Meningite bacteriana: uma revisão / Bacterial meningitis: a review

A meningite bacteriana é uma inflamação das leptomeninges que envolvem o Sistema Nervoso Central. Essa patologia, que possui diversos agentes etiológicos, apresenta-se na forma de síndrome, com quadro clínico grave. Entre as principais bactérias que causam a meningite, estão a Neisseria meningitis e Streptococcus pneumoniae. A transmissão ocorre através das vias aéreas por meio de gotículas, sendo a corrente sanguínea a principal rota para as bactérias chegarem à barreira hematoencefálica e, a partir dessa, até as meninges. Atualmente existem vários métodos de diagnóstico precisos, onde a cultura de líquido cefalorraquidiano (LCR) é o método padrão ouro. Ademais, a melhora na qualidade do tratamento com beta-lactâmicos e a maior possibilidade de prevenção, devido à elevação do número e da eficácia de vacinas, vem contribuindo para redução dos casos da doença e de sua gravidade. Porém, apesar desses avanços, ainda há um elevado número de mortalidades e sequelas causadas por essa síndrome.

Bacterial meningitis is an inflammation of the leptomeninges that surround the Central Nervous System. This pathology, which has several etiological agents, is presented as a syndrome with a severe clinical scenario. The main bacteria causing meningitis include Neisseria meningitis and Streptococcus pneumoniae. It can be transmitted by droplets through the airways, with the bacteria using the bloodstream as the main route to reach the blood-brain barrier, and from there to the meninges. There are currently several accurate diagnostic methods, with CSF culture being the gold standard. In addition, the improvement in the quality of beta-lactam treatment and the greater possibility of prevention due to the increased number and effectiveness of vaccines have contributed to reducing the number of cases and severity of the disease. Nevertheless, despite these advances, this syndrome still presents a high number of mortalities and sequelae.

Clinical factors associated with composition of lung microbiota and important taxa predicting clinical prognosis in patients with severe community-acquired pneumonia / 医学前沿

Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R2 = 0.033; P = 0.018), followed by acute kidney injury (AKI; R2 = 0.032; P = 0.011) and plasma MIP-1β level (R2 = 0.027; P = 0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients' lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.

Antibacterial effect of isoeugenol against Pseudomonas aeruginosa

Abatsract Pseudomonas aeruginosa is an important nosocomial pathogen and its clinical importance is mainly related to nosocomial infections. Increased rates of bacterial resistance in recent years has led WHO to publish a global priority list to guide research and discovery of new antibiotics, where P. aeruginosa is among the group of bacteria for which there is a critical level of priority for new drugs to be discovered. In this context, isoeugenol appears as an interesting alternative and the objective of this study was to investigate its action against P. aeruginosa. Isoeugenol presented significant antibacterial activity, with minimum inhibitory concentration (MIC) of 64µg/mL and minimum bactericidal concentration (MBC) of 128µg/mL, and was considered bactericidal against this species. Molecular docking revealed interactions that suggest that isoeugenol may bind to the enzyme Penicillin-Binding Protein 3 and interfere with the bacterial cell wall synthesis process. This study reinforces the antibacterial potential of this compound and emphasizes that more studies are needed in order to better investigate its mechanism of antibacterial action.

Antimicrobial photodynamic inactivation mediated by methylene blue: Analysis of inactivation kinetics and biochemical mechanisms / Inativação fotodinâmica antimicrobiana mediada por azul de metileno: Análises de cinética de inativação e mecanismos bioquímicos

The widespread use of antimicrobial chemotherapy in medicine and livestock production imposed an evolutive selection of drug-resistant strains worldwide. As a result, the effectiveness of our current antimicrobial armamentarium is constantly being reduced to alarming levels. Therefore, novel antimicrobial therapeutic strategies are urgently needed. Antimicrobial photodynamic therapy (APDT) comes to this scenario as a powerful tool to counteract the emergence of microbial drug-resistance. Its mechanisms of action are based on simultaneous oxidative damage of multiple targets and, therefore, it is much less likely to allow any type of microbial resistance. Therefore, the objectives of this study were focused into establishing 1) a mathematical tool to allow precise analysis of microbial photoinactivation; 2) a broad analysis of APDT effectiveness against global priority drug-resistant pathogens; 3) inhibition of ßlactamase enzymes; and 4) how the biochemical mechanisms of APDT avoid emergence of resistance. The main results obtained through the investigation led by this thesis were divided into 4 scientific articles regarding each of the above-mentioned objectives. In summary, we discovered that 1) a power-law function can precisely fit all microbial inactivation kinetics data and provide insightful information of tolerance factors and lethal doses; 2) there is no correlation between drug-resistance and APDT sensitivity, i.e., extensively drug resistant microorganisms are killed in the same kinetics as drug-sensitive controls; 3) ß-lactamases are very sensitive to photodynamic inhibition; 4) biochemical mechanisms of APDT promote oxidative damages to external cell membranes, DNA and proteins whereas the main cause of microbial death seems to be directly associated with protein degradation. Thus, we conclude that APDT is effective against a broad-spectrum of pathogens and has minimum chances of promoting resistance mechanisms

O amplo uso da quimioterapia antimicrobiana impôs uma seleção evolutiva de cepas resistentes a medicamentos. Como resultado, a eficácia dos fármacos antimicrobianos tem sido reduzida a níveis alarmantes. Portanto, novas estratégias terapêuticas antimicrobianas são urgentemente necessárias. A terapia fotodinâmica antimicrobiana (TFDA) entra neste cenário como uma ferramenta poderosa para combater a resistência microbiana. Seus mecanismos de ação são baseados no dano oxidativo sobre múltiplos alvos e, portanto, é muito menos provável que permita o surgimento de qualquer tipo de resistência. Os objetivos deste estudo foram focados ao estabelecimento de 1) modelo matemático para análise precisa da fotoinativação microbiana; 2) ampla análise da eficácia da TFDA contra patógenos resistentes a fármacos antimicrobianos de prioridade global; 3) inibição de ß-lactamases por TFDA; e 4) como os mecanismos bioquímicos da TFDA evitam o surgimento de resistência. Os principais resultados obtidos através da investigação conduzida por esta tese foram divididos em 4 artigos científicos. Em resumo, descobrimos que 1) uma função de lei de potência pode ajustar com precisão todos os dados de cinética de inativação microbiana e fornecer informações detalhadas sobre fatores de tolerância e doses letais; 2) não há correlação entre resistência à quimioterapia antimicrobiana e sensibilidade à TFDA, isto é, cepas extensivamente resistentes aos antimicrobianos são inativadas sob a mesma cinética que controles sensíveis aos antimicrobianos; 3) ß-lactamases são altamente sensíveis à inibição fotodinâmica; 4) os mecanismos bioquímicos da TFDA promovem danos oxidativos às membranas celulares e DNA, porém, a principal causa de morte microbiana é diretamente associada à degradação das proteínas. Assim, concluímos que a TFDA é eficaz contra um amplo espectro de patógenos e tem chances mínimas de promover mecanismos de resistência

Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir, India

BACKGROUND: Traditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS. RESULTS: The glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported. CONCLUSION: Results indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.

Correlation between Vitamin D Status and Gut Microbiota in Patients with Inflammatory Bowel Disease / 中国医学科学院学报

Objective To investigate the correlation between serum total 25-hydroxyvitamin D[T-25(OH)D]level and fecal microbiota in patients with inflammatory bowel disease(IBD). Methods Twenty-three patients with IBD completed the tests for serum T-25(OH)D,and the fecal microbiota was studied using V4 hypervariable region of 16S ribosomal RNA(rRNA)gene sequencing.According to serum T-25(OH)D level,the patients were divided into three groups including vitamin D normal group(

Gut microbiota in Mexican patients with common variable immunodeficiency

Introduction: Common variable immunodeficiency (CVID) is the main symptomatic primary immunodeficiency and is associated with complex immune disorders. Gut microbiota interacts closely with the immune system, and intestinal dysbiosis is related to multiple diseases. Objective: To describe for the first time the composition of gut microbiota in Mexican patients with CVID. Methods: Fecal samples from five patients with CVID were collected and massive sequencing of the V3-V4 region of 16S rRNA gene was carried out using illumina technology. Results: Bacterial relative abundance was observed at all taxonomic levels. Firmicutes, Actinobacteria and Verrucomicrobia were the predominant phyla. The Clostridia class and the Clostridial order were the most common in their respective taxon; the Ruminococcaceae family predominated. A total of 166 genera were reported, with the most abundant being Faecalibacterium. Five species were identified, but only Bifidobacterium longum was present in all patients. Conclusions: Unlike healthy subjects' gut microbiota, where Firmicutes and Bacteroidetes predominate, the microbiota of the patients with CVID considered in this study was abundant in Firmicutes, Actinobacteria and Verrucomicrobia. The low presence of Bacteroidetes and high abundance of Firmicutes might indicate the existence of intestinal dysbiosis in these patients.

Molecular identification and microbiological evaluation of isolates from equipments and food contact surfaces in a hospital Food and Nutrition Unit / Avaliação microbiológica e identificação molecular de isolados de equipamentos e superfícies de contato com alimentos em um hospital Unidade de Alimentação e Nutrição

Abstract The hygienic and sanitary control in Food and Nutrition Units (FNU) is considered a standard procedure to produce adequate meals and reduce the risk of foodborne diseases and hospital infections. This study aimed to evaluate the isolation and identification of bacteria from equipment and food contact surfaces in a hospital FNU as well as to evaluate the sanitary condition. Likewise, it was analyzed the adhesion of the microorganisms on polyethylene cutting boards. The presence of aerobic mesophilic microorganisms, yeasts, molds, coagulase-positive staphylococci, coliform and fecal coliform, and Escherichia coli were analyzed on eating tables, countertop surfaces and cutting boards used for meat or vegetable handling, and equipment such as microwaves and refrigerators. The molecular identification it was done by 16S rRNA gene sequencing. The adhesion of the microorganisms (biofilm formation) on meat and vegetable cutting boards was also evaluated by scanning electron microscopy. The results showed high numbers of all microorganisms, except for E. coli , which was not observed in the samples. The molecular analysis identified species of the Enterobacteriaceae family and species of the Pseudomonadaceae family. Scanning electron microscopy analyses revealed bacterial adhesion on the cutting board surfaces. The results obtained in this study indicated that the hygienic conditions of surfaces like plastic cutting boards and equipment in this hospital FNU were inadequate. The achievement and application of standard operating procedures could positively help in the standardization of sanitary control, reducing the microbial contamination and providing a safe food to hospitalized patients.

Resumo O controle higiênico e sanitário nas Unidades de Alimentação e Nutrição (UAN) é considerado um procedimento padrão para produzir refeições adequadas e reduzir o risco de doenças transmitidas pelos alimentos e infecções hospitalares. Este estudo teve como objetivo isolar e identificar bactérias de equipamentos e superfícies de contato com alimentos em uma UAN hospitalar, bem como avaliar a condição sanitária. Do mesmo modo, analisou-se a adesão dos micro-organismos em tábuas de corte de polietileno. A presença de micro-organismos aeróbios mesófilos, leveduras, fungos, Sthapylococcus coagulase-positivos, coliformes, coliformes fecais e Escherichia coli foi analisadas na superfície de mesas do refeitório, superfícies de bancada e tábuas de corte usadas para manuseio de carne ou vegetais e, em equipamentos como micro-ondas e refrigeradores. A identificação molecular foi feita pelo sequenciamento do gene 16S rRNA. A adesão dos micro-organismos (formação de biofilmes) em tábuas de corte de carne e de vegetais também foi avaliada por microscopia eletrônica de varredura. Os resultados mostraram elevada contagem para todos os micro-organismos analisados, exceto para E. coli, a qual não foi observada nas amostras. A análise molecular identificou espécies da família Enterobacteriaceae e Pseudomonadaceae. A análise de microscopia eletrônica de varredura revelaram adesão bacteriana nas superfícies das placsa de corte. Os resultados obtidos neste estudo indicaram que as condições higiênicas das superfícies e de equipamentos nesta UAN hospitalar estavam inadequadas. A aplicação de procedimentos operacionais padrão poderia auxiliar positivamente na padronização do controle higiênico-sanitário, reduzindo a contaminação microbiana e fornecendo um alimento seguro para pacientes hospitalizados.

Composition of bacterial community in enrichment cultures of shale by-products from Irati Formation, Brazil

ABSTRACT We examined microbial communities from enriched fine and retorted shale particles using sequencing of V4 variable region of 16S rRNA. High number of microbial genera was found in both enriched shale by-products that were dominate by Actinobacteria, Firmicutes and Proteobacteria, showing differences due to microbial colonization after the pyrolysis process.

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil

ABSTRACT Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic isolation site (São Paulo and Mato Grosso) but not the analyzed organs (utricle and stolon). We reported that six genera were common to both sample sites (São Paulo and Mato Grosso). These genera have previously been reported to be beneficial to plants, as well as related to the bioremediation process, showing that these isolates present great biotechnological and agricultural potential. This is the first report of an Acidobacteria isolated from U. breviscapa. The role of these bacteria inside the plant must be further investigated in order to understand their population dynamics within the host.

Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana

ABSTRACT Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.

Ammonia determines transcriptional profile of microorganisms in anaerobic digestion

ABSTRACT Anaerobic digestion is important for the management of livestock manure with high ammonia level. Although ammonia effects on anaerobic digestion have been comprehensively studied, the molecular mechanism underlying ammonia inhibition still remains elusive. In this study, based on metatranscriptomic analysis, the transcriptional profile of microbial community in anaerobic digestion under low (1500 mg L-1) and high NH4 + (5000 mg L-1) concentrations, respectively, were revealed. The results showed that high NH4 + concentrations significantly inhibited methane production but facilitated the accumulations of volatile fatty acids. The expression of methanogenic pathway was significantly inhibited by high NH4 + concentration but most of the other pathways were not significantly affected. Furthermore, the expressions of methanogenic genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase were significantly inhibited by high NH4 + concentration. The inhibition of the co-expressions of the genes which encode acetyl-CoA decarbonylase was observed. Some genes involved in the pathways of aminoacyl-tRNA biosynthesis and ribosome were highly expressed under high NH4 + concentration. Consequently, the ammonia inhibition on anaerobic digestion mainly focused on methanogenic process by suppressing the expressions of genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase. This study improved the accuracy and depth of understanding ammonia inhibition on anaerobic digestion.

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier

Abstract As a glacier retreats, barren areas are exposed, and these barren areas are ideal sites to study microbial succession. In this study, we characterized the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tianshan Mountains. The total number of culturable bacteria ranged from 2.19 × 105 to 1.30 × 106 CFU g-1 dw and from 9.33 × 105 to 2.53 × 106 CFU g-1 dw at 4 °C and 25 °C, respectively. The number of culturable bacteria in the soil increased at 25 °C but decreased at 4 °C along the chronosequence. The total organic carbon, total nitrogen content, and enzymatic activity were relatively low in the glacier foreland. The number of culturable bacteria isolated at 25 °C was significantly positively correlated with the TOC and TN as well as the soil urease, protease, polyphenoloxidase, sucrase, catalase, and dehydrogenase activities. We obtained 358 isolates from the glacier foreland soils that clustered into 35 groups using amplified ribosomal DNA restriction analysis. These groups are affiliated with 20 genera that belong to six taxa, namely, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteroides, and Deinococcus-Thermus, with a predominance of members of Actinobacteria and Proteobacteria in all of the samples. A redundancy analysis showed that the bacterial succession was divided into three periods, an early stage (10a), a middle stage (25-74a), and a late stage (100-130a), with the total number of culturable bacteria mainly being affected by the soil enzymatic activity, suggesting that the microbial succession correlated with the soil age along the foreland.

Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine

Abstract Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L )

Abstract Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p = 1.24e-12), Candidatus koribacter versatilis (p = 2.66e-10)] and fungi [(Fusarium oxysporum (p = 0.013), Talaromyces stipitatus (p = 0.219) and Pestalotiopsis fici (p = 0.443)] in terms of abundance in population and bacterial chemotaxis (p = 0.012), iron metabolism (p = 2.97e-5) with the reduction in abundance for pathogenicity islands (p = 7.30e-3), phages and prophages (p = 7.30e-3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p = 2.34e-4), and degradation of heterocyclic aromatic compounds (p = 3.59e-13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper.

Rubber gloves biodegradation by a consortium, mixed culture and pure culture isolated from soil samples

Abstract An increasing production of natural rubber (NR) products has led to major challenges in waste management. In this study, the degradation of rubber latex gloves in a mineral salt medium (MSM) using a bacterial consortium, a mixed culture of the selected bacteria and a pure culture were studied. The highest 18% weight loss of the rubber gloves were detected after incubated with the mixed culture. The increased viable cell counts over incubation time indicated that cells used rubber gloves as sole carbon source leading to the degradation of the polymer. The growth behavior of NR-degrading bacteria on the latex gloves surface was investigated using the scanning electron microscope (SEM). The occurrence of the aldehyde groups in the degradation products was observed by Fourier Transform Infrared Spectroscopy analysis. Rhodococcus pyridinivorans strain F5 gave the highest weight loss of rubber gloves among the isolated strain and posses latex clearing protein encoded by lcp gene. The mixed culture of the selected strains showed the potential in degrading rubber within 30 days and is considered to be used efficiently for rubber product degradation. This is the first report to demonstrate a strong ability to degrade rubber by Rhodococcus pyridinivorans.

A broad-range PCR technique for the diagnosis of infective endocarditis

Abstract Infective endocarditis (IE) remains a severe and potentially fatal disease demanding sophisticated diagnostic strategies for detection of the causative microorganisms. The aim of the present study was to develop a broad-range 16S ribosomal RNA gene polymerase chain reaction in the routine diagnostic of IE for the early diagnosis of fatal disease. A broad-range PCR technique was selected and evaluated in terms of its efficiency in the diagnosis of endocarditis using 19 heart valves from patients undergoing cardiovascular surgeries at the Habib Bourguiba Hospital of Sfax, Tunisia, on the grounds of suspected IE. The results demonstrated the efficiency of this technique particularly in cases involving a limited number of bacteria since it helped to increase detection sensitivity. The technique proved to be efficient, particularly, in the bacteriological diagnosis of IE in contexts involving negative results from conventional culture methods and other contexts involving bacterial species that were not amenable to identification by phenotypic investigations. Indeed, the sequencing of the partial 16S ribosomal RNA gene revealed the presence of Bartonella henselae, Enterobacter sp., and Streptococcus pyogenes in three heart valves with the negative culture. It should be noted that the results obtained from the polymerase chain reaction-sequencing identification applied to the heart valve and the strain isolated from the same tissue were not consistent with the ones found by the conventional microbiological methods in the case of IE caused by Gemella morbillorum. In fact, the results from the molecular identification revealed the presence of Lactobacillus jensenii. Overall, the results have revealed that the proposed method is sensitive, reliable and might open promising opportunities for the early diagnosis of IE.

Antagonistic endophytic bacteria associated with nodules of soybean (Glycine max L. ) and plant growth-promoting properties

Abstract A total of 276 endophytic bacteria were isolated from the root nodules of soybean (Glycine max L.) grown in 14 sites in Henan Province, China. The inhibitory activity of these bacteria against pathogenic fungus Phytophthora sojae 01 was screened in vitro. Six strains with more than 63% inhibitory activities were further characterized through optical epifluorescence microscopic observation, sequencing, and phylogenetic analysis of 16S rRNA gene, potential plant growth-promoting properties analysis, and plant inoculation assay. On the basis of the phylogeny of 16S rRNA genes, the six endophytic antagonists were identified as belonging to five genera: Enterobacter, Acinetobacter, Pseudomonas, Ochrobactrum, and Bacillus. The strain Acinetobacter calcoaceticus DD161 had the strongest inhibitory activity (71.14%) against the P. sojae 01, which caused morphological abnormal changes of fungal mycelia; such changes include fracture, lysis, formation of a protoplast ball at the end of hyphae, and split ends. Except for Ochrobactrum haematophilum DD234, other antagonistic strains showed the capacity to produce siderophore, indole acetic acid, and nitrogen fixation activity. Regression analysis suggested a significant positive correlation between siderophore production and inhibition ratio against P. sojae 01. This study demonstrated that nodule endophytic bacteria are important resources for searching for inhibitors specific to the fungi and for promoting effects for soybean seedlings.

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota

Abstract In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.

Polyhydroxyalkanoate biosynthesis by oxalotrophic bacteria from high Andean soil / Biosíntesis de polihidrxialcanoato por bacterias oxalotróficas de suelos altoandinos / Biossínteses de polihidroxialcanoato por bactérias oxalotróficas de solos andinos

Abstract Oxalate is a highly oxidized organic acid anion used as a carbon and energy source by oxalotrophic bacteria. Oxalogenic plants convert atmospheric CO2 into oxalic acid and oxalic salts. Oxalate-salt formation acts as a carbon sink in terrestrial ecosystems via the oxalate-carbonate pathway (OCP). Oxalotrophic bacteria might be implicated in other carbon-storage processes, including the synthesis of polyhydroxyalkanoates (PHAs). More recently, a variety of bacteria from the Andean region of Colombia in Narino have been reported for their PHA-producing abilities. These species can degrade oxalate and participate in the oxalate-carbonate pathway. The aim of this study was to isolate and characterize oxalotrophic bacteria with the capacity to accumulate PHA biopolymers. Plants of the genus Oxalis were collected and bacteria were isolated from the soil adhering to the roots. The isolated bacterial strains were characterized using biochemical and molecular biological methods. The consumption of oxalate in culture was quantified, and PHA production was monitored in batch fermentation. The polymeric composition was characterized using gas chromatography. Finally, a biosynthetic pathway based on our findings and on those from published sources is proposed. Strains of Bacillus spp. and Serratia sp. were found to metabolize calcium oxalate and synthesize PHA.

Resumen El oxalato es un anión de ácido orgánico altamente oxidado usado como fuente carbono y energía por bacterias oxalotróficas. Las plantas oxalogénicas convierten CO2 atmosférico en ácido oxálico y sales oxálicas. La formación de sales de oxalato actúa como un sumidero de carbono en ecosistemas terrestres via oxalato-carbonato (OCP). Las bacterias oxalotróficas podrían estar implicadas en otros procesos de almacenamiento de carbono, incluyendo la síntesis de polihidroxialcanoatos (PHAs). Recientemente, una variedad de bacterias de la región andina colombiana en Nariño ha sido reportada por su habilidad para producir PHAs. Estas especies pueden degradar oxalato y participar en la vía del oxalato-carbonato. El objetivo de este estudio fue aislar y caracterizar bacterias oxalotróficas con capacidad de acumular biopolímeros PHA. Se colectaron plantas del genero Oxalis y se aislaron bacterias del suelo adheridas a las raíces. Las cepas bacterianas aisladas se caracterizaron usando métodos bioquímicos y de biología molecular. Se cuantificó el consumo de oxalato en cultivo, y se monitoreó la producción de PHA en fermentación por lotes. La composición polimérica se caracterizó usando cromatografía de gases. Finalmente, se propone una via biosintética basada en nuestros hallazgos y en los de otras fuentes publicadas. Se encontró que las cepas de Bacillus spp. y Serratia sp. metabolizan oxalato de calcio y sintetizan PHA.

Resumo O oxalato é um ânion de ácido orgânico altamente oxidado utilizado como fonte de carbono e nergía por bactérias oxalotróficas. As plantas oxalogênicas convertem CO2 atmosférico em ácido oxálico e sais oxálicos. A formação de sais de oxalato atua como um sumidouro de carbono em ecossistemas terrestres via oxalato-carbono (OCP). As bactérias oxalotróficas poderiam estar envolvidas em outros processos de armazenamento de carbono, incluindo a sínteses de polihidroxialcanoatos (PHAs). Recentemente, uma variedade de bactérias da região Andina colombiana no Departamento de Nariño foi reportada devido a sua habilidade para produzir PHAs. Estas espécies podem degradar oxalato e participar na via oxalato-carbono. O objetivo de esse estudo foi isolar e caracterizar bactérias oxalotróficas com capacidade de acumular biopolímeros PHA. Plantas do género Oxalis foram coletadas e se isolaram bactérias do solo aderido a suas raízes. As cepas bacterianas isoladas se caracterizaram utilizando métodos bioquímicos e de biologia molecular. O consumo de oxalato em cultivo foi quantificado, e a produção de PHA foi monitorada em fermentação por lotes. A composição polimérica se caracterizou utilizando Cromatografia de Gases. Finalmente, se propõe uma via biossintética baseada em nossos resultados juntamente com resultados da literatura. Se encontrou que as cepas de Bacillus spp. e Serratia sp. metabolizam oxalato de cálcio e sintetizam PHA.