Genomic analysis of Enterococcus durans LAB18S, a potential probiotic strain isolated from cheese

Gut microbiota exerts a fundamental role in human health and increased evidence supports the beneficial role of probiotic microorganisms in the maintenance of intestinal health. Enterococcus durans LAB18S was previously isolated from soft cheese and showed some desirable in vitro probiotic properties, for that reason its genome was sequenced and evaluated for genes that can be relevant for probiotic activity and are involved in selenium metabolism. Genome sequencing was performed using the Illumina MiSeq System. A variety of genes potentially associated with probiotic properties, including adhesion capability, viability at low pH, bile salt resistance, antimicrobial activity, and utilization of prebiotic fructooligosaccharides (FOS) were identified. The strain showed tolerance to acid pH and bile salts, exhibited antimicrobial activity and thrived on prebiotic oligosaccharides. Six genes involved in selenium metabolism were predicted. Analysis of the SECIS element showed twelve known selenoprotein candidates. E. durans LAB18S was the only food isolate showing absence of plasmids, virulence and antimicrobial resistance genes, when compared with other 30 E. durans genomes. The results of this study provide evidence supporting the potential of E. durans LAB18S as alternative for probiotic formulations

Microbial community and physicochemical characterization of kombuchas produced and marketed in Brazil

Kombucha has recently become popular in the Brazilian beverage market as a healthy alternative to soft drinks. However, little is known about the microbial composition and physicochemical characteristics of products available on the market. To investigate the microbial profile of kombuchas, high-throughput sequencing of the 16S rRNA and ITS genes, in samples belonging to six brands was utilized. In addition, the drinks were characterized based on the physicochemical parameters of pH, total acidity and alcohol content. Through the metagenetic analysis, the most abundant prokaryotic species identified were Liquorilactobacillus nagelii, Oenococcus oeni, Komagataeibacter rhaeticus, Liquorilactobacillus ghanensis, Gluconobacter oxydans, Komagataeibacter saccharivorans, Acetobacter peroxydans and Pantoea stewartii, while the mainly eukaryotic species were Dekkera bruxellensis, Dekkera anomala, Saccharomyces cerevisiae and Lanchancea fermentati. Interestingly, we identified six different oligotypes of D. bruxellensis, showing a wide diversity of strains belonging to this species. The results obtained for the physicochemical analyses, within the shelf life of the products, presented a range between 2.88 ± 0.06 and 3.43 ± 0.04 of pH, values between 1.80 ± 0.59 and 4.86 ± 0.72 for the total titratable acidity and 1.03 ± 0.24 to 2.54 ± 0.39 referring to alcohol content, demonstrating significant differences between brand. In addition, all samples had alcohol content above 0.5%, resulting in the classification of alcoholic beverages, which need proper labelling. The data generated in this work helped to understand the composition of the kombuchas available in the Brazilian market, as well as in the development of the identity and quality standard of the drink

Evaluating Sardinella brasiliensis quality indicators through the quantification of histamine and bacterial communities

Primarily formed by the microbial decarboxylation of the amino acid histidine, histamine is the leading global cause of food poisoning from fish consumption worldwide. In the present work, the quality of 12 fresh and 12 frozen marketed sardines (Sardinella brasiliensis) were evaluated for histamine concentration using Highperformance Liquid Chromatography with Diode-Array Detection (HPLC-DAD), while the detection and quantification of histamine-producing bacteria were performed via quantitative Polymerase Chain Reaction (qPCR), and the microbiota composition of sardines was assessed through amplification of the 16S rRNA gene using highthroughput sequencing (HTS). According to the results obtained by HPLC-DAD, histamine concentration ranged from 226.14 to 583.87 mg kg 1. The histidine decarboxylase (hdc) genes from gram-negative bacteria (Morganella morganii, and Enterobacter aerogenes) were identified. The most abundant microorganisms present in fresh sardines belong to the genera Macrococcus spp., Acinetobacter spp., and Pseudomonas spp., while the genera Phyllobacterium spp., Pseudomonas spp., and Acinetobacter spp. were most abundant in frozen sardines

Zika virus envelope domain III recombinant protein delivered with saponin-based nanoadjuvant from Quillaja brasiliensis enhances anti-zika immune responses, including neutralizing antibodies and splenocyte proliferation

Nanoadjuvants that combine immunostimulatory properties and delivery systems reportedly bestow major improvements on the efficacy of recombinant, protein-based vaccines. Among these, self-assembled micellar formulations named ISCOMs (immune stimulating complexes) show a great ability to trigger powerful immunological responses against infectious pathogens. Here, a nanoadjuvant preparation, based on saponins from Quillaja brasiliensis, was evaluated together with an experimental Zika virus (ZIKV) vaccine (IQB80-zEDIII) and compared to an equivalent vaccine with alum as the standard adjuvant. The preparations were administered to mice in two doses (on days zero and 14) and immune responses were evaluated on day 28 post-priming. Serum levels of anti-Zika virus IgG, IgG1, IgG2b, IgG2c, IgG3 were significantly increased by the nanoadjuvant vaccine, compared to the mice that received the alum-adjuvanted vaccine or the unadjuvanted vaccine. In addition, a robust production of neutralizing antibodies and in vitro splenocyte proliferative responses were observed in mice immunized with IQB80-zEDIII nanoformulated vaccine. Therefore, the IQB80-zEDIII recombinant preparation seems to be a suitable candidate vaccine for ZIKV. Overall, this study identified saponin-based delivery systems as an adequate adjuvant for recombinant ZIKV vaccines and has important implications for recombinant protein-based vaccine formulations against other flaviviruses and possibly enveloped viruses

Changes in the ceca microbiota of broilers vaccinated for coccidiosis or supplemented with salinomycin

The objective of this study was to characterize differences in the cecal microbiota of chickens vaccinated for coccidiosis or receiving salinomycin in the diet. In this study, 140 male 1-day-old broiler chickens were divided in 2 groups: vaccine group (live vaccine) vaccinated at the first day and salinomycin group (125 ppm/kg since the first day until 35 d of age). Each treatment was composed for 7 replicates of 10 birds per pen. At 28 d, the cecal content of one bird per replicate was collected for microbiota analysis. The genetic sequencing was conducted by the Miseq Illumina platform. Vaccine group showed lower body weight, weight gain, and poorer feed conversion in the total period (P 0.05). The richness distribution in the salinomycin group was larger and more uniform than the vaccinated birds. Salinomycin group was related to the enrichment of Bacteroidetes, whereas Firmicutes and Proteobacteria phyla were in greater proportions in the vaccine group. The last phylum includes a wide variety of pathogenic bacteria. The vaccine did not decrease the species richness but decreased the percentage of Bacteroidetes, a phylum composed by genera that produce short-chain fatty acids improving intestinal health. Vaccine group also had higher Proteobacteria phylum, which may help explain its poorer performance

Genomic characterization of novel circular ssDNA viruses from insectivorous bats in southern Brazil

Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirusand the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop

Comparative analysis of the upper respiratory bacterial communities of pigs with or without respiratory clinical signs : from weaning to finishing phase

A prospective study was conducted to identify bacterial communities in the nasal and laryngeal cavities of pigs with or without clinical signs of respiratory disease in a longitudinal fashion, from weaning to the finishing phase. Nasal and laryngeal swabs were collected from asymptomatic pigs (n = 30), as well as from pigs with clinical signs of respiratory disease (n = 30) at the end of the weaning (T1—33 days) phase, end of the nursery phase (T2—71 days), and finishing (T3—173 days). Total DNA was extracted from each sample, and the V4 hypervariable region of the 16S rRNA gene was amplified and sequenced with the Illumina MiSeq platform. Principal coordinates analysis indicated no significant differences between the nasal and laryngeal bacterial communities. Nevertheless, the microbiota composition in the upper respiratory tract (URT) was clearly distinct between animals, with or without signs of respiratory disease, particularly at post-weaning and the end of nursery. In pigs with clinical signs of respiratory disease, Actinobacillus, Streptococcus Porphyromonas, Veillonella, and an unclassified genus of Pasteurellaceae were more abundant than in pigs with no signs. Metabolic prediction identified 28 differentially abundant pathways, mainly related to carbohydrate, energy, amino acid, anaerobic, and nucleotide metabolism in symptomatic pigs (especially in T2). These findings provide evidence that the composition of the URT bacterial microbiota differs significantly when comparing pigs with or without respiratory clinical signs after weaning, and this difference is maintained in the nursery phase; such differences, however, were not evident at the finishing phase

Evolution of the spontaneous sourdoughs microbiota prepared with organic or conventional whole wheat flours from South Brazil

The purpose of this study was to compare the composition and stability of bacteria and fungi communities during the propagation of sourdoughs prepared with organic or conventional whole wheat (Triticum aestivum) flours from South Brazil. Sourdoughs were prepared and samples were collected during different fermentation times (0 to 216 h). Total DNA of sourdough samples were extracted and the 16S rRNA gene and Internal Transcribed Spacer region were sequenced by MiSeq-Illumina. A total of 43 and 56 OTUs were identified and defined as core taxa in the bacterial and fungal communities, respectively. The analysis revealed increases in the relative abundances of the lactic acid (Pediococcus pentosaceus, Weissella hellenica and Limosilactobacillus pontis) and acetic acid bacteria (Gluconobacter frateurii and Acetobacter tropicalis) during the sourdough propagation. The filaments fungi, Alternaria tenuissima, Fusarium culmorum, Fusarium petersiae and Microdochium seminicola remained more stable in organic than conventional during propagation cycles. After 216 h of fermentation, both sourdoughs were dominated by acid- and salt-tolerant yeast Issatchenkia orientalis (syn Pichia kudriavzevii, and Candida glycerinogenes). In conclusion, there were no significant differences in microbial communities among the sourdough samples. This study revealed that both flours contain autochthonous LAB, AAB, and yeasts with biotechnological applications in sourdough bread-making

Complete genome sequences of two bovine alphaherpesvirus 5 subtype C strains from southeast Brazil

Bovine alphaherpesvirus 5 causes meningoencephalitis in cattle, belongs to the Herpesviridae family, and can be divided into subtypes a, b, and c. Limited information is available about subtype c. Here, we report the complete genome sequences of two strains, P160/96, and ISO97/45, isolated from cattle in southeast Brazil