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AIM: Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS: The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS: Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
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Endófitos , Oryza , Raízes de Plantas , Microbiologia do Solo , Solo , Oryza/microbiologia , Oryza/crescimento & desenvolvimento , Raízes de Plantas/microbiologia , Endófitos/genética , Endófitos/isolamento & purificação , Endófitos/classificação , Solo/química , Polimorfismo de Fragmento de Restrição , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Fixação de Nitrogênio , Oxirredutases/genéticaRESUMO
Although chronic hepatitis C has been effectively treated with direct-acting antivirals (DAAs), the use of conventional therapy with peg-interferon (Peg-IFN) or (predominantly) ribavirin (RBV), remains widespread. R70Q/H and L/C91M amino acid substitutions in the hepatitis C virus (HCV) core protein may modulate responses to IFN and/or RBV, and are associated with cirrhosis, hepatocellular carcinoma (HCC), insulin resistance, and liver steatosis. We evaluated the R70Q/H and L/C91M substitutions, clinical and epidemiological profiles, and risk factors of Brazilian patients chronically infected with HCV subgenotypes 1a and 1b (HCV-GT1a and HCV-GT1b) unresponsive to IFN and/or RBV therapy. Sequencing and pyrosequencing analyses and sociodemographic and clinical predictive variables were used to assess the relationship between R70Q/H and L/C91M substitutions. Leukocyte counts, ALT levels, and ALT/AST ratios were significantly reduced in treated individuals, but more of these patients had advanced fibrosis and cirrhosis. L91M was more prevalent (19.7%), occurring only in HCV-GT1b, followed by R70Q/P (11.5%) and R70P (1.4%). R70Q/P exhibited higher mean AST, ALT, and GGT values, whereas L91M showed higher mean GGT values. Pyrosequencing of the L91M position revealed mutant subpopulations in 43.75% of samples.
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Carcinoma Hepatocelular , Hepatite C Crônica , Hepatite C , Neoplasias Hepáticas , Humanos , Antivirais , Brasil/epidemiologia , Carcinoma Hepatocelular/tratamento farmacológico , Quimioterapia Combinada , Hepacivirus/genética , Hepatite C/tratamento farmacológico , Hepatite C Crônica/tratamento farmacológico , Interferon-alfa/uso terapêutico , Neoplasias Hepáticas/tratamento farmacológico , Polietilenoglicóis/uso terapêutico , Proteínas Recombinantes/uso terapêutico , Ribavirina/uso terapêuticoRESUMO
Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.
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Microbioma Gastrointestinal , Gastrópodes , Microbiota , Animais , Simpatria , Gastrópodes/microbiologia , Proteobactérias/genéticaRESUMO
Aim: This study investigated the influence of antidepressant drugs on methylation status of KCNE1, KCNH2 and SCN5A promoters and ECG parameters in adult psychiatric patients. Materials & methods: Electrocardiographic evaluation (24 h) and blood samples were obtained from 34 psychiatric patients before and after 30 days of antidepressant therapy. Methylation of promoter CpG sites of KCNE1, KCNH2 and SCN5A was analyzed by pyrosequencing. Results: Three CpG and four CpG sites of KCNE1 and SCN5A, respectively, had increased % methylation after treatment. Principal component analysis showed correlations of the methylation status with electrocardiographic variables, antidepressant doses and patient age. Conclusion: Short-term treatment with antidepressant drugs increase DNA methylation in KCNE1 and SCN5A promoters, which may induce ECG alterations in psychiatric patients.
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Antidepressivos , Metilação de DNA , Adulto , Antidepressivos/farmacologia , Antidepressivos/uso terapêutico , Células Sanguíneas , Ilhas de CpG , Humanos , Canais Iônicos , Regiões Promotoras GenéticasRESUMO
We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.
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BACKGROUND: Prenatal cocaine exposure (PCE) is associated with behavioral, cognitive, and social consequences in children that might persist into later development. However, there are still few data concerning epigenetic mechanisms associated with the effects of gestational cocaine exposure, particularly in human newborns. AIMS: We investigated the effects of PCE on DNA methylation patterns of the Oxytocin Receptor (OXTR) gene in the umbilical cord blood (UCB). The relationship between UCB DNA methylation levels and the severity of the mother's cocaine use during pregnancy was also evaluated. METHODS: In this cross-sectional study, 28 UCB samples of newborns with a history of crack cocaine exposure in utero and 30 UCB samples of non-exposed newborns (NEC) were compared for DNA methylation levels at two genomic loci located in exon III of the OXTR gene (OXTR1 and OXTR2) through pyrosequencing. Maternal psychopathology was investigated using the Mini International Neuropsychiatric Interview, and substance use characteristics and addiction severity were assessed using the Smoking and Substance Involvement Screening Test (ASSIST). RESULTS: No differences between newborns with a history of PCE and NEC were observed in OXTR1 or OXTR2 DNA methylation levels. However, regression analyses showed that maternal addiction severity for crack cocaine use predicted OXTR1 DNA methylation in newborns. CONCLUSION: These data suggest that OXTR methylation levels in the UCB of children are affected by the severity of maternal crack cocaine usage. Larger studies are likely to detect specific changes in DNA methylation relevant to the consequences of PCE.
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This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.
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Bactérias/classificação , Cacau/microbiologia , Análise de Sequência de DNA/métodos , Leveduras/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Fenômenos Fisiológicos Bacterianos , DNA Bacteriano/genética , DNA Fúngico/genética , Fermentação , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Leveduras/genética , Leveduras/isolamento & purificação , Leveduras/fisiologiaRESUMO
It is well known that one of the most outstanding adverse effects related to lead (Pb) exposure is oxidative stress; moreover, recent findings suggest that disturbances of the redox status of cells are associated with epigenetic responses, and metabolism of glutathione (GSH) plays an important role in this process. This study aimed to assess Pb exposure on % methylation of GSH-related genes' promoter regions (%CH3-CpG) and their influence on biomarkers of oxidative stress, in workers exposed to the metal. One hundred nine male workers participated in the study; ICP-MS determined blood lead levels (BLL); biochemical parameters related to redox status, named GSH, glutathione peroxidase (GPX) and glutathione-S-transferase (GST) were quantified by UV/Vis spectrophotometry. Determination of %CH3-CpG of genes GCLC, GPX1, GSR, and GSTP1 were done by pyrosequencing. Inverse associations were seen between BLL and %CH3-CpG-GCLC, and %CH3-CpG-GSTP1. Moreover, metal exposure did not impact GSH, GPX, and GST; however, negative associations were observed between %CH3-CpG-GPX1 and %CH3-CpG-GSTP1, and the activities of GPX and GST, respectively. Taken together, our results give further evidence about adaptive epigenetic response to avoid oxidative damage induced by Pb exposure, allowing a better understanding of the molecular mechanisms related to the metal toxicity.
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Glutationa , Chumbo , Epigênese Genética , Glutationa/metabolismo , Glutationa Peroxidase/metabolismo , Glutationa Transferase/genética , Glutationa Transferase/metabolismo , Humanos , Chumbo/toxicidade , Masculino , Estresse Oxidativo/genéticaRESUMO
The aim of the present study was to investigate the occurrence of Haemonchus contortus and Haemonchus placei in beef cattle and the frequency of single nucleotide polymorphisms associated with benzimidazole (BZ)-resistance in Haemonchus spp. in Brazil. For such, fecal samples were collected from 61 beef cattle ranches in 11 Brazilian states. Third-stage larvae (L3) were produced for morphological species identification and DNA extraction. PCR was performed for the analysis of the isotype 1 ß-tubulin gene and the products were sequenced to confirm the presence of H. placei and H. contortus. For each field population, pyrosequencing assays were performed to quantify the frequency of the F167Y, E198A and F200Y polymorphisms in the isotype-1 ß-tubulin gene. The results of the morphometric analysis of 2345 larvae showed that H. placei was present on all ranches. The analysis of the isotype 1 ß-tubulin gene confirmed 100% prevalence for H. placei and 23.7% for H. contortus. Pyrosequencing assays demonstrated single-nucleotide polymorphisms (SNPs) associated with BZ-resistance in all three codons (F167Y, E198A and F200Y) of the isotype 1 ß-tubulin gene in H. placei field populations. Frequencies of resistance-associated alleles above background (≥ 15%) were found for at least one codon in 11.4% of the field isolates and maximum frequencies of 30, 21 and 29% were found for codons 167, 198 and 200, respectively, on individual ranches. This study confirms the presence of H. contortus in beef cattle in the major livestock farming states in Brazil and demonstrates that genotypes associated with BZ resistance are present in field populations of Haemonchus spp..
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Anti-Helmínticos/farmacologia , Benzimidazóis/farmacologia , Doenças dos Bovinos/epidemiologia , Resistência a Medicamentos/genética , Hemoncose/veterinária , Haemonchus/fisiologia , Polimorfismo de Nucleotídeo Único/genética , Alelos , Animais , Biodiversidade , Brasil/epidemiologia , Bovinos , Doenças dos Bovinos/parasitologia , Hemoncose/epidemiologia , Hemoncose/parasitologia , Haemonchus/genética , Masculino , PrevalênciaRESUMO
The aim of this work was to gain a more comprehensive and perspicacious view of the endophytic diazotrophic community (EDC) of tomato plant bacteria and assess the effects of chemical fertilization and the plant phenologic stage on the status of those microbes. When the EDC of stem and roots from tomato plants grown in a greenhouse with and without exogenous chemical fertilization was examined by pyrosequencing the nifH gene during the growth cycle, a high taxonomic and phylogenetic diversity was observed. The abundant taxa were related to ubiquitous endophytes such as Rhizobium or Burkholderia but also involved anaerobic members usually restricted to flooded plant tissues, such as Clostridium, Geobacter, and Desulfovibrio. The EDC composition appeared to be dynamic during the growth phase of the tomato, with the structure of the community at the early stages of growth displaying major differences from the late stages. Inorganic fertilization negatively affected the diversity and modified the profile of the predominant components of the EDC in the different growth stages. Populations such as Burkholderia and Geobacter plus the Cyanobacteria appeared particularly affected by fertilization.Our work demonstrates an extensive endophytic diazotrophic diversity, suggesting a high potential for nitrogen fixation. The effect of the phenologic stage and inorganic-chemical soil fertilization on the community structure indicated a dynamic community that responded to environmental changes. These findings contribute to a better understanding of endophytic associations that could be helpful in assisting to shape the endomicrobiome that provides essential benefits to crops.