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2.
Science ; 364(6436)2019 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-30975860

RESUMO

To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.


Assuntos
Adaptação Fisiológica , Astronautas , Voo Espacial , Imunidade Adaptativa , Peso Corporal , Artérias Carótidas/diagnóstico por imagem , Espessura Intima-Media Carotídea , Dano ao DNA , Metilação de DNA , Microbioma Gastrointestinal , Instabilidade Genômica , Humanos , Masculino , Homeostase do Telômero , Fatores de Tempo , Estados Unidos , United States National Aeronautics and Space Administration
3.
Microbiome ; 7(1): 35, 2019 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-30819245

RESUMO

BACKGROUND: Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood. RESULTS: We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters. CONCLUSIONS: Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance.


Assuntos
Antibacterianos/farmacologia , Bactérias/classificação , Metagenômica/métodos , Esgotos/microbiologia , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/patogenicidade , Proteínas de Bactérias/genética , Praias , Estudos Transversais , Farmacorresistência Bacteriana , Humanos , Análise de Sequência de DNA , Uruguai , Microbiologia da Água
4.
Per Med ; 15(3): 199-208, 2018 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-29843583

RESUMO

Genomic medicine is transforming patient care. However, the speed of development has left a knowledge gap between discovery and effective implementation into clinical practice. Since 2010, the Training Residents in Genomics (TRIG) Working Group has found success in building a rigorous genomics curriculum with implementation tools aimed at pathology residents in postgraduate training years 1-4. Based on the TRIG model, the interprofessional Undergraduate Training in Genomics (UTRIG) Working Group was formed. Under the aegis of the Undergraduate Medical Educators Section of the Association of Pathology Chairs and representation from nine additional professional societies, UTRIG's collaborative goal is building medical student genomic literacy through development of a ready-to-use genomics curriculum. Key elements to the UTRIG curriculum are expert consensus-driven objectives, active learning methods, rigorous assessment and integration.

5.
Gates Open Res ; 2: 3, 2018 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-29630066

RESUMO

The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes' characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY-Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism's taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

6.
Microbiome ; 5(1): 125, 2017 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-28938903

RESUMO

BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals. RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation). CONCLUSIONS: While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.


Assuntos
Ambulâncias , Bactérias/isolamento & purificação , Metagenoma , Metagenômica , Consórcios Microbianos , Microbiota , Bactérias/classificação , Bactérias/genética , Bactérias/patogenicidade , Infecção Hospitalar/microbiologia , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Hospitais , Humanos , Consórcios Microbianos/genética , Microbiota/genética , Estados Unidos
7.
Genome Biol ; 18(1): 182, 2017 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-28934964

RESUMO

BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. CONCLUSIONS: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.


Assuntos
Benchmarking/métodos , Mapeamento de Sequências Contíguas/métodos , Código de Barras de DNA Taxonômico/métodos , Metagenoma , Análise de Sequência de DNA/métodos , Software , Benchmarking/normas , Mapeamento de Sequências Contíguas/normas , Código de Barras de DNA Taxonômico/normas , Humanos , Microbiota , Filogenia , Análise de Sequência de DNA/normas
8.
Sci Rep ; 7(1): 6589, 2017 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-28761145

RESUMO

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.

9.
Exp Hematol ; 54: 26-30, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28705639

RESUMO

Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy with an exceedingly poor prognosis: a 5-year overall survival rate of 40%-45% in the young and a 5-year survival rate of less than 10% in the elderly (>60 years of age). Although a high percentage of patients enters complete remission after chemotherapeutic intervention, the majority of patients relapse within 3 years. Such stark prognostic outcomes highlight the need for additional clinical research, basic discovery, and molecular delineation of the etiologies and mechanisms behind responses to therapy that lead to relapse. Here, we summarize recent discoveries in tumor heterogeneity at the genetic and epigenetic levels and their independent molecular trajectories and dynamics in response to therapy. These new discoveries may have significant implications for understanding, monitoring, and treating leukemia and other cancers.


Assuntos
Aberrações Cromossômicas , Epigênese Genética , Regulação Leucêmica da Expressão Gênica , Heterogeneidade Genética , Leucemia Mieloide Aguda/genética , Proteínas de Neoplasias/genética , Fatores Etários , Antineoplásicos/uso terapêutico , Resistencia a Medicamentos Antineoplásicos/genética , Humanos , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/tratamento farmacológico , Leucemia Mieloide Aguda/mortalidade , Mutação , Proteínas de Neoplasias/metabolismo , Prognóstico , Recidiva , Indução de Remissão , Análise de Célula Única , Análise de Sobrevida
10.
J Biomol Tech ; 28(1): 31-39, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28337070

RESUMO

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.


Assuntos
Microbiologia Ambiental , Microbiota/genética , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Ambientes Extremos , Metagenoma , Tipagem Molecular/normas , RNA Bacteriano/genética , RNA Bacteriano/isolamento & purificação , Padrões de Referência , Análise de Sequência de DNA/normas
11.
J Biomol Tech ; 28(1): 8-18, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28337071

RESUMO

Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data. Here we review current standards and their applications in genomics, including whole genomes, transcriptomes, mixed genomic samples (metagenomes), and the modified bases within each (epigenomes and epitranscriptomes). These standards, tools, and metrics are critical for quantifying the accuracy of NGS methods, which will be essential for robust approaches in clinical genomics and precision medicine.


Assuntos
Perfilação da Expressão Gênica/normas , Animais , DNA/genética , DNA/isolamento & purificação , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Metagenoma , Padrões de Referência , Análise de Sequência de DNA/normas , Software , Transcriptoma
12.
J Biomol Tech ; 28(1): 40-45, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28337072

RESUMO

Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear. Here, we present a robust protocol for the implementation and application of "precision metagenomics" across various sequencing platforms for clinical samples. Such a pipeline integrates DNA/RNA extraction, library preparation, sequencing, and bioinformatics analyses for taxonomic classification, antimicrobial resistance (AMR) marker screening, and functional analysis (biochemical and metabolic pathway abundance). Moreover, the pipeline has 3 tracks: STAT for results within 24 h; Comprehensive that affords a more in-depth analysis and takes between 5 and 7 d, but offers antimicrobial resistance information; and Targeted, which also requires 5-7 d, but with more sensitive analysis for specific pathogens. Finally, we discuss the challenges that need to be addressed before full integration in the clinical setting.


Assuntos
Doenças Transmissíveis/diagnóstico , Metagenômica/normas , Vigilância em Saúde Pública , Doenças Transmissíveis/microbiologia , Biologia Computacional , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Medicina de Precisão/normas , Padrões de Referência , Análise de Sequência de DNA , Pesquisa Médica Translacional
13.
J Biomol Tech ; 28(1): 46-55, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28344519

RESUMO

Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample. We extracted and sequenced genomic DNA (gDNA) from 8 environmental samples and compared the quality of the sequencing data for the MDA and their corresponding non-MDA samples. The degree of REPLI-g MDA bias was evaluated by sequence metrics, species composition, and cross-validating observed species abundance and species diversity estimates using the One Codex and MetaPhlAn taxonomic classification tools. Here, we provide evidence of the overall efficacy of REPLI-g MDA on retaining sequencing data quality and species abundance measurements while providing increased yields of high-fidelity DNA. We find that species abundance estimates are largely consistent across samples, even with REPLI-g amplification, as demonstrated by the Spearman's rank order coefficient (R2 > 0.8). However, REPLI-g MDA often produced fewer classified reads at the species, genera, and family level, resulting in decreased species diversity. We also observed some areas with the PCR "jackpot effect," with varying input DNA values for the Metagenomics Research Group (MGRG) controls at specific genomic loci. We visualize this effect in whole genome coverage plots and with sequence composition analyses and note these caveats of the MDA method. Despite overall concordance of species abundance between the amplified and unamplified samples, these results demonstrate that amplification of DNA using the REPLI-g method has some limitations. These concerns could be addressed by future improvements in the enzymes or methods for REPLI-g to be considered a >99% robust method for increasing the amount of high-fidelity DNA from low-biomass samples or at the very least, accounted for during computational analysis of MDA samples.


Assuntos
Microbiologia Ambiental , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Composição de Bases , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Genoma Bacteriano , Metagenômica , Microbiota/genética
14.
Br Med Bull ; 120(1): 27-33, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27941038

RESUMO

INTRODUCTION OR BACKGROUND: Crowdfunding and crowdsourcing of medical research has emerged as a novel paradigm for many biomedical disciplines to rapidly collect, process and interpret data from high-throughput and high-dimensional experiments. The novelty and promise of these approaches have led to fundamental discoveries about RNA mechanisms, microbiome dynamics and even patient interpretation of test results. However, these methods require robust training protocols, uniform sampling methods and experimental rigor in order to be useful for subsequent research efforts. Executed correctly, crowdfunding and crowdsourcing can leverage public resources and engagement to generate support for scientific endeavors that would otherwise be impossible due to funding constraints and or the large number of participants needed for data collection. SOURCES OF DATA: We conducted a comprehensive literature review of scientific studies that utilized crowdsourcing and crowdfunding to generate data. We also discuss our own experiences conducting citizen-science research initiatives (MetaSUB and PathoMap) in ensuring data robustness, educational outreach and public engagement. AREAS OF AGREEMENT: We demonstrate the efficacy of crowdsourcing mechanisms for revolutionizing microbiome and metagenomic research to better elucidate the microbial and genetic dynamics of cities around the world (as well as non-urban areas). Crowdsourced studies have been able to create an improved and unprecedented ability to monitor, design and measure changes at the microbial and macroscopic scale. Thus, the use of crowdsourcing strategies has dramatically altered certain genomics research to create global citizen-science initiatives that reveal new discoveries about the world's genetic dynamics. AREAS OF CONTROVERSY: The effectiveness of crowdfunding and crowdsourcing is largely dependent on the study design and methodology. One point of contention for the present discussion is the validity and scientific rigor of data that are generated by non-scientists. Selection bias, limited sample sizes and limitations for scientists in enforcing standardized protocols are all challenges for those who engage in citizen-science initiatives. GROWING POINTS: Despite the aforementioned concerns, crowdsourced data allow for greater inroads into the field of personalized medicine, whereby community members take an active role in generating data about their personal and environmental health. AREAS TIMELY FOR DEVELOPING RESEARCH: Crowdsourced viral and metagenomic studies are the next step in elucidating the genomic and epigenomic characterization of urban population health.


Assuntos
Pesquisa Biomédica , Crowdsourcing , Pesquisa Biomédica/economia , Pesquisa Biomédica/organização & administração , Pesquisa Biomédica/tendências , Ensaios Clínicos como Assunto , Crowdsourcing/economia , Crowdsourcing/métodos , Crowdsourcing/tendências , Humanos , Medicina de Precisão , Apoio à Pesquisa como Assunto , Sociedades Médicas
16.
Nat Commun ; 7: 10164, 2016 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-26836631

RESUMO

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on human blood and included genes from the Wolbachia endosymbiont, which shows a simultaneous and coordinated host/commensal response to haematophagous activity. These data provide a rich genetic resource for mapping activity and density of C. lectularius across human hosts and cities, which can help track, manage and control bed bug infestations.


Assuntos
Percevejos-de-Cama/genética , Regulação da Expressão Gênica no Desenvolvimento , Estágios do Ciclo de Vida/genética , Animais , Sangue , Mapeamento Cromossômico , Ingestão de Alimentos , Feminino , Perfilação da Expressão Gênica , Humanos , Masculino , Modelos Moleculares , Filogenia , Análise de Sequência de RNA
17.
Cell Syst ; 1(1): 72-87, 2015 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-26594662

RESUMO

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station's history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

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