@article{dagher_vaishnav_stanley_meilleur_edwards_bruno-barcena_2023, title={Structural analysis and functional evaluation of the disordered ß-hexosyltransferase region from <i>Hamamotoa (Sporobolomyces) singularis</i>}, volume={11}, ISSN={["2296-4185"]}, url={http://dx.doi.org/10.3389/fbioe.2023.1291245}, DOI={10.3389/fbioe.2023.1291245}, abstractNote={Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.}, journal={FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY}, author={Dagher, Suzanne F. and Vaishnav, Asmita and Stanley, Christopher B. and Meilleur, Flora and Edwards, Brian F. P. and Bruno-Barcena, Jose M.}, year={2023}, month={Dec} }
 @article{zuleta-correa_chinn_bruno-barcena_2022, title={Application of raw industrial sweetpotato hydrolysates for butanol production by Clostridium beijerinckii NCIMB 8052}, volume={8}, ISSN={["2190-6823"]}, url={https://doi.org/10.1007/s13399-022-03101-z}, DOI={10.1007/s13399-022-03101-z}, journal={BIOMASS CONVERSION AND BIOREFINERY}, author={Zuleta-Correa, Ana and Chinn, Mari S. and Bruno-Barcena, Jose M.}, year={2022}, month={Aug} }
 @article{gookin_strong_bruno-barcena_stauffer_williams_wassack_azcarate-peril_estrada_seguin_balzer_et al._2022, title={Randomized placebo-controlled trial of feline-origin Enterococcus hirae probiotic effects on preventative health and fecal microbiota composition of fostered shelter kittens}, volume={9}, ISSN={["2297-1769"]}, url={https://doi.org/10.3389/fvets.2022.923792}, DOI={10.3389/fvets.2022.923792}, abstractNote={IntroductionDiarrhea is the second most common cause of mortality in shelter kittens. Studies examining prevention strategies in this population are lacking. Probiotics are of particular interest but studies in cats are largely limited to healthy adults or those with induced disease. Only one study in domestic cats describes the use of host-derived bacteria as a probiotic. We previously identified Enterococcus hirae as a dominant species colonizing the small intestinal mucosa in healthy shelter kittens. Oral administration of a probiotic formulation of kitten-origin E. hirae (strain 1002-2) mitigated the increase in intestinal permeability and fecal water loss resulting from experimental enteropathogenic E. coli infection in purpose-bred kittens. Based on these findings, we hypothesized that administration of kitten-origin E. hirae to weaned fostered shelter kittens could provide a measurable preventative health benefit.}, journal={FRONTIERS IN VETERINARY SCIENCE}, author={Gookin, Jody L. L. and Strong, Sandra J. J. and Bruno-Barcena, Jose M. and Stauffer, Stephen H. H. and Williams, Shelby and Wassack, Erica and Azcarate-Peril, M. Andrea and Estrada, Marko and Seguin, Alexis and Balzer, Joerg and et al.}, year={2022}, month={Nov} }
 @article{arnold_whittington_dagher_roach_azcarate-peril_bruno-barcena_2021, title={Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome}, volume={8}, ISSN={["2296-861X"]}, url={https://www.frontiersin.org/article/10.3389/fnut.2021.640100}, DOI={10.3389/fnut.2021.640100}, abstractNote={Complex dietary carbohydrate structures including β(1–4) galacto-oligosaccharides (GOS) are resistant to digestion in the upper gastrointestinal (GI) tract and arrive intact to the colon where they benefit the host by selectively stimulating microbial growth. Studies have reported the beneficial impact of GOS (alone or in combination with other prebiotics) by serving as metabolic substrates for modulating the assembly of the infant gut microbiome while reducing GI infections. N-Acetyl-D-lactosamine (LacNAc, Galβ1,4GlcNAc) is found in breast milk as a free disaccharide. This compound is also found as a component of human milk oligosaccharides (HMOs), which have repeating and variably branched lactose and/or LacNAc units, often attached to sialic acid and fucose monosaccharides. Human glycosyl-hydrolases do not degrade most HMOs, indicating that these structures have evolved as natural prebiotics to drive the proper assembly of the infant healthy gut microbiota. Here, we sought to develop a novel enzymatic method for generating LacNAc-enriched GOS, which we refer to as humanized GOS (hGOS). We showed that the membrane-bound β-hexosyl transferase (rBHT) from Hamamotoa (Sporobolomyces) singularis was able to generate GOS and hGOS from lactose and N-Acetyl-glucosamine (GlcNAc). The enzyme catalyzed the regio-selective, repeated addition of galactose from lactose to GlcNAc forming the β-galactosyl linkage at the 4-position of the GlcNAc and at the 1-position of D-galactose generating, in addition to GOS, LacNAc, and Galactosyl-LacNAc trisaccharides which were produced by two sequential transgalactosylations. Humanized GOS is chemically distinct from HMOs, and its effects in vivo have yet to be determined. Thus, we evaluated its safety and demonstrated the prebiotic's ability to modulate the gut microbiome in 6-week-old C57BL/6J mice. Longitudinal analysis of gut microbiome composition of stool samples collected from mice fed a diet containing hGOS for 5 weeks showed a transient reduction in alpha diversity. Differences in microbiome community composition mostly within the Firmicutes phylum were observed between hGOS and GOS, compared to control-fed animals. In sum, our study demonstrated the biological synthesis of hGOS, and signaled its safety and ability to modulate the gut microbiome in vivo, promoting the growth of beneficial microorganisms, including Bifidobacterium and Akkermansia.}, journal={FRONTIERS IN NUTRITION}, author={Arnold, Jason W. and Whittington, Hunter D. and Dagher, Suzanne F. and Roach, Jeffery and Azcarate-Peril, M. Andrea and Bruno-Barcena, Jose M.}, year={2021}, month={Apr} }
 @article{arnold_roach_fabela_moorfield_ding_blue_dagher_magness_tamayo_bruno-barcena_et al._2021, title={The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut}, volume={9}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-020-00980-0}, abstractNote={Abstract}, number={1}, journal={MICROBIOME}, author={Arnold, Jason W. and Roach, Jeffery and Fabela, Salvador and Moorfield, Emily and Ding, Shengli and Blue, Eric and Dagher, Suzanne and Magness, Scott and Tamayo, Rita and Bruno-Barcena, Jose M. and et al.}, year={2021}, month={Jan} }
 @article{arnold_roach_fabela_moorfield_ding_blue_dagher_magness_tamayo_bruno-barcena_et al._2021, title={The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut (vol 9, 31, 2021)}, volume={9}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-021-01030-z}, abstractNote={An amendment to this paper has been published and can be accessed via the original article.}, number={1}, journal={MICROBIOME}, author={Arnold, Jason W. and Roach, Jeffery and Fabela, Salvador and Moorfield, Emily and Ding, Shengli and Blue, Eric and Dagher, Suzanne and Magness, Scott and Tamayo, Rita and Bruno-Barcena, Jose M. and et al.}, year={2021}, month={Feb} }
 @article{accelerated biodegradation of the agrochemical ametoctradin by soil-derived microbial consortia_2020, url={http://dx.doi.org/10.3389/fmicb.2020.01898}, DOI={10.3389/fmicb.2020.01898}, abstractNote={Pesticide-resistant plant pathogens are an increasing threat to the global food supply and have generated a need for novel, efficacious agrochemicals. The current regulatory process for approving new agrochemicals is a tedious but necessary process. One way to accelerate the safety evaluation process is to utilize in vitro systems to demonstrate pesticide degradation by soil microbes prior to ex vivo soil evaluations. This approach may have the capability to generate metabolic profiles free of inhibitory substances, such as humic acids, commonly present in ex vivo soil systems. In this study, we used a packed-bed microbial bioreactor to assess the role of the natural soil microbial community during biodegradation of the triazolopyrimidine fungicide, ametoctradin. Metabolite profiles produced during in vitro ametoctradin degradation were similar to the metabolite profiles obtained during environmental fate studies and demonstrated the degradation of 81% of the parent compound in 72 h compared to a half-life of 2 weeks when ametoctradin was left in the soil. The microbial communities of four different soil locations and the bioreactor microbiome were compared using high throughput sequencing. It was found that biodegradation of ametoctradin in both ex vivo soils and in vitro in the bioreactor correlated with an increase in the relative abundance of Burkholderiales, well characterized microbial degraders of xenobiotic compounds.}, journal={Frontiers in Microbiology}, year={2020}, month={Aug} }
 @article{an iterative approach to improve xylose consumption by clostridium autoethanogenum: from substrate concentration to ph adjustment_2020, url={http://dx.doi.org/10.1016/j.biombioe.2020.105663}, DOI={10.1016/j.biombioe.2020.105663}, abstractNote={Clostridium autoethanogenum is an autotrophic acetogen also able to utilize xylose as a carbon source. Here, we evaluated this organism's industrially relevant capability since the transformation of sugars derived from lignocellulosic materials to biofuels is of great interest. Initially, the organism was challenged with different initial xylose levels to determine xylose utilization and maximum inhibitory concentrations for C. autoethanogenum when grown in batch cultures. A critical factor that could limit xylose utilization is culture pH, and this factor was separately examined as a means to provide C. autoethanogenum with more suitable environmental conditions. Finally, optimum pH conditions for growth were tested to assess how efficiently initial xylose concentrations could be fully utilized. C. autoethanogenum specific growth rate was not impacted when cells were exposed to initial xylose concentrations up to 30 g L−1, while cultures amended with concentrations as high as 45 g L−1 showed a delay in growth and in formation of final fermentation product concentrations. Intermittent adjustment of the culture pH to 5.8 allowed for complete substrate utilization when step-wise fed-batch xylose additions were performed. Under these conditions the cultures showed a unique biphasic growth which enhanced biomass and end product formation. In C. autoethanogenum cultures exposed to an initial xylose concentration as high as 30 g L−1, pH adjustment to 5.8 supported full utilization of all available xylose and generation of up to 2.4 g L−1 ethanol and 9.5 g L−1 acetate. This work demonstrated that C. autoethanogenum can effectively biotransform xylose at concentrations typically present in lignocellulosic hydrolysate streams.}, journal={Biomass and Bioenergy}, year={2020}, month={Sep} }
 @article{moore_whittington_azcarate-peril_bruno-bárcena_2020, title={Draft Genome Sequence of Lactobacillus rhamnosus NCB 441, Isolated from Egyptian White Domiati Cheese}, url={https://doi.org/10.1128/MRA.01191-20}, DOI={10.1128/MRA.01191-20}, abstractNote={
            Here, we report the draft genome sequence of
            Lactobacillus rhamnosus
            NCB 441, which was isolated from pickled white cheese samples gathered at Farafra Oasis in New Valley Governorate, Egypt. The genome size is 2,969,245 bp, with a G+C content of 46.7%.
          }, journal={Microbiology Resource Announcements}, author={Moore, Madison A. and Whittington, Hunter D. and Azcarate-Peril, M. Andrea and Bruno-Bárcena, José M.}, editor={Stedman, Kenneth M.Editor}, year={2020}, month={Dec} }
 @article{natzke_bruno-bárcena_2020, title={Two-stage continuous conversion of carbon monoxide to ethylene by whole cells of Azotobacter vinelandii.}, volume={86}, url={https://doi.org/10.1128/AEM.00446-20}, DOI={10.1128/aem.00446-20}, abstractNote={
            Ethylene is an essential commodity feedstock used for the generation of a variety of consumer products, but its generation demands energy-intensive processes and is dependent on nonrenewable substrates. This work describes a continuous biological method for investigating the nitrogenase-mediated carbon monoxide reductive coupling involved in ethylene production using whole cells of
            Azotobacter vinelandii
            . If eventually adopted by industry, this technology has the potential to significantly reduce the total energy input required and the ethylene recovery costs, as well as decreasing greenhouse gas emissions associated with current production strategies.
          }, number={11}, journal={Applied and environmental microbiology}, publisher={American Society for Microbiology}, author={Natzke, Jace and Bruno-Bárcena, José M.}, editor={Vieille, ClaireEditor}, year={2020}, month={Mar} }
 @article{zuleta-correa_chinn_alfaro-córdoba_truong_yencho_bruno-bárcena_2020, place={George Craig Yencho}, title={Use of unconventional mixed Acetone-Butanol-Ethanol solvents for anthocyanin extraction from Purple-Fleshed sweetpotatoes}, volume={314}, ISSN={0308-8146}, url={http://dx.doi.org/10.1016/j.foodchem.2019.125959}, DOI={10.1016/j.foodchem.2019.125959}, abstractNote={Anthocyanins from purple-fleshed sweetpotatoes constitute highly valued natural colorants and functional ingredients. In the past, anthocyanin extraction conditions and efficiencies using a single acidified solvent have been assessed. However, the potential of solvent mixes that can be generated by fermentation of biomass-derived sugars have not been explored. In this study, the effects of single and mixed solvent, time, temperature, sweetpotato genotype and preparation, on anthocyanin and phenolic extraction were evaluated. Results indicated that unconventional diluted solvent mixes containing acetone, butanol, and ethanol were superior or equally efficient for extracting anthocyanins when compared to commonly used concentrated extractants. In addition, analysis of anthocyanidins concentrations including cyanidin (cy), peonidin (pe), and pelargonidin (pl), indicated that different ratios of pn/cy were obtained depending on the solvent used. These results could be useful when selecting processing conditions that better suit particular end-use applications and more environmentally friendly process development for purple sweetpotatoes.}, journal={Food Chemistry}, publisher={Elsevier BV}, author={Zuleta-Correa, Ana and Chinn, Mari Sum and Alfaro-Córdoba, Marcela and Truong, Van-Den and Yencho, George Craig and Bruno-Bárcena, José Manuel}, year={2020}, month={Jun}, pages={125959} }
 @book{how fermented foods feed a healthy gut microbiota: a nutrition continuum_2019, url={http://dx.doi.org/10.1007/978-3-030-28737-5}, DOI={10.1007/978-3-030-28737-5}, year={2019} }
 @article{watson_jacob_bruno-bárcena_amirsultan_stauffer_píqueras_frias_gookin_2019, title={Influence of the intestinal microbiota on disease susceptibility in kittens with experimentally-induced carriage of atypical enteropathogenic Escherichia coli}, volume={231}, ISSN={0378-1135}, url={http://dx.doi.org/10.1016/j.vetmic.2019.03.020}, DOI={10.1016/j.vetmic.2019.03.020}, abstractNote={Typical enteropathogenic E. coli (tEPEC) carries the highest hazard of death in children with diarrhea and atypical EPEC (aEPEC) was recently identified as significantly associated with diarrheal mortality in kittens. In both children and kittens there is a significant association between aEPEC burden and diarrheal disease, however the infection can be found in individuals with and without diarrhea. It remains unclear to what extent, under what conditions, or by what mechanisms aEPEC serves as a primary pathogen in individuals with diarrhea. It seems likely that a combination of host and bacterial factors enable aEPEC to cause disease in some individuals and not in others. The purpose of this study was to determine the impact of aEPEC on intestinal function and diarrhea in kittens following experimentally-induced carriage and the influence of a disrupted intestinal microbiota on disease susceptibility. Results of this study identify aEPEC as a potential pathogen in kittens. In the absence of disruption to the intestinal microbiota, kittens are resistant to clinical signs of aEPEC carriage but demonstrate significant occult changes in intestinal absorption and permeability. Antibiotic-induced disruption of the intestinal microbiota prior to infection increases subsequent intestinal water loss as determined by % fecal wet weight. Enrichment of the intestinal microbiota with a commensal member of the feline mucosa-associated microbiota, Enterococcus hirae, ameliorated the effects of aEPEC experimental infection on intestinal function and water loss. These observations begin to unravel the mechanisms by which aEPEC infection may be able to exploit susceptible hosts.}, journal={Veterinary Microbiology}, publisher={Elsevier BV}, author={Watson, Victoria E. and Jacob, Megan E. and Bruno-Bárcena, José M. and Amirsultan, Sophia and Stauffer, Stephen H. and Píqueras, Victoria O. and Frias, Rafael and Gookin, Jody L.}, year={2019}, month={Apr}, pages={197–206} }
 @inbook{whittington h.d._2019, place={Cham}, title={Production and Conservation of Starter Cultures: From “Backslopping” to Controlled Fermentations}, url={http://dx.doi.org/10.1007/978-3-030-28737-5_5}, DOI={10.1007/978-3-030-28737-5_5}, booktitle={How Fermented Foods Feed a Healthy Gut Microbiota: A Nutrition Continuum}, publisher={Springer}, author={Whittington H.D., Dagher S.F.}, editor={In: Azcarate-Peril M., Arnold R.Editor}, year={2019} }
 @article{azotobacter vinelandii nitrogenase activity, hydrogen production, and response to oxygen exposure_2018, url={https://publons.com/wos-op/publon/31684347/}, DOI={10.1128/AEM.01208-18}, abstractNote={
            A. vinelandii
            has been a focus of intense research for over 100 years. It has been investigated for a variety of functions, including agricultural fertilization and hydrogen production. All of these endeavors are centered around
            A. vinelandii
            's ability to fix nitrogen aerobically using three nitrogenase isoenzymes. The majority of research up to this point has targeted
            in vitro
            measurements of the molybdenum nitrogenase, and robust data contrasting how oxygen impacts the
            in vivo
            activity of each nitrogenase isoenzyme are lacking. This article aims to provide
            in vivo
            nitrogenase activity data using a real-time evaluation of hydrogen gas released by derepressed nitrogenase mutants lacking an uptake hydrogenase and PHB accumulation.
          }, journal={Applied and Environmental Microbiology}, year={2018} }
 @article{natzke_noar_bruno-bárcena_2018, title={Azotobacter vinelandii nitrogenase activity, hydrogen production, and response to oxygen exposure}, volume={84}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85051723159&partnerID=MN8TOARS}, DOI={10.1128/AEM.001208-18}, number={16}, journal={Applied and Environmental Microbiology}, author={Natzke, J. and Noar, J. and Bruno-Bárcena, J.M.}, year={2018} }
 @article{noar_bruno-bárcena_2018, title={Azotobacter vinelandii: The source of 100 years of discoveries and many more to come}, volume={164}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85045129894&partnerID=MN8TOARS}, DOI={10.1099/mic.0.000643}, abstractNote={
                  Azotobacter vinelandii has been studied for over 100 years since its discovery as an aerobic nitrogen-fixing organism. This species has proved useful for the study of many different biological systems, including enzyme kinetics and the genetic code. It has been especially useful in working out the structures and mechanisms of different nitrogenase enzymes, how they can function in oxic environments and the interactions of nitrogen fixation with other aspects of metabolism. Interest in studying A. vinelandii has waned in recent decades, but this bacterium still possesses great potential for new discoveries in many fields and commercial applications. The species is of interest for research because of its genetic pliability and natural competence. Its features of particular interest to industry are its ability to produce multiple valuable polymers – bioplastic and alginate in particular; its nitrogen-fixing prowess, which could reduce the need for synthetic fertilizer in agriculture and industrial fermentations, via coculture; its production of potentially useful enzymes and metabolic pathways; and even its biofuel production abilities. This review summarizes the history and potential for future research using this versatile microbe.}, number={4}, journal={Microbiology (United Kingdom)}, author={Noar, J.D. and Bruno-Bárcena, J.M.}, year={2018}, pages={421–436} }
 @article{arnold_simpson_roach_bruno-barcena_azcarate-peril_2018, title={Prebiotics for Lactose Intolerance: Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus}, volume={10}, ISSN={["2072-6643"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055079156&partnerID=MN8TOARS}, DOI={10.3390/nu10101517}, abstractNote={Lactose intolerance, characterized by a decrease in host lactase expression, affects approximately 75% of the world population. Galacto-oligosaccharides (GOS) are prebiotics that have been shown to alleviate symptoms of lactose intolerance and to modulate the intestinal microbiota, promoting the growth of beneficial microorganisms. We hypothesized that mechanisms of GOS utilization by intestinal bacteria are variable, impacting efficacy and response, with differences occurring at the strain level. This study aimed to determine the mechanisms by which human-derived Lactobacillus rhamnosus strains metabolize GOS. Genomic comparisons between strains revealed differences in carbohydrate utilization components, including transporters, enzymes for degradation, and transcriptional regulation, despite a high overall sequence identity (>95%) between strains. Physiological and transcriptomics analyses showed distinct differences in carbohydrate metabolism profiles and GOS utilization between strains. A putative operon responsible for GOS utilization was identified and characterized by genetic disruption of the 6-phospho-β-galactosidase, which had a critical role in GOS utilization. Our findings highlight the importance of strain-specific bacterial metabolism in the selection of probiotics and synbiotics to alleviate symptoms of gastrointestinal disorders including lactose intolerance.}, number={10}, journal={NUTRIENTS}, author={Arnold, Jason W. and Simpson, Joshua B. and Roach, Jeffery and Bruno-Barcena, Jose M. and Azcarate-Peril, M. Andrea}, year={2018}, month={Oct} }
 @article{sandoval-espinola_chinn_thon_bruno-bárcena_2017, title={Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii}, volume={7}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-017-12962-8}, DOI={10.1038/s41598-017-12962-8}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Sandoval-Espinola, W. J. and Chinn, M. S. and Thon, M. R. and Bruno-Bárcena, J. M.}, year={2017}, month={Oct} }
 @article{packed-bed reactors, dynamic culturing, and stress-directed microbiome selection; a case study of agrochemicals soil biodegradation_2017, url={https://publons.com/publon/31684349/}, journal={In Vitro Cellular and Developmental Biology - Animal}, year={2017} }
 @article{dagher_bruno-barcena_2016, title={A novel N-terminal region of the membrane beta-hexosyltransferase: its role in secretion of soluble protein by Pichia pastoris}, volume={162}, ISSN={["1465-2080"]}, url={http://europepmc.org/abstract/med/26552922}, DOI={10.1099/mic.0.000211}, abstractNote={The β-hexosyltransferase (BHT) from Sporobolomyces singularis is a membrane-bound enzyme that catalyses transgalactosylation reactions to synthesize galacto-oligosaccharides (GOSs). To increase the secretion of the active soluble version of this protein, we examined the uncharacterized novel N-terminal region (amino acids 1-110), which included two predicted endogenous structural domains. The first domain (amino acids 1-22) may act as a classical leader while a non-classical signal was located within the remaining region (amino acids 23-110). A functional analysis of these domains was performed by evaluating the amounts of the rBHT forms secreted by recombinant P. pastoris strains carrying combinations of the predicted structural domains and the α mating factor (MFα) from Saccharomyces cerevisiae as positive control. Upon replacement of the leader domain (amino acids 1-22) by MFα (MFα-rBht(23-594)), protein secretion increased and activity of both soluble and membrane-bound enzymes was improved 53- and 14-fold, respectively. Leader interference was demonstrated when MFα preceded the putative classical rBHT(1-22) leader (amino acids 1-22), explaining the limited secretion of soluble protein by P. pastoris (GS115 : : MFα-rBht(1-594)). To validate the role of the N-terminal domains in promoting protein secretion, we tested the domains using a non-secreted protein, the anti-β-galactosidase single-chain variable antibody fragment scFv13R4. The recombinants carrying chimeras of the N-terminal 1-110 regions of rBHT preceding scFv13R4 correlated with the secretion strength of soluble protein observed with the rBHT recombinants. Finally, soluble bioactive HIS-tagged and non-tagged rBHT (purified to homogeneity) obtained from the most efficient recombinants (GS115 : : MFα-rBht(23-594)-HIS and GS115 : : MFα-rBht(23-594)) showed comparable activity rates of GOS generation.}, number={1}, journal={MICROBIOLOGY-SGM}, author={Dagher, Suzanne F. and Bruno-Barcena, Jose M.}, year={2016}, month={Jan}, pages={23–34} }
 @article{whitham_schulte_bobay_bruno-barcena_chinn_flickinger_pawlak_grunden_2016, title={Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain}, volume={101}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/S00253-016-7978-6}, DOI={10.1007/s00253-016-7978-6}, abstractNote={A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing identified four unique single nucleotide polymorphisms (SNPs) in the C. ljungdahlii OTA1 genome. Among these, two SNPs were found in the gene coding for AcsA and HemL, enzymes involved in acetyl-CoA formation from CO/CO 2 . Homology models of the respective mutated enzymes revealed alterations in the size and hydrogen bonding of the amino acids in their active sites. Failed attempts to grow OTA1 autotrophically suggested that one or both of these mutated genes prevented acetyl-CoA synthesis from CO/CO 2 , demonstrating that its activity was required for autotrophic growth by C. ljungdahlii. An inoperable Wood-Ljungdahl pathway resulted in higher CO 2  and ethanol yields and lower biomass and acetate yields compared to WT for multiple growth conditions including heterotrophic and mixotrophic conditions. The two other SNPs identified in the C. ljungdahlii OTA1 genome were in genes coding for transcriptional regulators (CLJU_c09320 and CLJU_c18110) and were found to be responsible for deregulated expression of co-localized arginine catabolism and 2-deoxy-D-ribose catabolism genes. Growth medium supplementation experiments suggested that increased arginine metabolism and 2-deoxy-D-ribose were likely to have minor effects on biomass and fermentation product yields. In addition, in silico flux balance analysis simulating mixotrophic and heterotrophic conditions showed no change in flux to ethanol when flux through HemL was changed whereas limited flux through AcsA increased the ethanol flux for both simulations. In characterizing the effects of the SNPs identified in the C. ljungdahlii OTA1 genome, a non-autotrophic hyper ethanol-producing strain of C. ljungdahlii was identified that has utility for further physiology and strain performance studies and as a biocatalyst for industrial applications.}, number={4}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Nature}, author={Whitham, Jason M. and Schulte, Mark J. and Bobay, Benjamin G. and Bruno-Barcena, Jose M. and Chinn, Mari S. and Flickinger, Michael C. and Pawlak, Joel J. and Grunden, Amy M.}, year={2016}, month={Nov}, pages={1615–1630} }
 @article{monteagudo-mera_arthur_jobin_keku_bruno-barcena_azcarate-peril_2016, title={High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome.}, volume={7}, url={http://europepmc.org/abstract/med/26839072}, DOI={10.3920/bm2015.0114}, abstractNote={Prebiotics are selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon the host health. The aim of this study was to evaluate the influence of a β(1-4)galacto-oligosaccharides (GOS) formulation consisting of 90% pure GOS (GOS90), on the composition and activity of the mouse gut microbiota. Germ-free mice were colonised with microbiota from four pathogen-free wt 129 mice donors (SPF), and stools were collected during a feeding trial in which GOS90 was delivered orally for 14 days. Pyrosequencing of 16S rDNA amplicons showed that Bifidobacterium and specific Lactobacillus, Bacteroides and Clostridiales were more prevalent in GOS90-fed mice after 14 days, although the prebiotic impact on Bifidobacterium varied among individual mice. Prebiotic feeding also resulted in decreased abundance of Bacteroidales, Helicobacter and Clostridium. High-throughput quantitative PCR showed an increased abundance of Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Bifidobacterium lactis and Bifidobacterium gallicum in the prebiotic-fed mice. Control female mice showed a higher diversity (phylogenetic diversity (PD) = 15.1±3.4 in stools and PD = 13.0±0.6 in intestinal contents) than control males (PD = 7.8±1.6 in stool samples and PD = 9.5±1.0 in intestinal contents). GOS90 did not modify inflammatory biomarkers (interleukin (IL)-6, IL-12, IL-1β, interferon gamma and tumour necrosis factor alpha). Decreased butyrate, acetate and lactate concentrations in stools of prebiotic fed mice suggested an increase in colonic absorption and reduced excretion. Overall, our results demonstrate that GOS90 is capable of modulating the intestinal microbiome resulting in expansion of the probiome (autochtonous commensal intestinal bacteria considered to have a beneficial influence on health).}, number={2}, journal={Beneficial microbes}, author={Monteagudo-Mera, A. and Arthur, J.C. and Jobin, C. and Keku, T. and Bruno-Barcena, J.M. and Azcarate-Peril, M.A.}, year={2016}, pages={247–264} }
 @misc{noar_bruno-barcena_2016, title={Protons and pleomorphs: aerobic hydrogen production in Azotobacters}, volume={32}, ISSN={["1573-0972"]}, url={http://europepmc.org/abstract/med/26748806}, DOI={10.1007/s11274-015-1980-5}, abstractNote={As obligate aerobic soil organisms, the ability of Azotobacter species to fix nitrogen is unusual given that the nitrogenase complex requires a reduced cellular environment. Molecular hydrogen is an unavoidable byproduct of the reduction of dinitrogen; at least one molecule of H2 is produced for each molecule of N2 fixed. This could be considered a fault in nitrogenase efficiency, essentially a waste of energy and reducing equivalents. Wild-type Azotobacter captures this hydrogen and oxidizes it with its membrane-bound uptake hydrogenase complex. Strains lacking an active hydrogenase complex have been investigated for their hydrogen production capacities. What is the role of H2 in the energy metabolism of nitrogen-fixing Azotobacter? Is hydrogen production involved in Azotobacter species' protection from or tolerance to oxygen, or vice versa? What yields of hydrogen can be expected from hydrogen-evolving strains? Can the yield of hydrogen be controlled or increased by changing genetic, environmental, or physiological conditions? We will address these questions in the following mini-review.}, number={2}, journal={WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY}, author={Noar, Jesse D. and Bruno-Barcena, Jose M.}, year={2016}, month={Feb} }
 @article{noar_loveless_luis navarro-herrero_olson_bruno-barcena_2015, title={Aerobic Hydrogen Production via Nitrogenase in Azotobacter vinelandii CA6}, volume={81}, ISSN={["1098-5336"]}, url={http://europepmc.org/abstract/med/25911479}, DOI={10.1128/aem.00679-15}, abstractNote={ABSTRACT}, number={13}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Noar, Jesse and Loveless, Telisa and Luis Navarro-Herrero, Jose and Olson, Jonathan W. and Bruno-Barcena, Jose M.}, year={2015}, month={Jul}, pages={4507–4516} }
 @article{leite_troxell_bruno-bárcena_hassan_2015, title={Biology of reactive oxygen species, oxidative stress, and antioxidants in lactic acid bacteria}, url={https://publons.com/publon/31684350/}, DOI={10.21775/9781910190098.14}, journal={Probiotics and Prebiotics: Current Research and Future Trends}, author={Leite, M. C. T. and Troxell, B. and Bruno-Bárcena, José M and Hassan, H. M.}, year={2015}, pages={205–218} }
 @article{bruno-barcena_azcarate-peril_2015, title={Galacto-oligosaccharides and colorectal cancer: Feeding our intestinal probiome}, volume={12}, ISSN={["1756-4646"]}, url={http://europepmc.org/abstract/med/25584074}, DOI={10.1016/j.jff.2014.10.029}, abstractNote={Prebiotics are ingredients selectively fermented by the intestinal microbiota that promote changes in the microbial community structure and/or their metabolism, conferring health benefits to the host. Studies show that β (1-4) galacto-oligosaccharides [β (1-4) GOS], lactulose and fructo-oligosaccharides increase intestinal concentration of lactate and short chain fatty acids, and stool frequency and weight, and they decrease fecal concentration of secondary bile acids, fecal pH, and nitroreductase and β-glucuronidase activities suggesting a clear role in colorectal cancer (CRC) prevention. This review summarizes research on prebiotics bioassimilation, specifically β (1-4) GOS, and their potential role in CRC. We also evaluate research that show that the impact of prebiotics on host physiology can be direct or through modulation of the gut intestinal microbiome, specifically the probiome (autochtonous beneficial bacteria), we present studies on a potential role in CRC progression to finally describe the current state of β (1-4) GOS generation for industrial production.}, journal={JOURNAL OF FUNCTIONAL FOODS}, author={Bruno-Barcena, Jose M. and Azcarate-Peril, M. Andrea}, year={2015}, month={Jan}, pages={92–108} }
 @article{sandoval-espinola_chinn_bruno-barcena_2015, title={Inoculum optimization of Clostridium beijerinckii for reproducible growth}, volume={362}, ISSN={1574-6968}, url={http://dx.doi.org/10.1093/femsle/fnv164}, DOI={10.1093/femsle/fnv164}, abstractNote={Spore-forming solventogenic Clostridium spp. are receiving renewed attention due to their butanol production abilities. However, there is an absence of literature describing the preparation of dense, vigorous and homogeneous seed cultures of Clostridium spp., guaranteeing reproducibility during fermentation. Therefore, we performed a series of growth experiments of Clostridium beijerinckii NCIMB 8052 and its offspring SA-1 to evaluate the influence of inoculum age (harvest time) on the subsequent population's maximum specific growth rate, as a signal of population homogeneity. The organisms were cultivated in Reinforced Clostridial Medium and supplemented sweet sorghum juice. The best inoculum ages coincided with the late-exponential growth phase: between 9 and 11 h in the conditions tested. Additionally, the harvest time was delayed up to 4 h by pre-adapting the seed culture with 0.75 g L(-1) butyric acid. These findings were validated by performing a series of bench-top batch fermentations showcasing reproducibility in growth kinetics with 95% confidence limits. Overall, these experiments allowed us to understand the transient nature of seed cultures of C. beijerinckii NCIMB 8052 and SA-1, while enabling reproducibility and consistent culture performance.}, number={19}, journal={FEMS Microbiology Letters}, publisher={Oxford University Press (OUP)}, author={Sandoval-Espinola, Walter J. and Chinn, Mari and Bruno-Barcena, Jose M.}, editor={Sauer, MichaelEditor}, year={2015}, month={Sep}, pages={fnv164} }
 @article{utturkar_klingeman_bruno-barcena_chinn_grunden_köpke_brown_2015, title={Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies}, volume={2}, ISSN={2052-4463}, url={http://dx.doi.org/10.1038/SDATA.2015.14}, DOI={10.1038/sdata.2015.14}, abstractNote={During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequence datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.}, number={1}, journal={Scientific Data}, publisher={Springer Science and Business Media LLC}, author={Utturkar, Sagar M and Klingeman, Dawn M and Bruno-Barcena, José M and Chinn, Mari S and Grunden, Amy M and Köpke, Michael and Brown, Steven D}, year={2015}, month={Apr} }
 @article{complete genome sequence of solvent-tolerant clostridium beijerinckii strain sa-1_2014, url={https://publons.com/publon/274767/}, DOI={10.1128/GENOMEA.01310-14.COPYRIGHT}, journal={Microbiology Resource Announcements}, year={2014} }
 @article{noar_makwana_bruno-bárcena_2014, title={Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1.}, volume={2}, url={http://europepmc.org/abstract/med/25523769}, DOI={10.1128/genomea.01310-14}, abstractNote={ABSTRACT}, number={6}, journal={Genome announcements}, author={Noar, J. and Makwana, S.T. and Bruno-Bárcena, J.M.}, year={2014} }
 @article{sandoval-espinola_makwana_chinn_thon_andrea azcarate-peril_bruno-barcena_2013, title={Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052}, volume={159}, ISSN={["1465-2080"]}, url={http://europepmc.org/abstract/med/24068240}, DOI={10.1099/mic.0.069534-0}, abstractNote={Production of butanol by solventogenic clostridia is controlled through metabolic regulation of the carbon flow and limited by its toxic effects. To overcome cell sensitivity to solvents, stress-directed evolution methodology was used three decades ago on Clostridium beijerinckii NCIMB 8052 that spawned the SA-1 strain. Here, we evaluated SA-1 solventogenic capabilities when growing on a previously validated medium containing, as carbon- and energy-limiting substrates, sucrose and the products of its hydrolysis d-glucose and d-fructose and only d-fructose. Comparative small-scale batch fermentations with controlled pH (pH 6.5) showed that SA-1 is a solvent hyper-producing strain capable of generating up to 16.1 g l(-1) of butanol and 26.3 g l(-1) of total solvents, 62.3 % and 63 % more than NCIMB 8052, respectively. This corresponds to butanol and solvent yields of 0.3 and 0.49 g g(-1), respectively (63 % and 65 % increase compared with NCIMB 8052). SA-1 showed a deficiency in d-fructose transport as suggested by its 7 h generation time compared with 1 h for NCIMB 8052. To potentially correlate physiological behaviour with genetic mutations, the whole genome of SA-1 was sequenced using the Illumina GA IIx platform. PCR and Sanger sequencing were performed to analyse the putative variations. As a result, four errors were confirmed and validated in the reference genome of NCIMB 8052 and a total of 10 genetic polymorphisms in SA-1. The genetic polymorphisms included eight single nucleotide variants, one small deletion and one large insertion that it is an additional copy of the insertion sequence ISCb1. Two of the genetic polymorphisms, the serine threonine phosphatase cbs_4400 and the solute binding protein cbs_0769, may possibly explain some of the observed physiological behaviour, such as rerouting of the metabolic carbon flow, deregulation of the d-fructose phosphotransferase transport system and delayed sporulation.}, number={PART 12}, journal={MICROBIOLOGY-SGM}, author={Sandoval-Espinola, Walter J. and Makwana, Satya T. and Chinn, Mari S. and Thon, Michael R. and Andrea Azcarate-Peril, M. and Bruno-Barcena, Jose M.}, year={2013}, month={Dec}, pages={2558–2570} }
 @article{noar_bruno-bárcena_2013, title={Complete Genome Sequences of Azotobacter vinelandii Wild-Type Strain CA and Tungsten-Tolerant Mutant Strain CA6.}, volume={6}, url={http://europepmc.org/abstract/med/23792740}, DOI={10.1128/genomea.00313-13}, abstractNote={ABSTRACT}, number={3}, journal={Genome announcements}, author={Noar, J.D. and Bruno-Bárcena, J.M.}, year={2013}, month={Jun} }
 @article{bruno-barcena_chinn_grunden_2013, title={Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide}, volume={1}, ISSN={2169-8287}, url={http://dx.doi.org/10.1128/genomeA.00628-13}, DOI={10.1128/genomea.00628-13}, abstractNote={ABSTRACT}, number={4}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Bruno-Barcena, J. M. and Chinn, M. S. and Grunden, A. M.}, year={2013}, month={Aug} }
 @article{dagher_azcarate-peril_bruno-barcena_2013, title={Heterologous Expression of a Bioactive beta-Hexosyltransferase, an Enzyme Producer of Prebiotics, from Sporobolomyces singularis}, volume={79}, ISSN={["1098-5336"]}, url={http://europepmc.org/abstract/med/23241974}, DOI={10.1128/aem.03491-12}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Dagher, Suzanne F. and Azcarate-Peril, M. Andrea and Bruno-Barcena, Jose M.}, year={2013}, month={Feb}, pages={1241–1249} }
 @article{heluane_evans_dagher_bruno-barcena_2011, title={Meta-Analysis and Functional Validation of Nutritional Requirements of Solventogenic Clostridia Growing under Butanol Stress Conditions and Coutilization of D-Glucose and D-Xylose}, volume={77}, ISSN={["1098-5336"]}, url={http://europepmc.org/abstract/med/21602379}, DOI={10.1128/aem.00116-11}, abstractNote={ABSTRACT}, number={13}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Heluane, Humberto and Evans, Matthew R. and Dagher, Sue F. and Bruno-Barcena, Jose M.}, year={2011}, month={Jul}, pages={4473–4485} }
 @misc{azcarate-peril_sikes_bruno-barcena_2011, title={The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?}, volume={301}, ISSN={["1522-1547"]}, url={http://europepmc.org/abstract/med/21700901}, DOI={10.1152/ajpgi.00110.2011}, abstractNote={Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States, and, even though 5–15% of the total CRC cases can be attributed to individual genetic predisposition, environmental factors could be considered major factors in susceptibility to CRC. Lifestyle factors increasing the risks of CRC include elevated body mass index, obesity, and reduced physical activity. Additionally, a number of dietary elements have been associated with higher or lower incidence of CRC. In this context, it has been suggested that diets high in fruit and low in meat might have a protective effect, reducing the incidence of colorectal adenomas by modulating the composition of the normal nonpathogenic commensal microbiota. In addition, it has been demonstrated that changes in abundance of taxonomic groups have a profound impact on the gastrointestinal physiology, and an increasing number of studies are proposing that the microbiota mediates the generation of dietary factors triggering colon cancer. High-throughput sequencing and molecular taxonomic technologies are rapidly filling the knowledge gaps left by conventional microbiology techniques to obtain a comprehensive catalog of the human intestinal microbiota and their associated metabolic repertoire. The information provided by these studies will be essential to identify agents capable of modulating the massive amount of gut bacteria in safe noninvasive manners to prevent CRC. Probiotics, defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” ( 219 ), are capable of transient modulation of the microbiota, and their beneficial effects include reinforcement of the natural defense mechanisms and protection against gastrointestinal disorders. Probiotics have been successfully used to manage infant diarrhea, food allergies, and inflammatory bowel disease; hence, the purpose of this review was to examine probiotic metabolic activities that may have an effect on the prevention of CRC by scavenging toxic compounds or preventing their generation in situ. Additionally, a brief consideration is given to safety evaluation and production methods in the context of probiotics efficacy.}, number={3}, journal={AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY}, author={Azcarate-Peril, M. Andrea and Sikes, Michael and Bruno-Barcena, Jose M.}, year={2011}, month={Sep}, pages={G401–G424} }
 @article{dagher_ragout_sineriz_bruno-barcena_2010, title={Cell Immobilization for Production of Lactic Acid: Biofilms Do It Naturally}, volume={71}, ISBN={["978-0-12-380993-3"]}, ISSN={["0065-2164"]}, url={http://europepmc.org/abstract/med/20378053}, DOI={10.1016/s0065-2164(10)71005-4}, abstractNote={Interest in natural cell immobilization or biofilms for lactic acid fermentation has developed considerably over the last few decades. Many studies report the benefits associated with biofilms as industrial methods for food production and for wastewater treatment, since the formation represents a protective means of microbial growth offering survival advantages to cells in toxic environments. The formation of biofilms is a natural process in which microbial cells adsorb to a support without chemicals or polymers that entrap the cells and is dependent on the reactor environment, microorganism, and characteristics of the support. These unique characteristics enable biofilms to cause chronic infections, disease, food spoilage, and devastating effects as in microbial corrosion. Their distinct resistance to toxicity, high biomass potential, and improved stability over cells in suspension make biofilms a good tool for improving the industrial economics of biological lactic acid production. Lactic acid bacteria and specific filamentous fungi are the main sources of biological lactic acid. Over the past two decades, studies have focused on improving the lactic acid volumetric productivity through reactor design development, new support materials, and improvements in microbial production strains. To illustrate the operational designs applied to the natural immobilization of lactic acid producing microorganisms, this chapter presents the results of a search for optimum parameters and how they are affected by the physical, chemical, and biological variables of the process. We will place particular emphasis upon the relationship between lactic acid productivity attained by various types of reactors, supports, media formulations, and lactic acid producing microorganisms.}, journal={ADVANCES IN APPLIED MICROBIOLOGY, VOL 71}, author={Dagher, Suzanne F. and Ragout, Alicia L. and Sineriz, Faustino and Bruno-Barcena, Jose M.}, year={2010}, pages={113–148} }
 @article{bruno-barcena_azcarate-peril_hassan_2010, title={Role of Antioxidant Enzymes in Bacterial Resistance to Organic Acids}, volume={76}, ISSN={["1098-5336"]}, url={http://europepmc.org/abstract/med/20305033}, DOI={10.1128/aem.02718-09}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Bruno-Barcena, Jose M. and Azcarate-Peril, M. Andrea and Hassan, Hosni M.}, year={2010}, month={May}, pages={2747–2753} }
 @article{carroll_andrus_bruno-barcena_klaenhammer_hassan_threadgill_2007, title={Anti-inflammatory properties of Lactobacillus gasseri expressing manganese superoxide dismutase using the interleukin 10-deficient mouse model of colitis}, volume={293}, ISSN={["1522-1547"]}, url={http://europepmc.org/abstract/med/17640978}, DOI={10.1152/ajpgi.00132.2007}, abstractNote={Emerging evidence has implicated reactive oxygen species (ROS) in the pathogenesis of inflammatory bowel disease (IBD). Although intestinal epithelial cells produce the ROS-neutralizing enzyme superoxide dismutase (SOD), the protein and activity levels of copper/zinc (Cu/Zn) and manganese (Mn) SOD are perturbed in inflamed tissues of IBD patients. Thus we investigated the ability of MnSOD from Streptococcus thermophilus to reduce colitis symptoms in interleukin (IL) 10-deficient mice using Lactobacillus gasseri as a delivery vehicle. Cohorts of 13–15 IL-10-deficient mice were left untreated or supplemented with native L. gasseri or L. gasseri expressing MnSOD for 4 wk. Colonic tissue was collected and inflammation was histologically scored. The presence of innate immune cells was investigated by immunohistochemistry and the host antioxidant response was determined by quantitative PCR. It was demonstrated that L. gasseri was stably maintained in mice for at least 3 days. L. gasseri producing MnSOD significantly reduced inflammation in IL-10-deficient mice compared with untreated controls ( P < 0.05), whereas the anti-inflammatory effects of both native and MnSOD producing L. gasseri were more pronounced in males. The anti-inflammatory effects of L. gasseri were associated with a reduction in the infiltration of neutrophils and macrophages. Transcripts of antioxidant genes were equivalent in colonic tissues obtained from control and probiotic-treated IL-10-deficient mice. This study demonstrates that L. gasseri producing MnSOD has significant anti-inflammatory activity that reduces the severity of colitis in the IL-10-deficient mouse.}, number={4}, journal={AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY}, author={Carroll, Ian M. and Andrus, Jason M. and Bruno-Barcena, Jose M. and Klaenhammer, Todd R. and Hassan, Hosni M. and Threadgill, Deborah S.}, year={2007}, month={Oct}, pages={G729–G738} }
 @article{pico-marco_navarro_bruno-barcena_2006, title={A closed loop exponential feeding law: Invariance and global stability analysis}, volume={16}, ISSN={["1873-2771"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-29144509840&partnerID=MN8TOARS}, DOI={10.1016/j.jprocont.2005.06.014}, abstractNote={This article addresses the computation of invariant control laws [A. Fradkov, I. Miroshnik, V. Nikiforov, Nonlinear and Adaptive Control of Complex Systems, Kluwer, 1999] for fed-batch fermenters represented by two standard models. It will be shown how to derive partial state feedbacks that, assuming ideal conditions and perfect model, keep the specific growth rate μ constant provided the initial conditions are adequate. The invariant control law is the closed loop version of the exponential feeding already suggested in several references as shown later. The paper presents an analysis of invariance and a study of global stability within the framework of partial stability. That is, stability with respect to some of the state variables. This enables us to treat the case with Haldane-like or non-monotonous kinetics.}, number={4}, journal={JOURNAL OF PROCESS CONTROL}, author={Pico-Marco, E and Navarro, JL and Bruno-Barcena, JM}, year={2006}, month={Apr}, pages={395–402} }
 @article{azcarate-peril_bruno-barcena_hassan_klaenhammer_2006, title={Transcriptional and functional analysis of oxalyl-coenzyme A (CoA) decarboxylase and formyl-CoA transferase genes from Lactobacillus acidophilus}, volume={72}, ISSN={["1098-5336"]}, url={http://europepmc.org/abstract/med/16517636}, DOI={10.1128/AEM.72.3.1891-1899.2006}, abstractNote={ABSTRACT}, number={3}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Azcarate-Peril, MA and Bruno-Barcena, JM and Hassan, HM and Klaenhammer, TR}, year={2006}, month={Mar}, pages={1891–1899} }
 @article{bruno-barcena_azcarate-peril_klaenhammer_hassan_2005, title={Marker-free chromosomal integration of the manganese superoxide dismutase gene (sodA) from Streptococcus thermophilus into Lactobacillus gasseri}, volume={246}, ISSN={["1574-6968"]}, url={http://europepmc.org/abstract/med/15869967}, DOI={10.1016/j.femsle.2005.03.044}, abstractNote={A strategy for functional gene replacement in the chromosome of Lactobacillus gasseri is described. The phospho-β-galactosidase II gene (lacII) was functionally replaced by the manganese superoxide dismutase (MnSOD) gene (sodA) from Streptococcus thermophilus, by adapting the insertional inactivation method described for lactobacilli [Russell, W.M. and Klaenhammer, T.R. 2001 Efficient system for directed integration into the Lactobacillus acidophilus and Lactobacillus gasseri chromosomes via homologous recombination. Appl. Environ. Microbiol. 67, 4361–4364]. L. gasseri carrying the heterologous sodA gene grew on lactose as efficiently as the wild-type parent. An active MnSOD was expressed in the transgenic strain, and the enzyme migrated on PAGE-SOD activity gels to the same position as that of MnSOD from S. thermophilus. The expression of MnSOD from a single copy of sodA integrated in the chromosome of L. gasseri provided enhanced tolerance to hydrogen peroxide, and extended the viability of carbon/energy starved cultures stored at 25 °C. This is the first report showing the successful utilization of the pORI plasmids system to generate marker-free gene integration in L. gasseri strains.}, number={1}, journal={FEMS MICROBIOLOGY LETTERS}, author={Bruno-Barcena, JM and Azcarate-Peril, MA and Klaenhammer, TR and Hassan, HM}, year={2005}, month={May}, pages={91–101} }
 @article{pérez-torrado_bruno-bárcena_matallana_2005, title={Monitoring stress-related genes during the process of biomass propagation of Saccharomyces cerevisiae strains used for wine making.}, volume={11}, url={http://europepmc.org/abstract/med/16269716}, DOI={10.1128/aem.71.11.6831-6837.2005}, abstractNote={ABSTRACT}, number={11}, journal={Applied and Environmental Microbiology}, author={Pérez-Torrado, R. and Bruno-Bárcena, J.M. and Matallana, E.}, year={2005}, month={Nov}, pages={6831–6837} }
 @article{bruno-barcena_andrus_libby_klaenhammer_hassan_2004, title={Expression of a heterologous manganese superoxide dismutase gene in intestinal lactobacilli provides protection against hydrogen peroxide toxicity}, volume={70}, ISSN={["1098-5336"]}, url={http://europepmc.org/abstract/med/15294805}, DOI={10.1128/AEM.70.8.4702-4710.2004}, abstractNote={ABSTRACT}, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Bruno-Barcena, JM and Andrus, JM and Libby, SL and Klaenhammer, TR and Hassan, HM}, year={2004}, month={Aug}, pages={4702–4710} }
 @article{ph regulation of enzyme production in aspergillus nidulans growing in aerobic batch fermenter._2002, volume={4}, url={http://europepmc.org/abstract/AGR/IND23282191}, DOI={10.1023/a:1014868726188}, number={7}, journal={Biotechnology letters}, year={2002}, month={Apr}, pages={567–572} }
 @article{continuous production of l(+)-lactic acid by lactobacillus casei in two-stage systems._1999, volume={3}, url={http://europepmc.org/abstract/med/10222580}, DOI={10.1007/s002530051397}, abstractNote={A two-stage two-stream chemostat system and a two-stage two-stream immobilized upflow packed-bed reactor system were used for the study of lactic acid production by Lactobacillus casei subsp casei. A mixing ratio of D12/D2 = 0.5 (D = dilution rate) resulted in optimum production, making it possible to generate continuously a broth with high lactic acid concentration (48 g l-1) and with a lowered overall content of initial yeast extract (5 g l-1), half the concentration supplied in the one-step process. In the two-stage chemostat system, with the first stage at pH 5.5 and 37 degrees C and a second stage at pH 6.0, a temperature change from 40 degrees C to 45 degrees C in the second stage resulted in a 100% substrate consumption at an overall dilution rate of 0.05 h-1. To increase the cell mass in the system, an adhesive strain of L. casei was used to inoculate two packed-bed reactors, which operated with two mixed feedstock streams at the optimal conditions found above. Lactic acid fermentation started after a lag period of cell growth over foam glass particles. No significant amount of free cells, compared with those adhering to the glass foam, was observed during continuous lactic acid production. The extreme values, 57.5 g l-1 for lactic acid concentration and 9.72 g l-1 h-1 for the volumetric productivity, in upflow packed-bed reactors were higher than those obtained for free cells (48 g l-1 and 2.42 g l-1 h-1) respectively and the highest overall L(+)-lactic acid purity (96.8%) was obtained in the two-chemostat system as compared with the immobilized-cell reactors (93%).}, number={3}, journal={Applied microbiology and biotechnology}, year={1999}, month={Mar}, pages={316–324} }
 @article{raya-tonetti_córdoba_bruno-bárcena_siñeriz_perotti_1999, title={Fluidized bed ion exchange for improving purification of lactic acid from fermentation.}, volume={3}, url={http://europepmc.org/abstract/AGR/IND21990968}, DOI={10.1023/a:1008909031995}, number={3}, journal={Biotechnology techniques.}, author={Raya-Tonetti, G. and Córdoba, P. and Bruno-Bárcena, J. and Siñeriz, F. and Perotti, N.}, year={1999}, month={Mar}, pages={201–205} }
 @article{chemostat production of plantaricin c by <i>lactobacillus plantarum</i> ll441_1998, url={https://publons.com/wos-op/publon/28290537/}, journal={Applied and Environmental Microbiology}, year={1998} }
 @article{chemostat production of plantaricin c by lactobacillus plantarum ll441_1998, volume={64}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-3543035172&partnerID=MN8TOARS}, number={9}, journal={Applied and Environmental Microbiology}, year={1998}, pages={3512–3514} }
 @article{chemostat production of plantaricin c by lactobacillus plantarum ll441._1998, volume={9}, url={http://europepmc.org/abstract/med/9726907}, journal={Applied and environmental microbiology}, year={1998}, month={Sep} }
 @article{fragile cells of lactobacillus casei suitable for plasmid dna isolation_1998, url={https://publons.com/publon/31684369/}, journal={Biotechnology Techniques}, year={1998} }
 @article{bruno-bárcena_azcárate-peril_ragout_font de valdez_raya_siñeriz_1998, title={Fragile cells of Lactobacillus casei suitable for plasmid DNA isolation.}, volume={2}, url={http://europepmc.org/abstract/AGR/IND20904300}, DOI={10.1023/a:1017139713930}, number={2}, journal={Biotechnology techniques.}, author={Bruno-Bárcena, J.M. and Azcárate-Peril, M.A. and Ragout, A. and Font De Valdez, G. and Raya, R. and Siñeriz, F.}, year={1998}, month={Feb}, pages={97–99} }
 @article{microbial physiology applied to process optimisation: lactic acid bacteria_1998, url={https://publons.com/publon/31684361/}, DOI={10.1007/978-94-017-0643-8_6}, journal={Advances in Bioprocess Engineering Volume Ii}, year={1998} }
 @article{de valdez_ragout_bruno-bárcena_diekmann_siñeriz_1997, title={Shifts in pH affect the maltose/glycerol co-fermentation by Lactobacillus reuteri}, volume={19}, url={https://publons.com/publon/31684362/}, DOI={10.1023/A:1018334714278}, number={7}, journal={Biotechnology Letters}, author={De Valdez, G.F. and Ragout, A. and Bruno-Bárcena, J.M. and Diekmann, H. and Siñeriz, F.}, year={1997}, pages={645–649} }