Healthcare and Epidemiological Surveillance Costs of Hepatitis A Outbreaks in Spain in Regions with and without Universal Hepatitis A Vaccination of Children during 2010-2018.

The aim of this study was to evaluate and compare hepatitis A outbreak-associated healthcare and epidemiological surveillance costs in Spain in two types of autonomous regions during 2010-2018: (1) regions with a prevention strategy based on universal hepatitis A vaccination of children and vaccination of high-risk population groups (Catalonia) and (2) regions with a prevention strategy based on vaccinating high-risk population groups (Castile and Leon, Murcia, Navarra, Community of Madrid, Community of Valencia). Healthcare costs were determined based on the resources used to treat hepatitis A outbreak-associated cases and hospitalizations. Epidemiological surveillance costs were calculated from the resources used during surveillance activities. The ratios for total, healthcare and epidemiological surveillance costs (regions without universal hepatitis A vaccination of children vs. Catalonia) were used to compare the two hepatitis A prevention strategies. From 2010 to 2018, the total, healthcare and epidemiological surveillance costs per million population were 1.75 times (EUR 101,671 vs. EUR 58,032), 1.96 times (EUR 75,500 vs. EUR 38,516) and 1.34 times greater (EUR 26,171 vs. EUR 19,515) in regions without universal hepatitis A vaccination of children than in Catalonia, respectively. The ratios tended to increase over time during 2010-2018. In 2015-2018, total, healthcare and epidemiological surveillance costs per million population were 2.68 times (EUR 69,993 vs. EUR 26,158), 2.86 times (EUR 53,807 vs. EUR 18,825) and 2.21 times greater (EUR 16,186 vs. EUR 7333) in regions without universal hepatitis A vaccination of children than in Catalonia, respectively. These findings suggest that universal hepatitis A vaccination of children could reduce hepatitis A outbreak-associated costs.

Integrated transcriptomic landscape of the effect of anti-steatotic treatments in high-fat diet mouse models of non-alcoholic fatty liver disease.

High-fat diet (HFD) mouse models are widely used in research to develop medications to treat non-alcoholic fatty liver disease (NAFLD), as they mimic the steatosis, inflammation, and hepatic fibrosis typically found in this complex human disease. The aims of this study were to identify a complete transcriptomic signature of these mouse models and to characterize the transcriptional impact exerted by different experimental anti-steatotic treatments. For this reason, we conducted a systematic review and meta-analysis of liver transcriptomic studies performed in HFD-fed C57BL/6J mice, comparing them with control mice and HFD-fed mice receiving potential anti-steatotic treatments. Analyzing 21 studies broaching 24 different treatments, we obtained a robust HFD transcriptomic signature that included 2,670 differentially expressed genes and 2,567 modified gene ontology biological processes. Treated HFD mice generally showed a reversion of this HFD signature, although the extent varied depending on the treatment. The biological processes most frequently reversed were those related to lipid metabolism, response to stress, and immune system, whereas processes related to nitrogen compound metabolism were generally not reversed. When comparing this HFD signature with a signature of human NAFLD progression, we identified 62 genes that were common to both; 10 belonged to the group that were reversed by treatments. Altered expression of most of these 10 genes was confirmed in vitro in hepatocytes and hepatic stellate cells exposed to a lipotoxic or a profibrogenic stimulus, respectively. In conclusion, this study provides a vast amount of information about transcriptomic changes induced during the progression and regression of NAFLD and identifies some relevant targets. Our results may help in the assessment of treatment efficacy, the discovery of unmet therapeutic targets, and the search for novel biomarkers. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Assessing the Ecotoxicity of Eight Widely Used Antibiotics on River Microbial Communities.

Global prevalence of antibiotic residues (ABX) in rivers requires ecotoxicological impact assessment. River microbial communities serve as effective bioindicators for this purpose. We quantified the effects of eight commonly used ABXs on a freshwater river microbial community using Biolog EcoPlates™, enabling the assessment of growth and physiological profile changes. Microbial community characterization involved 16S rRNA gene sequencing. The river community structure was representative of aquatic ecosystems, with the prevalence of Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. Our findings reveal that all ABXs at 100 µg/mL reduced microbial community growth and metabolic capacity, particularly for polymers, carbohydrates, carboxylic, and ketonic acids. Chloramphenicol, erythromycin, and gentamicin exhibited the highest toxicity, with chloramphenicol notably impairing the metabolism of all studied metabolite groups. At lower concentrations (1 µg/mL), some ABXs slightly enhanced growth and the capacity to metabolize substrates, such as carbohydrates, carboxylic, and ketonic acids, and amines, except for amoxicillin, which decreased the metabolic capacity across all metabolites. We explored potential correlations between physicochemical parameters and drug mechanisms to understand drug bioavailability. Acute toxicity effects at the river-detected low concentrations (ng/L) are unlikely. However, they may disrupt microbial communities in aquatic ecosystems. The utilization of a wide array of genetically characterized microbial communities, as opposed to a single species, enables a better understanding of the impact of ABXs on complex river ecosystems.

A deep transcriptome meta-analysis reveals sex differences in multiple sclerosis.

BACKGROUND: Multiple sclerosis (MS), a chronic auto-immune, inflammatory, and degenerative disease of the central nervous system, affects both males and females; however, females suffer from a higher risk of developing MS (2-3:1 ratio relative to males). The precise sex-based factors influencing risk of MS are currently unknown. Here, we explore the role of sex in MS to identify molecular mechanisms underlying observed MS sex differences that may guide novel therapeutic approaches tailored for males or females. METHODS: We performed a rigorous and systematic review of genome-wide transcriptome studies of MS that included patient sex data in the Gene Expression Omnibus and ArrayExpress databases following PRISMA statement guidelines. For each selected study, we analyzed differential gene expression to explore the impact of the disease in females (IDF), in males (IDM) and our main goal: the sex differential impact of the disease (SDID). Then, for each scenario (IDF, IDM and SDID) we performed 2 meta-analyses in the main tissues involved in the disease (brain and blood). Finally, we performed a gene set analysis in brain tissue, in which a higher number of genes were dysregulated, to characterize sex differences in biological pathways. RESULTS: After screening 122 publications, the systematic review provided a selection of 9 studies (5 in blood and 4 in brain tissue) with a total of 474 samples (189 females with MS and 109 control females; 82 males with MS and 94 control males). Blood and brain tissue meta-analyses identified, respectively, 1 (KIR2DL3) and 13 (ARL17B, CECR7, CEP78, IFFO2, LOC401127, NUDT18, RNF10, SLC17A5, STMP1, TRAF3IP2-AS1, UBXN2B, ZNF117, ZNF488) MS-associated genes that differed between males and females (SDID comparison). Functional analyses in the brain revealed different altered immune patterns in females and males (IDF and IDM comparisons). The pro-inflammatory environment and innate immune responses related to myeloid lineage appear to be more affected in females, while adaptive responses associated with the lymphocyte lineage in males. Additionally, females with MS displayed alterations in mitochondrial respiratory chain complexes, purine, and glutamate metabolism, while MS males displayed alterations in stress response to metal ion, amine, and amino acid transport. CONCLUSION: We found transcriptomic and functional differences between MS males and MS females (especially in the immune system), which may support the development of new sex-based research of this disease. Our study highlights the importance of understanding the role of biological sex in MS to guide a more personalized medicine.

Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite.

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called "RNASeq" and "VariantSeq" to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, "RNASeq" and "VariantSeq" are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. "RNASeq" and "VariantSeq" are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. "RNASeq" and "VariantSeq" also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software.

Impact of eight widely consumed antibiotics on the growth and physiological profile of natural soil microbial communities.

Antibiotics' (ATBs) occurrence in soil ecosystems has a relevant effect in the structure and functionality of edaphic microbial communities, mainly because of their amendment with manure and biosolids that alter their key ecological functions. In this study, the impact of eight widely consumed ATBs on a natural soil microbial community, characterized through 16 S rRNA gene sequencing, was evaluated. Changes induced by the ATBs in the growth of the soil microbiota and in the community-level physiological profiling (CLPP), using Biolog EcoPlates™, were measured as endpoint. The eight assayed ATBs lead to a significant decrease in the growth of soil microbial communities in a dose-dependent way, ordered by its effect as follows: chloramphenicol > gentamycin > erythromycin > ampicillin > penicillin > amoxicillin > tetracycline > streptomycin. Chloramphenicol, gentamycin, and erythromycin adversely affected the physiological profile of the soil community, especially its ability to metabolize amino acids, carboxylic and ketonic acids and polymers. The analysis of the relationship between the physico-chemical properties of ATBs, as well as their mechanism of action, revealed that, except for the aminoglycosides, each ATB is influenced by a different physico-chemical parameters, even for ATBs of the same family. Significant effects were detected from 100 µg mL to 1, concentrations that can be found in digested sludge, biosolids and even in fertilized soils after repeated application of manure, so cumulative and long-term effects of these antibiotics on soil environment cannot be ruled out.

Biological relevance of Granzymes A and K during E. coli sepsis.

Aims: Recent in vitro findings suggest that the serine protease Granzyme K (GzmK) may act as a proinflammatory mediator. However, its role in sepsis is unknown. Here we aim to understand the role of GzmK in a mouse model of bacterial sepsis and compare it to the biological relevance of Granzyme A (GzmA). Methods: Sepsis was induced in WT, GzmA-/- and GzmK-/- mice by an intraperitoneal injection of 2x108 CFU from E. coli. Mouse survival was monitored during 5 days. Levels of IL-1α, IL-1ß, TNFα and IL-6 in plasma were measured and bacterial load in blood, liver and spleen was analyzed. Finally, profile of cellular expression of GzmA and GzmK was analyzed by FACS. Results: GzmA and GzmK are not involved in the control of bacterial infection. However, GzmA and GzmK deficient mice showed a lower sepsis score in comparison with WT mice, although only GzmA deficient mice exhibited increased survival. GzmA deficient mice also showed reduced expression of some proinflammatory cytokines like IL1-α, IL-ß and IL-6. A similar result was found when extracellular GzmA was therapeutically inhibited in WT mice using serpinb6b, which improved survival and reduced IL-6 expression. Mechanistically, active extracellular GzmA induces the production of IL-6 in macrophages by a mechanism dependent on TLR4 and MyD88. Conclusions: These results suggest that although both proteases contribute to the clinical signs of E. coli-induced sepsis, inhibition of GzmA is sufficient to reduce inflammation and improve survival irrespectively of the presence of other inflammatory granzymes, like GzmK.

Isolation of Candida auris in large hospitals in the Autonomous Community of Valencia; population-based study (2013-2017).

BACKGROUND: Candida auris is an emerging multidrug-resistant and highly virulent yeast that spreads easily among patients. AIMS: To describe the characteristics of candidemia caused by C. auris in the southeast of Spain (Autonomous Community of Valencia - ACV) through a 5-year population-based study. METHODS: An analysis of all the episodes of candidemia diagnosed in the ACV, with approximately 4,500,000 inhabitants, during 2013-2017, was done. Data were obtained from the Epidemiological Surveillance Valencian Network, a network that collects all the microbiological data from the hospitals in the study region. RESULTS: Based on the records, 1.9% of the isolates recovered from the positive blood cultures (corresponding to 1789 patients) were yeasts. This implies an annual rate of 7.09 cases/100,000 inhabitants. Of the 23 yeast species isolated, Candida albicans was the most frequent (37.3%), showing a higher frequency than Candida parapsilosis (28.4%) and Candida glabrata (15.6%) (p<0.0001). It is remarkable the emergence of C. auris during 2016 and 2017, as this species became the fourth more prevalent in 2016 (9.2%), and the third in 2017 (15.7%). Fungemia was more common in hospitals with >500 beds (63.3% versus 36.7% in small hospitals) (p<0.0001), and C. auris was mostly isolated in large hospitals (8.5% versus 0.3%); its incidence was higher in autumn and among the age group of 65-84 years. CONCLUSIONS: The information about the local epidemiology of candidemia is essential in order to decide the best empirical treatment approach. This study reports the novel presence of C. auris in large hospitals. This pathogen has usually resistance to several antifungals and causes severe fungemia, so the results of this work reveal the need to monitor the presence of this species systematically.

Nutrigenetic Interactions Might Modulate the Antioxidant and Anti-Inflammatory Status in Mastiha-Supplemented Patients With NAFLD.

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease with no therapeutic consensus. Oxidation and inflammation are hallmarks in the progression of this complex disease, which also involves interactions between the genetic background and the environment. Mastiha is a natural nutritional supplement known to possess antioxidant and anti-inflammatory properties. This study investigated how a 6-month Mastiha supplementation (2.1 g/day) could impact the antioxidant and inflammatory status of patients with NAFLD, and whether genetic variants significantly mediate these effects. We recruited 98 patients with obesity (BMI ≥ 30 kg/m2) and NAFLD and randomly allocated them to either the Mastiha or the placebo group for 6 months. The anti-oxidative and inflammatory status was assessed at baseline and post-treatment. Genome-wide genetic data was also obtained from all participants, to investigate gene-by-Mastiha interactions. NAFLD patients with severe obesity (BMI > 35kg/m2) taking the Mastiha had significantly higher total antioxidant status (TAS) compared to the corresponding placebo group (P value=0.008). We did not observe any other significant change in the investigated biomarkers as a result of Mastiha supplementation alone. We identified several novel gene-by-Mastiha interaction associations with levels of cytokines and antioxidant biomarkers. Some of the identified genetic loci are implicated in the pathological pathways of NAFLD, including the lanosterol synthase gene (LSS) associated with glutathione peroxidase activity (Gpx) levels, the mitochondrial pyruvate carrier-1 gene (MPC1) and the sphingolipid transporter-1 gene (SPNS1) associated with hemoglobin levels, the transforming growth factor-beta-induced gene (TGFBI) and the micro-RNA 129-1 (MIR129-1) associated with IL-6 and the granzyme B gene (GZMB) associated with IL-10 levels. Within the MAST4HEALTH randomized clinical trial (NCT03135873, www.clinicaltrials.gov) Mastiha supplementation improved the TAS levels among NAFLD patients with severe obesity. We identified several novel genome-wide significant nutrigenetic interactions, influencing the antioxidant and inflammatory status in NAFLD. Clinical Trial Registration: ClinicalTrials.gov, identifier NCT03135873.

Effect of Mastiha supplementation on NAFLD: The MAST4HEALTH Randomised, Controlled Trial.

SCOPE: Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease with poor therapeutic strategies. Mastiha possesses antioxidant/anti-inflammatory and lipid-lowering properties. The authors investigate the effectiveness of Mastiha as a nonpharmacological intervention in NAFLD. METHODS AND RESULTS: Ninety-eight patients with NAFLD in three countries (Greece, Italy, Serbia) are randomly allocated to either Mastiha or Placebo for 6 months, as part of a multicenter, randomized, double-blind, placebo-controlled, parallel-group clinical trial. The authors assess NAFLD severity via magnetic resonance imaging (MRI) scanning and LiverMultiScan technique and evaluate the effectiveness of Mastiha through medical, anthropometric, biochemical, metabolomic, and microbiota assessment. Mastiha is not superior to Placebo on changes in iron-corrected T1 (cT1) and Liver Inflammation Fibrosis score (LIF) in entire patient population; however, after BMI stratification (BMI ≤ 35 kg m-2 and BMI > 35 kg m-2 ), severely obese patients show an improvement in cT1 and LIF in Mastiha versus Placebo. Mastiha increases dissimilarity of gut microbiota, as shown by the Bray-Curtis index, downregulates Flavonifractor, a known inflammatory taxon and decreases Lysophosphatidylcholines-(LysoPC) 18:1, Lysophosphatidylethanolamines-(LysoPE) 18:1, and cholic acid compared to Placebo. CONCLUSION: Mastiha supplementation improves microbiota dysbiosis and lipid metabolite levels in patients with NAFLD, although it reduces parameters of liver inflammation/fibrosis only in severely obese patients.

SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files.

MOTIVATION: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis. RESULT: SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets. AVAILABILITYAND IMPLEMENTATION: SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Etiology of bloodstream infections at a population level during 2013-2017 in the Autonomous Community of Valencia, Spain / Etiología de las bacteriemias a nivel poblacional durante 2013-2017 en la Comunidad Autónoma de Valencia, España

INTRODUCTION: Bloodstream Infections has become in one of the priorities for the antimicrobial stewardship teams due to their high mortality and morbidity rates. Usually, the first antibiotic treatment for this pathology must be empirical, without microbiology data about the microorganism involved. For this reason, the population studies about the etiology of bacteremia are a key factor to improve the selection of the empirical treatment, because they describe the main microorganisms associated to this pathology in each area, and this data could facilitate the selection of correct antibiotic therapy. MATERIAL AND METHODS: This study describes the etiology of bloodstream infections in the Southeast of Spain. The etiology of bacteremia was analysed by a retrospective review of all age-ranged patients from every public hospital in the Autonomous Community of Valencia (approximately 5,000,000 inhabitants) for five years. RESULTS: A total of 92,097 isolates were obtained, 44.5% of them were coagulase-negative staphylococci. Enterobacteriales was the most prevalent group and an increase in frequency was observed along the time. Streptococcus spp. were the second microorganisms more frequently isolated. Next, the most prevalent were Staphylococcus aureus and Enterococcus spp., both with a stable incidence along the study. Finally, Pseudomonas aeruginosa was the fifth microorganism more frequently solated. CONCLUSIONS: These data constitute a useful tool that can help in the choice of empirical treatment for bloodstream infections, since the knowledge of local epidemiology is key to prescribe a fast and appropriate antibiotic therapy, aspect capital to improve survival

INTRODUCCIÓN: Las bacteriemias se han convertido en una de las prioridades de los Programas de Optimización de uso de Antimicrobianos (PROA) debido a sus altas tasas de morbimortalidad. Normalmente, el tratamiento antibiótico tiene que ser pautado de forma empírica, sin datos del microorganismo implicado. Por esto, los estudios poblacionales sobre la etiología de las bacteriemias son un factor clave para mejorar la elección del tratamiento empírico, ya que describen los principales microorganismos asociados a esta patología en cada área, lo que facilita en gran medida la selección del antibiótico correcto. MATERIAL Y MÉTODOS: Este estudio describe la etiología de las bacteriemias en el sureste de España durante los años 2013-2017. La etología fue analizada de forma retrospectiva estudiando los microorganismos implicados en todas las bacteriemias diagnosticadas en la Comunidad Valenciana (5.000.000 de habitantes). RESULTADOS: Se obtuvieron un total de 92.097 aislados clínicos, de los cuales un 44,5% fueron Staphylococcus coagulasa negativos. Las enterobacterias fueron el grupo más prevalente, su frecuencia se incrementó durante el estudio. Los cocos grampositivos, tipo Streptococcus, fueron los siguientes microorganismos que se aislaron de forma más frecuente, su frecuencia disminuyó a lo largo del periodo estudiado. A continuación, Staphylococcus aureus y Enterococcus spp. les siguieron en prevalencia, manteniéndose sus tasas estables a lo largo del estudio. Por último, el quinto microorganismo más prevalente fue Pseudomonas aeruginosa. CONCLUSIONES: Los datos obtenidos en este estudio constituyen una herramienta que puede facilitar la elección correcta del tratamiento empírico inicial que debe aplicarse en estos procesos

Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish.

Intestinal microbiota is key for many host functions, such as digestion, nutrient metabolism, disease resistance, and immune function. With the growth of the aquaculture industry, there has been a growing interest in the manipulation of fish gut microbiota to improve welfare and nutrition. Intestinal microbiota varies with many factors, including host species, genetics, developmental stage, diet, environment, and sex. The aim of this study was to compare the intestinal microbiota of adult gilthead sea bream (Sparus aurata) from three groups of age and sex (1-year-old males and 2- and 4-year-old females) maintained under the same conditions and fed exactly the same diet. Microbiota diversity and richness did not differ among groups. However, bacterial composition did, highlighting the presence of Photobacterium and Vibrio starting at 2 years of age (females) and a higher presence of Staphylococcus and Corynebacterium in 1-year-old males. The core microbiota was defined by 14 Operational Taxonomic Units (OTUs) and the groups that showed more OTUs in common were 2- and 4-year-old females. Discriminant analyses showed a clear separation by sex and age, with bacteria belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria driving the separation. Pathway analysis performed with the inferred metagenome showed significant differences between 1-year-old males and 4-year-old females, with an increase in infection-related pathways, nitrotoluene degradation and sphingolipid metabolism, and a significant decrease in carbohydrate metabolism pathways with age. These results show, for the first time, how intestinal microbiota is modulated in adult gilthead sea bream and highlight the importance of reporting age and sex variables in these type of studies in fish.

Corrigendum: Phylogeny of Vibrio vulnificus From the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy.

[This corrects the article DOI: 10.3389/fmicb.2017.02613.].

A metagenomic study of patients with alveolar osteitis after tooth extraction. A preliminary case-control study.

OBJECTIVE: To identify the microbiome in sockets with alveolar osteitis and compare it with a control group using metagenomic techniques. MATERIALS AND METHODS: A case-control study was conducted in subjects that had undergone a tooth extraction. Microbiological samples were taken from the sockets of 10 patients with dry socket after tooth extraction (AO group) and 10 patients in whom exodontia resulted in no postoperative complications (control group). Bacterial DNA was isolated, and the 16S rRNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by Metagenomic Rapid Annotation. RESULTS: A total of 151 different species were found: 55 bacteria were only found in the AO group, 51 were specific to the control group, and 45 were common to both groups. The most frequently found genera in both groups were Prevotella. Prevotella nanceiensis, Actinomyces odontolyticus, Treponema maltophilum, Veillonella dispar, Tannerella forsythia, and Leuconostoc mesenteroides were found in several patients with alveolar osteitis, with an abundance greater than 0.5%, and were absent in all the control group samples. CONCLUSIONS: Patients who develop alveolar osteitis after dental extractions might have a different microbiota from that of patients without postoperative complications. Since this is a preliminary report, further research is needed to assess whether bacteria play an important role in the etiology of dry socket. CLINICAL RELEVANCE: This study seems to indicate that bacteria may play an important role in the alveolar osteitis etiology. Thus, new prevention and treatment strategies should be considered.

Analysis of the Transcriptome of the Red Seaweed Grateloupia imbricata with Emphasis on Reproductive Potential.

Grateloupia imbricata is an intertidal marine seaweed and candidate model organism for both industry and academic research, owing to its ability to produce raw materials such as carrageenan. Here we report on the transcriptome of G. imbricata with the aim of providing new insights into the metabolic pathways and other functional pathways related to the reproduction of Grateloupia species. Next-generation sequencing was carried out with subsequent de novo assembly and annotation using state-of-the-art bioinformatic protocols. The results show the presence of transcripts required for the uptake of glycerol, which is a specific carbon source for in vitro culture of G. imbricata and nucleotide sequences that are involved in polyamine-based biosynthesis, polyamine degradation, and metabolism of jasmonates and ethylene. Polyamines, ethylene and methyl jasmonate are plant growth regulators that elicit the development and maturation of cystocarps and the release of spores from seaweeds. Our results will inform studies of the mechanisms that control polysaccharide accumulation, cystocarp formation and spore release. Moreover, our transcriptome information clarifies aspects of red seaweed carposporogenesis with potential benefits for enhancing reproduction.

Genome of wild olive and the evolution of oil biosynthesis.

Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.

New Insights into the Genome Organization of Yeast Killer Viruses Based on "Atypical" Killer Strains Characterized by High-Throughput Sequencing.

Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located around the central poly(A) region. A continuous sequence of the ScV-M2 genome was obtained for the first time. M1 virus was found for the first time in wine yeasts, coexisting with Mbarr-1 virus in T. delbrueckii. Extra 5'- and 3'-sequences were found in all M-genomes. The presence of repeated short sequences in the non-coding 3'-region of most M-genomes indicates that they have a common phylogenetic origin. High identity between amino acid sequences of killer toxins and some unclassified proteins of yeast, bacteria, and wine grapes suggests that killer viruses recruited some sequences from the genome of these organisms, or vice versa, during evolution.

Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An In Vivo Model.

BACKGROUND: The microbiota colonizing dental implants has been said to be similar to the microbiome surrounding teeth. In the absence of inflammation, a biofilm with pathologic bacteria can cover implant surfaces exposed to the oral cavity, for example, due to a remodeling process. The aim of the present study is to identify microbiota surrounding exposed dental implants in patients with and without a history of periodontitis through a deep-sequencing approach. METHODS: An experimental abutment with the same surface and structure as a commercially available dental implant was used. Bacterial DNA was isolated, and the 16S ribosomal RNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by metagenomic rapid annotation. RESULTS: A wide variety of bacteria, 96 species, were identified. The most frequently found bacteria were Fusobacterium nucleatum and Prevotella denticola. Some species generally associated with periodontitis were found to a greater extent in patients without a history of periodontitis. Some bacteria that have never been described as part of the oral microbiome were identified in the present sample. CONCLUSIONS: Analysis of data suggests that the bacteria surrounding exposed dental implants form a diverse microbiome regardless of the periodontal profile of patients. Further research is needed to clarify the role of these microorganisms in the oral environment.

Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy.

Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name "piscis."