Publications

Below are some recent publications. For a full list of publications, see Google Scholar.

Tannous, J, CM Cosetta, MT Drott, TA Rush, PE Abraham, RJ Giannone, NP Keller, BE Wolfe. 2023. LaeA-regulated fungal traits mediate bacterial community assembly. mBio 14:e00769-23

Cosetta, CM, B Niccum, N Kamkari, M Dente, M Podniesinski, Wolfe BE. 2023. Bacterial–fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species. The ISME Journal. 31:1-3

Ye, R, C Tomo, N Chan, and BE Wolfe. 2023. Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum. mSphere. 4:e00047-23

Wolfe, BE. 2023. Are fermented foods an overlooked reservoir and vector of antimicrobial resistance? Current Opinion in Food Science. 51:101018

Louw, N, K Lele, R Ye, C Edwards, BE Wolfe. 2023. Microbiome assembly in fermented foods. Annual Review of Microbiology 77:381-402

Landis, EA, E Fogarty, JC Edwards, O Popa, A Murat Eren, BE Wolfe. 2022. Microbial diversity and interaction specificity in kombucha tea fermentations. mSystems e00157-22

Landis, EA, AM Oliverio, EA McKenny, LM Nichols, N Kfoury, M Biango-Daniels, LK Shell, AA Madden, LR Shapiro, SK Sakunala, K Drake, A Robbat, M Booker, RR Dunn, N Fierer, BE Wolfe. 2021. The structure and function of sourdough starter microbiomes. eLife 10:e61644

Pierce, EC, M Morin, JC Little, RB Liu, J Tannous, NP Keller, BE Wolfe, LM Sanchez, and RJ Dutton. 2021. High-throughput genetic screen reveals diverse impacts of cheese-associated fungi on bacteria. Nature Microbiology6:87-102

Marco, ML, ME Sanders, M Gänzle, MC Arrieta, PD Cotter, LD Vuyst, C Hill, W Holzapfel, SLebeer, D Merenstein, G Reid, BE Wolfe, and R Hutkins. 2021. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology 18:196–208 

Cosetta, CM and BE Wolfe. 2020. Fungal volatiles mediate cheese rind microbiome assembly. Environmental Microbiology 22:4745–4760

Fulcher, MR, ML Bolton, MD Millican, MJ Michalska-Smith, JP Dundore-Arias, J Handelsman, JL Klassen, KC Milligan-Myhre, AShade, BE Wolfe, LL Kinkel. 2020. Broadening participation in scientific conferences during the era of social distancing. Trends in Microbiology 28:949-952.

Niccum, BA, EK Kastman, N Kfoury, A Robbat, BE Wolfe. 2020. Strain-level diversity impacts cheese rind microbiome assembly and function. mSystems 5: e00149-20

Bodinaku, IA, J Shaffer, AB Connors, JL Steenwyk, MN Biango-Daniels, EK Kastman, A Rokas, A Robbat, and BE Wolfe. 2019. Rapid phenotypic and metabolomic domestication of wild Penicillium molds on cheese. mBio e02445-19

Cosetta, CM and BE Wolfe. 2019. Causes and consequences of biotic interactions within microbiomes. Current Opinion in Microbiology 50:35-41

Cosetta, CM and BE Wolfe. 2019. Deconstructing and reconstructing cheese rind microbiomes. Current Protocols in Microbiology 56:e95

Miller, EA, PJ Kearns, BA Niccum, J O’Mara Schwartz, A Ornstein, EK Kastman, BE Wolfe. 2019. Establishment limitation constrains the abundance of lactic acid bacteria in the Napa cabbage phyllosphere. Applied and Environmental Microbiology 85:e00269-19

Bonham KS, Wolfe BE, Dutton RJ. 2017. Extensive horizontal gene transfer in cheese-associated bacteria. eLife. 6: e22144

Schaeffer R,C Wilson, L Radville, E Whitney, M Barrett, S Roitman, E Miller, BE Wolfe, C Thornber, C Orians, E Preisser. 2017. Individual and non-additive effects of exotic sap-feeders on root functional and mycorrhizal traits of a shared conifer host. Functional Ecology 31: 2024-2033

Fu X, SG Harshman, X Shen, DB Haytowitz, JP Karl, BE Wolfe, SL Booth. 2017. Multiple vitamin K forms exist in dairy foods. Current Developments in Nutrition 1: e000638

Morokuma J, FR Durant, KB Williams, JM Finkelstein, DJ Blackiston, T Clements, DW Reed, M Roberts, M Jain, K Kimel, SA Trauger, BE Wolfe, M Levin. 2017. Planarian regeneration in space: persistent anatomical, behavioral, and bacteriological changes induced by space travel. Regeneration  4: 85-102

Kastman, EK, N Kamelamela, J Norville, C Cosetta, RJ Dutton, and BE Wolfe. 2016. Biotic interactions shape the ecological distributions of Staphylococcus species. mBio 7(5):e01157-16.

Bokulich, N, JR Rideout, W Mercurio, A Shiffer, BE Wolfe, C Maurice, R Dutton, P Turnbaugh, R Knight, JG Caporaso. 2016. Mockrobiota: a public resource for microbiome bioinformatics benchmarking. mSystems 1(5): e00062-16

Karl, JP, X Fu, X Wang, Y Zhao, J Shen, C Zhang, BE Wolfe, E Saltzman, L Zhao, and SL Booth. 2015. Fecal menaquinone profiles of overweight adults are associated with gut microbiota composition during a gut microbiota–targeted dietary intervention. The American Journal of Clinical Nutrition: ajcn109496.

Wolfe, BE, and RJ Dutton. 2015. Fermented foods as experimentally tractable microbial ecosystems. Cell 161:49-55.

Wolfe, BE, JE Button, M Santarelli, RJ Dutton. 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158: 422-433.

Hess, J, I Skrede, BE Wolfe, K LaButti, RA Ohm, IV Grigoriev, and A Pringle. 2014. Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi. Genome Biology and Evolution 6: 1564-1578.

Lawrence, DA, CF Maurice, RN Carmody, DB Gootenberg, JE Button, BE Wolfe, AV Ling, S Devlin, M Fischbach, SB Biddinger, RJ Dutton, PJ Turnbaugh. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559-563.

Cheng-Chih H, MS ElNaggar, Y Peng, J Fang, LM Sanchez, SJ Mascuch, KA Møller, EK Alazzeh, J Pikula, RA Quinn, Y Zeng, BE Wolfe, RJ Dutton, L Gerwick, L Zhang, X Liu, M Mansson, and Pieter C. Dorrestein. 2013. Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. Analytical Chemistry 85: 7014−7018.

Wolfe, BE, RE Tulloss, and A Pringle. 2012. The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis.  PLoS One 7(7): e39597.