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Lactobacillus Genome

Matthew J Scarborough, Christopher E Lawson, Joshua J Hamilton, Timothy J Donohue, Daniel R Noguera
Biomanufacturing from renewable feedstocks can offset fossil fuel-based chemical production. One potential biomanufacturing strategy is production of medium-chain fatty acids (MCFA) from organic feedstocks using either pure cultures or microbiomes. While the set of microbes in a microbiome can often metabolize organic materials of greater diversity than a single species can and while the role of specific species may be known, knowledge of the carbon and energy flow within and between organisms in MCFA-producing microbiomes is only now starting to emerge...
November 2018: MSystems
Eugenia Pennacchietti, Chiara D'Alonzo, Luca Freddi, Alessandra Occhialini, Daniela De Biase
Neutralophilic bacteria have developed several strategies to overcome the deleterious effects of acid stress. In particular, the amino acid-dependent systems are widespread, with their activities overlapping, covering a rather large pH range, from 6 to <2. Recent reports showed that an acid resistance (AR) system relying on the amino acid glutamine (AR2_Q), the most readily available amino acid in the free form, is operative in Escherichia coli, Lactobacillus reuteri , and some Brucella species. This system requires a glutaminase active at acidic pH and the antiporter GadC to import L -glutamine and export either glutamate (the glutamine deamination product) or GABA...
2018: Frontiers in Microbiology
Jaeyoung Heo, Donghyun Shin, Sung Yong Chang, Paul Bogere, Mi Ri Park, Sangdon Ryu, Woong Ji Lee, Bohyun Yun, Hak Kyo Lee, Younghoon Kim, Sangnam Oh
In the current study, the probiotic potential of approximately 250 strains of lactic acid bacteria (LAB) isolated from piglet fecal samples were investigated; among them Lactobacillus plantarum strain JDFM LP11, which possesses significant probiotic potential, with enhanced acid/bile tolerance, attachment to porcine intestinal epithelial cells (IPEC-J2), and antimicrobial activity. The genetic characteristics of strain JDFM LP11 were explored by performing whole genome sequencing (WGS) using a PacBio system...
October 2018: Korean Journal for Food Science of Animal Resources
Fabien J Cousin, Rozenn Le Guellec, Victoria Chuat, Marion Dalmasso, Jean-Marie Laplace, Marina Cretenet
Lactobacillus, Pediococcus, Oenococcus and Leuconostoc are the main Lactic Acid Bacteria (LAB) genera present in cider as they are able to survive this hostile environment. LAB play a significant role in cider quality, for example in the process of malolactic fermentation, even though they can also be involved in spoilage of cider (production of biogenic amines, exopolysaccharides, off-flavours…). In this context a better monitoring of the fermentation process is a matter of interest to guarantee cider quality...
November 6, 2018: International Journal of Food Microbiology
Alessandra Fontana, Carla Zacconi, Lorenzo Morelli
Lactobacillus casei/Lactobacillus paracasei group of species contains strains adapted to a wide range of environments, from dairy products to intestinal tract of animals and fermented vegetables. Understanding the gene acquisitions and losses that induced such different adaptations, implies a comparison between complete genomes, since evolutionary differences spread on the whole sequence. This study compared 12 complete genomes of L. casei/paracasei dairy-niche isolates and 7 genomes of L. casei/paracasei isolated from other habitats (i...
2018: Frontiers in Microbiology
Md-Nafiz Hamid, Iddo Friedberg
Motivation: Antibiotic resistance constitutes a major public health crisis, and finding new sources of antimicrobial drugs is crucial to solving it. Bacteriocins, which are bacterially-produced antimicrobial peptide products, are candidates for broadening the available choices of antimicrobials. However, the discovery of new bacteriocins by genomic mining is hampered by their sequences' low complexity and high variance, which frustrates sequence similarity-based searches. Results: Here we use word embeddings of protein sequences to represent bacteriocins, and apply a word embedding method that accounts for amino acid order in protein sequences, to predict novel bacteriocins from protein sequences without using sequence similarity...
November 10, 2018: Bioinformatics
Shao K Huang, Kun T Ye, Wei F Huang, Bi H Ying, Xin Su, Li H Lin, Jiang H Li, Yan P Chen, Ji L Li, Xiu L Bao, Jian Z Hu
The gut microbiota plays an essential role in the health of bees. To elucidate the effect of feed and Nosema ceranae infection on the gut microbiota of honey bee (Apis cerana), we used 16S rRNA sequencing to survey the gut microbiota of honey bee workers fed with sugar water or beebread and inoculated with or without N. ceranae. The gut microbiota of A. cerana is dominated by Serratia , Snodgrassella , and Lactobacillus genera. The overall gut microbiota diversity was show to be significantly differential by feeding type...
November 2018: MSystems
Mustafa Özçam, Restituto Tocmo, Jee-Hwan Oh, Amin Afrazi, Joshua D Mezrich, Stefan Roos, Jan Claesen, Jan-Peter van Pijkeren
Mechanistic understanding of microbe-host interactions is critical to developing therapeutic strategies for targeted modulation of the host immune system. Different members of the gut symbiont species Lactobacillus reuteri modulate host health by, for example, reduction of intestinal inflammation. Previously, it was shown that L. reuteri activates the aryl-hydrocarbon receptor (AhR)-a ligand-activated transcription factor that plays an important role in the mucosal immune system-by production of tryptophan catabolites...
November 2, 2018: Applied and Environmental Microbiology
Daniel Wüthrich, Stefan Irmler, Hélène Berthoud, Barbara Guggenbühl, Elisabeth Eugster, Rémy Bruggmann
Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei - a flavor-enhancing adjunct culture species - can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L...
2018: Frontiers in Microbiology
Gyu-Sung Cho, Claudia Cappello, Katrin Schrader, Olakunle Fagbemigum, Folarin A Oguntoyinbo, Claudia Csovcsics, Niels Rösch, Jan Kabisch, Horst Neve, Wilhelm Bockelmann, Karlis Briviba, Monica Modesto, Elisabetta Cilli, Paola Mattarelli, Charles M A P Franz
The lactobacilli associated with a fermented goat milk product from Tajikistan were isolated to characterize their technological properties and antibiotic resistances in order to assess their suitability for development as starter cultures. In this study, twenty three strains were identified by 16S rRNA sequencing as typical dairy-associated lactic acid bacterial strains, i.e. L. plantarum , L. pentosus , L. delbrueckii , L. helveticus and L. paracasei strains. These strains were generally susceptible to most antibiotics tested in this study and this allowed a selection of strains as safe starters...
October 19, 2018: Journal of Microbiology and Biotechnology
Ilenia Campedelli, Harsh Mathur, Elisa Salvetti, Siobhán Clarke, Mary C Rea, Sandra Torriani, R Paul Ross, Colin Hill, Paul W O'Toole
Lactobacillus species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for Qualified Presumption of Safety status, the safety of Lactobacillus species and their carriage of antibiotic resistance (AR) genes is under continuing ad hoc review. To comprehensively update the identification of AR in the genus Lactobacillus , we determined the antibiotic susceptibility patterns of 182 Lactobacillus type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes...
October 26, 2018: Applied and Environmental Microbiology
Bowen Yan, Yuan Yao Chen, Weilan Wang, Jianxin Zhao, Wei Chen, Michael Gänzle
Kokumi-active γ-glutamyl dipeptides (γ-GPs) accumulate in fermented food. γ-Glutamyl transferase, glutaminase, glutathione synthetase, and γ-glutamyl cysteine ligase (GCL) may synthesize γ-GPs. The genome of Lactobacillus reuteri encodes GCL but not glutathione synthetase or glutamyl transferase; therefore, this study investigated the role of GCL in γ-GP synthesis by L. reuteri LTH5448. Phylogenomic analysis of gcl in lactobacilli demonstrated that three genes coding for GCL are present in L. reuteri; two of these are present in L...
November 7, 2018: Journal of Agricultural and Food Chemistry
Eldho Paul, Abhishek Albert, Sasikumar Ponnusamy, Sangeetha Venkatesan, Selvam Govindan Sadasivam
Lactobacillus plantarum WCFS1 (L. plantarum WCFS1) is commonly used as a potential cell factory because of its 'generally recognized as safe' status. The plasmid instability and the presence of antibiotic selection marker complicate the application of genetically modified L. plantarum in human clinical trials. In the present study, we aimed to integrate oxalate decarboxylase (oxdC) gene of Bacillus subtilis origin by targeted chromosomal mutation in L. plantarum using mobile genetic element Ll.LtrB as a therapeutic tool against calcium oxalate stone disease...
October 22, 2018: Archives of Microbiology
Narendrakumar M Chaudhari, Anupam Gautam, Vinod Kumar Gupta, Gagneet Kaur, Chitra Dutta, Sandip Paul
The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM ( - a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project...
2018: Frontiers in Microbiology
Zigui Chen, Yun Kit Yeoh, Mamie Hui, Po Yee Wong, Martin C W Chan, Margaret Ip, Jun Yu, Robert D Burk, Francis K L Chan, Paul K S Chan
Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques (N = 116) and compared the compositions with the healthy communities from Human Microbiome Project. The macaque microbiota was dominated by Bacteroidetes, Firmicutes and Proteobacteria; however, there were marked differences in phylotypes enriched across body sites indicative of strong niche specialization...
October 22, 2018: Scientific Reports
Marion E Fraunhofer, Andreas J Geißler, Jürgen Behr, Rudi F Vogel
Lactobacillus (L.) brevis represents a versatile, ubiquitistic species of lactic acid bacteria, occurring in various foods, as well as plants and intestinal tracts. The ability to deal with considerably differing environmental conditions in the respective ecological niches implies a genomic adaptation to the particular requirements to use it as a habitat beyond a transient state. Given the isolation source, 24 L. brevis genomes were analyzed via comparative genomics to get a broad view of the genomic complexity and ecological versatility of this species...
October 19, 2018: Current Microbiology
Di Xu, Julia Bechtner, Jürgen Behr, Lara Eisenbach, Andreas J Geißler, Rudi F Vogel
Water kefir is a traditional fermented beverage made from sucrose, water, kefir granules, dried or fresh fruits. In our water kefir granules, Lactobacillus (L.) hordei is one of the predominant lactic acid bacteria (LAB) species of this presumed symbiotic consortium. It faces abundant sucrose versus limitation of amino- and fatty acids in an acidic environment. Sequencing of the genome of L. hordei TMW 1.1822 revealed one chromosome plus three plasmids. The size of the chromosome was 2.42 Mbp with a GC content of 35% GC and 2461 predicted coding sequences...
October 9, 2018: International Journal of Food Microbiology
Jason W Arnold, Joshua B Simpson, Jeffery Roach, Jose M Bruno-Barcena, M Andrea Azcarate-Peril
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...
October 16, 2018: Nutrients
Lois Bayigga, David P Kateete, Deborah J Anderson, Musa Sekikubo, Damalie Nakanjako
The vaginal microbial community ("microbiota") is a key component of the reproductive health of women, providing protection against urogenital infections. In Sub-Saharan Africa, there is a high prevalence of bacterial vaginosis (BV), a condition defined by bacterial overgrowth and a shift away from a lactobacillus-dominated profile towards increased percentages of strict anaerobic species. BV is associated with an increased risk of HIV acquisition and transmission, as well as an increased risk of acquiring other sexually transmitted infections , pre-term births and pelvic inflammatory disease...
October 12, 2018: American Journal of Obstetrics and Gynecology
Paulraj Kanmani, Leonardo Albarracin, Hisakazu Kobayashi, Elvira Maria Hebert, Lucila Saavedra, Ryoya Komatsu, Brian Gatica, Ayako Miyazaki, Wakako Ikeda-Ohtsubo, Yoshihito Suda, Hisashi Aso, Shintaro Egusa, Takashi Mishima, Alexis Salas-Burgos, Hideki Takahashi, Julio Villena, Haruki Kitazawa
In lactic acid bacteria, the synthesis of exopolysaccharides (EPS) has been associated with some favorable technological properties as well as health-promoting benefits. Research works have shown the potential of EPS produced by lactobacilli to differentially modulate immune responses. However, most studies were performed in immune cells and few works have concentrated in the immunomodulatory activities of EPS in non-immune cells such as intestinal epithelial cells. In addition, the cellular and molecular mechanisms involved in the immunoregulatory effects of EPS have not been studied in detail...
2018: Frontiers in Immunology
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