Publications

2023

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.
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.

2022

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.. (2022). Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago. BioRxiv, 2022–2004.

2021

Cohen, A. B., Klepac-Ceraj, V., Butler, K., Weber, F., Garber, A. I., Christensen, L. N., Cram, J., McCormick M.L., & Taylor, G. T. (2021). Particle-associated and free-living microbial assemblages are distinct in a permanently redox-stratified freshwater lake. BioRxiv, 2021–2011
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.
Abo-Sido, N., Goss, J. W., Griffith, A. B., & Klepac-Ceraj, V. (2021). Microbial transformation of traditional fermented fertilizer bokashi alters chemical composition and improves plant growth. Biorxiv, 2021–2008.
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.
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.
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.
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.
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.

2020

Bonham, K. S., Bruchhage, M. M. K., Rowland, S., Volpe, A. R., Dyer, K., D’Sa, V., Huttenhower, C., Deoni, S. C. L, Klepac-Ceraj, V., & RESONANCE Consortium. (2020). Gut microbes and their genes are associated with brain development and cognitive function in healthy children. bioRxiv. https://doi.org/10.1101/2020.02.13.944181

Full text (via DOI) · Google Scholar

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. https://doi.org/10.3389/fmicb.2020.00796

Full text (via DOI) · Google Scholar

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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio

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. https://doi.org/10.1038/s41586-019-1804-0

Full text (via DOI) · Google Scholar

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. https://doi.org/10.1101/691378

Full text (via DOI) · Google Scholar

2018

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. In Press. https://doi.org/10.9734/IJPSS/2018/40403

Full text (via DOI) · Google Scholar

Rowland, S. & Klepac-Ceraj, V. Sallie “Penny” Chisholm and Oceans of Prochlorococcus. Women in Microbiology. Eds: RJ Whitaker, HA. Barton. doi: 10.1128/9781555819545.

Full text (via DOI) · Google Scholar

2004

Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V., & Polz, M. F. (2004). Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons. Journal of Bacteriology, 186(9), 2629–2635. doi:10.1128/JB.186.9.2629-2635.2004

Full text (via DOI) · Google Scholar · Epistemio
Klepac-Ceraj, V., Bahr, M., Crump, B. C., Teske, A. P., Hobbie, J. E., & Polz, M. F. (2004). High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environmental Microbiology, 6(7), 686–698. doi:10.1111/j.1462-2920.2004.00600.x

Full text (via DOI) · Google Scholar · Epistemio
Acinas, S. G., Klepac-Ceraj, V., Hunt, D. E., Pharino, C., Ceraj, I., Distel, D. L., & Polz, M. F. (2004). Fine-scale phylogenetic architecture of a complex bacterial community. Nature, 430(6999), 551–554. doi:10.1038/nature02649

Full text (via DOI) · Google Scholar · Epistemio

2005

Acinas, S. G., Sarma-Rupavtarm, R., Klepac-Ceraj, V., & Polz, M. F. (2005). PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample. Applied and Environmental Microbiology, 71(12), 8966–8969. doi:10.1128/AEM.71.12.8966-8969.2005

Full text (via DOI) · Google Scholar · Epistemio
Bahr, M., Crump, B. C., Klepac-Ceraj, V., Teske, A., Sogin, M. L., & Hobbie, J. E. (2005). Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environmental Microbiology, 7(8), 1175–1185. doi:10.1111/j.1462-2920.2005.00796.x

Full text (via DOI) · Google Scholar · Epistemio
Klepac-Ceraj, V., Zhang, X. V., McNamara, C. J., Polz, M. F., Martin, S. T., Berke, N., & Mitchell, R. (2005). Binding of Harvested Bacterial Exopolymers to the Surface of Calcite. Environmental Science & Technology, 39(22), 8770–8775. doi:10.1021/es0508368

Full text (via DOI) · Google Scholar · Epistemio

2006

Hunt, D. E., Klepac-Ceraj, V., Acinas, S. G., Gautier, C., Bertilsson, S., & Polz, M. F. (2006). Evaluation of 23S rRNA PCR Primers for Use in Phylogenetic Studies of Bacterial Diversity. Applied and Environmental Microbiology, 72(3), 2221–2225. doi:10.1128/AEM.72.3.2221-2225.2006 Full text (via DOI) · Google Scholar · Epistemio

2010

Klepac-Ceraj, V., Lemon, K. P., Martin, T. R., Allgaier, M., Kembel, S. W., Knapp, A. A., Lory, S., Brodie, E. L., Lynch, S. V., Bohannan, B. J. M., Green, J. L., Maurer, B. A., & Kolter, R. (2010). Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa: Ecology of the cystic fibrosis respiratory tract bacterial community. Environmental Microbiology, 12(5), 1293–1303. doi:10.1111/j.1462-2920.2010.02173.x

Full text (via DOI) · Google Scholar · Epistemio
Udiković Kolić, N., Hršak, D., Devers, M., Klepac-Ceraj, V., Petrić, I., & Martin-Laurent, F. (2010). Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil. Journal of Applied Microbiology. doi:10.1111/j.1365-2672.2010.04700.x

Full text (via DOI) · Google Scholar · Epistemio

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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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: UGI Microbiome Beta-Diversity Associated with BMI. Obesity, 23(4), 862–869. doi:10.1002/oby.21020

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio

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

Full text (via DOI) · Google Scholar · Epistemio
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: Uptake of Hduring the life cycle of soil actinobacteria. Environmental Microbiology Reports, 6(3), 226–238. doi:10.1111/1758-2229.12116

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio
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

Full text (via DOI) · Google Scholar · Epistemio

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
Full text (via DOI) · Google Scholar · Epistemio
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
Full text (via DOI) · Google Scholar · Epistemio
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
Full text (via DOI) · Google Scholar · Epistemio

2012

Torlakovic, L., Klepac-Ceraj, V., Øgaard, B., Cotton, S. L., Paster, B. J., & Olsen, I. (2012). Microbial community succession on developing lesions on human enamel. Journal of Oral Microbiology, 4(1), 16125. doi:10.3402/jom.v4i0.16125

Full text (via DOI) · Google Scholar · Epistemio
Bosak, T., Liang, B., Wu, T. - D., Templer, S. P., Evans, A., Vali, H., Guerquin‐Kern, J. - L., Klepac‐Ceraj, V., Sim, M. S., & Mui, J. (2012). Cyanobacterial diversity and activity in modern conical microbialites. Geobiology, 10(5), 384–401. doi:10.1111/j.1472-4669.2012.00334.x

Full text (via DOI) · Google Scholar · Epistemio
Klepac-Ceraj, V., Hayes, C. A., Gilhooly, W. P., Lyons, T. W., Kolter, R., & Pearson, A. (2012). Microbial diversity under extreme euxinia: Mahoney Lake, Canada: Microbial diversity of a stratified saline lake. Geobiology, 10(3), 223–235. doi:10.1111/j.1472-4669.2012.00317.x

Full text (via DOI) · Google Scholar · Epistemio
Sim, M. S., Liang, B., Petroff, A. P., Evans, A., Klepac-Ceraj, V., Flannery, D. T., Walter, M. R., & Bosak, T. (2012). Oxygen-Dependent Morphogenesis of Modern Clumped Photosynthetic Mats and Implications for the Archean Stromatolite Record. Geosciences, 2(4), 235–259. doi:10.3390/geosciences2040235

Full text (via DOI) · Google Scholar · Epistemio
Shaddox, L. M., Huang, H., Lin, T., Hou, W., Harrison, P. L., Aukhil, I., Walker, C. B., Klepac-Ceraj, V., & Paster, B. J. (2012). Microbiological Characterization in Children with Aggressive Periodontitis. Journal of Dental Research, 91(10), 927–933. doi:10.1177/0022034512456039

Full text (via DOI) · Google Scholar · Epistemio
Hunter, R. C., Klepac-Ceraj, V., Lorenzi, M. M., Grotzinger, H., Martin, T. R., & Newman, D. K. (2012). Phenazine Content in the Cystic Fibrosis Respiratory Tract Negatively Correlates with Lung Function and Microbial Complexity. American Journal of Respiratory Cell and Molecular Biology, 47(6), 738–745. doi:10.1165/rcmb.2012-0088OC

Full text (via DOI) · Google Scholar · Epistemio
Bohorquez, L. C., Delgado-Serrano, L., López, G., Osorio-Forero, C., Klepac-Ceraj, V., Kolter, R., Junca, H., Baena, S., & Zambrano, M. M. (2012). In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes. Microbial Ecology, 63(1), 103–115. doi:10.1007/s00248-011-9943-3

Full text (via DOI) · Google Scholar · Epistemio

2011

Ng, R., Singh, F., Papamanou, D. A., Song, X., Patel, C., Holewa, C., Patel, N., Klepac-Ceraj, V., Fontana, C. R., Kent, R., Pagonis, T. C., Stashenko, P. P., & Soukos, N. S. (2011). Endodontic Photodynamic Therapy Ex Vivo. Journal of Endodontics, 37(2), 217–222. doi:10.1016/j.joen.2010.10.008

Full text (via DOI) · Google Scholar · Epistemio
Shank, E. A., Klepac-Ceraj, V., Collado-Torres, L., Powers, G. E., Losick, R., & Kolter, R. (2011). Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proceedings of the National Academy of Sciences, 108(48), E1236–E1243. doi:10.1073/pnas.1103630108

Full text (via DOI) · Google Scholar · Epistemio
Klepac-Ceraj, V., Patel, N., Song, X., Holewa, C., Patel, C., Kent, R., Amiji, M. M., & Soukos, N. S.(2011). Photodynamic effects of methylene blue-loaded polymeric nanoparticles on dental plaque bacteria: PHOTODESTRUCTION OF ORAL BACTERIA. Lasers in Surgery and Medicine, 43(7), 600–606. doi:10.1002/lsm.21069

Full text (via DOI) · Google Scholar · Epistemio
Guss, A. M., Roeselers, G., Newton, I. L. G., Young, C. R., Klepac-Ceraj, V., Lory, S., & Cavanaugh, C. M. (2011). Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. The ISME Journal, 5(1), 20–29. doi:10.1038/ismej.2010.88

Full text (via DOI) · Google Scholar · Epistemio