RESUMO
Respiratory pathogens infecting the human respiratory system are characterized by their diversity, high infectivity, rapid transmission, and acute onset. Traditional detection methods are time-consuming, have low sensitivity, and lack specificity, failing to meet the needs of rapid clinical diagnosis. Nucleic acid aptamers, as an emerging and innovative detection technology, offer novel solutions with high specificity, affinity, and broad target applicability, making them particularly promising for respiratory pathogen detection. This review highlights the progress in the research and application of nucleic acid aptamers for detecting respiratory pathogens, discussing their selection, application, potential in clinical diagnosis, and future development. Notably, these aptamers can significantly enhance the sensitivity and specificity of detection when combined with detection techniques such as fluorescence, colorimetry and electrochemistry. This review offers new insights into how aptamers can address the limitations of traditional diagnostic methods and advance clinical diagnostics. It also highlights key challenges and future research directions for the clinical application of nucleic acid aptamers.
Assuntos
Aptâmeros de Nucleotídeos , Infecções Respiratórias , Sensibilidade e Especificidade , Humanos , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Infecções Respiratórias/microbiologia , Vírus/isolamento & purificação , Vírus/genética , Vírus/classificação , Bactérias/isolamento & purificação , Bactérias/genética , Técnica de Seleção de Aptâmeros/métodos , Viroses/diagnóstico , Viroses/virologia , Técnicas de Diagnóstico Molecular/métodosRESUMO
Aerosol-transmitted viruses possess strong infectivity and can spread over long distances, earning the difficult-to-control title. They cause various human diseases and pose serious threats to human health. Mutations can increase the transmissibility and virulence of the strains, reducing the protection provided by vaccines and weakening the efficacy of antiviral drugs. In this study, we established a manually curated database (termed AVM) to store information on aerosol-transmitted viral mutations (VMs). The current version of the AVM contains 42,041 VMs (including 2613 immune escape mutations), 45 clinical information datasets, and 407 drugs/antibodies/vaccines. Additionally, we recorded 88 human diseases associated with viruses and found that the same virus can target multiple organs in the body, leading to diverse diseases. Furthermore, the AVM database offers a straightforward user interface for browsing, retrieving, and downloading information. This database is a comprehensive resource that can provide timely and valuable information on the transmission, treatment, and diseases caused by aerosol-transmitted viruses (http://www.bio-bigdata.center/AVM).
Assuntos
Aerossóis , Mutação , Humanos , Antivirais/farmacologia , Bases de Dados Genéticas , Vírus/genética , Vírus/classificação , Vírus/patogenicidade , Viroses/transmissão , Viroses/virologia , Viroses/genética , Bases de Dados Factuais , Curadoria de Dados/métodosRESUMO
BACKGROUND: Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read. RESULTS: Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3-40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes. CONCLUSION: PenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities. Video Abstract.
Assuntos
Bactérias , Genoma Viral , Metagenômica , RNA Ribossômico 16S , RNA Ribossômico 16S/genética , Genoma Viral/genética , Metagenômica/métodos , Bactérias/genética , Bactérias/classificação , Bactérias/virologia , Software , Humanos , Teorema de Bayes , Vírus/genética , Vírus/classificação , MetagenomaRESUMO
Background: When individuals infected with human immunodeficiency virus (HIV) experience pulmonary infections, they often exhibit severe symptoms and face a grim prognosis. Consequently, early, rapid, and accurate pathogen diagnosis is vital for informing effective treatment strategies. This study aimed to use metagenomic next-generation sequencing (mNGS) and targeted mNGS (tNGS) to elucidate the characteristics of pulmonary infections in HIV and non-HIV individuals. Methods: This study enrolled 90 patients with pulmonary infection at the Department of Infectious Diseases of The First Hospital of Jilin University from June 2022 to May 2023, and they were divided into HIV (n=46) and non-HIV (n=44) infection groups. Their bronchoalveolar lavage fluid (BALF) was collected for mNGS analysis to evaluate the differences in pulmonary infection pathogens, and tNGS detection was performed on BALF samples from 15 HIV-infected patients. Results: A total of 37 pathogens were identified in this study, including 21 bacteria, 5 fungi, 5 viruses, 5 mycobacteria, and 1 mycoplasma. The sensitivity of mNGS was 78.9% (71/90), which is significantly higher than that of conventional methods (CTM) (39/90, P=1.5E-8). The combination of mNGS with CTM can greatly enhance the sensitivity of pathogen detection. The prevalence of Pneumocystis jirovecii (82.6% vs. 9.1%), cytomegalovirus (CMV) (58.7% vs. 0%), and Epstein-Barr virus (EBV) (17.4% vs. 2.3%) was significantly higher in the HIV infection group than in the non-HIV infection group (P<0.05). Although no statistically significant difference was observed, the detection rate of Mycobacteria was higher in HIV-infected patients (17.4%) than in the non-HIV group (6.8%). Furthermore, the tNGS results of BALF from 15 HIV-infected patients were not entirely consistent with the mNGS results., and the concordance rate of tNGS for the detection of main pathogens reached 86.7% (13/15). Conclusion: Next-generation sequencing (NGS) can accurately detect pathogens in the BALF of patients with pulmonary infection. The sensitivity of tNGS is comparable to that of mNGS. Therefore, this technique should be promoted in the clinic for better patient outcomes.
Assuntos
Líquido da Lavagem Broncoalveolar , Infecções por HIV , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Infecções por HIV/complicações , Infecções por HIV/virologia , Masculino , Feminino , Metagenômica/métodos , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Pessoa de Meia-Idade , Adulto , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Idoso , Sensibilidade e Especificidade , Vírus/genética , Vírus/isolamento & purificação , Vírus/classificação , Metagenoma , Infecções Respiratórias/virologia , Infecções Respiratórias/microbiologia , Infecções Respiratórias/diagnósticoRESUMO
Background: Although the emerging NGS-based assays, metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), have been extensively utilized for the identification of pathogens in pulmonary infections, there have been limited studies systematically evaluating differences in the efficacy of mNGS and multiplex PCR-based tNGS in bronchoalveolar lavage fluid (BALF) specimens. Methods: In this study, 85 suspected infectious BALF specimens were collected. Parallel mNGS and tNGS workflows to each sample were performed; then, we comparatively compared their consistency in detecting pathogens. The differential results for clinically key pathogens were confirmed using PCR. Results: The microbial detection rates of BALF specimens by the mNGS and tNGS workflows were 95.18% (79/83) and 92.77% (77/83), respectively, with no significant difference. mNGS identified 55 different microorganisms, whereas tNGS detected 49 pathogens. The comparative analysis of mNGS and tNGS revealed that 86.75% (72/83) of the specimens were complete or partial concordance. Particularly, mNGS and tNGS differed significantly in detection rates for some of the human herpesviruses only, including Human gammaherpesvirus 4 (P<0.001), Human betaherpesvirus 7 (P<0.001), Human betaherpesvirus 5 (P<0.05) and Human betaherpesvirus 6 (P<0.01), in which tNGS always had higher detection rates. Orthogonal testing of clinically critical pathogens showed a total coincidence rate of 50% for mNGS and PCR, as well as for tNGS and PCR. Conclusions: Overall, the performance of mNGS and multiplex PCR-based tNGS assays was similar for bacteria and fungi, and tNGS may be superior to mNGS for the detection of DNA viruses. No significant differences were seen between the two NGS assays compared to PCR.
Assuntos
Líquido da Lavagem Broncoalveolar , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Feminino , Masculino , Pessoa de Meia-Idade , Adulto , Reação em Cadeia da Polimerase Multiplex/métodos , Idoso , Bactérias/isolamento & purificação , Bactérias/genética , Bactérias/classificação , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Infecções Respiratórias/microbiologia , Vírus/isolamento & purificação , Vírus/genética , Vírus/classificação , Técnicas de Diagnóstico Molecular/métodos , Adulto JovemRESUMO
The role of gut microbiota in health and disease is being thoroughly examined in various contexts, with a specific focus on the bacterial fraction due to its significant abundance. However, despite their lower abundance, viruses within the gut microbiota are gaining recognition for their crucial role in shaping the structure and function of the intestinal microbiota, with significant effects on the host as a whole, particularly the immune system. Similarly, environmental factors such as stress are key in modulating the host immune system, which in turn influences the composition of the gut virome and neurological functions through the bidirectional communication of the gut-brain axis. In this context, alterations in the host immune system due to stress and/or dysbiosis of the gut virome are critical factors in the development of both infectious and noninfectious diseases. The molecular mechanisms and correlation patterns between microbial species are not yet fully understood. This literature review seeks to explore the interconnected relationship between stress and the gut virome, with a focus on how this interaction is influenced by the host's immune system. We also discuss how disturbances in this finely balanced system can lead to the onset and/or progression of diseases.
Assuntos
Disbiose , Microbioma Gastrointestinal , Estresse Fisiológico , Viroma , Humanos , Microbioma Gastrointestinal/fisiologia , Doenças Transmissíveis/virologia , Doenças Transmissíveis/microbiologia , Animais , Vírus/classificaçãoRESUMO
Holobionts are highly organized assemblages of eukaryotic hosts, cellular microbial symbionts, and viruses, whose interactions and evolution involve complex biological processes. It is largely unknown which specific determinants drive similarity or individuality in genetic diversity between holobionts. Here, we combine short- and long-read sequencing and DNA-proximity-linkage technologies to investigate intraspecific diversity of the microbiomes, including host-resolved viruses, in individuals of a model marine sponge. We find strong impacts of the sponge host and the cellular hosts of viruses on strain-level organization of the holobiont, whereas substantial overlap in nucleotide diversity between holobionts suggests frequent exchanges of microbial cells and viruses at intrastrain level in the local sponge population. Immune-evasive arms races likely restricted virus-host co-evolution at the intrastrain level, generated holobiont-specific genome variations, and linked virus-host genetics through recombination. Our work shows that a decoupling of strain- and intrastrain-level interactions is a key factor in the genetic diversification of holobionts.
Assuntos
Microbiota , Poríferos , Simbiose , Animais , Microbiota/genética , Poríferos/microbiologia , Poríferos/virologia , Variação Genética , Vírus/genética , Vírus/classificação , FilogeniaRESUMO
The emergence of SARS-CoV-2 and the non-pharmacological interventions adopted to counter its spread appear to have led to changes in the normal circulation and seasonality of respiratory viruses. Our study aims to investigate changes related to the circulation of respiratory viruses, not SARS-CoV-2, among hospitalized patients in Perugia, Central Italy, between 2019 and 2023. The samples were collected from individuals who went to the emergency room (ER) or were hospitalized and analyzed using a molecular multiplex test. The results underline that non-pharmaceutical interventions altered the typical seasonal circulation patterns of different respiratory viruses. Those mostly affected were enveloped viruses like influenza viruses that disappeared in 2021; the least impact was recorded for Rhinovirus, which was detected during the pandemic period, maintaining the same seasonality observed in the pre-pandemic period although with a reduction in the number of positive samples. Our data underline the importance of the continuous monitoring of these viruses, especially to understand the timing with which prevention measures, not only non-pharmacological interventions but also the equipment of vaccine doses and monoclonal antibodies, should be adopted to reduce their circulation, particularly in the population at risk of developing severe forms of lower respiratory tract infection.
Assuntos
COVID-19 , Hospitalização , Infecções Respiratórias , Estações do Ano , Humanos , Itália/epidemiologia , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/virologia , Hospitalização/estatística & dados numéricos , COVID-19/epidemiologia , COVID-19/virologia , COVID-19/prevenção & controle , SARS-CoV-2 , Rhinovirus/isolamento & purificação , Vírus/isolamento & purificação , Vírus/classificação , Vírus/genética , Feminino , Masculino , Idoso , Pessoa de Meia-IdadeRESUMO
Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of "big data", which has also affected the field of virology. The collaboration between the communities of bioinformaticians and virologists already started a few decades ago and it was strongly enhanced by the recent SARS-CoV-2 pandemics. In this article, which is the first in a series on how bioinformatics can enhance virus research, we show that highly useful information is retrievable from selected general and dedicated databases. Indeed, an enormous amount of information-both in terms of nucleotide/protein sequences and their annotation-is deposited in the general databases of international organisations participating in the International Nucleotide Sequence Database Collaboration (INSDC). However, more and more virus-specific databases have been established and are progressively enriched with the contents and features reported in this article. Since viruses are intracellular obligate parasites, a special focus is given to host-pathogen protein-protein interaction databases. Finally, we illustrate several phylogenetic and phylodynamic tools, combining information on algorithms and features with practical information on how to use them and case studies that validate their usefulness. Databases and tools for functional inference will be covered in the next article of this series: Bioinformatics goes viral: II. Sequence-based and structure-based functional analyses for boosting virus research.
Assuntos
Biologia Computacional , Filogenia , Biologia Computacional/métodos , Humanos , Vírus/genética , Vírus/classificação , SARS-CoV-2/genética , SARS-CoV-2/classificação , Genoma Viral , COVID-19/virologia , COVID-19/epidemiologia , Bases de Dados Genéticas , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
Shrews (Soricidae) are common small wild mammals. Some species of shrews, such as Asian house shrews (Suncus murinus), have a significant overlap in their habitats with humans and domestic animals. Currently, over 190 species of viruses in 32 families, including Adenoviridae, Arenaviridae, Arteriviridae, Astroviridae, Anelloviridae, Bornaviridae, Caliciviridae, Chuviridae, Coronaviridae, Filoviridae, Flaviviridae, Hantaviridae, Hepadnaviridae, Hepeviridae, Nairoviridae, Nodaviridae, Orthoherpesviridae, Orthomyxoviridae, Paramyxoviridae, Parvoviridae, Phenuiviridae, Picobirnaviridae, Picornaviridae, Polyomaviridae, Poxviridae, Rhabdoviridae, Sedoreoviridae, Spinareoviridae, and three unclassified families, have been identified in shrews. Diverse shrew viruses, such as Borna disease virus 1, Langya virus, and severe fever with thrombocytopenia syndrome virus, cause diseases in humans and/or domestic animals, posing significant threats to public health and animal health. This review compiled fundamental information about shrews and provided a comprehensive summary of the viruses that have been detected in shrews, with the aim of facilitating a deep understanding of shrews and the diversity, epidemiology, and risks of their viruses.
Assuntos
Musaranhos , Viroses , Vírus , Animais , Musaranhos/virologia , Vírus/classificação , Vírus/isolamento & purificação , Vírus/genética , Viroses/veterinária , Viroses/virologia , Filogenia , HumanosRESUMO
Advances in sequencing technologies and bioinformatics have led to breakthroughs in the study of virus biodiversity. Millipedes (Diplopoda, Myriapoda, Arthropoda) include more than 12,000 extant species, yet data on virus diversity in Diplopoda are scarce. This study aimed to explore the virome of the millipedes collected in the Dong Nai Biosphere Reserve in Vietnam. We studied 14 species of millipedes and managed to assemble and annotate the complete coding genomes of 16 novel viruses, the partial coding genomes of 10 more viruses, and several fragmented viral sequences, which may indicate the presence of about 54 more viruses in the studied samples. Among the complete and partial genomes, 27% were putative members of the order Picornavirales. Most of the discovered viruses were very distant from the viruses currently present in the relevant databases. At least eight viruses meet the criteria to be recognized as a new species by the International Committee on Taxonomy of Viruses, and, for two of them, a higher taxonomic status (genus and even family) can be suggested.
Assuntos
Artrópodes , Biodiversidade , Genoma Viral , Filogenia , Vírus , Vírus/classificação , Vírus/genética , Vírus/isolamento & purificação , Animais , Vietnã , Artrópodes/virologia , Artrópodes/classificação , Viroma/genética , Variação GenéticaRESUMO
Blood feeding ectoparasites of bats have been found to contain insect-specific and vertebrate-infecting viruses of agricultural and medical importance. While it is plausible that some of these are of bat origin, those would be sourced either from the bat exterior or their blood meal. Bats, in addition to their regular diets, consume numerous ectoparasites during grooming. All microbes on and in the ectoparasites would then be introduced into the bat gut upon ingestion of the ectoparasites. To investigate the potential impact of bat ectoparasite viromes on the gut viral microbiome of bats, we compared virus sequences from bats and their blood feeding ectoparasites collected from Yunnan Province, China. Although all the co-occurring viruses were bacteriophages, we observed that bats contained a larger set of viruses than their ectoparasites, and that the set of predicted viruses present in the bats were more diverse than those present in bat ectoparasites. Our analysis suggests that despite a heavy influx of ectoparasites into the digestive tract of bats through consumption, there are only few co-occurring/shared viruses between bats and their ectoparasites, and that these ectoparasites may not be a major driver of bat virome diversity. Our findings provide necessary preliminary data for the evaluation of bat ectoparasites as a potential source of bat infecting viruses.
Assuntos
Artrópodes , Quirópteros , Viroma , Animais , Quirópteros/virologia , Quirópteros/parasitologia , China , Ectoparasitoses/veterinária , Ectoparasitoses/parasitologia , Vírus/classificação , Vírus/isolamento & purificação , Vírus/genéticaRESUMO
Neurotropic viruses, characterized by their capacity to invade the central nervous system, present a considerable challenge to public health and are responsible for a diverse range of neurological disorders. This group includes a diverse array of viruses, such as herpes simplex virus, varicella zoster virus, poliovirus, enterovirus and Japanese encephalitis virus, among others. Some of these viruses exhibit high neuroinvasiveness and neurovirulence, while others demonstrate weaker neuroinvasive and neurovirulent properties. The clinical manifestations of infections caused by neurotropic viruses can vary significantly, ranging from mild symptoms to severe life-threatening conditions. Extracellular vesicles (EVs) have garnered considerable attention due to their pivotal role in intracellular communication, which modulates the biological activity of target cells via the transport of biomolecules in both health and disease. Investigating EVs in the context of virus infection is crucial for elucidating their potential role contribution to viral pathogenesis. This is because EVs derived from virus-infected cells frequently transfer viral components to uninfected cells. Importantly, EVs released by virus-infected cells have the capacity to traverse the blood-brain barrier (BBB), thereby impacting neuronal activity and inducing neuroinflammation. In this review, we explore the roles of EVs during neurotropic virus infections in either enhancing or inhibiting viral pathogenesis. We will delve into our current comprehension of the molecular mechanisms that underpin these roles, the potential implications for the infected host, and the prospective diagnostic applications that could arise from this understanding.
Assuntos
Barreira Hematoencefálica , Vesículas Extracelulares , Vesículas Extracelulares/virologia , Vesículas Extracelulares/metabolismo , Humanos , Barreira Hematoencefálica/virologia , Animais , Vírus/patogenicidade , Vírus/classificação , Viroses/virologia , Vírus da Encefalite Japonesa (Espécie)/patogenicidade , Vírus da Encefalite Japonesa (Espécie)/fisiologia , Herpesvirus Humano 3/patogenicidade , Herpesvirus Humano 3/fisiologia , Enterovirus/patogenicidade , Enterovirus/fisiologiaRESUMO
Human enteric and some respiratory viruses are identified to be involved with acute gastroenteritis that can be shed in feces of infected persons into the environment. Understanding the abundance of these viruses in wastewater is significant when assessing the public health impacts associated with discharge of wastewater into the environment. This study aimed to investigate the prevalence and seasonal variation of human enteric adenovirus (HAdV), Aichi virus (AiV-1), bocavirus (HBoV), and respiratory syndrome coronavirus 2 virus (SARS-CoV-2) in wastewater as well as their prevalence among hospitalized children with acute gastroenteritis. The viruses were detected and quantified with real-time PCR. HAdV was the most detected virus in raw sewage (88.5%), treated sewage (28%), and stool gastroenteritis (74%), followed by HBoV (45.8% for raw sewage, 14.6% for treated sewage, and 55.3% for stool samples). The detection rate of AiV-1 was 59.4%, 19.8%, and 62.6% in raw sewage, treated sewage, and stool samples, respectively. The rate of SARS-CoV-2 detection in raw sewage, treated sewage, and stool samples was 33.3%, 7.3%, and 20.6%, respectively. The viral concentrations ranged between 4.50 × 101 and 8.75 × 107 GC/ml in raw sewage samples, 1.20 × 101 and 5.43 × 106 GC/ml in treated sewage samples, and 4.80 × 101 and 9.88 × 108 GC/gram in stool samples. The overall log means of virus reduction during the wastewater treatment process ranged from 1.68 log10 (HAdV) to 3.31 log10 (AiV-1). The peak prevalence of the four viruses in raw sewage samples occurred during the winter season. This study showed the high detection rates of the four targeted viruses in wastewater and demonstrated that virological surveillance of wastewater in local wastewater treatment plants is a suitable model for epidemiological monitoring of diarrheal and respiratory diseases in middle- and low-resource countries.
Assuntos
Fezes , Gastroenterite , Estações do Ano , Esgotos , Águas Residuárias , Humanos , Gastroenterite/virologia , Gastroenterite/epidemiologia , Águas Residuárias/virologia , Prevalência , Esgotos/virologia , Criança , Fezes/virologia , Pré-Escolar , Criança Hospitalizada , Lactente , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Vírus/isolamento & purificação , Vírus/classificação , Vírus/genética , Kobuvirus/isolamento & purificação , Kobuvirus/genética , Bocavirus Humano/isolamento & purificação , Bocavirus Humano/genética , MasculinoRESUMO
BACKGROUND: Febrile respiratory syndrome (FRS) is often associated with viral infections. The aim of this study was to identify the viral pathogens responsible for FRS in Liaoning Province, China. METHODS: We tested eight respiratory viruses, namely, influenza virus (IFV), rhinovirus (RV), human adenovirus (HAdV), human bocavirus (HBoV), human parainfluenza virus (HPIV), human coronavirus (HCoV), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV), using reverse transcription-polymerase chain reaction (RT-PCR). Statistical analyses were performed using SPSS version 25.0, and the data were plotted using RStudio 4.2.1 software. RESULTS: IFV was the most frequently identified pathogen, followed by RV, HAdV, HBoV, HPIV, HCoV, RSV, and HMPV. RSV/HBoV coinfection occurred most frequently among the mixed cases. The rate of respiratory virus detection was highest in children under one year of age and decreased significantly with age. Seasonal trends showed a peak in virus detection during the winter months. CONCLUSIONS: IFV is the leading cause of FRS in Liaoning Province, China, with single-virus infections prevailing over coinfections. Observations indicate a differential virus detection rate across age groups and seasons, highlighting the need for focused preventive strategies to mitigate the transmission of respiratory viruses, particularly among susceptible populations in the colder season.
Assuntos
Infecções Respiratórias , Humanos , China/epidemiologia , Lactente , Pré-Escolar , Masculino , Feminino , Criança , Adulto , Pessoa de Meia-Idade , Adolescente , Adulto Jovem , Infecções Respiratórias/virologia , Infecções Respiratórias/epidemiologia , Idoso , Estações do Ano , Coinfecção/epidemiologia , Coinfecção/virologia , Viroses/epidemiologia , Viroses/virologia , Vírus/isolamento & purificação , Vírus/classificação , Vírus/genética , Recém-Nascido , Idoso de 80 Anos ou maisAssuntos
Inteligência Artificial , Dobramento de Proteína , Vírus , Animais , Humanos , Vírus/química , Vírus/classificação , Vírus/patogenicidade , Filogenia , Evolução MolecularRESUMO
Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE: Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.
Assuntos
Estuários , Metagenômica , Microbiota , Vírus , Microbiota/genética , Metagenômica/métodos , São Francisco , Vírus/genética , Vírus/classificação , Vírus/isolamento & purificação , Metagenoma/genética , Bactérias/genética , Bactérias/classificação , Archaea/genética , Archaea/virologia , Eucariotos/genética , Genoma Viral/genéticaRESUMO
The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.