., Kononoff, P. (2012). The effect of brown midrib corn silage and dried distillers' grains with solubles on milk production, nitrogen utilization and microbial community structure in dairy cows. Canadian journal of Animal Science, 92(3), 365-380.
    Role: Was the lead for bioinformatics analysis of the microbiome
  33. Fernando S.C., Purvis II H.T., Najar F.Z., Sukharnikov L., Nagaraja T.G., Krehbiel C.R., Roe B.A., DeSilva U. (2010) Rumen microbial population dynamics during adaptation to high-grain diet. Applied and Environmental Microbiology 76(22): 7482-7490
  34. Davis, R.L., Buck, D.J., Saffarian, N., Shekher, M., DeSilva, U., Fernando, S.C., and Stevens, C.W. (2008) β-Funaltrexamine inhibits inducible nitric-oxide synthase expression in human astroglial cells. journal of neuroimmune pharmacology 3(3): 150-153
  35. Fernando, S. C., Najar, F. Z., Guo, X., Zhou, L., Fu, Y., Geisert, R. D., Roe, B. A., and DeSilva, U. (2007) Isolation and characterization of the porcine kallikrein gene family: Genomic structure, radiation-hybrid mapping and differential expression analysis. Genomics 89(3):429-38
  36. Bommineni, Y.R., Dai, H., Gong, Y. X., Soulages, J. L., Fernando, S. C., DeSilva, U., Prakash, O., and Zhang, G. (2007) Fowlicidin-3 is an alpha-helical cationic host defense peptide with potent antibacterial and lipopolysaccharide-neutralizing activities. FEBS J. 274(2):418-28
  37. Fernando, S. C., Ashworth, M.S., Ross, J. W., Geisert, R. D., and DeSilva, U. (2006) Porcine endometrial and conceptus tissue kallikrein 1,4,11 and 14 gene expression. Reproduction 132,1-10
  38. Xiao, Y., Cai, Y., Bommineni, Y.R., Fernando, S.C., Prakash, O., Gilliland, S.E. and Zhang, G. (2006) Identification and functional characterization of three chicken cathelicidins with potent antimicrobial activity. J. Biol. Chem. 281(5) 2858-2867
  39. DeSilva, U., Guo, X., Kupfer, D. M., Fernando, S. C., Pillai, A. T. V., Najar, F. Z., So, S., Fitch, G. Q., and Roe, B. A. (2003). Allelic variants of ovine prion protein gene (PRNP) in Oklahoma sheep. Cytogenet. Genome Res. 102(1-4):89-94
  40.  Vonnahme K. A., Fernando, S. C., Ross, J. A., Ashworth, M. D., DeSilva, U., Malayer, J. R., and Geisert, R. D. (2003). Porcine endometrial and conceptus expression of kininogens and plasma kallikrein in cyclic and pregnant gilts. Biol. Reprod. 70(1): 132-138

Funding Acknowledgements

USDA NIFA Logo
Department of Justice Logo
Nebraska Beef Council Logo
Nebraska Environmental Trust Logo
National Institutes of Health Logo
National Cattlemen's Beef Association Logo
Nebraska Corn Board logo
Nebraska Pork Producers Association Logo