Publications

For a complete list see here.

2024

Bottino GF, Bonham KS, Pate F, McCann S, Zieff M, Naspolini N, Ho D, Portlock T, Joos R, Midani FS, Schüroff P, Das A, Shennon I, Wilson BC, O’Sullivan JM, Britton RA, Murray DM, Kiely ME, Taddei CR, Beltrão-Braga PCB, Campos AC, Polanczyk GV, Huttenhower C, Donald KA, Klepac-Ceraj V*. Early life microbial succession in the gut follows common patterns in humans across the globe. BioRxiv: doi: https://doi.org/10.1101/2024.07.25.605223.
Bonham KS, Margolis, ET, Bottino G, Patel F, McCann S, Zieff MR, Donald KA, Gabard-Durnam LJ*, Klepac-Ceraj V*. Co-development of gut microbial metabolism and visual neural circuitry in human infants. medRxiv: doi: https://doi.org/10.1101/2024.07.24.24310884. (*=co-corresponding author)
Laue HE, Bonham KS, Coker MO, Moroishi, Y, Hoen AG, Karagas MR; Klepac-Ceraj V*, Madan JC*. Prospective association of the infant gut microbiome with autism-related behaviors in the ECHO consortium. Molecular Autism 15, 21 (2024). https://doi.org/10.1186/s13229-024-00597-2. (*=co-corresponding author)
Margolis ET, Davel L, Bourke NJ, Bosco C, Zieff MR, Monachino AD, Mazubane T, Williams SR, Miles M, Jacobs CA, Williams S, Bradford L, Knipe C, Madi Z, Methola B, Mhlakwaphalwa T, Mlandu N, Nkubungu K, Goolam Nabi Z, Pan T, Samuels R, Pini N, Klepac-Ceraj V, Fifer WP, Alexander DC, Jones DK, Williams SCR, Amso D, Donald KA, Gabard-Durnam LJ. Longitudinal effects of prenatal alcohol exposure on visual neurodevelopment over infancy. Dev Psychol. 2024 Mar 21. doi: 10.1037/dev0001727. Epub ahead of print. PMID: 38512192.
Zieff, MR, Miles M, Mbale E, Eastman E, Ginnell L, Williams SCR, Alexander DC, Wijeratne PA, Gabard-Durnam LJ, Klepac-Ceraj V, Bonham KS, Pini N, Sania A, Lucchini M, Deoni S, Fifer WP, Gladstone M, Amso D, Donald KA. Characterizing developing executive functions in the first 1000 days in South Africa and Malawi: The Khula Study. [version 1; peer review: 2 approved with reservations]. Wellcome Open Res 2024, 9:157 https://doi.org/10.12688/wellcomeopenres.19638.1.

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.