Due to the high pressure on the use of antibiotics, especially in food animals, and the high demand for new therapeutic strategies, any achievement of microbiome research and the potential use of metagenomic tools to prevent disease and to detect risk factors for disease development to the diagnostic process would have an immediate impact on animal health and production; and simultaneously lower the risk of emergence of antibiotic-resistant bacterial strains. Therefore, uncovering the microbial communities of distinct niches of the body is an important component of detection of patterns and understanding the effects of the microbiome on animal health.

The goals for my MS dissertation projects were to bring new insight on the infectious disease epidemiologic triangle that is illustrated by the interaction of epidemiologic factors that contribute to the outbreak of an infectious disease: the host, the pathogen or disease-causing organism, and the environment.  To accomplish these studies, I have used advanced epidemiological and statistical methods in conjunction to a variety of molecular and biomedical techniques and modern genomics approaches. I would expect that those studies would shed light on the understanding of how the factors associated with the host, the pathogens, and the environment influence the risk of the uterine diseases. And because the earliest source of microbial colonizers in the newborn calves might be influenced by the dam’s own microbiota, from the passage through the birth canal including contamination from fecal microbiota, I am currently investigating a community-wide perspective of the microbial relationships shared between dam and calves, as well as the influence of the dam pre-partum vaginal and fecal microbiota on the calves early-life microbial community and calf health.

1. Doctor of Veterinary Medicine (DVM) [1997-2002] at Federal University of Goias, Brazil.
2. Internship in Ambulatory Medicine [2006-2007] at the Department of Population Medicine and Diagnostic Sciences, Cornell University
3. Master of Science (MS) [2013-2016] in the field of Animal Sciences with concentration in Animal Science, and minors in Epidemiology, and Microbiology. Cornell University.

1. Silva, L.A.F.; Bittar, E.J.; Pires, L.B.F.; Souza, M.L.; Boechat, T.A.; Fioravanti, M.C.S.; Lopes, E.L. Uso do Azaperone na operação cesariana em porcas (Use of Azaperone in Cesarean Section in Sows). Ciência Animal Brasileira, Goiânia, v.1, p.221, out. 2000. Suplemento

2. Gardener, R.B.; Nydam D.V.; Luna J.A., Bicalho M.L.S., Matychak M.B.; Flaminio M.J. B. 2007 Serum opsonization capacity, phagocytosis and oxidative burst activity in neonatal foals in the intensive care unit. J Vet Intern Med. 2007 Jul-Aug; 21(4):797-805.

3. Bicalho R.C.; Santos T.M.; Gilbert R.O.; Caixeta L.S.; Teixeira L.M.; Bicalho M.L.; Machado V.S. Susceptibility of Escherichia coli isolated from uteri of postpartum dairy cows to antibiotic and environmental bacteriophages. Part I: Isolation and lytic activity estimation of bacteriophages. J Dairy Sci. 2010 Jan; 93(1):93-104.

4. Santos T. M. A., Bicalho R. C., Gilbert R. O., Caixeta L. S., Bicalho M. L.; Machado V. S. 2010. Susceptibility of Escherichia coli isolated from uterus of postpartum dairy cows to antibiotic and environmental bacteriophages, PART II: In vitro antimicrobial activity evaluation of a bacteriophage cocktail and several antibiotics. J. Dairy Sci. 93:105-114.

5. Bicalho R. C., Santos T. M. A.; Gilbert R. O., Caixeta L. S. , Bicalho M. L.; Machado V. S. 2010. Antimicrobial resistance and presence of virulence factor genes in Arcanobacterium pyogenes isolated from the uterus of postpartum dairy cows. Vet. Microbiology. 145(1-2): 84 - 89.

6. Bicalho R.C., Machado V.S., Bicalho M.L.S., Gilbert R.O., Teixeira A.G.V., Caixeta L.S.,Pereira  R.V.V. Molecular and epidemiological characterization of  bovine intrauterine Escherichia coli. J. Dairy Sci. 2010 Nov; 93:5818–5830.

7. Santos T. M. A., Ledbetter Eric C., Caixeta L. S., Bicalho M. L., R. C. Bicalho.. Isolation and characterization of two bacteriophages with strong in vitro antimicrobial activity against a broad range of multidrug resistant Pseudomonas aeruginosa. AJVR, Vol 72, No. 8, August 2011.

8. Pereira R. V. V., Santos T. M. A., Bicalho M. L.; Caixeta L. S., Machado V. S. and R. C. Bicalho. 2010. Antimicrobial resistance and prevalence of virulence factor genes in fecal Escherichia coli of Holstein calves receiving or not antimicrobial growth promoter. J Dairy Sci. 2011 Sep; 94(9):4556-65.

9. Machado V. S., M. L. S. Bicalho, W. A. Knauer, R. O. Gilbert, and R. C. Bicalho. 2011. A novel diagnostic technique to determine uterine health of Holstein cows at 35 days postpartum. J Dairy Sci. 2012 Mar; 95(3):1349-57.

10. Bicalho M. L. S., T. M. A. Santos, D. V. Nydam, V. S. Machado, and R. C. Bicalho. 2011. Evaluation of bacteriophages oral administration in neonatal calves: phage survivability, impact on fecal Escherichia coli and calf health. Livestock Science. Volume 144, Issue 3, Pages 294-299, April 2012

11. Bicalho M. L. S., V. S. Machado, Oikonomou G., R. O. Gilbert, and R. C. Bicalho. 2011. Association between virulence factors of Escherichia coli, Fusobacterium necrophorum, and Arcanobacterium pyogenes and uterine diseases of dairy cows. Vet Microbiol. 2012 May 25;157(1-2):125-31.

12. Machado V. S, M. L. S. Bicalho, R. V. Pereira, L. S. Caixeta, J. H. J. Bittar, G. Oikonomou, R. O. Gilbert, and R. C. Bicalho. The effect of intrauterine administration of mannose and bacteriophage, and intrauterine presence of Escherichia coli and Arcanobacterium pyogenes on uterine health and reproductive performance of lactating Holstein cows. J.Dairy Sci. 2012 Jun; 95(6):3100-9.

13. Machado V.S., G .Oikonomou, M.L. Bicalho, W.A. Knauer, R.O. Gilbert, R.C. Bicalho. Investigation of postpartum dairy cows uterine microbial diversity using metagenomic pyrosequencing of the 16S rRNA gene. Vet Microbiol. 2012 Oct 12; 159(3-4):460-9.

14. Machado V. S., M. L. S. Bicalho, R. V. Pereira, L. S. Caixeta, W. A. Knauer, G. Oikonomou, R. O. Gilbert, and R. C. Bicalho. The effect of injectable trace mineral (selenium, copper, zinc, and manganese) on health and production of lactating Holstein cows. Vet J. 2013 Aug;197(2):451-6.

15. Teixeira AG, M.L. S. Bicalho, V. S Machado, G. Oikonomou; C. Kacar, C. Foditsch; R. Young, W.A. Knauer, D.V. Nydam, Bicalho RC. Heat and ultraviolet light treatment of colostrum and hospital milk: effects on colostrum and hospital milk characteristics and calf health and growth parameters. Vet J. 2013 Aug;197(2):175-81.

16. Oikonomou G, A.G. Teixeira , C.  Foditsch C, M.L.S. Bicalho , V.S. Machado, Bicalho RC. Fecal microbial diversity in pre-weaned dairy calves as described by pyrosequencing of metagenomic 16S rDNA. Associations of Faecalibacterium species with health and growth. PLoS One. 2013 Apr 30; 8(4):e63157.

17. Oikonomou G., M.L.S Bicalho, E. Meira, R.E Rossi, C.Foditsch, V.S Machado, A.G. Teixeira, C. Santisteban, Y.H. Suchukken, R.C. Bicalho. Microbiota of Cow's Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters. 2014. PloS One. 2014 Jan 20; 9(1):e85904.

18. Machado V. S. , G. Oikonomou , S. F. Lima , M. L. S. Bicalho , C. Kacar , C. Foditsch , M. J. Felippe , R. O. Gilbert , and R. C. Bicalho. The effect of injectable trace mineral (selenium, copper, zinc, and manganese) on peripheral blood leucocytes activity and serum superoxide dismutase activity of lactating Holstein cows. Vet. J. 2014 May; 200 (2) 299-304.

19. Machado V. S. , M. L. S. Bicalho, Meira EB Jr , G. Oikonomou , S. F. Lima , C. Foditsch , R. O. Gilbert , and R. C. Bicalho. Subcutaneous Immunization with Inactivated Bacterial Components and Purified Protein of Escherichia coli, Fusobacterium necrophorum and Trueperella pyogenes Prevents Puerperal Metritis in Holstein Dairy Cows. PloS One. 2014 March 9;(3):e91734.

20. Bicalho M.L.S., F.S. Lima, E.K. Ganda, C. Foditsch , V.S. Machado, A.G. Teixeira, G. Oikonomou, R. O. Gilbert, R. C. Bicalho. Effect of trace mineral supplementation on selected minerals, energy metabolites, oxidative stress, and immune parameters and its association with uterine diseases in dairy cattle. J. Dairy Sci. 97 :4281–4295.2014.

21. Teixeira A. G. V., S.F. Lima, M. L. S. Bicalho, A. Kussler, F. S. Lima, and R. C. Bicalho. Effect of an injectable trace mineral supplement containing selenium, copper, zinc, and manganese on immunity, health, and growth of dairy calves. J. Dairy Sci. 97:4216–4226. 2014.

22. Oikonomou G, P. Trojacanec, E.K. Ganda, M.L. Bicalho, R.C. Bicalho. Association of digital cushion thickness with sole temperature measured with the use of infrared thermography. J. Dairy Sci. 97:4208–4215. 2014.

23. Machado V.S.; M.L.S. Bicalho; R.O. Gilbert and R.C. Bicalho. Short communication: Relationship between natural antibodies and postpartum uterine health in dairy cows. J.Dairy Sci 97 :1–5. 2014.

24. Pereira R. V. V., M. L. Bicalho; S. Lima; V.S. Machado; l.d Warnick, and R. C. Bicalho. Evaluation of the effects of ultraviolet light on bacterial contaminants inoculated into whole milk and colostrum, and on colostrum immunoglobulin G. J.Dairy Sci 97:2866–2875. 2014.

25. Oultram J., Phipps E., Teixeira A. G. V., Foditsch C., Bicalho M. L., Machado V. S., Bicalho R. C., G. Oikonomou. Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity. 2015. The Veterinary record 177(23). DOI: 10.1136/vr.103320

26. Foditsch C., G., Oikonomou V.S .Machado, M.L.S Bicalho, E. Ganda,  S. Lima, R. Rossi, B. Ribeiro,  A. Kussler,  and  R.C. Bicalho . Lameness prevalence and risk factors in large dairy farms in upstate New York. Model development for the prediction of claw horn disruption lesions. PLoS One. 2016 Jan 21;11(1): e0146718. doi: 10.1371/journal.pone.0146718.

27. Bicalho M.L.S., Lima FS, Machado VS, Meira Jr EB, Ganda EK, Foditsch C, Bicalho RC, Gilbert RO, Associations among Trueperella pyogenes endometritis diagnosis and pregnancy outcomes in dairy cows, Theriogenology (2016), doi: 10.1016/j.theriogenology.2016.09.04

28.  Foditsch C., G., Oikonomou; V. S. Machado, M.L.S Bicalho, E. Ganda, S. Lima, R. Rossi, B. Ribeiro, R.C. Bicalho. Lameness prevalence and risk factors in large dairy farms in upstate New York. Model development for the prediction of claw horn disruption lesions. PLoS One. 2016 Jan 21;11(1): e0146718. doi: 10.1371/journal.pone.0146718

29.E.K. Ganda, R.S. Bisinotto, A.K. Vasquez, A.G.V. Teixeira, V.S. Machado, C. Foditsch, M. Bicalho, F.S. Lima, L. Stephens, M.S. Gomes, J.M. Dias, R.C. Bicalho, Effects of injectable trace mineral supplementation in lactating dairy cows with elevated somatic cell counts. (2016) Journal of Dairy Science. Volume 99, Issue 9, September 2016, Pages 7319–7329

30. Bicalho M. L. S., E.C. Marques, Bicalho R.C. and R.O Gilbert. 2016. The association of plasma glucose, BHBA, and NEFA with postpartum uterine diseases of Holstein dairy cows. Theriogenology (2016) 10.1016/j.theriogenology.2016.09.036.30.

31. Bicalho M.L.S., F.S. Lima; G. Oikonomou; C. Foditsch, K.B. Krieger; R.C. Bicalho and R.O. Gilbert. Effects of injectable trace minerals supplementation on oxidative stress parameters, testosterone serum concentration, and semen quality of bulls. Submitted for peer review at Theriogenology Journal.

32. Bicalho M.L.S, T. Santin, M.X. Rodrigues, C.E. Marques, S.F. Lima, and R.C. Bicalho. 2017. Dynamics of the microbiome found in the vagina of dairy cows during the transition period: associations with Uterine diseases and reproductive outcome. Journal of Dairy Science, Volume 100, Issue 4, April 2017, Pages 3043-3058.

33. Bicalho M.L.S., V. S. Machado, C. H. Higgins, F. S. Lima, and R. C. Bicalho. 2017. Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus Healthy. Journal of Dairy Science, Volume 100, Issue 5, May 2017, Pages 3850-3862

34. Bicalho, M.L.S., S. Lima, C. H. Higgins, V. S. Machado, F. S. Lima, and R. C. Bicalho.2017. Genetic and functional analysis of the bovine uterine microbiota. Part II: purulent vaginal discharge versus Healthy. Journal of Dairy Science, Volume 100, Issue 5, May 2017, Pages 3863-3874

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