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1.
Water Res ; 170: 115277, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-31756613

RESUMO

The emergence and spread of resistance to antibiotics among bacteria is the most serious global threat to public health in recent and coming decades. In this study, we characterized qualitatively and quantitatively ß-lactamase and carbapenemase genes in the wastewater resistome of Central Wastewater Treatment Plant in Kozieglowy, Poland. The research concerns determination of the frequency of genes conferring resistance to ß-lactam and carbapenem antibiotics in the genomes of culturable bacteria, as well as in the wastewater metagenome at three stages of treatment: raw sewage, aeration tank, and final effluent. In the final effluent we found bacteria with genes that pose the greatest threat to public health, including genes of extended spectrum ß-lactamases - blaCTX-M, carbapenemases - blaNDM, blaVIM, blaGES, blaOXA-48, and showed that during the wastewater treatment their frequency increased. Moreover, the wastewater treatment process leads to significant increase in the relative abundance of blaTEM and blaGES genes and tend to increase the relative abundance of blaCTX-M, blaSHV and blaOXA-48 genes in the effluent metagenome. The biodiversity of bacterial populations increased during the wastewater treatment and there was a correlation between the change in the composition of bacterial populations and the variation of relative abundance of ß-lactamase and carbapenemase genes. PCR-based quantitative metagenomic analysis combined with analyses based on culture methods provided significant information on the routes of ARBs and ARGs spread through WWTP. The limited effectiveness of wastewater treatment processes in the elimination of antibiotic-resistant bacteria and resistance genes impose the need to develop an effective strategy and implement additional methods of wastewater disinfection, in order to limit the increase and the spread of antibiotic resistance in the environment.


Assuntos
Metagenoma , Águas Residuárias , Antibacterianos , Proteínas de Bactérias , Polônia , beta-Lactamases
2.
Water Res ; 169: 115250, 2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-31726395

RESUMO

The use of irrigation water sourced from reclamation facilities and untreated surface water bodies may be a practical solution to attenuate the burden on diminishing groundwater aquifers. However, comprehensive microbial characterizations of these water sources are generally lacking, especially with regard to variations through time and across multiple water types. To address this knowledge gap we used a shotgun metagenomic approach to characterize the taxonomic and functional variations of microbial communities within two agricultural ponds, two freshwater creeks, two brackish rivers, and three water reclamation facilities located in the Mid-Atlantic, United States. Water samples (n = 24) were collected from all sites between October and November 2016, and filtered onto 0.2 µm membrane filters. Filters were then subjected to total DNA extraction and shotgun sequencing on the Illumina HiSeq platform. From these data, we found that Betaproteobacteria dominated the majority of freshwater sites, while Alphaproteobacteria were abundant at times in the brackish waters. One of these brackish sites was also host to a greater abundance of the bacterial genera Gimesia and Microcystis. Furthermore, predicted microbial features (e.g. antibiotic resistance genes (ARGs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays) varied based on specific site and sampling date. ARGs were found across samples, with the diversity and abundance highest in those from a reclamation facility and a wastewater-impacted freshwater creek. Additionally, we identified over 600 CRISPR arrays, containing ∼2600 unique spacers, suggestive of a diverse and often site-specific phage community. Overall, these results provide a better understanding of the complex microbial community in untreated surface and reclaimed waters, while highlighting possible environmental and human health impacts associated with their use in agriculture.


Assuntos
Metagenoma , Águas Residuárias , Resistência Microbiana a Medicamentos , Humanos , Rios , Microbiologia da Água
3.
Arch Microbiol ; 202(1): 31-41, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31456050

RESUMO

Anaerobic digestion, a recently hot technology to produce biogases especially methane generation for biofuel from wastewater, is considered an effective explanation for energy crisis and global pollution threat. A complex microbiome population is present in sludge, which plays an important role in the digestion of complex polymer into simple monomers. 16S rRNA approaches simply are not enough for amplification due to the involvement of extreme complex population. However, Illumina sequencing is a recent powerful technology to reveal the entire microbiome structure and methane generation pathways in anaerobic digestion. Metagenomic sequencing was tested to reveal the microbial structure of a digested sludge from a local wastewater treatment plant in Beijing. The Illumina HiSeq program was used to extract about 5 GB of data for metagenomic analysis. The classification investigation revealed about 97.64% dominancy of bacteria while 1.78% were detected to be archaea using MG-RAST server. The most abundant bacterial communities were reported to be Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Furthermore, the important microbiome involved in methane generation was revealed. The dominant methanogens were detected (Methanosaeta and Methanosarcina), with affiliation of dominant genes involved in acetoclastic methanogenesis in a digesting sludge. The metagenomic analysis showed that microbial structure and methane generation pathways were successfully dissected in an anaerobic digester.


Assuntos
Biocombustíveis/microbiologia , Genoma Microbiano/genética , Metagenoma/genética , Metano/metabolismo , Esgotos/microbiologia , Anaerobiose , Archaea/genética , Bactérias/genética , Sequenciamento de Nucleotídeos em Larga Escala , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
4.
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
5.
Huan Jing Ke Xue ; 41(1): 313-320, 2020 Jan 08.
Artigo em Chinês | MEDLINE | ID: mdl-31854932

RESUMO

Wastewater treatment plants hold a vast pool of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The aim of this study is to analyze the ARB and ARGs in a pharmaceutical and chemical wastewater treatment plant using a metagenomic technique. The results of taxonomic annotation revealed that bacteria were the predominant domain. The most abundant phyla and genus was Proteobacteria and Hyphomicrobium, respectively. A total of 74 categories of ARGs were predicted using CARD with the most dominant types being sav 1866, dfrE, and mfd. Furthermore, a network analysis was conducted to investigate the co-occurrence patterns between ARGs and microbial taxa. ARGs were found to be highly connected to microbial taxa at the genus level. With respect to the antibiotic resistance mechanisms, antibiotic-specific efflux pumps appeared to be the most common mechanisms. Among these, resistance-nodulation-cell division (RND) was the major type. The most important functional pathway of this microbial community was metabolic correlation. Interestingly, there were many genes related to human diseases, among which bacterial infectious diseases were the main ones. On the one hand, these data further confirmed that pharmaceutical and chemical wastewater treatment plants are rich in ARB and ARGs. The accumulation of ARGs increases the potential environmental risks, and hence it is necessary to strengthen the active monitoring of ARB and ARGs in pharmaceutical and chemical wastewater treatment plants. On the other hand, research on ARB and ARGs offers important information for the selection of deep processing technology to effectively remove ARB and ARGs.


Assuntos
Bactérias/classificação , Farmacorresistência Bacteriana , Genes Bacterianos , Águas Residuárias , Purificação da Água , Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Humanos , Metagenoma , Preparações Farmacêuticas
6.
Water Res ; 171: 115425, 2020 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-31881499

RESUMO

Stimulating Methanothrix-dominant communities with ethanol is recently considered as a promising strategy of improving the efficiency and stability of anaerobic digestion (AD), while the effects on methanogenic pathway and energy metabolism linked to the establishment of direct interspecies electron transfer (DIET) were not investigated yet. The results showed that, Methanothrix species were the dominant and metabolically active methanogens in the methanogenic sludge fed with the ethanol-type fermentation products, and the abundance of genes that encoded the key enzymes involved in the reduction of carbon dioxide was significantly higher than that fed with the other products, such as propionate and butyrate. Conversely, the abundance of genes that encoded the key enzymes involved in acetate decarboxylation among all the methanogenic sludge were nearly same. In the presence of ethanol, the abundance of gene for pilA significantly increased. The gene for pliA was primarily derived from Sphaerochaeta, Sedimentibacter and Pseudomonas species that were specially abundant and metabolically active. Further analysis showed that, the abundance of genes that encoded V/A-type ATPase in the methanogenic digesters fed with the ethanol-type fermentation products was 1.3-1.5 folds higher than that fed with the other products. As a result, the concentration of total ATP in the cells was increased by 1.8-2.3 folds. These results, and the fact that DIET is the only electron donor to support the reduction of carbon dioxide in Methanothrix species for the first time revealed the mechanisms involved in the establishment of DIET-based methanogenic metabolism with ethanol.


Assuntos
Etanol , Metano , Anaerobiose , Reatores Biológicos , Metagenoma , Methanosarcinaceae
7.
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
8.
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
9.
Food Microbiol ; 85: 103302, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500708

RESUMO

This study dealt with the influence of the temperature on the bacterial dynamics of two spontaneously fermented wheat sourdoughs, propagated at 21 ±â€¯1 °C (SD1) and 30 ±â€¯1 °C (SD2), during nine backslopping steps (BS1 to BS9). Proteobacteria was the only phylum found in flour. Escherichia hermannii was predominant, followed by Kosakonia cowanii, besides species belonging to the genera Pantoea and Pseudomonas. After one step of propagation, Clostridium and Bacillus cereus group became predominant. Lactobacillus curvatus was found at low relative abundance. For the second backslopping step, Clostridium was flanked by L. curvatus and Lactobacillus farciminis. From BS4 (6th day) onward, lactic acid bacteria (LAB) became predominant. L. farciminis overcame L. curvatus and remained dominant until the end of propagations for both sourdoughs. At 21 °C, Bacillus, Clostridium, Pseudomonas, and Enterobacteriaceae were gradually inhibited. At the end of propagation, SD1 harbored only LAB. Otherwise, the temperature of 30 °C favored the persistence of atypical bacteria in SD2, as Pseudomonas and Enterobacteriaceae. Therefore, the temperature of 21 °C was more suitable for sourdough propagation in Brazil. This study enhanced the knowledge of temperature's influence on microbial assembly and contributed to the elucidation of sourdough microbial communities in Brazil.


Assuntos
Pão/microbiologia , Fermentação , Metagenoma , Proteobactérias/classificação , Brasil , Contagem de Colônia Microbiana , DNA Bacteriano/genética , Farinha/microbiologia , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota , Proteobactérias/crescimento & desenvolvimento , RNA Ribossômico 16S/genética , Temperatura Ambiente
10.
Sci Total Environ ; 701: 134682, 2020 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-31704413

RESUMO

Biofilm formation on membranes in activated sludge membrane bioreactors (MBR), commonly identified as biofouling, is a significant problem for MBR operations. A better understanding of microbial species involved in the biofilm formation is needed to develop anti-biofilm measures. A read-based and genome-resolved shotgun metagenomic approach was applied to characterize the composition and functional potential of the sludge and early stage biofilm microbial communities in an MBR process. Read-based analysis revealed that the prevalence of different phyla are relatively similar in both the sludge and biofilm samples, with Proteobacteria as the most dominant, followed by Chloroflexi, Bacteroidetes and Planctomycetes. However, the relative abundance of these phyla slightly varies between the sludge and biofilm. Phyla such as Actinobacteria, bacterial candidate phyla, Chlamydiae, Cyanobacteria/Melainabacteria and Firmicutes are 2 to 4 times more abundant in the biofilm than in the sludge. At the genus level, genera belonging to Proteobacteria (Legionella, Caulobacter, Sphingomonas, Acinetobacter and Rhizobium), Cyanobacteria (Hassallia), and Spirochaetes (Turneriella) are at least twice more abundant in the biofilm. These genera, especially those belonging to Phylum Proteobacteria, are known to play an important role in the formation of biofilms on surfaces. The Alpha diversity is found slightly higher in the biofilm, compared with sludge samples. Functional classification of reads through the SEED subsystem shows that functional classes such as those involved in the metabolism of various molecules are significantly different in the biofilm and sludge. A phylogenomic analysis of the six extracted metagenome assembled genomes (MAGs) shows that three MAGs belong to Proteobacteria, and one MAG belong to each of Chloroflexi, Bacteroidetes and Planctomycetes. The relative abundance of the MAG belonging to Alphaproteobacteria is higher in the biofilm. A functional potential analysis of the MAGs reveals their potential to metabolize carbon and nitrogen sources, as well as the prevalence of antibiotic resistance genes.


Assuntos
Biofilmes , Reatores Biológicos/microbiologia , Microbiota , Eliminação de Resíduos Líquidos , Incrustação Biológica , Membranas Artificiais , Metagenoma , Esgotos/microbiologia
11.
Environ Monit Assess ; 191(12): 778, 2019 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-31784843

RESUMO

The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing technology to analyze microbial communities and their metabolic capabilities in polluted environments. A total of 1113884 sequences of v3-v4 hypervariable region of the 16S rRNA were obtained using Illumina sequencing and assigned to the corresponding taxonomical ranks using Greengenes databases. Proteobacteria and Bacteroidetes were dominantly present in all the four studied sites (solid waste dumping site (SWD); Chite river site (CHR), Turial river site (TUR), and Tuikual river site (TUKR)). It was found that the SWD was dominated by Firmicutes, Actinobacteria; CHR by Acidobacteria, Verrucomicrobia, Planctomycetes; TUR by Verrucomicrobia, Acidobacteria; and TUKR by Verrucomicrobia and Firmicutes, respectively. The dominant bacterial genus present in all samples was Acinetobacter, Flavobacterium, Prevotella, Corynebacterium, Comamonas, Bacteroides, Wautersiella, Cloacibacterium, Stenotrophomonas, Sphingobacterium, and Pseudomonas. Twenty-seven putative bacterial pathogens were identified from the contaminated sites belonging to Salmonella enterica, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Functional analysis showed a high representation of genes in the KEGG pathway involved in the metabolism of amino acids and carbohydrates and identified several genes associated with antibiotic resistance and xenobiotic degradation in these environments, which can be a serious problem for human health and environment. The results from this research will provide a new understanding of the possible management practices to minimize the spread of pathogenic microorganisms in the environment.


Assuntos
Bactérias , Microbiologia Ambiental , Microbiota , Microbiologia do Solo , Bactérias/classificação , Bactérias/genética , Monitoramento Ambiental , Metagenoma , Microbiota/genética , RNA Ribossômico 16S/genética , Rios/química , Rios/microbiologia , Instalações de Eliminação de Resíduos
12.
Sheng Wu Gong Cheng Xue Bao ; 35(11): 2050-2060, 2019 Nov 25.
Artigo em Chinês | MEDLINE | ID: mdl-31814353

RESUMO

As flame retardants, organophosphate is recognized as a global environmental contaminant because of its wide application. This contaminant is hardly degradable by hydrolysis in the environment due to its special physicochemical properties. Therefore, it is of urgent needs to study the microbial degradation of organophosphate. Through continuous enrichment, we isolated one bacterial consortium, named YC-BJ1, from leachate of waste treatment plant in Beijing. The bacterial consortium YC-BJ1 could efficiently degrade 99.8% of triphenyl phosphate (TPhP) and 91.9% of tricresyl phosphate (TCrP) with the concentration of 100 mg/L within 4 days. Besides aryl phosphates, it could degrade chloro-phosphates, tris(1,3-dichloroisopropyl) phosphate (TDCPP) and tris(2-chloroethyl) phosphate (TCEP) by 16.5% and 22.0% respectively. The degradation of the consortium on TPhP was optimized through a broad range of temperature (15-40 ℃), pH (5.0-12.0) and salinity (0%-4%). 16S rRNA gene-based metagenomic analysis revealed that Hyphomicrobium (38.80%), Chryseobacterium (17.57%) and Sphingopyxis (17.46%) were the dominant genera of the consortium YC-BJ1. Compared with the reported organophosphorus flame retardants (OPFRs) degrading bacteria and microflora, the mixed microflora YC-BJ1 exhibited great advantages in degradation efficiency and environmental adaptability, demonstrating its wide application potential. The enrichment and isolation of highly efficient degrading flora can provide abundant microbial resources for the degradation of OPFRs and the bioremediation towards OPFRs-contaminated environments, and also lay a solid foundation for the exploration of its degradation mechanism.


Assuntos
Bactérias , Recuperação e Remediação Ambiental , Retardadores de Chama , Metagenoma , Compostos Organofosforados , RNA Ribossômico 16S , Bactérias/classificação , Bactérias/genética , Retardadores de Chama/metabolismo , Compostos Organofosforados/metabolismo , RNA Ribossômico 16S/genética
13.
Nat Med ; 25(12): 1873-1884, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31806906

RESUMO

Herpes simplex virus-1 (HSV-1) encephalitis (HSE) is typically sporadic. Inborn errors of TLR3- and DBR1-mediated central nervous system cell-intrinsic immunity can account for forebrain and brainstem HSE, respectively. We report five unrelated patients with forebrain HSE, each heterozygous for one of four rare variants of SNORA31, encoding a small nucleolar RNA of the H/ACA class that are predicted to direct the isomerization of uridine residues to pseudouridine in small nuclear RNA and ribosomal RNA. We show that CRISPR/Cas9-introduced bi- and monoallelic SNORA31 deletions render human pluripotent stem cell (hPSC)-derived cortical neurons susceptible to HSV-1. Accordingly, SNORA31-mutated patient hPSC-derived cortical neurons are susceptible to HSV-1, like those from TLR3- or STAT1-deficient patients. Exogenous interferon (IFN)-ß renders SNORA31- and TLR3- but not STAT1-mutated neurons resistant to HSV-1. Finally, transcriptome analysis of SNORA31-mutated neurons revealed normal responses to TLR3 and IFN-α/ß stimulation but abnormal responses to HSV-1. Human SNORA31 thus controls central nervous system neuron-intrinsic immunity to HSV-1 by a distinctive mechanism.


Assuntos
Encefalite por Herpes Simples/genética , Herpesvirus Humano 1/genética , Neurônios/imunologia , RNA Nucleolar Pequeno/genética , Adulto , Sistema Nervoso Central/imunologia , Sistema Nervoso Central/virologia , Pré-Escolar , Encefalite por Herpes Simples/imunologia , Encefalite por Herpes Simples/patologia , Encefalite por Herpes Simples/virologia , Feminino , Predisposição Genética para Doença , Herpesvirus Humano 1/imunologia , Herpesvirus Humano 1/patogenicidade , Humanos , Imunidade/genética , Lactente , Masculino , Metagenoma/genética , Metagenoma/imunologia , Pessoa de Meia-Idade , Neurônios/virologia , RNA Nucleolar Pequeno/imunologia
14.
Science ; 366(6471): 1309-1310, 2019 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-31831655
15.
Nat Methods ; 16(12): 1201, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31780826
16.
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
17.
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
18.
J Microbiol ; 57(12): 1095-1104, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31758395

RESUMO

Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.


Assuntos
Sedimentos Geológicos/microbiologia , Hidrogênio/metabolismo , Metagenoma , Microbiota/fisiologia , Regiões Antárticas , Archaea/classificação , Archaea/enzimologia , Archaea/genética , Archaea/metabolismo , Bactérias/classificação , Bactérias/enzimologia , Bactérias/genética , Bactérias/metabolismo , Ciclo do Carbono , Crescimento Quimioautotrófico , Comamonadaceae/enzimologia , Comamonadaceae/metabolismo , Genes Arqueais/genética , Genes Bacterianos/genética , Hidrogenase/classificação , Hidrogenase/genética , Hidrogenase/isolamento & purificação , Redes e Vias Metabólicas , Microbiota/genética , Nitratos/metabolismo , Fosforilação Oxidativa , Fotossíntese , Análise de Sequência de DNA
19.
World J Microbiol Biotechnol ; 35(11): 176, 2019 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-31673867

RESUMO

The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.


Assuntos
Bactérias/classificação , Bactérias/metabolismo , Clima , Endófitos/classificação , Ipomoea batatas/microbiologia , Metagenoma , Microbiota , Solo/química , Bactérias/genética , Sequência de Bases , Biodiversidade , DNA Bacteriano/análise , DNA Mitocondrial/análise , Endófitos/genética , Microbiota/genética , Filogenia , RNA Ribossômico 16S/genética , Microbiologia do Solo
20.
BMC Bioinformatics ; 20(1): 552, 2019 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-31694525

RESUMO

BACKGROUND: Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS: Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors. CONCLUSIONS: MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub .


Assuntos
Aprendizado Profundo/normas , /métodos , Bases de Dados Genéticas , Humanos , Metagenoma , Melhoria de Qualidade , Software
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