Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 6.071
Filtrar
2.
BMC Bioinformatics ; 21(1): 471, 2020 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-33087062

RESUMO

BACKGROUND: Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Functional annotation of shotgun metagenomic data has become an increasingly popular method for identifying the aggregate functional capacities encoded by the community's constituent microbes. Currently available metagenomic functional annotation pipelines, however, suffer from several shortcomings, including limited pipeline customization options, lack of standard raw sequence data pre-processing, and insufficient capabilities for integration with distributed computing systems. RESULTS: Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun metagenomic data as input and generate functional profiles. MetaLAFFA is implemented as a Snakemake pipeline, which enables convenient integration with distributed computing clusters, allowing users to take full advantage of available computing resources. Default pipeline settings allow new users to run MetaLAFFA according to common practices while a Python module-based configuration system provides advanced users with a flexible interface for pipeline customization. MetaLAFFA also generates summary statistics for each step in the pipeline so that users can better understand pre-processing and annotation quality. CONCLUSIONS: MetaLAFFA is a new end-to-end metagenomic functional annotation pipeline with distributed computing compatibility and flexible customization options. MetaLAFFA source code is available at https://github.com/borenstein-lab/MetaLAFFA and can be installed via Conda as described in the accompanying documentation.


Assuntos
Metagenômica/métodos , Software , Humanos , Microbiota
3.
Gigascience ; 9(10)2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-33057676

RESUMO

BACKGROUND: Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments. FINDINGS: We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. CONCLUSION: The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.


Assuntos
Betacoronavirus/genética , Computação em Nuvem , Infecções por Coronavirus/virologia , Metagenoma , Metagenômica/métodos , Pneumonia Viral/virologia , Betacoronavirus/patogenicidade , Infecções por Coronavirus/diagnóstico , Bases de Dados Genéticas , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Pandemias , Pneumonia Viral/diagnóstico , Software
4.
Nat Commun ; 11(1): 5085, 2020 10 08.
Artigo em Inglês | MEDLINE | ID: mdl-33033250

RESUMO

Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cultivars as well as Tibetan landraces. We demonstrate that high-altitude environments can trigger extensive reshaping of wheat genomes, and also uncover that Tibetan wheat accessions accumulate high-altitude adapted haplotypes of related genes in response to harsh environmental constraints. Moreover, we find that Tibetan semi-wild wheat is a feral form of Tibetan landrace, and identify two associated loci, including a 0.8-Mb deletion region containing Brt1/2 homologs and a genomic region with TaQ-5A gene, responsible for rachis brittleness during the de-domestication episode. Our study provides confident evidence to support the hypothesis that Tibetan semi-wild wheat is de-domesticated from local landraces, in response to high-altitude extremes.


Assuntos
Adaptação Fisiológica , Altitude , Triticum/fisiologia , Adaptação Fisiológica/genética , Domesticação , Ecótipo , Genoma de Planta , Geografia , Metagenômica , Fenótipo , Análise de Componente Principal , Tibet , Triticum/genética
5.
Nat Commun ; 11(1): 4988, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-33020496
6.
Water Res ; 185: 116127, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33086465

RESUMO

Antibiotic resistance has become a global public health concern, rendering common infections untreatable. Given the widespread occurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance gene (ARG) dissemination outside the clinical realm. Studies during the past decade have clearly proved the increased ARG pollution trend along with gradient of anthropogenic interference, mainly through marker-ARG detection by PCR-based approaches. However, accurate source-tracking has been always confounded by various factors in previous studies, such as autochthonous ARG level, spatiotemporal variability and environmental resistome complexity, as well as inherent method limitation. The rapidly developed metagenomics profiles ARG occurrence within the sample-wide genomic context, opening a new avenue for source tracking of environmental ARG pollution. Coupling with machine-learning classification, it has been demonstrated the potential of metagenomic ARG profiles in unambiguously assigning source contribution. Through identifying indicator ARG and recovering ARG-host genomes, metagenomics-based analysis will further increase the resolution and accuracy of source tracking. In this review, challenges and progresses in source-tracking studies on environmental ARG pollution will be discussed, with specific focus on recent metagenomics-guide approaches. We propose an integrative metagenomics-based framework, in which coordinated efforts on experimental design and metagenomic analysis will assist in realizing the ultimate goal of robust source-tracking in environmental ARG pollution.


Assuntos
Antibacterianos , Genes Bacterianos , Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos/genética , Genes Bacterianos/genética , Metagenoma , Metagenômica
7.
Nat Commun ; 11(1): 5494, 2020 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-33127895

RESUMO

Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.


Assuntos
Archaea/classificação , Archaea/genética , Duplicação Gênica , Genoma Arqueal , Filogenia , Archaea/metabolismo , Ecossistema , Evolução Molecular , Transferência Genética Horizontal , Metagenômica , Proteoma
8.
Nat Commun ; 11(1): 5490, 2020 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-33127909

RESUMO

Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.


Assuntos
Archaea/classificação , Archaea/genética , Euryarchaeota/genética , Genoma Arqueal , Filogenia , Archaea/metabolismo , Proteínas Arqueais/metabolismo , Euryarchaeota/classificação , Euryarchaeota/metabolismo , Evolução Molecular , Transferência Genética Horizontal , Genes Bacterianos , Metagenômica , Metano/metabolismo , Família Multigênica , RNA Ribossômico 16S/genética
9.
BMC Bioinformatics ; 21(1): 459, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33059593

RESUMO

BACKGROUND: High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established. RESULTS: Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency. CONCLUSION: Our benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.


Assuntos
Benchmarking , Simulação por Computador , Metagenoma , Fases de Leitura Aberta/genética , Algoritmos , Humanos , Metagenômica , Microbiota/genética , Valor Preditivo dos Testes
10.
PLoS One ; 15(10): e0239741, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33022000

RESUMO

The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when dealing with increasing problems sizes, making in this way the usage of High Performance Computing (HPC) technologies such as the message passing interface (MPI) a promising alternative. Recently, MetaCacheSpark, an Apache Spark based software for detection and quantification of species composition in food samples has been proposed. This tool can be used to analyze high throughput sequencing data sets of metagenomic DNA and allows for dealing with large-scale collections of complex eukaryotic and bacterial reference genome. In this work, we propose MetaCache-MPI, a fast and memory efficient solution for computing clusters which is based on MPI instead of Apache Spark. In order to evaluate its performance a comparison is performed between the original single CPU version of MetaCache, the Spark version and the MPI version we are introducing. Results show that for 32 processes, MetaCache-MPI is 1.65× faster while consuming 48.12% of the RAM memory used by Spark for building a metagenomics database. For querying this database, also with 32 processes, the MPI version is 3.11× faster, while using 55.56% of the memory used by Spark. We conclude that the new MetaCache-MPI version is faster in both building and querying the database and uses less RAM memory, when compared with MetaCacheSpark, while keeping the accuracy of the original implementation.


Assuntos
Big Data , Genoma Bacteriano/genética , Metagenoma/genética , Metagenômica , Algoritmos , Metodologias Computacionais , DNA/genética , Software
11.
Int J Food Microbiol ; 335: 108894, 2020 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-33032033

RESUMO

A metagenome-based approach was used to assess the taxonomic affiliation and functional potential for bacteriocin production of the bacterial community in cow's milk artisanal cheeses from Northwestern Argentina. Three different samples were analyzed by high-throughput sequencing of the V4 region of the 16S rRNA gene and shotgun metagenomics. Taxonomic analysis showed that cheese A and C were quite similar whereas cheese B displayed a rather different bacterial composition. Overall, two families, Streptococceae and Enterococceae, dominated the artisanal cheese microbiota, being the former family prevalent in cheese B and the later family the most important in samples A and C. Besides the usual species associated to cheeses, a number of bacterial taxa that have not been previously found in Argentinean artisanal cheeses were reported in the present work such as Macrococcus caseolyticus and Streptococcus macedonicus Functional metagenomics analysis using the bacteriocin mining software BAGEL3, identified 2 ORFs encoding antimicrobial peptides in cheese B and 42 different peptides in sample C. The bacteriocin genes found showed good correlation with taxonomy. Based on the microbial diversity and functional features found through shotgun metagenomic sequencing, a culture-dependent approach was applied aiming to isolate bacteriocin-producing bacteria able to inhibit the growth of the foodborne pathogen Listeria monocytogenes. From 151 bacterial colonies derived from the cheese samples, 10 were associated to high anti-Listeria activity. Based on partial 16S rRNA gene sequencing and RAPD-PCR analysis, all bacteriocinogenic isolates were identified as Enterococcus faecium. Finally, we carried out a pilot experiment with L. monocytogenes-contaminated cheese using one of the enterococcal isolates as a bioprotective adjunct culture. The use of E. faecium CRL1879 during artisanal cheese manufacturing did not alter the main organoleptic properties of the cheese and ensured an efficient control of the foodborne pathogen up to 30 days. This finding supports the use of E. faecium CRL1879 as an adjunct culture in the cheese-making process with a combination of both safety and minimal processing.


Assuntos
Antibacterianos/biossíntese , Bactérias/isolamento & purificação , Bacteriocinas/biossíntese , Queijo/microbiologia , Microbiota , Animais , Antibacterianos/análise , Argentina , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Bacteriocinas/análise , Bacteriocinas/genética , Bovinos , Queijo/análise , Metagenômica , Microbiota/genética , RNA Ribossômico 16S/genética
12.
Nat Commun ; 11(1): 5281, 2020 10 19.
Artigo em Inglês | MEDLINE | ID: mdl-33077707

RESUMO

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Microbiota , Águas Residuárias/microbiologia , Bactérias/classificação , Bactérias/isolamento & purificação , Reatores Biológicos/microbiologia , Ecossistema , Metabolômica , Metagenoma , Metagenômica , Proteômica , Fatores de Tempo
13.
BMC Bioinformatics ; 21(1): 488, 2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-33126862

RESUMO

BACKGROUND: Microbiome/metagenomic data have specific characteristics, including varying total sequence reads, over-dispersion, and zero-inflation, which require tailored analytic tools. Many microbiome/metagenomic studies follow a longitudinal design to collect samples, which further complicates the analysis methods needed. A flexible and efficient R package is needed for analyzing processed multilevel or longitudinal microbiome/metagenomic data. RESULTS: NBZIMM is a freely available R package that provides functions for setting up and fitting negative binomial mixed models, zero-inflated negative binomial mixed models, and zero-inflated Gaussian mixed models. It also provides functions to summarize the results from fitted models, both numerically and graphically. The main functions are built on top of the commonly used R packages nlme and MASS, allowing us to incorporate the well-developed analytic procedures into the framework for analyzing over-dispersed and zero-inflated count or proportion data with multilevel structures (e.g., longitudinal studies). The statistical methods and their implementations in NBZIMM particularly address the data characteristics and the complex designs in microbiome/metagenomic studies. The package is freely available from the public GitHub repository https://github.com/nyiuab/NBZIMM . CONCLUSION: The NBZIMM package provides useful tools for complex microbiome/metagenomics data analysis.


Assuntos
Análise de Dados , Metagenômica , Microbiota/genética , Modelos Estatísticos , Algoritmos , Humanos , Metagenoma , Análise Multinível
14.
Bioresour Technol ; 318: 124043, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32911364

RESUMO

Obligate aerobic methanotrophs have been proven to oxidize methane and participate in denitrification under hypoxic conditions. However, this phenomenon and its metabolic mechanism have not been investigated in detail in aerobic methane oxidation coupled to denitrification (AME-D) process. In this study, a type of hypoxic AME-D consortium was enriched and operated for a long time in a CH4-cycling bioreactor with strict anaerobic control and the nitrite removal rate reached approximately 50 mg N/L/d. Metagenomics combined with DNA stable-isotope probing demonstrated that the genus Methylomonas, which constitutes type I aerobic methanotrophs, was the dominant member and contributed to methane oxidation and partial denitrification. Metagenomic binning recovered a near-complete (98%) draft genome affiliated with the family Methylococcaceae containing essential genes that encode nitrite reductase (nirK), nitric oxide reductase (norBC) and hydroxylamine dehydrogenase (hao). Metabolic reconstruction of the selected Methylococcaceae genomes also revealed a potential link between methanotrophy and partial denitrification.


Assuntos
Metano , Methylomonas , Desnitrificação , Isótopos , Metagenômica , Oxirredução
15.
PLoS Genet ; 16(9): e1009027, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32966296

RESUMO

The availability of genomes for many species has advanced our understanding of the non-protein-coding fraction of the genome. Comparative genomics has proven itself to be an invaluable approach for the systematic, genome-wide identification of conserved non-protein-coding elements (CNEs). However, for many non-mammalian model species, including chicken, our capability to interpret the functional importance of variants overlapping CNEs has been limited by current genomic annotations, which rely on a single information type (e.g. conservation). We here studied CNEs in chicken using a combination of population genomics and comparative genomics. To investigate the functional importance of variants found in CNEs we develop a ch(icken) Combined Annotation-Dependent Depletion (chCADD) model, a variant effect prediction tool first introduced for humans and later on for mouse and pig. We show that 73 Mb of the chicken genome has been conserved across more than 280 million years of vertebrate evolution. The vast majority of the conserved elements are in non-protein-coding regions, which display SNP densities and allele frequency distributions characteristic of genomic regions constrained by purifying selection. By annotating SNPs with the chCADD score we are able to pinpoint specific subregions of the CNEs to be of higher functional importance, as supported by SNPs found in these subregions are associated with known disease genes in humans, mice, and rats. Taken together, our findings indicate that CNEs harbor variants of functional significance that should be object of further investigation along with protein-coding mutations. We therefore anticipate chCADD to be of great use to the scientific community and breeding companies in future functional studies in chicken.


Assuntos
Galinhas/genética , DNA Intergênico/genética , Genômica/métodos , Alelos , Animais , Sequência Conservada/genética , DNA Intergênico/metabolismo , Evolução Molecular , Frequência do Gene/genética , Variação Genética/genética , Genoma/genética , Íntrons/genética , Metagenômica/métodos , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência/métodos
16.
Arch Virol ; 165(12): 2891-2901, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32893316

RESUMO

Genomoviruses (family Genomoviridae) are circular single-stranded DNA viruses that have been mainly identified through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the genera Gemykolovirus (n = 37), Gemyduguivirus (n = 9), Gemygorvirus (n = 8), Gemykroznavirus (n = 6), Gemycircularvirus (n = 21) and Gemykibivirus (n = 17).


Assuntos
Infecções por Vírus de DNA/virologia , Vírus de DNA/isolamento & purificação , Genoma Viral , Plantas/virologia , Austrália , Brasil , Vírus de DNA/classificação , França , Metagenômica , Filogenia , África do Sul , Estados Unidos
17.
Arch Virol ; 165(12): 2921-2926, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32989573

RESUMO

In this study, we present an analysis of metagenome sequences obtained from a filtrate of a siphon tissue homogenate of otter clams (Lutraria rhynchaena) with swollen-siphon disease. The viral signal was mined from the metagenomic data, and a novel circular ssDNA virus was identified. Genomic features and phylogenetic analysis showed that the virus belongs to the phylum Cressdnaviricota, which consists of viruses with circular, single-stranded DNA (ssDNA) genomes. Members of this phylum have been identified in various species and in environmental samples. The newly found virus is distantly related to the currently known members of the phylum Cressdnaviricota.


Assuntos
Bivalves/genética , Vírus de DNA/classificação , DNA Viral/genética , Genoma Viral , Animais , Vírus de DNA/isolamento & purificação , DNA Circular/genética , DNA de Cadeia Simples/genética , Microbiologia Ambiental , Metagenômica , Filogenia , Análise de Sequência de DNA
18.
J Clin Virol ; 131: 104594, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32866812

RESUMO

INTRODUCTION: The SARS-CoV-2 pandemic of 2020 is a prime example of the omnipresent threat of emerging viruses that can infect humans. A protocol for the identification of novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to pandemic preparedness. AIM: The aim of this study is to validate a metagenomic virus discovery protocol as a tool for coronavirus pandemic preparedness. METHODS: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery. RESULTS: Classification of NGS reads using Centrifuge and Genome Detective resulted in assignment of the reads to the closest relatives of the emerging coronaviruses. Low nucleotide and amino acid identity (81% and 84%, respectively, for SARS-CoV-2) in combination with up to 98% genome coverage were indicative for a related, novel coronavirus. Capture probes targeting vertebrate viruses, designed in 2015, enhanced both sequencing depth and coverage of the SARS-CoV-2 genome, the latter increasing from 71% to 98%. CONCLUSION: The model used for simulation of virus discovery enabled validation of the metagenomic sequencing protocol. The metagenomic protocol with virus probes designed before the pandemic, can assist the detection and identification of novel coronaviruses directly in clinical samples.


Assuntos
Infecções por Coronavirus/virologia , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Pneumonia Viral/virologia , Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Biologia Computacional , Infecções por Coronavirus/diagnóstico , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/isolamento & purificação , Nasofaringe/virologia , Pandemias , Vírus da SARS/isolamento & purificação
19.
BMC Bioinformatics ; 21(1): 412, 2020 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-32957925

RESUMO

BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of "incremental learning" addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data. RESULTS: We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model's knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4th of the non-incremental time with no accuracy loss. CONCLUSIONS: It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources.


Assuntos
Microbioma Gastrointestinal/genética , Genoma Bacteriano , Aprendizado de Máquina , Metagenômica/métodos , Algoritmos , Bactérias/genética , Teorema de Bayes , Humanos , Metagenoma , Análise de Sequência de DNA/métodos
20.
Ecotoxicol Environ Saf ; 203: 111037, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32888596

RESUMO

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.


Assuntos
Adaptação Biológica/genética , Antibacterianos/toxicidade , Resistência Microbiana a Medicamentos/genética , Poluentes Ambientais/toxicidade , Genes Bacterianos/efeitos dos fármacos , Camada de Gelo/microbiologia , Metais Pesados/toxicidade , Adaptação Biológica/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Negativas/genética , Camada de Gelo/química , Índia , Metagenômica , Siquim
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA