RESUMO
We report the microbial 16S rRNA gene and internal transcribed spacer (ITS) sequencing data of maize and soybean plants and field soil from eight locations in Brazil. Enterobacter and Pseudomonas were among the most abundant genera. The data suggest the presence of several species that have not been documented for Brazil.
RESUMO
Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.
Assuntos
Alcaligenes faecalis/genética , Citrus/microbiologia , Genoma Bacteriano , Sequenciamento Completo do Genoma , Alcaligenes faecalis/efeitos dos fármacos , Animais , Antibacterianos/farmacologia , Sequência de Bases , Citrus/parasitologia , DNA Circular/genética , Resistência Microbiana a Medicamentos/efeitos dos fármacos , Resistência Microbiana a Medicamentos/genética , Ilhas Genômicas/genética , Ferro/metabolismo , Metais Pesados/toxicidade , Mimosa/microbiologia , Nematoides/fisiologia , Fenóis/metabolismo , FilogeniaRESUMO
Obesity is linked with altered microbial short-chain fatty acids (SCFAs), which are a signature of gut dysbiosis and inflammation. In the present study, we investigated whether tributyrin, a prodrug of the SCFA butyrate, could improve metabolic and inflammatory profiles in diet-induced obese mice. Mice fed a high-fat diet for eight weeks were treated with tributyrin or placebo for another six weeks. We show that obese mice treated with tributyrin had lower body weight gain and an improved insulin responsiveness and glucose metabolism, partly via reduced hepatic triglycerides content. Additionally, tributyrin induced an anti-inflammatory state in the adipose tissue by reduction of Il-1ß and Tnf-a and increased Il-10, Tregs cells and M2-macrophages. Moreover, improvement in glucose metabolism and reduction of fat inflammatory states associated with tributyrin treatment were dependent on GPR109A activation. Our results indicate that exogenous targeting of SCFA butyrate attenuates metabolic and inflammatory dysfunction, highlighting a potentially novel approach to tackle obesity.
Assuntos
Obesidade/sangue , Obesidade/tratamento farmacológico , Pró-Fármacos/administração & dosagem , Receptores Acoplados a Proteínas G/metabolismo , Transdução de Sinais/efeitos dos fármacos , Triglicerídeos/administração & dosagem , Tecido Adiposo/efeitos dos fármacos , Tecido Adiposo/metabolismo , Animais , Butiratos/sangue , Citocinas/metabolismo , Dieta Hiperlipídica/efeitos adversos , Microbioma Gastrointestinal , Técnicas de Inativação de Genes , Inflamação/tratamento farmacológico , Inflamação/metabolismo , Resistência à Insulina , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Obesidade/etiologia , Receptores Acoplados a Proteínas G/genética , Triglicerídeos/sangue , Aumento de Peso/efeitos dos fármacosRESUMO
Gut microbiota composition is influenced by environmental factors and has been shown to impact body metabolism. OBJECTIVE: To assess the gut microbiota profile before and after Roux-en-Y gastric bypass (RYGB) and the correlation with food intake and postoperative type 2 diabetes remission (T2Dr). DESIGN: Gut microbiota profile from obese diabetic women was evaluated before (n = 25) and 3 (n = 20) and 12 months (n = 14) after RYGB, using MiSeq Illumina-based V4 bacterial 16S rRNA gene profiling. Data on food intake (7-day record) and T2Dr (American Diabetes Association (ADA) criteria) were recorded. RESULTS: Preoperatively, the abundance of five bacteria genera differed between patients with (57%) and without T2Dr (p < 0.050). Preoperative gut bacteria genus signature was able to predict the T2Dr status with 0.94 accuracy ROC curve (receiver operating characteristic curve). Postoperatively (vs. preoperative), the relative abundance of some gut bacteria genera changed, the gut microbial richness increased, and the Firmicutes to Bacteroidetes ratio (rFB) decreased (p < 0.05) regardless of T2Dr. Richness levels was correlated with dietary profile pre and postoperatively, mainly displaying positive and inverse correlations with fiber and lipid intakes, respectively (p < 0.05). CONCLUSIONS: Gut microbiota profile was influenced by RYGB and correlated with diet and T2Dr preoperatively, suggesting the possibility to assess its composition to predict postoperative T2Dr.
Assuntos
Diabetes Mellitus Tipo 2/microbiologia , Ingestão de Alimentos/fisiologia , Derivação Gástrica , Microbioma Gastrointestinal/fisiologia , Obesidade Mórbida/microbiologia , Adulto , Diabetes Mellitus Tipo 2/etiologia , Diabetes Mellitus Tipo 2/cirurgia , Feminino , Microbioma Gastrointestinal/genética , Humanos , Pessoa de Meia-Idade , Obesidade Mórbida/complicações , Obesidade Mórbida/cirurgia , Período Pós-Operatório , RNA Ribossômico 16S/análise , Indução de Remissão , Resultado do TratamentoRESUMO
Obesity is linked with altered microbial short-chain fatty acids (SCFAs), which are a signature of gut dysbiosis and inflammation. In the present study, we investigated whether tributyrin, a prodrug of the SCFA butyrate, could improve metabolic and inflammatory profiles in diet-induced obese mice. Mice fed a high-fat diet for eight weeks were treated with tributyrin or placebo for another six weeks. We show that obese mice treated with tributyrin had lower body weight gain and an improved insulin responsiveness and glucose metabolism, partly via reduced hepatic triglycerides content. Additionally, tributyrin induced an anti-inflammatory state in the adipose tissue by reduction of Il-1β and Tnf-a and increased Il-10, Tregs cells and M2-macrophages. Moreover, improvement in glucose metabolism and reduction of fat inflammatory states associated with tributyrin treatment were dependent on GPR109A activation. Our results indicate that exogenous targeting of SCFA butyrate attenuates metabolic and inflammatory dysfunction, highlighting a potentially novel approach to tackle obesity
RESUMO
Antibiotic-induced dysbiosis is a key factor predisposing intestinal infection by Clostridium difficile. Here, we show that interventions that restore butyrate intestinal levels mitigate clinical and pathological features of C. difficile-induced colitis. Butyrate has no effect on C. difficile colonization or toxin production. However, it attenuates intestinal inflammation and improves intestinal barrier function in infected mice, as shown by reduced intestinal epithelial permeability and bacterial translocation, effects associated with the increased expression of components of intestinal epithelial cell tight junctions. Activation of the transcription factor HIF-1 in intestinal epithelial cells exerts a protective effect in C. difficile-induced colitis, and it is required for butyrate effects. We conclude that butyrate protects intestinal epithelial cells from damage caused by C. difficile toxins via the stabilization of HIF-1, mitigating local inflammatory response and systemic consequences of the infection.
Assuntos
Butiratos/administração & dosagem , Clostridioides difficile/patogenicidade , Colite/prevenção & controle , Fator 1 Induzível por Hipóxia/metabolismo , Administração Oral , Animais , Antibacterianos/farmacologia , Butiratos/farmacologia , Clostridioides difficile/metabolismo , Colite/etiologia , Colite/microbiologia , Células Epiteliais/citologia , Células Epiteliais/efeitos dos fármacos , Células Epiteliais/metabolismo , Ácidos Graxos Voláteis/metabolismo , Humanos , Insulina/administração & dosagem , Mucosa Intestinal/citologia , Mucosa Intestinal/patologia , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Microbiota/efeitos dos fármacos , Permeabilidade/efeitos dos fármacos , Junções Íntimas/metabolismo , Toxinas Biológicas/toxicidade , Triglicerídeos/administração & dosagemRESUMO
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.
Assuntos
Compostagem , Consórcios Microbianos , Microbiologia do Solo , Bactérias/genética , Biodegradação Ambiental , Biomassa , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Lignina/metabolismo , Metagenômica , RNA Ribossômico 16S/genéticaRESUMO
Lower-grade gliomas (LGGs), which are uniformly fatal in young adults, are classified as grades II-III tumors according to their histological features. The NFκB transcription factor, a crucial player in cancer initiation and progression, is inactivated in the cytoplasm by inhibitory proteins (IκBs) that have been shown to exert tumor-suppressor activity. Therefore, using The Cancer Genome Atlas copy number alteration and RNA-Seq data from 398 patients, we evaluated the association between the expression and dosage of NFKBIA, which encodes IκBα, and the overall malignancy of LGGs. Deletion and low expression of NFKBIA were associated with enhanced tumor aggressiveness and poor prognosis in LGGs. Accordingly, the dosage and expression of NFKBIA were independent prognostic factors for 5-year survival (dosage: P = 0.016; expression: P = 0.002) and 5-year recurrence-free survival (dosage: P = 0.009; expression: P = 0.005). Moreover, gene set enrichment analyses and co-expression network analyses indicated a role for NFKBIA in the negative regulation of cell proliferation, possibly through the modulation of downstream NFκB activation. Overall, the present findings reveal the prognostic value of NFKBIA in LGGs, reinforcing the relevance of NFκB signaling in the development and progression of gliomas.
Assuntos
Neoplasias Encefálicas/genética , Deleção de Genes , Regulação Neoplásica da Expressão Gênica , Glioma/genética , Proteínas I-kappa B/genética , Adulto , Idoso , Neoplasias Encefálicas/mortalidade , Neoplasias Encefálicas/patologia , Proliferação de Células/genética , Variações do Número de Cópias de DNA , Feminino , Glioma/mortalidade , Glioma/patologia , Humanos , Proteínas I-kappa B/metabolismo , Estimativa de Kaplan-Meier , Masculino , Pessoa de Meia-Idade , Análise Multivariada , Inibidor de NF-kappaB alfa , NF-kappa B/genética , NF-kappa B/metabolismo , Gradação de Tumores , Prognóstico , Transdução de Sinais/genéticaRESUMO
BACKGROUND: Today there are more than 2 billion alcohol users and about 1.3 billion tobacco users worldwide. The chronic and heavy use of these two substances is at the heart of numerous diseases and may wreak havoc on the human oral microbiome. This study delves into the changes that alcohol and tobacco may cause on biofilms of the human oral microbiome. To do so, we used swabs to sample the oral biofilm of 22 subjects; including 9 control-individuals with no or very low consumption of alcohol and no consumption of tobacco, 7 who were chronic and heavy users of both substances and 6 active smokers that reported no significant alcohol consumption. DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. DNA sequences were clustered and OTUs were assigned using the ARB SILVA database and Qiime. RESULTS: We found no differences in species diversity and evenness among the groups. However, we found a significant decrease in species richness in only smokers and in smokers/drinkers when compared to controls. We found that Neisseria abundance was significantly decreased in both groups when compared to controls. Smokers had significant increases in Prevotella and Capnocytophaga and reductions in Granulicatella, Staphylococcus, Peptostreptococcus and Gemella when compared to the two other groups. Controls showed higher abundance of Aggregibacter, whilst smokers/drinkers had lower abundances of Fusobacteria. Samples from only smokers clustered closer together than to controls and smokers/drinkers, and also had a significant reduction in inter-group dissimilarity distances, indicating a more homogenous group than controls. CONCLUSIONS: Our results indicate that the continued use of tobacco or alcohol plus tobacco significantly reduces bacterial richness, which apparently leads to a reduction in inter-group variability, turning the respective biofilms into a more homogenous microenvironment in terms of bacterial community composition, with possible consequences for human oral diseases.
Assuntos
Consumo de Bebidas Alcoólicas , Bactérias/classificação , Biofilmes/crescimento & desenvolvimento , Biota/efeitos dos fármacos , Mucosa Bucal/microbiologia , Uso de Tabaco , Idoso , Bactérias/genética , Bactérias/isolamento & purificação , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
Álcool e tabaco são os agentes externos mais importantes para o surgimento do câncer da cavidade oral. Outro elemento exógeno que talvez seja importante na composição deste cenário é a microbiota da cavidade oral, que atua de forma marcante contribuindo para gerar agentes potencialmente carcinogênicos, tais como o acetaldeído. Neste projeto, avaliamos a composição da microbiota oral bacteriana utilizando sequenciamento em larga escala, um método que independe do crescimento ou cultivo de bactérias in vitro, e permite a identificação e quantificação de táxons bacterianos após análises de bioinformática. Para avaliar as populações bacterianas presentes em biofilmes de pacientes com câncer da cavidade oral, três grupos foram estudados: 1) 10 indivíduos sem câncer de cavidade oral e que não usam álcool ou tabaco; 2) 5 indivíduos sem câncer de cavidade oral e que fazem uso diário de tabaco e álcool e 3) 11 indivíduos portadores de câncer oral e que fazem uso destas duas drogas. Para tal, amplificamos regiões polimórficas do gene 16S-rDNA, marcamos as sequências oriundas de cada indivíduo com tags específicas e sequenciamos os amplicons na plataforma Ion Torrent&*61668;. As sequências obtidas foram anotadas utilizando bancos de dados públicos. Os dados obtidos sugerem uma maior diversidade bacteriana nos pacientes com câncer oral, quando comparados aos grupos-controle sem câncer, sendo esta ainda mais elevada entre os pacientes com estadiamento tumoral mais avançado (T3-T4). Bactérias do gênero Actinomyces se mostraram mais prevalentes nos pacientes e controles que fumam e bebem. Os resultados obtidos devem auxiliar na compreensão da composição da microbiota bacteriana oral de pacientes com câncer, representando o primeiro passo para uma avaliação do papel de carcinógenos comuns sobre microbiota e o papel de ambos no desenvolvimento do câncer de cavidade oral.
Alcohol and tobacco are the two most important external agents that cause oral squamous cell carcinomas (OSCC). The oral cavity's microbiota is also another exogenous element that may have an important role in this scenario, generating potentially carcinogenic agents, such as acetaldehyde. In this project, the oral cavity's bacterial microbiota composition was evaluated using metagenomic largescale sequencing, a method that doesn't rely on the in vivo growth or cultivation of bacteria, and allows their identification and quantification after in silico analysis. In order to evaluate the bacterial populations present in the biofilms of patients with OSCC, three groups were studied: 1) 10 individuals without OSCC that do not smoke nor drink, 2) 5 individuals without OSCC that smoke and drink on a daily basis, 3) 11 individuals that have OSCC and use these two drugs. To do so, polymorphic regions of the 16S-rDNA gene were amplified by PCR and the resulting amplicons were barcoded with specific sequences for each individual and were then sequenced on the Ion Torrent™ platform. The resulting sequences were compared to those present in public databases. The data suggests a higher bacterial diversity in patients with OSCC, when compared to the group without cancer, the group withoutcancer that smoke and drank and even more so in patients with advanced tumours (T3-T4). The bacterial genus Actinomyces was found to be more abundant in patients with OSSC then both control groups. The results obtained in this study should help understand the bacterial composition of patients with oral cancer, a first step in evaluating the role that common carcinogns play on the microbiota and oral cavity cancer.