Publications

For a complete list see here.

2023

Bonham K.S., Fahur Bottino G., McCann S.H., Beauchemin J., Weisse E., Barry F., Cano Lorente R.; RESONANCE Consortium; Huttenhower C., Bruchhage M., D'Sa V., Deoni S., Klepac-Ceraj V. (2023). Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children. Science Advances. 9(51):eadi0497. doi: 10.1126/sciadv.adi0497.
Schoenborn, A. A., Yannarell, S. M., MacVicar, C. T., Barriga-Medina, N. N., Markillie, M., Mitchell, H., Bonham, K.S., Leon-Reyes, A., Riveros-Iregui, D., Klepac-Ceraj, V.*, & Shank, E.A.* (2023). Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago. Environmental Microbiology. 2023 Mar 7. DOI: 10.1111/1462-2920.16361. (*=co-corresponding author)
Rahman, T., Sarwar, P. F., Potter, C., Comstock, S.*, & Klepac-Ceraj, V*. (2023). Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema. Frontiers in Pediatrics, 11, 315. doi: 10.3389/fped.2023.1090048. (*=co-corresponding author)
Cohen, A. B., Klepac-Ceraj, V., Bidas, K., Weber, F., Garber, A. I., Christensen, L. N., Cram, J.A., McCormick, M.L., & Taylor, G. T. (2023). Deep photoautotrophic prokaryotes contribute substantially to carbon dynamics in oxygen-deficient waters in a permanently redox-stratified freshwater lake. Limnology and Oceanography, 68(1), 232–247. doi: 10.1002/lno.12262.

2021

Bonham, K. S., Kayisire, A. A., Luo, A. S., & Klepac-Ceraj, V. (2021). Microbiome. jl and BiobakeryUtils. jl-Julia packages for working with microbial community data. Journal of Open Source Software, 6(67), 3876. https://joss.theoj.org/papers/10.21105/joss.03876.
Lewis, C. R., Bonham, K. S., McCann, S. H., Volpe, A. R., D’sa, V., Naymik, M. De Both, M.D., Huentelman, M.J., Lemery-Chalfant, K., Highlander, S.K., Deoni, S.C.L., & Klepac-Ceraj, V. (2021). Family SES is associated with the gut microbiome in infants and children. Microorganisms, 9(8), 1608. doi:10.3390/microorganisms9081608.
Ferro, L. E., Sugino, K. Y., Klepac-Ceraj, V., & Comstock, S. S. (2021). The Abundance of Human Milk Oligosaccharide (HMO)-Metabolizing Genes in Fecal Samples from Six-Month-Old Human Infants. Microorganisms, 9(7), 1352. doi:10.3390/microorganisms9071352.
Ferro, L., Sugino, K., Klepac-Ceraj, V., & Comstock, S. (2021). Human Milk Oligosaccharide (HMO) Metabolizing Gene Abundances in Human Infant Fecal Samples. Current Developments in Nutrition, 5(Supplement_2), 741–741.
Tso, L., Bonham, K. S., Fishbein, A., Rowland, S., & Klepac-Ceraj, V. (2021). Targeted high-resolution taxonomic identification of Bifidobacterium Longum Subsp. Infantis using human milk oligosaccharide metabolizing genes. Nutrients, 13(8), 2833. doi:10.3390/nu13082833.
Peterson, D., Bonham, K. S., Rowland, S., Pattanayak, C. W., Consortium, R., & Klepac-Ceraj, V. (2021). Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes. Frontiers in Microbiology, 12, 670336. doi:10.3389/fmicb.2021.670336.
Rojas, C. A., De Santiago Torio, A., Park, S., Bosak, T., & Klepac-Ceraj, V. (2021). Organic electron donors and terminal electron acceptors structure anaerobic microbial communities and interactions in a permanently stratified sulfidic lake. Frontiers in Microbiology, 12, 620424. doi:10.3389/fmicb.2021.620424.

2020

Hough, M., McClure, A., Bolduc, B., Dorrepaal, E., Saleska, S., Klepac-Ceraj, V.*, & Rich, V.* (2020). Biotic and environmental drivers of plant microbiomes across a permafrost thaw gradient. Frontiers in Microbiology. doi:10.3389/fmicb.2020.00796. (*=co-corresponding author)

2019

Daye, M., Klepac-Ceraj, V., Pajusalu, M., Rowland, S., Farrell-Sherman, A., Beukes, N., Tamura, N., Fournier, G., & Bosak, T. (2019). Light-driven anaerobic microbial oxidation of manganese. Nature, 576(7786). 311-314. doi:10.1038/s41586-019-1804-0.
Shapiro, L. R., Youngblom, M., Scully, E. D., Rocha, J., Paulson, J. N., Klepac-Ceraj, V., Cibrián-Jaramillo, A., & López-Uribe, M. M. (2019). Bacterial communities of herbivores and pollinators that have co-evolved Cucurbita spp. bioRXiv. doi:10.1101/691378.

2018

Shapiro L.R., Paulson J.N., Arnold B.J., Scully E.D., Zhaxybayeva O., Pierce N.E., Rocha J., Klepac-Ceraj V., Holton K., & Kolter R. (2018) An Introduced crop plant is driving diversification of the virulent bacterial pathogen Erwinia tracheiphila. mBio. 9(5):e01307-18. doi: 10.1128/mBio.01307-18.
Howard, M. M., Plotkin, M. M., McClure, A. R., Klepac-Ceraj, V., Griffith, A. B., Brabander, D. J., & Jones, K. N. Comfrey mulch enriches soil but does not improve an indicator crop within one season. International Journal of Plant & Soil Science. doi:10.9734/IJPSS/2018/4040.
Rowland, S. & Klepac-Ceraj, V. Sallie “Penny” Chisholm and Oceans of Prochlorococcus. Women in Microbiology. Eds: RJ Whitaker, HA. Barton. doi: 10.1128/9781555819545.

2017

McDonough, J., Goudsouzian, L. K., Papaj, A., Maceli, A. R., Klepac-Ceraj, V. & Peterson, C. N. (2017). Stressing Escherichia coli to educate students about research: A CURE to investigate multiple levels of gene regulation : CURE: Identifying Regulators of RpoS. Biochemistry and Molecular Biology Education. doi:10.1002/bmb.21055.
O'Reilly, S. S., Mariotti, G., Winter, A. R., Newman, S. A., Matys, E. D., McDermott, F., Pruss, S. B., Bosak, T., Summons, R. E., & Klepac‐Ceraj, V. (2017). Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas. Geobiology, 15(1), 112–130. doi:10.1111/gbi.12196.
Newman, S. A., Klepac-Ceraj, V., Mariotti, G., Pruss, S. B., Watson, N., & Bosak, T. (2017). Experimental fossilization of mat-forming cyanobacteria in coarse-grained siliciclastic sediments. Geobiology. doi:10.1111/gbi.12229.

2015

Elabdeen, H. R. Z., Mustafa, M., Hasturk, H., Klepac-Ceraj, V., Ali, R. W., Paster, B. J., Van Dyke, T., & Bolstad, A. I. (2015). Subgingival microbial profiles of Sudanese patients with aggressive periodontitis. Journal of Periodontal Research, 50(5), 674–682. doi:10.1111/jre.12250.
Belstrøm, D., Fiehn, N. - E., Nielsen, C. H., Klepac-Ceraj, V., Paster, B. J., Twetman, S., & Holmstrup, P. (2015). Differentiation of salivary bacterial profiles of subjects with periodontitis and dental caries. Journal of Oral Microbiology, 7(1), 27429. doi:10.3402/jom.v7.27429.
Lin, S. - W., Freedman, N. D., Shi, J., Gail, M. H., Vogtmann, E., Yu, G., Klepac‐Ceraj, V., Paster, B. J., Dye, B. A., Wang, G. - Q., Wei, W. - Q., Fan, J. - H., Qiao, Y. - L., Dawsey S. M., & Abnet, C. C. (2015). Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index. Obesity, 23(4), 862–869. doi:10.1002/oby.21020.
Vogtmann, E., Flores, R., Yu, G., Freedman, N. D., Shi, J., Gail, M. H., Dye, B. A., Wang, G. - Q., Klepac-Ceraj, V., Paster, B. J., Wei, W. - Q., Guo, H. - Q., Dawsey, S. M., Qiao, Y. - L., & Abnet, C. C. (2015). Association between tobacco use and the upper gastrointestinal microbiome among Chinese men. Cancer Causes & Control, 26(4), 581–588. doi:10.1007/s10552-015-0535-2.
Smith, V. H., Rubinstein, R. J., Park, S., Kelly, L., & Klepac-Ceraj, V. (2015). Microbiology and Ecology Are Vitally Important to Premedical Curricula. Evolution, Medicine, and Public Health, eov014. doi:10.1093/emph/eov014.

2014

Yu, G., Dye, B. A., Gail, M. H., Shi, J., Klepac-Ceraj, V., Paster, B. J., Wang, G. - Q., Wei, W. - Q., Fan, J. - H., Qiao, Y. - L., Dawsey, S. M., Freedman, N. D., & Abnet, C. C.(2014). The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China. BMC Public Health, 14(1), 1110. doi:10.1186/1471-2458-14-1110.
Meredith, L. K., Rao, D., Bosak, T., Klepac-Ceraj, V., Tada, K. R., Hansel, C. M., Ono, S., & Prinn, R. G.(2014). Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria. Environmental Microbiology Reports, 6(3), 226–238. doi:10.1111/1758-2229.12116.
Yu, G., Gail, M. H., Shi, J., Klepac-Ceraj, V., Paster, B. J., Dye, B. A., Wang, G. - Q., Wei, W. - Q., Fan, J. - H., Qiao, Y. - L., Dawsey, S. M, Freedman, N. D., & Abnet, C. C. (2014). Association between upper digestive tract microbiota and cancer-predisposing states in the esophagus and stomach. Cancer Epidemiology Biomarkers & Prevention, 23(5), 735–741. doi:10.1158/1055-9965.EPI-13-0855.
Belstrøm, D., Holmstrup, P., Nielsen, C. H., Kirkby, N., Twetman, S., Heitmann, B. L., Klepac-Ceraj, V., Paster, B. J., & Fiehn, N. - E. (2014). Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status. Journal of Oral Microbiology, 6(1), 23609. doi:10.3402/jom.v6.23609.
Belstrøm, D., Fiehn, N. - E., Nielsen, C. H., Holmstrup, P., Kirkby, N., Klepac-Ceraj, V., Paster, B. J., & Twetman, S. (2014). Altered bacterial profiles in saliva from adults with caries lesions: a case-cohort study. Caries Research, 48(5), 368–375. doi:10.1159/000357502.
Belstrøm, D., Fiehn, N. - E., Nielsen, C. H., Kirkby, N., Twetman, S., Klepac-Ceraj, V., Paster, B. J., & Holmstrup, P. (2014). Differences in bacterial saliva profile between periodontitis patients and a control cohort. Journal of Clinical Periodontology, 41(2), 104–112. doi:10.1111/jcpe.12190.
Nascimento, M. M., Browngardt, C., Xiaohui, X., Klepac-Ceraj, V., Paster, B. J., & Burne, R. A. (2014). The effect of arginine on oral biofilm communities. Molecular Oral Microbiology, 29(1), 45–54. doi:10.1111/omi.12044.
Song, X., Yaskell, T., Klepac-Ceraj, V., Lynch, M. C., & Soukos, N. S. (2014). Antimicrobial action of minocycline microspheres versus 810-nm diode laser on human dental plaque microcosm biofilms. Journal of Periodontology, 85(2), 335–342. doi:10.1902/jop.2013.130007.

2013

Cugini, C., Klepac-Ceraj, V., Rackaityte, E., Riggs, J. E., & Davey, M. E. (2013). Porphyromonas gingivalis: keeping the pathos out of the biont. Journal of Oral Microbiology, 5(1), 19804. doi:10.3402/jom.v5i0.19804.
Nascimento, M. M., Browngardt, C., Xiaohui, X., Klepac-Ceraj, V., Paster, B. J., & Burne, R. A. (2013). The effect of arginine on oral biofilm communities. Molecular Oral Microbiology, n/a–n/a. doi:10.1111/mom.12044.
Gonçalves, P. F., Klepac-Ceraj, V., Huang, H., Paster, B. J., Aukhil, I., Wallet, S. M., & Shaddox, L. M. (2013). Correlation of Aggregatibacter actinomycetemcomitans detection with clinical/immunoinflammatory profile of localized aggressive periodontitis using a 16S rRNA microarray method: a cross-sectional study. (P. j Planet, Eds.) PLoS ONE, 8(12), e85066. doi:10.1371/journal.pone.0085066.