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1.
BMC Bioinformatics ; 21(Suppl 8): 299, 2020 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-32938362

RESUMO

BACKGROUND: The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxonomic classification of metagenomic reads, i.e., identifying the microorganisms that are present in a sample collected directly from the environment. The analysis of environmental samples (metagenomes) are particularly important to figure out the microbial composition of different ecosystems and it is used in a wide variety of fields: for instance, metagenomic studies in agriculture can help understanding the interactions between plants and microbes, or in ecology, they can provide valuable insights into the functions of environmental communities. RESULTS: In this paper, we describe a new lightweight alignment-free and assembly-free framework for metagenomic classification that compares each unknown sequence in the sample to a collection of known genomes. We take advantage of the combinatorial properties of an extension of the Burrows-Wheeler transform, and we sequentially scan the required data structures, so that we can analyze unknown sequences of large collections using little internal memory. The tool LiME (Lightweight Metagenomics via eBWT) is available at https://github.com/veronicaguerrini/LiME . CONCLUSIONS: In order to assess the reliability of our approach, we run several experiments on NGS data from two simulated metagenomes among those provided in benchmarking analysis and on a real metagenome from the Human Microbiome Project. The experiment results on the simulated data show that LiME is competitive with the widely used taxonomic classifiers. It achieves high levels of precision and specificity - e.g. 99.9% of the positive control reads are correctly assigned and the percentage of classified reads of the negative control is less than 0.01% - while keeping a high sensitivity. On the real metagenome, we show that LiME is able to deliver classification results comparable to that of MagicBlast. Overall, the experiments confirm the effectiveness of our method and its high accuracy even in negative control samples.


Assuntos
Algoritmos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Humanos , Reprodutibilidade dos Testes
2.
Viruses ; 12(9)2020 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-32872469

RESUMO

The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.


Assuntos
Infecções Respiratórias/virologia , Viroses/virologia , Zoonoses/virologia , Animais , Coronavirus/genética , Coronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Metagenoma , Metagenômica/métodos , Pandemias , Filogenia , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Infecções Respiratórias/diagnóstico , Viroses/diagnóstico , Zoonoses/diagnóstico
3.
Chemosphere ; 258: 127392, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32947654

RESUMO

Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.


Assuntos
Farmacorresistência Bacteriana/genética , Metagenoma , Bactérias/efeitos dos fármacos , Monitoramento Ambiental , Fezes/microbiologia , Genes Bacterianos/efeitos dos fármacos , Humanos , Macrolídeos , Metagenômica/métodos , Microbiota/efeitos dos fármacos , Águas Residuárias/microbiologia , beta-Lactamas
4.
BMC Bioinformatics ; 21(Suppl 13): 390, 2020 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-32938391

RESUMO

BACKGROUND: Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud. RESULTS: MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph. CONCLUSIONS: We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.


Assuntos
Classificação/métodos , Computadores/normas , Metagenômica/métodos , Humanos
5.
PLoS One ; 15(9): e0237975, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32960892

RESUMO

The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.


Assuntos
Ecologia , Genômica/métodos , Metabolômica/métodos , Metagenômica/métodos , Doenças das Plantas/etiologia , Plantas/imunologia , Proteômica/métodos , Microbiota , Plantas/metabolismo , Biologia de Sistemas
6.
Ecotoxicol Environ Saf ; 205: 111267, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32992213

RESUMO

Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.


Assuntos
Actinobacteria/efeitos dos fármacos , Arsênico/toxicidade , Firmicutes/efeitos dos fármacos , Metagenômica/métodos , Proteobactérias/efeitos dos fármacos , Poluentes do Solo/toxicidade , Actinobacteria/citologia , Actinobacteria/genética , Arsênico/análise , Biodegradação Ambiental , Meios de Cultura/química , Farmacorresistência Bacteriana/efeitos dos fármacos , Firmicutes/citologia , Firmicutes/genética , Ouro , Testes de Sensibilidade Microbiana , Microbiota/efeitos dos fármacos , Microbiota/genética , Mineração , Proteobactérias/citologia , Proteobactérias/genética , RNA Ribossômico 16S/genética , Solo/química , Microbiologia do Solo , Poluentes do Solo/análise
7.
Am J Hum Genet ; 107(2): 175-182, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32763188

RESUMO

Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment "to leveraging the benefits of genomics in the health system for all Australians." They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.


Assuntos
Metagenômica/métodos , Grupos Populacionais/genética , Austrália , Variação Genética/genética , Humanos
8.
Lancet Infect Dis ; 20(10): e251-e260, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32768390

RESUMO

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.


Assuntos
Metagenômica/métodos , Metagenômica/estatística & dados numéricos , Biologia Computacional , Humanos , Epidemiologia Molecular , Projetos de Pesquisa/normas
9.
BMC Bioinformatics ; 21(1): 345, 2020 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-32778056

RESUMO

BACKGROUND: Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. RESULTS: Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/ , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. CONCLUSIONS: With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.


Assuntos
Classificação , Internet , Metagenômica/métodos , Software , Estatística como Assunto , Interface Usuário-Computador , Líquidos Corporais/microbiologia , Pré-Escolar , Fezes/microbiologia , Humanos , Metagenoma , Microbiota , RNA Ribossômico 16S/genética , Fluxo de Trabalho
10.
Medicine (Baltimore) ; 99(30): e21315, 2020 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-32791721

RESUMO

INTRODUCTION: There is evidence that caesarean section (CS) is associated with increased risk of childhood obesity, asthma, and coeliac disease. The gut microbiota of CS-born babies differs to those born vaginally, possibly due to reduced exposure to maternal vaginal bacteria during birth. Vaginal seeding is a currently unproven practice intended to reduce such differences, so that the gut microbiota of CS-born babies is similar to that of babies born vaginally. Our pilot study, which uses oral administration as a novel form of vaginal seeding, will assess the degree of maternal strain transfer and overall efficacy of the procedure for establishing normal gut microbiota development. METHODS AND ANALYSIS: Protocol for a single-blinded, randomized, placebo-controlled pilot study of a previously untested method of vaginal seeding (oral administration) in 30 CS-born babies. A sample of maternal vaginal bacteria is obtained prior to CS, and mixed with 5 ml sterile water to obtain a supernatant. Healthy babies are randomized at 1:1 to receive active treatment (3 ml supernatant) or placebo (3 ml sterile water). A reference group of 15 non-randomized vaginal-born babies are also being recruited. Babies' stool samples will undergo whole metagenomic shotgun sequencing to identify potential differences in community structure between CS babies receiving active treatment compared to those receiving placebo at age 1 month (primary outcome). Secondary outcomes include differences in overall gut community between CS groups (24 hours, 3 months); similarity of CS-seeded and placebo gut profiles to vaginally-born babies (24 hours, 1 and 3 months); degree of maternal vaginal strain transfer in CS-born babies (24 hours, 1 and 3 months); anthropometry (1 and 3 months) and body composition (3 months). ETHICS AND DISSEMINATION: Ethics approval by the Northern A Health and Disability Ethics Committee (18/NTA/49). Results will be published in peer-reviewed journals and presented at international conferences. REGISTRATION: Australian New Zealand Clinical Trials Registry (ACTRN12618000339257).


Assuntos
Cesárea/efeitos adversos , Microbiota/fisiologia , Placebos/administração & dosagem , Vagina/microbiologia , Adulto , Antropometria/métodos , Asma/epidemiologia , Asma/etiologia , Fenômenos Fisiológicos Bacterianos , Composição Corporal , Estudos de Casos e Controles , Doença Celíaca/epidemiologia , Doença Celíaca/etiologia , Parto Obstétrico/tendências , Fezes , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Metagenômica/métodos , Microbiota/genética , Nova Zelândia/epidemiologia , Obesidade Pediátrica/epidemiologia , Obesidade Pediátrica/etiologia , Gravidez
11.
BMC Bioinformatics ; 21(1): 334, 2020 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-32723290

RESUMO

BACKGROUND: Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research. Both supervised and unsupervised machine learning methods have been employed in binning. Genome binning belonging to unsupervised method clusters contigs into individual genome bins by machine learning methods without the assistance of any reference databases. So far a lot of genome binning tools have emerged. Evaluating these genome tools is of great significance to microbiological research. In this study, we evaluate 15 genome binning tools containing 12 original binning tools and 3 refining binning tools by comparing the performance of these tools on chicken gut metagenomic datasets and the first CAMI challenge datasets. RESULTS: For chicken gut metagenomic datasets, original genome binner MetaBat, Groopm2 and Autometa performed better than other original binner, and MetaWrap combined the binning results of them generated the most high-quality genome bins. For CAMI datasets, Groopm2 achieved the highest purity (> 0.9) with good completeness (> 0.8), and reconstructed the most high-quality genome bins among original genome binners. Compared with Groopm2, MetaBat2 had similar performance with higher completeness and lower purity. Genome refining binners DASTool predicated the most high-quality genome bins among all genomes binners. Most genome binner performed well for unique strains. Nonetheless, reconstructing common strains still is a substantial challenge for all genome binner. CONCLUSIONS: In conclusion, we tested a set of currently available, state-of-the-art metagenomics hybrid binning tools and provided a guide for selecting tools for metagenomic binning by comparing range of purity, completeness, adjusted rand index, and the number of high-quality reconstructed bins. Furthermore, available information for future binning strategy were concluded.


Assuntos
Bases de Dados Genéticas , Metagenoma/genética , Metagenômica/métodos , Animais , Galinhas/microbiologia , Genoma Microbiano , Aprendizado de Máquina , Análise de Sequência de DNA/métodos , Aprendizado de Máquina não Supervisionado
12.
PLoS One ; 15(7): e0235682, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32645030

RESUMO

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.


Assuntos
Chaperonina 60/genética , Código de Barras de DNA Taxonômico/métodos , Metagenômica/métodos , Microbiota/genética , Bactérias/genética , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Vagina/microbiologia
13.
Nat Med ; 26(7): 1089-1095, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32632193

RESUMO

Modern lifestyles increase the risk of chronic diseases, in part by modifying the microbiome, but the health effects of lifestyles enforced on ethnic minorities are understudied1-3. Lifestyle affects the microbiome early in life, when the microbiome is assembled and the immune system is undergoing maturation4-6. Moreover, the influence of lifestyle has been separated from genetic and geographic factors by studies of genetically similar populations and ethnically distinct groups living in the same geographic location7-11. The lifestyle of Irish Travellers, an ethnically distinct subpopulation, changed with legislation in 2002 that effectively ended nomadism and altered their living conditions. Comparative metagenomics of gut microbiomes shows that Irish Travellers retain a microbiota similar to that of non-industrialized societies. Their microbiota is associated with non-dietary factors and is proportionately linked with risk of microbiome-related metabolic disease. Our findings suggest there are microbiome-related public health implications when ethnic minorities are pressured to change lifestyles.


Assuntos
Doença Crônica/epidemiologia , Microbioma Gastrointestinal/genética , Sistema Imunitário/imunologia , Estilo de Vida , Adulto , Grupos Étnicos/genética , Fezes/microbiologia , Microbioma Gastrointestinal/imunologia , Genética Populacional , Humanos , Sistema Imunitário/microbiologia , Irlanda/epidemiologia , Masculino , Metagenômica/métodos , Microbiota/genética , Microbiota/imunologia , Filogenia , Roma/genética , Migrantes
14.
BMC Infect Dis ; 20(1): 467, 2020 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-32615925

RESUMO

BACKGROUND: Urinary tract infection (UTI) caused by various pathogenic microorganisms is ubiquitous in the parts of the urinary system such as kidney, ureter, bladder, and urethra. Currently, clinical detection of UTI is mainly focused on urine culture; however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate, especially in patients who have used antibiotics. Generally, treatment for UTI relies on empirical medication rather than pathogen diagnosis, which leads to the inappropriate use of antimicrobial agents and a significant increase in resistant strains. Comparatively, metagenomic next-generation sequencing (mNGS) is capable of overcoming the disadvantages of clinical culture, and identifying pathogens for further treatment. CASE PRESENTATION: A 33-year-old male patient was admitted to hospital with a high fever and chills. None of his autoimmune disease or thyroid function related indicators were positive, and he had no risk of endocarditis. His white blood cell count, C-reactive protein, procalcitonin, interleukin 6, and neutrophil proportion were markedly elevated. He was initially diagnosed as having an infection of unknown etiology. Since empirical treatment of Sulperazon and Metronidazole did not relieve his symptoms, both the blood and urine specimens were examined using traditional culture, serological testing, and mNGS assay. Traditional culture and serological testing produced negative results, while the mNGS assay revealed the presence of a potential pathogen, Enterococcus faecalis, in the urine specimen, which was further confirmed by both Sanger sequencing and qPCR analysis. A CT scan of the patient's whole abdomen showed stones in the right kidney. Once targeted antibiotic therapy was administered, the patient recovered quickly. CONCLUSIONS: Our case illustrated that mNGS, as a novel culture-independent approach, demonstrated the capability of rapid, sensitive, and accurate pathogen identification. Furthermore, this technology provides strong support for guiding clinicians to determine appropriate treatment.


Assuntos
Enterococcus faecalis/genética , Infecções por Bactérias Gram-Positivas/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Infecções Urinárias/diagnóstico , Adulto , Antibacterianos/uso terapêutico , DNA Bacteriano/genética , Seguimentos , Infecções por Bactérias Gram-Positivas/tratamento farmacológico , Infecções por Bactérias Gram-Positivas/microbiologia , Infecções por Bactérias Gram-Positivas/urina , Humanos , Linezolida/uso terapêutico , Masculino , Resultado do Tratamento , Infecções Urinárias/tratamento farmacológico , Infecções Urinárias/urina , Infecções Urinárias/virologia
15.
PLoS One ; 15(6): e0234860, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32555605

RESUMO

Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as "biominer"), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.


Assuntos
Bactérias/classificação , Biologia Computacional/métodos , Microbioma Gastrointestinal , Metagenômica/métodos , Software , Animais , Bactérias/genética , Conjuntos de Dados como Assunto , Camundongos , RNA Ribossômico 16S/genética
17.
BMC Bioinformatics ; 21(1): 257, 2020 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-32571209

RESUMO

BACKGROUND: Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. RESULTS: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. CONCLUSIONS: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.


Assuntos
Metagenômica/métodos , Software , Metagenoma , Anotação de Sequência Molecular , Fluxo de Trabalho
18.
PLoS One ; 15(6): e0232610, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32497137

RESUMO

Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery. However, in most cases, the causative agent cannot be identified, which is partly due to the limited spectrum of pathogens covered by current diagnostics based on nucleic acid amplification. Therefore, in this study, we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. From April to July 2017, 32 hospitalized children with severe nonresponding pneumonia in Shenzhen Children's Hospital were included in this study. Blood tests were conducted immediately after hospitalization to assess cell counts and inflammatory markers, oropharyngeal swabs were collected to identify common pathogens by qPCR and culture. After bronchoscopy, bronchoalveolar lavage fluid (BALF) samples were collected for further pathogen identification using standardized diagnostic tests and mNGS. Blood tests were normal in 3 of the 32 children. In 9 oropharyngeal swabs, bacterial pathogens were detected, in 5 of these Mycoplasma pneumoniae was detected. Adenovirus was detected in 5 BALF samples, using the Direct Immunofluorescence Assay (DFA). In 15 cases, no common pathogens were found in BALF samples, using the current standard diagnostic tests, while in all 32 BALFs, pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus and bocavirus. This study shows that, with mNGS, the sensitivity of detection of the causative pathogens in children with severe nonresponding pneumonia is significantly improved. In addition, mNGS gives more strain specific information, helps to identify new pathogens and could potentially help to trace and control outbreaks. In this study, we have shown that it is possible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.


Assuntos
Coinfecção , Metagenômica/métodos , Pneumonia Bacteriana/diagnóstico , Pneumonia Viral/diagnóstico , Contagem de Células Sanguíneas , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Criança , Pré-Escolar , China/epidemiologia , Coinfecção/microbiologia , Coinfecção/virologia , DNA Bacteriano/análise , DNA Viral/análise , Feminino , Técnica Direta de Fluorescência para Anticorpo , Humanos , Lactente , Pacientes Internados , Masculino , Metagenoma , Orofaringe/microbiologia , Orofaringe/virologia , Pneumonia Bacteriana/epidemiologia , Pneumonia Bacteriana/microbiologia , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Estudo de Prova de Conceito , RNA Viral/análise , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
19.
mSphere ; 5(3)2020 05 06.
Artigo em Inglês | MEDLINE | ID: covidwho-186537

RESUMO

In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the "virome" keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265-269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270-273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/veterinária , Eutérios/virologia , Pneumopatias/veterinária , Metagenômica/métodos , Animais , Sequência de Bases , Quirópteros/virologia , Infecções por Coronavirus/virologia , Pulmão/virologia , Pneumopatias/virologia , Alinhamento de Sequência
20.
Nat Commun ; 11(1): 2500, 2020 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-32427907

RESUMO

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.0, an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences. For individual clades of interest, it reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers. At the other extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species. Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses.


Assuntos
Bactérias/genética , Genoma Bacteriano , Metagenômica/métodos , Filogenia , Bactérias/classificação , Bactérias/isolamento & purificação , Genoma Microbiano , Metagenoma
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