Dr. Karen Kalanetra PhD

Dr. Karen Kalanetra portrait

Position Title
Staff Research Associate

Department of Viticulture and Enology


Research Interests

Our lab is one of several that collaborate to connect the relationship of human milk oligosaccharides (HMO) composition and concentration in breast milk to the abundance and diversity of beneficial microbial populations in the infant gut (e.g. Bifidobacteria). In the Mills Research Group I am a microbial ecologist investigating the role of microbes in the infant gut. I follow large temporal changes in the composition of microbial communities in relation to diet (e.g. breast milk versus formula), as well as focusing on Bifidobacteria population shifts.  Projects that I am working on include (among others) investigating gut microbial community changes in 1) full term healthy infants over time and 2) preterm infants in response to supplementation with probiotics (Bifidobacteria spp.), breast milk, formula, and complex oligosaccharides (HMOs, galactooligosaccharides). Because premature infants are practically sterile when delivered, they are susceptible to devastating complications such as necrotizing enterocolitis. I would like to be able to use next generation sequencing, whether by pyro- or Illumina sequencing or metagenomics, to understand the microbial community changes that occur in these infants.

Professional Experience

  • Staff Research Associate III Department of Viticulture and Enology, University of California, Davis, CA, 2010 to present
  • Postdoctoral Scholar Department of Public Health Sciences, University of California, 2007 to 2010
  • Postdoctoral Scholar Department of Marine Sciences, University of Georgia, Athens, GA, 2005 to 2007


  • Ph.D. Microbiology, Microbiology Graduate Group, University of California, Davis, CA         2005
  • B.S.   Marine Biology, Department of Biology, University of West Florida, Pensacola, FL     1995


  • Porcellato, D., M. E. Johnson. K. Houck. S. B. Skeie. D. A. Mills. K. M. Kalanetra, J. L. Steele. 2015. Potential of Lactobacillus curvatus LFC1 to produce slits in Cheddar cheese. Food Microbiology (In Press).
  • De Leoza, M. L. A., K. M. Kalanetra, N. A. Bokulich, J. S. Strum, M. A. Underwood, J. B. German, D. A. Mills, and C. B. Lebrilla.  2015. Human milk glycomics and gut microbial genomics in infant feces shows correlation between human milk oligosaccharides and gut microbiota: A proof-of-concept study. Journal of Proteome Research 14:491–502.
  • Underwood, M., J. Arriola, C. Gerber, A. Kaveti, K. Kalanetra, A. Kananurak, C. Bevins, D. A. Mills, and B. Dvorak. 2014. Bifidobacterium longumsubsp. infantis in experimental necrotizing enterocolitis: alterations in inflammation, innate immune response, and the microbiota.  Pediatric Research 76: 326–333.
  • Huda, M N., Z. Lewis, K. Kalanetra, M. Rashid, S. Ahmad, R. Raqib, F. Qadri, M. A. Underwood, D. A. Mills and C. Stephensen. 2014. Stool microbiota and vaccine responses of infants. Pediatrics 134:2 e362-e372.
  • Underwood, M. A., K. M. Kalanetra, N. A. Bokulich, M. Mirmiran, D. Barile, D. J. Tancredi, J. B. German, C. B. Lebrilla and D. A. Mills.  2014. Prebiotic oligosaccharides in premature infants. Journal of Pediatric Gastroenterology & Nutrition 58:352-360.
  • Underwood, M., K. Kalanetra, N. Bokulich, Z. T. Lewis, M. Mirmiran, D. Tancredi and D. A. Mills.  2013. A comparison of two probiotic strains of bifidobacteria in premature infants.  Journal of Pediatrics 163:1585-1591.
  • Ellis, C. L., N. A. Bokulich, K. M. Kalanetra, M. Mirmiran, J. Elumalai, L. Haapanen, T. Schegg, J. C. Rutledge, G. Raff, D. A. Mills, M. A. Underwood. 2013.  Probiotic administration in congenital heart disease: A pilot study.  Journal of Perinatology33:691-697.
  • Lewis, Z. T., N. A. Bokulich, K. M. Kalanetra, S. Ruiz-Moyano, M. A Underwood and D. A Mills.  2013. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities.  Anaerobe 19:62-69.
  • De Leoz, M. L., S. Gaerlan, J. Strum, L. Dimapasoc, M. Mirmiran, D. Tancredi, J. Smilowitz, K. Kalanetra, D. A. Mills, J. B.  German, C. B. Lebrilla,  M. Underwood.  2012. Lacto-N-tetraose, fucosylation, and secretor status are highly variable in human milk oligosaccharides from women delivering preterm. Journal of Proteome Research 11:4662-4672.
  • Albrecht, H., B. Durbin-Johnson, R. Yunis, K. M. Kalanetra, S. Wu, R. Chen, T. R. Stevenson, and D. M. Rocke. 2012. Transcriptional response of ex vivo human skin to ionizing radiation: comparison between low- and high dose effects. Radiation Research. 177:69-83.
  • Kalanetra, K. M. and D. C. Nelson. Vacuolate-attached filaments: highly productive Ridgeia piscesae epibionts at the Juan de Fuca hydrothermal vents. 2010. Mar Biol. 157:791-800.
  • Kalanetra, K. M., N. Bano, and J. T. Hollibaugh. Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters. 2009.Environ Microbiol. 11:2434-2445.
  • Caffrey, J. M., N. Bano, K. Kalanetra, and J. T. Hollibaugh. Ammonia oxidation and ammonia-oxidizing bacteria and archaea from esuaries with differing histories of hypoxia. 2007. ISME J. 1:660-662.
  • Bailey, J. V., S. B. Joye, K. Kalanetra, B. E. Flood, and F. A. Corsetti. Palaeontology - Undressing and redressing Ediacaran embryos - Reply. 2007. Nature. 446:E10-E11.
  • Bailey, J. V. S. B. Joye, K. Kalanetra, B. E. Flood, and F. A. Corsetti. Evidence of giant sulphur bacteria in Neoproterozoic phosphorites. 2007. Nature. 445:198-201.
  • Ahmad, A., K. Kalanetra, and D. C. Nelson. Cultivated Beggiatoa spp. define the phylogenetic root of morphologically divers, noncultured, vacuolate sulfur bacteria. 2006. Can J Microbiol. 52:591-598.
  • Kalanetra, K. M., S. B. Joye, N. R. Sunseri, and D. C. Nelson. Novel vacuolate sulfur bacteria from the Gulf of Mexico reproduce by reductive division in three dimensions. 2005. Environ Microbiol. 7:1451-1460.
  • Kalanetra, K. M., S. L. Huston, and D. C. Nelson. Novel, attached, sulfur-oxidizing bacteria at shallow hydrothermal vents possess vacuoles not involved in respiratory nitrate accumulation. 2004. Appl Env Microbiol. 70:7487-7496.
  • Hamilton, P. V. and K. M. Koch (Kalanetra). Orientation toward natural and artificial grass beds by swimming bay scallops, Argopectens irradians (Lamarck, 1819). 1996. J Exp Mar Biol Ecol. 199:79-88.