@inproceedings{baugher_jaykus_2016, title={Natural microbiota of raspberries (Rubus idaeus) and strawberries (Fragaria x ananassa): Microbial survey, bacterial isolation and identification, and biofilm characterization}, volume={1133}, booktitle={Xi international rubus and ribes symposium}, author={Baugher, J. L. and Jaykus, L. A.}, year={2016}, pages={521–526} }
 @article{baugher_durmaz_klaenhammer_2014, title={Spontaneously Induced Prophages in Lactobacillus gasseri Contribute to Horizontal Gene Transfer}, volume={80}, ISSN={["1098-5336"]}, DOI={10.1128/aem.04092-13}, abstractNote={Lactobacillus gasseri is an endogenous species of the human gastrointestinal tract and vagina. With recent advances in microbial taxonomy, phylogenetics, and genomics, L. gasseri is recognized as an important commensal and is increasingly being used in probiotic formulations. L. gasseri strain ADH is lysogenic and harbors two inducible prophages. In this study, prophage adh was found to spontaneously induce in broth cultures to populations of ∼ 10(7) PFU/ml by stationary phase. The adh prophage-cured ADH derivative NCK102 was found to harbor a new, second inducible phage, vB_Lga_jlb1 (jlb1). Phage jlb1 was sequenced and found to be highly similar to the closely related phage LgaI, which resides as two tandem prophages in the neotype strain L. gasseri ATCC 33323. The common occurrence of multiple prophages in L. gasseri genomes, their propensity for spontaneous induction, and the high degree of homology among phages within multiple species of Lactobacillus suggest that temperate bacteriophages likely contribute to horizontal gene transfer (HGT) in commensal lactobacilli. In this study, the host ranges of phages adh and jlb1 were determined against 16 L. gasseri strains. The transduction range and the rate of spontaneous transduction were investigated in coculture experiments to ascertain the degree to which prophages can promote HGT among a variety of commensal and probiotic lactobacilli. Both adh and jlb1 particles were confirmed to mediate plasmid transfer. As many as ∼10(3) spontaneous transductants/ml were obtained. HGT by transducing phages of commensal lactobacilli may have a significant impact on the evolution of bacteria within the human microbiota.}, number={11}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Baugher, J. L. and Durmaz, E. and Klaenhammer, T. R.}, year={2014}, month={Jun}, pages={3508–3517} }
 @misc{baugher_klaenhammer_2011, title={Invited review: Application of omics tools to understanding probiotic functionality}, volume={94}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2011-4384}, abstractNote={The human gut microbiota comprises autochthonous species that colonize and reside at high levels permanently and allochthonous species that originate from another source and are transient residents of the human gut. The interactions between bacteria and the human host can be classified as a continuum from symbiosis and commensalism (mutualism) to pathogenesis. Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Recent advances in omics tools and sequencing techniques have furthered our understanding of probiotic functionality and the specific interactions between probiotics and their human hosts. Although it is known that not all probiotics use the same mechanisms to confer benefits on hosts, some specific mechanisms of action have been revealed through omic investigations. These include competitive exclusion, bacteriocin-mediated protection against intestinal pathogens, intimate interactions with mucin and the intestinal epithelium, and modulation of the immune system. The ability to examine fully sequenced and annotated genomes has greatly accelerated the application of genetic approaches to elucidate many important functional roles of probiotic microbes.}, number={10}, journal={JOURNAL OF DAIRY SCIENCE}, author={Baugher, J. L. and Klaenhammer, T. R.}, year={2011}, month={Oct}, pages={4753–4765} }