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1.
Medicine (Baltimore) ; 100(31): e26802, 2021 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-34397834

RESUMO

RATIONALE: Listeria monocytogenes (L. monocytogenes) is a compatible intracellular bacterial pathogen that can invade different mammalian cells and reach the central nervous system (CNS), leading to meningoencephalitis and brain abscesses. In the diagnosis of L. monocytogenes meningoencephalitis (LMM), conventional tests are often reported as negative due to antibiotic therapy or low bacterial content in cerebrospinal fluid. To date, prompt diagnosis and accurate treatment remain a challenge for patients with Listeria infections. PATIENT CONCERNS: Here, we report a case of a 64-year-old male diagnosed with LMM by using metagenomics next-generation sequencing (mNGS). DIAGNOSIS: LMM was confirmed by mNGS analysis of cerebrospinal fluid. INTERVENTIONS: The patient was treated with piperacillin and sensitive antibiotics. OUTCOMES: The patient could walk independently about 1 month after admission and was discharged from the hospital. LESSONS: This case highlights the value of mNGS in the diagnosis of LMM and emphasizes the inadequate sensitivity of conventional diagnostic methods for Listeria infection.


Assuntos
Encéfalo/diagnóstico por imagem , Líquido Cefalorraquidiano , Hemorragias Intracranianas , AVC Isquêmico , Listeria monocytogenes/isolamento & purificação , Meningite por Listeria , Piperacilina/administração & dosagem , Antibacterianos/administração & dosagem , Líquido Cefalorraquidiano/citologia , Líquido Cefalorraquidiano/microbiologia , Angiografia por Tomografia Computadorizada/métodos , Diagnóstico Diferencial , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Hemorragias Intracranianas/diagnóstico por imagem , Hemorragias Intracranianas/etiologia , AVC Isquêmico/diagnóstico , AVC Isquêmico/etiologia , Imageamento por Ressonância Magnética/métodos , Masculino , Meningite por Listeria/diagnóstico , Meningite por Listeria/tratamento farmacológico , Meningite por Listeria/fisiopatologia , Metagenômica/métodos , Pessoa de Meia-Idade , Tomografia Computadorizada por Raios X/métodos , Resultado do Tratamento
2.
Medicine (Baltimore) ; 100(31): e26842, 2021 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-34397856

RESUMO

INTRODUCTION: Opportunistic infection with multiple pathogens currently has become less uncommon since the application of immunosuppressant or corticosteroid in non- Human immunodeficiency virus patients. However, the clinical diagnosis of the co-infection remains difficult since the uncertainty and deficiency of the microbiologic testing methods. PATIENT CONCERNS: A 66-year-old male patient was admitted to our hospital with chest stuffiness, shortness of breath and elevated body temperature. DIAGNOSIS: He was diagnosed with the co-infection of Pneumocystis jiroveci and cytomegalovirus by metagenomic next-generation sequencing of bronchoalveolar lavage fluid after bronchoscopy. INTERVENTIONS: The patient was empirically treated with broad-spectrum antibiotics, trimethoprim/ sulfamethoxazole and ganciclovir in the beginning of the admission. OUTCOMES: The condition of this patient was not improved even with the intervention at the early stage of the disease. His family requested discharge after 24 inpatient days. LESSONS: This case highlights the application of metagenomic next-generation sequencing in the clinical diagnosis of pulmonary co-infection. Suitable prophylaxis, necessary clinical awareness and accurate diagnosis are indispensable for immunocompromised patients with pulmonary infection.


Assuntos
Líquido da Lavagem Broncoalveolar/microbiologia , Infecções por Citomegalovirus , Citomegalovirus , Ganciclovir/administração & dosagem , Pneumocystis carinii , Pneumonia por Pneumocystis , Combinação Trimetoprima e Sulfametoxazol/administração & dosagem , Idoso , Anti-Infecciosos/administração & dosagem , Broncoscopia/métodos , Coinfecção/diagnóstico , Coinfecção/microbiologia , Citomegalovirus/genética , Citomegalovirus/isolamento & purificação , Infecções por Citomegalovirus/diagnóstico , Infecções por Citomegalovirus/fisiopatologia , Infecções por Citomegalovirus/terapia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Masculino , Metagenômica/métodos , Metilprednisolona/uso terapêutico , Síndrome Nefrótica/tratamento farmacológico , Pneumocystis carinii/genética , Pneumocystis carinii/isolamento & purificação , Pneumonia por Pneumocystis/diagnóstico , Pneumonia por Pneumocystis/fisiopatologia , Pneumonia por Pneumocystis/terapia
3.
Avian Dis ; 65(1): 40-45, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-34339120

RESUMO

We performed viral metagenomics analysis of Japanese quail affected with enteritis to elucidate the viral etiology. Metagenomics generated 21,066,442 sequence reads via high-throughput sequencing, with a mean length of 136 nt. Enrichment in viral sequences suggested that at least three viruses were present in quail samples. Coronavirus and picornavirus were identified and are known as pathogens causing quail enteritis that match the observed morphology. Abundant reads of coronavirus from quail samples yielded four fragment sequences exhibiting six genomes of avian coronavirus. Sequence analysis showed that this quail coronavirus was related to turkey coronavirus and chicken infectious bronchitis virus. Quail picornavirus 8177 bp in size was identified and was similar to the QPV1/HUN/01 virus detected in quails without clinical symptoms in Hungary with 84.6% nucleotide and 94.6% amino acid identity. Our results are useful for understanding the genetic diversity of quail viruses. Further studies must be performed to determine whether quail coronavirus and quail picornavirus are pathogens of the digestive tract of quails.


Assuntos
Infecções por Coronavirus/veterinária , Coronavirus/genética , Coturnix/virologia , Enterite/veterinária , Metagenômica/métodos , Doenças das Aves Domésticas/virologia , Animais , Coronavirus/isolamento & purificação , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Enterite/epidemiologia , Enterite/virologia , Genoma Viral , Picornaviridae/isolamento & purificação , Infecções por Picornaviridae/epidemiologia , Infecções por Picornaviridae/veterinária , Infecções por Picornaviridae/virologia , Doenças das Aves Domésticas/epidemiologia , República da Coreia/epidemiologia
4.
NPJ Biofilms Microbiomes ; 7(1): 55, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34210980

RESUMO

Little is known about the replication and dynamic transcription of probiotics during their "passenger" journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.


Assuntos
Microbioma Gastrointestinal , Perfilação da Expressão Gênica , Lactobacillus casei/genética , Metagenoma , Metagenômica , Transcriptoma , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Regulação Bacteriana da Expressão Gênica , Humanos , Metagenômica/métodos
5.
Nat Commun ; 12(1): 4522, 2021 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-34312399

RESUMO

Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.


Assuntos
Antozoários/fisiologia , Recifes de Corais , Ecossistema , Oxigênio/metabolismo , Animais , Bactérias/classificação , Bactérias/genética , Região do Caribe , Mudança Climática , Peixes/fisiologia , Geografia , Metagenômica/métodos , Modelos Biológicos , Panamá , Filogenia , Água do Mar/microbiologia
6.
Nat Commun ; 12(1): 4485, 2021 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-34301928

RESUMO

High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.


Assuntos
Biologia Computacional/métodos , Genoma Bacteriano/genética , Metagenoma/genética , Metagenômica/métodos , Bactérias/classificação , Bactérias/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Especificidade da Espécie
7.
Medicine (Baltimore) ; 100(27): e26514, 2021 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-34232184

RESUMO

RATIONALE: Chlamydia psittaci (C psittaci) is a gram-negative obligate intracellular parasite, with birds as main hosts. The main route of infection in humans is inhalation of aerosols from contaminated animal excreta through the respiratory tract. The main manifestation of C psittaci infection is pneumonia. Patients suffering from severe infection are prone to sepsis and multiple organ failure. We report a case of simultaneous detection of C psittaci in blood and bronchoalveolar lavage fluid using metagenomic next-generation sequencing (mNGS) technology. PATIENT CONCERNS: The 71-year-old male patient was a farmer with a long history of raising poultry and initial symptoms of fever and muscle pain accompanied by limb weakness and paroxysmal cough. DIAGNOSES: The patient was diagnosed with sepsis, severe pneumonia, and multiple organ failure. INTERVENTIONS: Anti-infective therapy with doxycycline and meropenem was applied. OUTCOMES: The patient's body temperature and infection indicators improved and the chest X-ray findings showed the amelioration of lesions after 18 days of treatment. The patient was discharged without treatment on hospital day 19 due to financial constraints and subsequently died after 7 days. LESSONS: mNGS is an excellent diagnostic tool when specific pathogens are undetected by traditional assays.


Assuntos
Líquido da Lavagem Broncoalveolar/microbiologia , Chlamydophila psittaci/genética , Metagenômica/métodos , Pneumonia Bacteriana/diagnóstico , Psitacose/diagnóstico , Idoso , Chlamydophila psittaci/isolamento & purificação , Humanos , Masculino , Pneumonia Bacteriana/microbiologia , Psitacose/microbiologia
8.
Nat Commun ; 12(1): 4642, 2021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34330907

RESUMO

The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.


Assuntos
Archaea/genética , Vírus de Archaea/genética , Genoma Viral/genética , Metagenoma/genética , Metagenômica/métodos , Archaea/classificação , Archaea/virologia , Vírus de Archaea/metabolismo , Vírus de Archaea/fisiologia , Biofilmes/crescimento & desenvolvimento , Ecossistema , Genômica/métodos , Interações Hospedeiro-Patógeno/genética , Lisogenia/genética , Microscopia de Fluorescência , Filogenia , RNA Ribossômico 16S/genética , Especificidade da Espécie , Ativação Viral/genética
9.
Int J Mol Sci ; 22(13)2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34202141

RESUMO

Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.


Assuntos
Microbioma Gastrointestinal , Lepidópteros/microbiologia , Análise de Variância , Animais , Biologia Computacional/métodos , Interações Hospedeiro-Parasita , Metagenômica/métodos , Plantas/parasitologia , RNA Ribossômico 16S/genética
10.
Int J Mol Sci ; 22(13)2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34202675

RESUMO

Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.


Assuntos
Alho/microbiologia , Metagenoma , Metagenômica , Microbiota , Bactérias/classificação , Bactérias/genética , Biologia Computacional/métodos , Metagenômica/métodos , Especificidade de Órgãos , Filogenia , Análise de Sequência de RNA
11.
Infect Immun ; 89(9): e0015721, 2021 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-34061623

RESUMO

Zebrafish (Danio rerio) is an attractive model organism to use for an array of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic and can be significantly altered due to external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae for colonization, and subsequent disease, to occur. Many studies have explored a variety of aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms but few have researched how a V. cholerae infection changes the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was used to examine how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and that specific microbes that are targeted depend on the V. cholerae genotype.


Assuntos
Cólera/microbiologia , Suscetibilidade a Doenças , Microbioma Gastrointestinal , Interações Hospedeiro-Patógeno , Interações Microbianas , Vibrio cholerae/fisiologia , Animais , Modelos Animais de Doenças , Metagenômica/métodos , RNA Ribossômico 16S , Peixe-Zebra
12.
Am J Hum Genet ; 108(7): 1270-1282, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34157305

RESUMO

Publicly available genetic summary data have high utility in research and the clinic, including prioritizing putative causal variants, polygenic scoring, and leveraging common controls. However, summarizing individual-level data can mask population structure, resulting in confounding, reduced power, and incorrect prioritization of putative causal variants. This limits the utility of publicly available data, especially for understudied or admixed populations where additional research and resources are most needed. Although several methods exist to estimate ancestry in individual-level data, methods to estimate ancestry proportions in summary data are lacking. Here, we present Summix, a method to efficiently deconvolute ancestry and provide ancestry-adjusted allele frequencies (AFs) from summary data. Using continental reference ancestry, African (AFR), non-Finnish European (EUR), East Asian (EAS), Indigenous American (IAM), South Asian (SAS), we obtain accurate and precise estimates (within 0.1%) for all simulation scenarios. We apply Summix to gnomAD v.2.1 exome and genome groups and subgroups, finding heterogeneous continental ancestry for several groups, including African/African American (∼84% AFR, ∼14% EUR) and American/Latinx (∼4% AFR, ∼5% EAS, ∼43% EUR, ∼46% IAM). Compared to the unadjusted gnomAD AFs, Summix's ancestry-adjusted AFs more closely match respective African and Latinx reference samples. Even on modern, dense panels of summary statistics, Summix yields results in seconds, allowing for estimation of confidence intervals via block bootstrap. Given an accompanying R package, Summix increases the utility and equity of public genetic resources, empowering novel research opportunities.


Assuntos
Grupos de Populações Continentais/genética , Interpretação Estatística de Dados , Metagenômica/métodos , Linhagem , Alelos , Simulação por Computador , Frequência do Gene , Humanos , Padrões de Herança , Software
13.
Infect Immun ; 89(9): e0015121, 2021 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-34097462

RESUMO

Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae, an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was important for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, the presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.


Assuntos
Cólera/microbiologia , Microbioma Gastrointestinal , Interações entre Hospedeiro e Microrganismos , Interações Hospedeiro-Patógeno , Sistemas de Secreção Tipo VI/fisiologia , Vibrio cholerae/fisiologia , Animais , Modelos Animais de Doenças , Suscetibilidade a Doenças , Metagenômica/métodos , RNA Ribossômico 16S , Peixe-Zebra
14.
Viruses ; 13(6)2021 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-34064231

RESUMO

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.


Assuntos
Metagenoma , Metagenômica , Fagos de Pseudomonas/fisiologia , Pseudomonas/virologia , Ensaio de Placa Viral , Viroma , Biologia Computacional , Especificidade de Hospedeiro , Metagenômica/métodos , Fagos de Pseudomonas/classificação , Ensaio de Placa Viral/métodos
15.
Viruses ; 13(6)2021 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-34072878

RESUMO

In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or "core gene sets", of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus-host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total "infectome" within a diverse range of vertebrate hosts.


Assuntos
Replicação do DNA , Vírus de DNA/genética , Vírus de RNA/genética , Transcrição Reversa , Vertebrados/virologia , Animais , Biologia Computacional , Vírus de DNA/classificação , Evolução Molecular , Perfilação da Expressão Gênica , Regulação Viral da Expressão Gênica , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Interações Hospedeiro-Patógeno , Metagenoma , Metagenômica/métodos , Filogenia , Vírus de RNA/classificação , Retroviridae/classificação , Retroviridae/genética , Análise de Sequência de RNA , Transcriptoma
16.
Viruses ; 13(6)2021 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-34073397

RESUMO

Viruses transmitted by the sweet potato whitefly (Bemisia tabaci) have been detrimental to the sustainable production of cucurbits in the southeastern USA. Surveys were conducted in the fall of 2019 and 2020 in Georgia, a major cucurbit-producing state of the USA, to identify the viruses infecting cucurbits and their distribution. Symptomatic samples were collected and small RNA libraries were prepared and sequenced from three cantaloupes, four cucumbers, and two yellow squash samples. An analysis of the sequences revealed the presence of the criniviruses cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and the begomovirus cucurbit leaf crumple virus (CuLCrV). CuLCrV was detected in 76%, CCYV in 60%, and CYSDV in 43% of the total samples (n = 820) tested. The level of mixed infections was high in all the cucurbits, with most plants tested being infected with at least two of these viruses. Near-complete genome sequences of two criniviruses, CCYV and CYSDV, were assembled from the small RNA sequences. An analysis of the coding regions showed low genetic variability among isolates from different hosts. In phylogenetic analysis, the CCYV isolates from Georgia clustered with Asian isolates, while CYSDV isolates clustered with European and USA isolates. This work enhances our understanding of the distribution of viruses on cucurbits in South Georgia and will be useful to develop strategies for managing the complex of whitefly-transmitted viruses in the region.


Assuntos
Coinfecção/virologia , Hemípteros/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Doenças das Plantas/virologia , Vírus de Plantas/classificação , Vírus de Plantas/genética , Animais , Crinivirus/genética , Crinivirus/isolamento & purificação , Genoma Viral , Georgia/epidemiologia , Metagenômica/métodos , Fenótipo , Filogenia , Prevalência , RNA Viral
17.
Viruses ; 13(5)2021 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-34065683

RESUMO

Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.


Assuntos
Metagenoma , Metagenômica , Poaceae/virologia , Saccharum/virologia , Viroma , Metagenômica/métodos , Filogenia , Doenças das Plantas/virologia , Quarentena , Vírion
18.
Viruses ; 13(5)2021 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-34066683

RESUMO

Bat flies (Hippoboscoidea: Nycteribiidae and Streblidae) are obligate hematophagous ectoparasites of bats. We collected streblid bat flies from the New World (México) and the Old World (Uganda), and used metagenomics to identify their viruses. In México, we found méjal virus (Rhabdoviridae; Vesiculovirus), Amate virus (Reoviridae: Orbivirus), and two unclassified viruses of invertebrates. Méjal virus is related to emerging zoonotic encephalitis viruses and to the agriculturally important vesicular stomatitis viruses (VSV). Amate virus and its sister taxon from a bat are most closely related to mosquito- and tick-borne orbiviruses, suggesting a previously unrecognized orbivirus transmission cycle involving bats and bat flies. In Uganda, we found mamucuso virus (Peribunyaviridae: Orthobunyavirus) and two unclassified viruses (a rhabdovirus and an invertebrate virus). Mamucuso virus is related to encephalitic viruses of mammals and to viruses from nycteribiid bat flies and louse flies, suggesting a previously unrecognized orthobunyavirus transmission cycle involving hippoboscoid insects. Bat fly virus transmission may be neither strictly vector-borne nor strictly vertical, with opportunistic feeding by bat flies occasionally leading to zoonotic transmission. Many "bat-associated" viruses, which are ecologically and epidemiologically associated with bats but rarely or never found in bats themselves, may actually be viruses of bat flies or other bat ectoparasites.


Assuntos
Dípteros/virologia , Tropismo Viral , Animais , Código de Barras de DNA Taxonômico , Dípteros/classificação , Dípteros/genética , Geografia , Especificidade de Hospedeiro , Metagenômica/métodos , México , Filogenia , Uganda
19.
PLoS One ; 16(6): e0252534, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34133435

RESUMO

Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.


Assuntos
Quirópteros/virologia , Fezes/virologia , Metagenômica/métodos , Viroma/genética , Vírus/genética , Zoonoses/virologia , Adenoviridae/classificação , Adenoviridae/genética , Animais , Quirópteros/classificação , Reservatórios de Doenças/virologia , Variação Genética , Genoma Viral/genética , Hepevirus/classificação , Hepevirus/genética , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/classificação , Coronavírus da Síndrome Respiratória do Oriente Médio/genética , Filogenia , Rotavirus/classificação , Rotavirus/genética , Análise de Sequência de DNA/métodos , Suíça , Vírus/classificação
20.
Nat Commun ; 12(1): 3562, 2021 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-34117246

RESUMO

While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.


Assuntos
Benchmarking/métodos , Biologia Computacional/métodos , Microbiota , Classificação , Disbiose/microbiologia , Processamento Eletrônico de Dados/métodos , Humanos , Metagenoma , Metagenômica/métodos , Viés de Seleção
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