@article{hassan_mendoza_dickey_2024, title={Complete genome sequences of <i>Lactobacillus acidophilus</i> strain P42 and <i>Limosilactobacillus reuteri</i> strain P43 isolated from chicken cecum}, volume={3}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/mra.01140-23}, DOI={10.1128/mra.01140-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Hassan, Hosni M. and Mendoza, Mary and Dickey, Allison N.}, editor={Hotopp, Julie C. DunningEditor}, year={2024}, month={Mar} }
 @article{troxell_mendoza_ali_koci_hassan_2020, title={Attenuated Salmonella enterica Serovar Typhimurium, Strain NC983, Is Immunogenic, and Protective against Virulent Typhimurium Challenges in Mice}, volume={8}, ISSN={["2076-393X"]}, DOI={10.3390/vaccines8040646}, abstractNote={Non-typhoidal Salmonella (NTS) serovars are significant health burden worldwide. Although much effort has been devoted to developing typhoid-based vaccines for humans, currently there is no NTS vaccine available. Presented here is the efficacy of a live attenuated serovar Typhimurium strain (NC983). Oral delivery of strain NC983 was capable of fully protecting C57BL/6 and BALB/c mice against challenge with virulent Typhimurium. Strain NC983 was found to elicit an anti-Typhimurium IgG response following administration of vaccine and boosting doses. Furthermore, in competition experiments with virulent S. Typhimurium (ATCC 14028), NC983 was highly defective in colonization of the murine liver and spleen. Collectively, these results indicate that strain NC983 is a potential live attenuated vaccine strain that warrants further development.}, number={4}, journal={VACCINES}, author={Troxell, Bryan and Mendoza, Mary and Ali, Rizwana and Koci, Matthew and Hassan, Hosni}, year={2020}, month={Dec} }
 @article{meinders_mendoza_dickey_scholl_hassan_2020, title={Complete Genome Sequences of Six Lactobacilli Isolated from American Quarter Horses}, volume={9}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00997-20}, DOI={10.1128/MRA.00997-20}, abstractNote={
            We report the complete circular genome sequences of six
            Lactobacillus
            strains and their plasmids, if any, from the fecal material of quarter horses at different ages.
          }, number={47}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, publisher={American Society for Microbiology}, author={Meinders, Rachael I. and Mendoza, Mary and Dickey, Allison N. and Scholl, Elizabeth H. and Hassan, Hosni M.}, editor={Rasko, DavidEditor}, year={2020}, month={Nov} }
 @article{allali_arnold_roach_cadenas_butz_hassan_koci_ballou_mendoza_ali_et al._2017, title={A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome}, volume={17}, ISSN={["1471-2180"]}, DOI={10.1186/s12866-017-1101-8}, abstractNote={Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies.}, journal={BMC MICROBIOLOGY}, author={Allali, Imane and Arnold, Jason W. and Roach, Jeffrey and Cadenas, Maria Belen and Butz, Natasha and Hassan, Hosni M. and Koci, Matthew and Ballou, Anne and Mendoza, Mary and Ali, Rizwana and et al.}, year={2017}, month={Sep} }
 @article{azcarate-peril_butz_cadenas_koci_ballou_mendoza_ali_hassan_2017, title={An Attenuated
                    Salmonella enterica
                    Serovar Typhimurium Strain and Galacto-Oligosaccharides Accelerate Clearance of
                    Salmonella
                    Infections in Poultry through Modifications to the Gut Microbiome}, volume={84}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.02526-17}, DOI={10.1128/aem.02526-17}, abstractNote={ABSTRACT}, number={5}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Azcarate-Peril, M. Andrea and Butz, Natasha and Cadenas, Maria Belen and Koci, Matthew and Ballou, Anne and Mendoza, Mary and Ali, Rizwana and Hassan, Hosni}, editor={Schottel, Janet L.Editor}, year={2017}, month={Dec} }
 @article{troxell_petri_daron_pereira_mendoza_hassan_koci_2015, title={Poultry Body Temperature Contributes to Invasion Control through Reduced Expression of Salmonella Pathogenicity Island 1 Genes in Salmonella enterica Serovars Typhimurium and Enteritidis}, volume={81}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.02622-15}, DOI={10.1128/aem.02622-15}, abstractNote={ABSTRACT}, number={23}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Troxell, Bryan and Petri, Nicholas and Daron, Caitlyn and Pereira, Rafaela and Mendoza, Mary and Hassan, Hosni M. and Koci, Matthew D.}, editor={Elkins, C. A.Editor}, year={2015}, month={Sep}, pages={8192–8201} }
 @article{husain_jones-carson_liu_song_saah_troxell_mendoza_hassan_vazquez-torresa_2014, title={Ferric Uptake Regulator-Dependent Antinitrosative Defenses in Salmonella enterica Serovar Typhimurium Pathogenesis}, volume={82}, ISSN={["1098-5522"]}, DOI={10.1128/iai.01201-13}, abstractNote={ABSTRACT}, number={1}, journal={INFECTION AND IMMUNITY}, author={Husain, Maroof and Jones-Carson, Jessica and Liu, Lin and Song, Miryoung and Saah, J. Royden and Troxell, Bryan and Mendoza, Mary and Hassan, Hosni and Vazquez-Torresa, Andres}, year={2014}, month={Jan}, pages={333–340} }