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1.
Water Res ; 169: 115279, 2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-31734392

RESUMO

Nitrate production during anammox can decrease total nitrogen removal efficiency, which will negatively impact its usefulness for the removal of nitrogen from waste streams. However, neither the performance characteristics nor physiological shifts associated with nitrate accumulation in anammox reactors under different nitrogen loading rates (NLRs) is well understood. Consequently, these parameters were studied in a lower NLR anammox reactor, termed R1, producing higher than expected levels of nitrate and compared with a higher NLR reactor, termed R2, showing no excess nitrate production. While both reactors showed high NH4+-N removal efficiencies (>90%), the total nitrogen removal efficiency (<60%) was much lower in R1 due to higher nitrate production. Metagenomic analysis found that the number of reads derived from anammox bacteria were significantly higher in R2. Another notable trend in reads occurrence was the relatively higher levels of reads from genes predicted to be nitrite oxidoreductases (nxr) in R1. Binning yielded 27 high quality draft genomes from the two reactors. Analysis of bin occurrence found that R1 showing both a decrease in anammox bacteria and an unexpected increase in nxr. In-situ assays confirmed that R1 had higher rates of nitrite oxidation to nitrate and suggested that it was not solely due to obligate NOB, but other nxr-containing bacteria are important contributors as well. Our results demonstrate that nitrate accumulation can be a serious operational concern for the application of anammox technology to low-strength wastewater treatment and provide insight into the community changes leading to this outcome.


Assuntos
Microbiota , Nitrogênio , Reatores Biológicos , Desnitrificação , Metagenômica , Oxirredução
2.
Scand J Immunol ; 91(1): e12805, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31267543

RESUMO

Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by a mutation in the WAS gene that encodes the WAS protein (WASp); up to 5-10% of these patients develop inflammatory bowel disease (IBD). The mechanisms by which WASp deficiency causes IBD are unclear. Intestinal microbial dysbiosis and imbalances in host immune responses play important roles in the pathogenesis of polygenetic IBD; however, few studies have conducted detailed examination of the microbial alterations and their relationship with IBD in WAS. Here, we collected faecal samples from 19 children (all less than 2 years old) with WAS and samples from WASp-KO mice with IBD and subjected them to 16S ribosomal RNA sequencing. We found that microbial community richness and structure in WAS children were different from those in controls; WAS children revealed reduced microbial community richness and diversity. Relative abundance of Bacteroidetes and Verrucomicrobiain in WAS children was significantly lower, while that of Proteobacteria was markedly higher. WASp-KO mice revealed a significantly decreased abundance of Firmicutes. Faecal microbial dysbiosis caused by WASp deficiency is similar to that observed for polygenetic IBD, suggesting that WASp may play crucial function in microbial homoeostasis and that microbial dysbiosis may contribute to IBD in WAS. These microbial alterations may be useful targets for monitoring and therapeutically managing intestinal inflammation in WAS.


Assuntos
Disbiose , Fezes/microbiologia , Microbioma Gastrointestinal , Síndrome de Wiskott-Aldrich/etiologia , Animais , Biodiversidade , Biomarcadores , Estudos de Casos e Controles , Pré-Escolar , Modelos Animais de Doenças , Feminino , Humanos , Lactente , Doenças Inflamatórias Intestinais/etiologia , Masculino , Metagenoma , Metagenômica/métodos , Camundongos , Camundongos Knockout , Mutação , RNA Ribossômico 16S/genética , Síndrome de Wiskott-Aldrich/diagnóstico , Proteína da Síndrome de Wiskott-Aldrich/deficiência
3.
BJOG ; 127(2): 159-169, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31376240

RESUMO

OBJECTIVES: To resolve the controversy regarding the presence of a microbiota in the placenta. DESIGN: Classical and molecular microbiological study. SETTING: All samples were collected during caesarean section. POPULATION: A total of 28 human placentas and six murine placentas. METHODS: All 28 human placentas were checked for 16S rRNA gene amplification products. Three locations from four selected human placentas and three 'environmental controls' for each placenta were placed in seven culture media. The four selected human placentas were further analysed using Gram stain, immunohistochemistry for bacteria, electron microscopy, and TaqMan RT-qPCR. Six placentas from three SPF mice were cut into four pieces each, and further analysed for 16S rRNA gene amplification. MAIN OUTCOME MEASURES: Microbiological and molecular evidence of bacteria. RESULTS: None of the placental cultures used for the full analysis, or their environmental cultures, was positive for bacterial growth. None of the other methods showed any evidence of bacteria. Immunohistochemistry showed negligible bacterial counts. None of the murine placentas showed evidence of 16S rRNA gene amplification. CONCLUSIONS: Our results support that the fetal environment in the womb is sterile. Based on the immunohistochemistry and the limit of detection of the other methods used, if a placental microbiome exists, it is of extreme low biomass, and thus its effect on clinical phenotypes is probably minor, if it exists at all. TWEETABLE ABSTRACT: Using several microbiological and molecular methods in parallel, we found no compelling evidence of bacteria in human and mouse placentas.


Assuntos
Líquido Amniótico/microbiologia , Microbioma Gastrointestinal/fisiologia , Microbiota/genética , Placenta/microbiologia , RNA Ribossômico 16S/fisiologia , Líquido Amniótico/imunologia , Animais , Feminino , Microbioma Gastrointestinal/imunologia , Humanos , Imuno-Histoquímica , Metagenômica , Camundongos , Placenta/imunologia , Gravidez , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
4.
BJOG ; 127(2): 147-158, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31587490

RESUMO

The female reproductive tract represents a continuum between the vagina and the upper genital tract. New evidence from cultivation-independent studies suggests that the female upper genital tract is not sterile; however, the significance of this for reproductive health and disease remains to be elucidated fully. Further, diagnosis and treatment of infectious reproductive tract pathologies using cultivation-independent technologies represents a largely unchartered area of modern medical science. The challenge now is to design well-controlled experiments to account for the ease of contamination known to confound molecular-based studies of low-biomass niches, including the uterus and placenta. This will support robust assessment of the potential function of microorganisms, microbial metabolites, and cell-free bacterial DNA on reproductive function in health and disease. TWEETABLE ABSTRACT: Molecular microbial studies of low-biomass niches require stringent experimental controls to reveal causal relations in reproductive health and disease.


Assuntos
Biomassa , Microbioma Gastrointestinal/fisiologia , Placenta/microbiologia , Saúde Reprodutiva , Infecções do Sistema Genital/microbiologia , Vagina/microbiologia , Feminino , Microbioma Gastrointestinal/genética , Microbioma Gastrointestinal/imunologia , Humanos , Metagenômica , Placenta/imunologia , Gravidez , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vagina/imunologia
5.
Food Microbiol ; 85: 103295, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500701

RESUMO

Fermented red pepper (FRP) sauce has been eaten in worldwide for many years. The salt content and resident microbial community influences the quality of the FRP sauce and may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers in some circumstances; however, the salt-mediated alteration of microbial community and antibiotic resistance genes are little known. In this study, a combination of whole genome sequencing and amplicon analysis was used to investigate the changes in microbial community and antimicrobial resistance genes in response to different salt content during red pepper fermentation. While the family Enterobacteriaceae dominated in high-salt (15-25%) samples, Lactobacillaceae quickly became the dominant population in place of Enterobacteriaceae after 24 days in 10% salt samples. Compared to 0.05 antibiotic resistance genes (ARGs) per cell number on average in 10% salt sample, 16.6 ARGs were present in high-salt samples, wherein the bacterial hosts were major assigned to Enterobacteriaceae including genera Enterobacter, Citrobacter, Escherichia, Salmonella and Klebsiella. Multidrug resistance genes were the predominant ARG type. Functional profiling showed that histidine kinase functions were of much higher abundance in high-salt samples and included several osmotic stress-related two-component systems that simultaneously encoded ARGs. These results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.


Assuntos
Capsicum/química , Farmacorresistência Bacteriana/genética , Enterobacteriaceae/genética , Lactobacillaceae/genética , Metagenoma , Microbiota , Cloreto de Sódio/química , Enterobacteriaceae/crescimento & desenvolvimento , Fermentação , Genes Bacterianos , Lactobacillaceae/crescimento & desenvolvimento , Metagenômica , Pressão Osmótica
6.
Food Microbiol ; 85: 103278, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500705

RESUMO

The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.


Assuntos
Queijo/virologia , Metagenoma , Metagenômica/métodos , Vírion/genética , Bacteriófagos/genética , Microbiota , Virologia/métodos
7.
Chemosphere ; 238: 124596, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31524629

RESUMO

Deteriorated environmental conditions during the bioremediation of trichloroethene (TCE)-polluted groundwater cause decreased treatment efficiencies. This study assessed the effect of applying immobilized Clostridium butyricum (a hydrogen-producing bacterium) in silica gel on enhancing the reductive dechlorination efficiency of TCE with the slow polycolloid-releasing substrate (SPRS) supplement in groundwater. The responses of microbial communities with the immobilized system (immobilized Clostridium butyricum and SPRS amendments) were also characterized by the metagenomics assay. A complete TCE removal in microcosms was obtained within 30 days with the application of this immobilized system via reductive dechlorination processes. An increase in the population of Dehalococcoides spp. was observed using the quantitative polymerase chain reaction (qPCR) analysis. Results of metagenomics assay reveal that the microbial communities in the immobilized system were distinct from those in systems with SPRS only. Bacterial communities associated with TCE biodegradation also increased in microcosms treated with the immobilized system. The immobilized system shows a great potential to promote the TCE dechlorination efficiency, and the metagenomics-based approach provides detailed insights into dechlorinating microbial community dynamics. The results would be helpful in designing an in situ immobilized system to enhance the bioremediation efficiency of TCE-contaminated groundwater.


Assuntos
Chloroflexi/metabolismo , Clostridium butyricum/metabolismo , Água Subterrânea/química , Tricloroetileno/metabolismo , Biodegradação Ambiental , Chloroflexi/crescimento & desenvolvimento , Halogenação , Metagenômica , Microbiota/fisiologia , Sílica Gel
8.
Sheng Wu Gong Cheng Xue Bao ; 35(11): 2081-2091, 2019 Nov 25.
Artigo em Chinês | MEDLINE | ID: mdl-31814356

RESUMO

Lignocellulose is widely found in the nature. The highly efficient degradation of lignocellulose requires synergistic interactions of varieties of microorganisms. The mechanism of synergistic interaction relationship is not entirely clear because it needs multitudinous microorganisms to participate in the process of lignocellulose degradation. With the development of microbial molecular biology and omics technology, some new methods will be provided for the research on the mechanism of microbial synergistic degradation of lignocellulose. Our previous research found that the bacterial composite microbial system shows strong degradation ability of lignocellulose at 50 °C. The consortium is composed of cultured and uncultured bacteria, but the former has no degradation ability. Metagenomics and metatranscriptomics show that the expression levels of some genes related to lignocellulosic degradation change significantly. It is possible to explain the microbiological and enzymatic mechanisms of lignocellulosic degradation by microorganisms through omics in the future. The research progress of lignocellulose microbial degradation is reviewed from the aspects of enzyme, pure culture strain, and microbial consortium. The current situation and application prospect of omics technology in analyzing the function mechanism of microbial consortium are also introduced, to provide reference for exploring synergistic interactions of lignocellulose microbial degradation.


Assuntos
Bactérias , Lignina , Bactérias/classificação , Bactérias/enzimologia , Bactérias/metabolismo , Lignina/metabolismo , Metagenômica
9.
Int. microbiol ; 22(4): 429-435, dic. 2019. graf, tab
Artigo em Inglês | IBECS | ID: ibc-185061

RESUMO

Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen


No disponible


Assuntos
Animais , Camelus , Metagenômica/métodos , Microbioma Gastrointestinal , Ativação Enzimática/genética , Cabras , Trato Gastrointestinal/microbiologia , Intestino Delgado/microbiologia , Intestino Grosso/microbiologia , Estômago de Ruminante/enzimologia , Estômago de Ruminante/microbiologia , Ruminantes/microbiologia
10.
Int. microbiol ; 22(4): 437-449, dic. 2019. graf, tab
Artigo em Inglês | IBECS | ID: ibc-185062

RESUMO

Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level


No disponible


Assuntos
Azurina/genética , Técnicas In Vitro/métodos , Variação Genética/efeitos dos fármacos , Microbioma Gastrointestinal/genética , Azurina/uso terapêutico , Bacteriocinas/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Metagenômica , Biologia Computacional/métodos , Antineoplásicos/farmacologia
11.
N Engl J Med ; 381(26): 2569-2580, 2019 12 26.
Artigo em Inglês | MEDLINE | ID: mdl-31881145

RESUMO

Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.


Assuntos
Surtos de Doenças , Doenças Transmitidas por Alimentos/epidemiologia , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Influenza Humana/epidemiologia , Saúde Pública , Tuberculose/epidemiologia , Animais , Bactérias/genética , Doenças Transmitidas por Alimentos/diagnóstico , Doenças Transmitidas por Alimentos/microbiologia , Doenças Transmitidas por Alimentos/parasitologia , Humanos , Influenza Humana/diagnóstico , Influenza Humana/microbiologia , Metagenômica , Parasitos/genética , Tuberculose/diagnóstico , Vírus/genética
12.
BMC Bioinformatics ; 20(Suppl 9): 367, 2019 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-31757198

RESUMO

MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths. RESULTS: In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.


Assuntos
Algoritmos , Mapeamento de Sequências Contíguas , Metagenoma , Metagenômica , Probabilidade , Estatística como Assunto , Análise por Conglomerados , Bases de Dados Genéticas , Microbiota/genética
13.
BMC Bioinformatics ; 20(Suppl 9): 416, 2019 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-31757204

RESUMO

BACKGROUND: In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data. RESULTS: In this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available at http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand https://gitlab.com/sysbiobig/metasparsim. CONCLUSION: metaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica , RNA Ribossômico 16S/genética , Software , Animais , Simulação por Computador , DNA Ribossômico/genética , Bases de Dados Genéticas , Humanos , Metagenoma
15.
Adv Exp Med Biol ; 1168: 147-156, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31713170

RESUMO

The microbiome comprises all the genetic material within a microbiota, that represents tenfold higher than that of our cells. The microbiota it includes a wide variety of microorganisms such as bacteria, viruses, protozoans, fungi, and archaea, and this ecosystem is personalized in any body space of every individual. Balanced microbial communities can positively contribute to training the immune system and maintaining immune homeostasis. Dysbiosis is a change in the normal microbiome composition that can initiate chronic inflammation, epithelial barrier breaches, and overgrowth of harmful bacteria. The next-generation sequencing methods have revolutionized the study of the microbiome. Bioinformatic tools to manage large volumes of new information, it became possible to assess species diversity and measure dynamic fluctuations in microbial communities. The burden of infections that are associated to human cancer is increasing but is underappreciated by the cancer research community. The rich content in microbes of normal and tumoral tissue reflect could be defining diverse physiological or pathological states. Genomic research has emerged a new focus on the interplay between the human microbiome and carcinogenesis and has been termed the 'oncobiome'. The interactions among the microbiota in all epithelium, induce changes in the host immune interactions and can be a cause of cancer. Microbes have been shown to have systemic effects on the host that influence the efficacy of anticancer drugs. Metagenomics allows to investigate the composition of microbial community. Metatranscriptome analysis applies RNA sequencing to microbial samples to determine which species are present. Cancer can be caused by changes in the microbiome. The roles of individual microbial species in cancer progression have been identified long ago for various tissue types. The identification of microbiomes of drug resistance in the treatment of cancer patients has been the subject of numerous microbiome studies. The complexity of cancer genetic alterations becomes irrelevant in certain cancers to explain the origin, the cause or the oncogenic maintenance by the oncogene addiction theory.


Assuntos
Microbiota , Neoplasias , Bactérias/genética , Disbiose , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Metagenômica , Microbiota/genética , Microbiota/fisiologia , Neoplasias/microbiologia
16.
Nature ; 574(7778): 304-305, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31616086
17.
Genome Biol ; 20(1): 217, 2019 10 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640809

RESUMO

Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.


Assuntos
Classificação/métodos , Genoma Microbiano , Metagenômica/métodos , Algoritmos , Fases de Leitura Aberta
18.
Ecotoxicol Environ Saf ; 186: 109771, 2019 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-31629904

RESUMO

In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used antibiotics in food-production. Yet, although useful to prevent infections, antibiotics may reshape aquatic animals' microbiome, disturbing hosts' welfare. However, the impact of this exposure to the organism microbiome and its surrounding environment is poorly understood. Then, the objective of this study was to analyze in detail the long-term effect of OTC in both zebrafish gut and water microbiomes. Zebrafish adults were exposed, via water, for two months to three concentrations of OTC (0, 10 and 10000 µg/L). Total DNA was extracted from gut and water samples and the V3-V4 region of the bacterial 16 S rRNA gene was sequenced using Illumina technology. Results of alpha and beta-diversity analyses revealed that long-term exposure to OTC impacted both zebrafish gut and water microbiomes. In water samples, effects were observed even at the lowest (10 µg/L) OTC concentration tested resulting in an increase in Deltaproteobacteria, namely the Myxococcales and Bdellovibrionales orders. On the other hand, effects on zebrafish gut were only observed at the highest concentration with the selection of Alphaproteobacteria and Actinobacteria classes. Although these classes are common in fish gut, the increase of Actinobacteria may represent a health problem since some genera like Gordonia are linked to some human infection disease. Nevertheless, in both gut and water, it was observed a decrease in Gamaproteobacteria, probably due to OTC mode of action. In silico functional metagenomic analysis revealed that OTC exposure selected general detoxification mechanisms. In addition, the abundance of functional genes involved in Quorum Sensing (QS) increased under OTC exposure suggesting that QS may help bacteria to survive OTC stress. Thus, future studies should consider post-exposure scenarios for a deeper analysis of the water and zebrafish gut resistome, since bacteria may react differently after exposure ceased.


Assuntos
Antibacterianos/toxicidade , Microbioma Gastrointestinal/efeitos dos fármacos , Metagenoma/efeitos dos fármacos , Poluentes Químicos da Água/toxicidade , Peixe-Zebra/microbiologia , Animais , Aquicultura , Microbioma Gastrointestinal/genética , Humanos , Metagenoma/genética , Metagenômica , RNA Ribossômico 16S/genética , Peixe-Zebra/genética
19.
BMC Bioinformatics ; 20(1): 486, 2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31581946

RESUMO

BACKGROUND: Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains over 220,000 genomes, and current metagenomic technology supports assemblies of many draft-quality genomes from a single sample, most of which will be novel. DESCRIPTION: We have added two quality assessment tools to the PATRIC annotation pipeline. EvalCon uses supervised machine learning to calculate an annotation consistency score. EvalG implements a variant of the CheckM algorithm to estimate contamination and completeness of an annotated genome.We report on the performance of these tools and the potential utility of the consistency score. Additionally, we provide contamination, completeness, and consistency measures for all genomes in PATRIC and in a recent set of metagenomic assemblies. CONCLUSION: EvalG and EvalCon facilitate the rapid quality control and exploration of PATRIC-annotated draft genomes.


Assuntos
Bases de Dados Genéticas , Genoma Arqueal , Genoma Bacteriano , Aprendizado de Máquina , Metagenômica/métodos , Metagenômica/normas , Software
20.
Vet Microbiol ; 237: 108390, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31585652

RESUMO

Parvovirosis is a highly contagious disease in dogs, often causing acute hemorrhagic enteritis and altering the intestinal microflora. In this study, real-time PCR was used to detect the viral copy numbers in dogs diagnosed with the disease. Hematological and hemobiochemical parameters were also determined. The species and abundances of the fecal microbial flora in both sick and healthy dogs were determined and compared via metagenomic sequencing. The viral copy numbers in the sick dogs were infected with little difference in the positive samples. The blood coagulation time was significantly shorter and the number of white blood cells was significantly greater in the sick dogs. The serum calcium content was slightly increased and the phosphorus content was reduced in the sick dogs. The LDH and CK activities were significantly elevated in the sick dogs. Metagenomic sequencing and analysis revealed relatively more Escherichia, Lachnoclostridium, gnavus group (Ruminococcus), and uncultured_bacterium_f_lachnospiraceae in the infected dogs, whereas the abundance of Collinsella was relatively reduced. Alloprevotella and Sutterella were absent among the fecal microorganisms of the infected dogs. The relative abundances of Romboutsia, Erysipelatoclostridium, Anaerotruncus, and Blautia were significantly increased in the infected dogs. Functional analysis of the metagenomes of the samples indicated a significant enrichment of the 'replication, recombination and repair', 'nucleotide transport and metabolism', 'transcription', and 'defense metabolism' functions in the fecal microbial flora of the infected dogs. In summary, this study provides a scientific theoretical basis for preventing and controlling diarrhea caused by the canine parvovirus.


Assuntos
Bactérias/classificação , Doenças do Cão/virologia , Fezes/microbiologia , Infecções por Parvoviridae/veterinária , Animais , Cães , Metagenômica , Infecções por Parvoviridae/virologia , Parvovirus Canino , Reação em Cadeia da Polimerase em Tempo Real
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