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1.
Nutrients ; 16(9)2024 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-38732575

RESUMO

Osteosarcopenia, the concurrent presence of sarcopenia and osteopenia/osteoporosis, poses a significant health risk to older adults, yet its impact on clinical outcomes is not fully understood. The aim of this prospective, longitudinal multicentre study was to examine the impact of osteosarcopenia on 3-year mortality and unplanned hospitalizations among 572 older hospitalized patients (mean age 75.1 ± 10.8 years, 78% female). Sarcopenia and low bone mineral density (BMD) were evaluated using Dual Energy X-ray Absorptiometry and the European Working Group on Sarcopenia in Older People (EWGSOP2) and WHO criteria, respectively. Among participants, 76% had low BMD, 9% were sarcopenic, and 8% had osteosarcopenia. Individuals with osteosarcopenia experienced a significantly higher rate of mortality (46%, p < 001) and unplanned hospitalization (86%, p < 001) compared to those without this condition. Moreover, "healthy" subjects-those without sarcopenia or low BMD-showed markedly lower 3-year mortality (9%, p < 001) and less unplanned hospitalization (53%, p < 001). The presence of osteosarcopenia (p = 0.009) increased the 3-year mortality risk by 30% over sarcopenia alone and by 8% over low BMD alone, underscoring the severe health implications of concurrent muscle and bone deterioration. This study highlights the substantial impact of osteosarcopenia on mortality among older adults, emphasizing the need for targeted diagnostic and therapeutic strategies.


Assuntos
Densidade Óssea , Doenças Ósseas Metabólicas , Hospitalização , Osteoporose , Sarcopenia , Humanos , Sarcopenia/mortalidade , Sarcopenia/complicações , Sarcopenia/epidemiologia , Feminino , Idoso , Masculino , Hospitalização/estatística & dados numéricos , Idoso de 80 Anos ou mais , Estudos Prospectivos , Osteoporose/mortalidade , Osteoporose/complicações , Doenças Ósseas Metabólicas/mortalidade , Estudos Longitudinais , Absorciometria de Fóton , Fatores de Risco
3.
PLoS One ; 17(12): e0277831, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36584002

RESUMO

Accurate measurement of cortical bone parameters may improve fracture risk assessment and help clinicians on the best treatment strategy. Patients at risk of fracture are currently detected using the current X-Ray gold standard DXA (Dual XRay Absorptiometry). Different alternatives, such as 3D X-Rays, Magnetic Resonance Imaging or Quantitative Ultrasound (QUS) devices, have been proposed, the latter having advantages of being portable and sensitive to mechanical and geometrical properties. The objective of this cross-sectional study was to evaluate the performance of a Bi-Directional Axial Transmission (BDAT) device used by trained operators in a clinical environment with older subjects. The device, positioned at one-third distal radius, provides two velocities: VFAS (first arriving signal) and VA0 (first anti-symmetrical guided mode). Moreover, two parameters are obtained from an inverse approach: Ct.Th (cortical thickness) and Ct.Po (cortical porosity), along with their ratio Ct.Po/Ct.Th. The areal bone mineral density (aBMD) was obtained using DXA at the femur and spine. One hundred and six patients (81 women, 25 men) from Marien Hospital and St. Anna Hospital (Herne, Germany) were included in this study. Age ranged from 41 to 95 years, while body mass index (BMI) ranged from 16 to 47 kg.m-2. Three groups were considered: 79 non-fractured patients (NF, 75±13years), 27 with non-traumatic fractures (F, 80±9years) including 14 patients with non-vertebral fractures (NVF, 84±7years). Weak to moderate significant Spearman correlations (R ranging from 0.23 to 0.53, p < 0.05) were found between ultrasound parameters and age, BMI. Using multivariate Partial Least Square discrimination analyses with Leave-One-Out Cross-Validation (PLS-LOOCV), we found the combination of VFAS and the ratio Ct.Po/Ct.Th to be predictive for all non traumatic fractures (F) with the odds ratio (OR) equals to 2.5 [1.6-3.4] and the area under the ROC curve (AUC) equal to 0.63 [0.62-0.65]. For the group NVF, combination of four parameters VA0. Ct.Th, Ct.Po and Ct.Po/Ct.Po, along with age provides a discrimination model with OR and AUC equals to 7.5 [6.0-9.1] and 0.75 [0.73-0.76]. When restricted to a smaller population (87 patients) common to both BDAT and DXA, BDAT ORs and AUCs are comparable or slightly higher to values obtained with DXA. The fracture risk assessment by BDAT method in older patients, in a clinical setting, suggests the benefit of the affordable and transportable device for the routine use.


Assuntos
Fraturas Ósseas , Masculino , Humanos , Feminino , Idoso , Adulto , Pessoa de Meia-Idade , Idoso de 80 Anos ou mais , Estudos Transversais , Fraturas Ósseas/diagnóstico por imagem , Densidade Óssea , Absorciometria de Fóton/métodos , Fêmur
4.
Nutrients ; 13(11)2021 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-34836043

RESUMO

Osteoporosis and sarcopenia are two chronic conditions, which widely affect older people and share common risk factors. We investigated the prevalence of low bone mineral density (BMD) and sarcopenia, including the overlap of both conditions (osteosarcopenia) in 572 older hospitalized patients (mean age 75.1 ± 10.8 years, 78% women) with known or suspected osteoporosis in this prospective observational multicenter study. Sarcopenia was assessed according to the revised definition of the European Working Group on Sarcopenia in Older People (EWGSOP2). Low BMD was defined according to the World Health Organization (WHO) recommendations as a T-score < -1.0. Osteosarcopenia was diagnosed when both low BMD and sarcopenia were present. Low BMD was prevalent in 76% and the prevalence of sarcopenia was 9%, with 90% of the sarcopenic patients showing the overlap of osteosarcopenia (8% of the entire population). Conversely, only few patients with low BMD demonstrated sarcopenia (11%). Osteosarcopenic patients were older and frailer and had lower BMI, fat, and muscle mass, handgrip strength, and T-score compared to nonosteosarcopenic patients. We conclude that osteosarcopenia is extremely common in sarcopenic subjects. Considering the increased risk of falls in patients with sarcopenia, they should always be evaluated for osteoporosis.


Assuntos
Doenças Ósseas Metabólicas/epidemiologia , Osteoporose/epidemiologia , Sarcopenia/epidemiologia , Idoso , Idoso de 80 Anos ou mais , Doenças Ósseas Metabólicas/complicações , Feminino , Humanos , Pacientes Internados/estatística & dados numéricos , Masculino , Osteoporose/complicações , Prevalência , Estudos Prospectivos , Sarcopenia/complicações , Síndrome
5.
Nutrients ; 13(8)2021 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-34444668

RESUMO

There are few data on the longitudinal association of cytokine and appetite among older hospitalized patients. We aimed to investigate the impact of the changes of inflammatory cytokines on appetite in older hospitalized patients. A total of 191 patients (mean age 81.3 ± 6.6 years, 64% women) participated in this prospective longitudinal observational study. Appetite was evaluated using the Edmonton Symptom Assessment System on admission and after seven days. Serum cytokines such as IL-1ß, IL-6, IL-8, IL-10, IL-12p70, IL-17, IL-18, IL-23 and IL-33, IFN-α2, IFN-γ, TNF-α and MCP-1 were measured both times. No significant differences in the mean serum levels of all the cytokines could be detected overtime in relation to appetite changes, except for IL-18. Appetite significantly deteriorated overtime in patients with increasing IL-18 levels and improved in those without significant changes in IL-18 levels. In a stepwise regression analysis, changes of IL-18 levels were the major independent predictor for the changes of patients' appetite and explained 4% of the variance, whereas other cytokines and variables, such as age, sex, infection and disease, did not show any impact on appetite changes. We conclude that IL-18 seems to exert a significant impact on appetite in acutely ill older hospitalized patients and should, therefore, be considered as a potential target in the diagnosis, prevention and treatment of malnutrition.


Assuntos
Regulação do Apetite , Citocinas/sangue , Hospitalização , Mediadores da Inflamação/sangue , Pacientes Internados , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Biomarcadores/sangue , Feminino , Avaliação Geriátrica , Humanos , Interleucina-18/sangue , Estudos Longitudinais , Masculino , Estudos Prospectivos , Fatores de Tempo
6.
Appetite ; 166: 105470, 2021 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-34139296

RESUMO

It has already been confirmed that the decline in appetite during disease is a common issue and the biologic players of inflammation such as cytokines may serve as mediators of this effect. This study aimed to investigate the association of appetite with individual cytokines that could be involved in the inflammation-associated loss of appetite in acutely ill older hospitalized patients. 191 patients (mean age 81.3 ± 6.6 years, 64% women) participated in this prospective observational study. Risk of malnutrition and patient's appetite were evaluated using the Mini Nutritional Assessment Short Form and the Simplified Nutritional Appetite Questionnaire on admission, respectively. Serum C-reactive protein (CRP) and serum cytokines such as Interleukin 1 beta (IL-1ß), IL-6, IL-8, IL-10, IL-12p70, IL-17, IL-18, IL-23 and IL-33, interferon alpha-2, interferon gamma, tumor necrosis factor alpha and monocyte chemoattractant protein-1 (MCP-1) were measured. Of total population, 30% had CRP>3.0 (mg/dL), 31% were malnourished and 31% demonstrated poor and very poor appetite. There were significant differences in the mean concentrations of a number of cytokines including IL-1ß, MCP-1, IL-6, IL-10, IL-12p70, IL-18 and IL-23 across the appetite scores. In a regression analysis, an increased IL-18 level (P = 0.049) was the most prominent biomarker for poor appetite. No other significant associations between appetite and circulating levels of other cytokines were found in the regression analysis, except for IL-6 and IL-33, which were only significantly associated in the unadjusted model. The association of IL-18 with decreased appetite was independent from the severity of CRP-level and infections. In this study, certain cytokines, in particular IL-18 were associated with poor appetite in acutely diseased patients and should therefore be considered as a potential target of the prevention and treatment of malnutrition.


Assuntos
Apetite , Desnutrição , Idoso , Idoso de 80 Anos ou mais , Proteína C-Reativa , Citocinas , Feminino , Humanos , Masculino , Avaliação Nutricional
7.
Sci Rep ; 11(1): 11726, 2021 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-34083692

RESUMO

Acute diarrhea is associated with a reduced absorption of both vitamin K antagonists (VKA) and vitamin K itself. To date, the net effect on the coagulation status of subjects with VKA remains elusive. We performed a systematic retrospective single-center analysis using an electronic data extraction approach to identify subjects with plasmatic anticoagulation (either VKA or direct oral anticoagulant (DOAC)) and diarrhea in a German University Hospital over a period of eight years. Acute diarrhea and complete documentation of coagulation status on admission were defined as inclusion criteria, anticoagulation other than VKA/DOAC and obvious inadherence as exclusion criteria. Subjects with VKA/DOAC admitted for hypertension served as control group. Data extraction yielded 356 subjects with gastrointestinal diagnoses and 198 hypertensive subjects, 55 and 83 of whom fulfilled all in- and exclusion criteria. INR values of subjects with VKA were significantly higher in subjects with diarrhea than in hypertensive controls (4.3 ± 3.7 vs. 2.3 ± 0.7, p < 0.001). The distribution of subjects having INR values lower, higher or within the target range differed significantly among groups with a substantially higher prevalence of overanticoagulation in the diarrhea group (46.4% vs. 14.3%, p < 0.001). In a multinomial logistic regression model, acute diarrhea was significantly associated with overanticoagulation (odds ratio 7.2, 95% confidence interval 2.163-23.921; p < 0.001), whereas age, sex, creatinine, and indication of anticoagulation were not (p > 0.05 each). Acute diarrhea is associated with a highly increased risk for overanticoagulation in patients with VKA. Thus, gastroenteritis necessitates a close monitoring of INR in order to identify subjects needing a temporary pause of VKA therapy.


Assuntos
Anticoagulantes/farmacocinética , Coagulação Sanguínea/efeitos dos fármacos , Diarreia/sangue , Vitamina K/antagonistas & inibidores , Administração Oral , Idoso , Idoso de 80 Anos ou mais , Anticoagulantes/administração & dosagem , Anticoagulantes/uso terapêutico , Diarreia/diagnóstico , Diarreia/tratamento farmacológico , Diarreia/epidemiologia , Registros Eletrônicos de Saúde , Feminino , Alemanha/epidemiologia , Pesquisas sobre Atenção à Saúde , Humanos , Masculino , Pessoa de Meia-Idade , Razão de Chances
8.
Preprint em Inglês | medRxiv | ID: ppmedrxiv-21253869

RESUMO

ObjectivesIt has recently been shown that von Willebrand factor (vWf) multimers may be a key driver of immunothrombosis in Coronavirus disease 2019 (COVID-19). Since COVID-19 is associated with an increased risk of autoreactivity, the present study investigates, whether the generation of autoantibodies to ADAMTS13 contributes to this finding. DesignObservational prospective controlled multicenter study. SettingBlood samples and clinical data of patients with COVID-19 were collected regularly during hospitalization in the period from April to November 2020. Patients90 patients with confirmed COVID-19 of mild to critical severity and 30 healthy controls participated in this study. Measuerements and Main ResultsAntibodies to ADAMTS13 occurred in 31 (34.4%) patients with COVID-19. Generation of ADAMTS13 antibodies was associated with a significantly lower ADAMTS13 activity (56.5%, interquartile range (IQR) 21.25 vs. 71.5%, IQR 24.25, p=0.0041), increased disease severity (severe or critical disease in 90% vs. 62.3%, p=0.0189), and a trend to a higher mortality (35.5% vs. 18.6%, p=0.0773). Median time to antibody development was 11 days after first positive SARS-CoV-2-PCR specimen. ConclusionThe present study demonstrates for the first time, that generation of antibodies to ADAMTS13 is a frequent finding in COVID-19. Generation of these antibodies is associated with a lower ADAMTS13 activity and an increased risk of an adverse course of the disease suggesting an inhibitory effect on the protease. These findings provide a rationale to include ADAMTS13 antibodies in the diagnostic workup of SARS-CoV-2 infections.

9.
Br J Nutr ; 124(10): 1069-1075, 2020 11 28.
Artigo em Inglês | MEDLINE | ID: mdl-32618518

RESUMO

The present study aimed to investigate the effect of acute changes in serum C-reactive protein (CRP) on appetite and food intake among older hospitalised patients. A total of 200 patients (age range 65-94 years, 62·5 % women) participated in this prospective longitudinal observational study. Risk of malnutrition was measured according to the Mini Nutritional Assessment Short Form. The Simplified Nutritional Appetite Questionnaire (SNAQ) and Edmonton Symptom Assessment System (ESAS) were used to evaluate patients' appetite at the time of hospital admission (baseline) and after 7 d (follow-up). Food intake was measured according to the plate diagram and serum CRP was analysed at baseline and follow-up. At baseline, 30·5 % of the patients had moderate to severe inflammation, 31·0 % were malnourished and 48·0 % had food intake <75 % of the meals offered. Also, 32·5 and 23·5 % reported poor and very poor appetite or severe loss of appetite according to the SNAQ and ESAS, respectively. Of the patients, 40 % displayed a pronounced reduction in median CRP levels by -1·2 mg/dl and 19 % demonstrated an increase in median CRP levels by +1·2 mg/dl. Appetite significantly improved (P = 0·006) in patients with a decrease in CRP level and deteriorated in those with an increase in CRP level (P = 0·032). Changes in CRP levels did not show any significant impact on food intake. In a regression analysis, changes of inflammation were the major independent predictor for changes of patients' appetite. We conclude that inflammation has a significant impact on appetite and should therefore be considered in the diagnosis and treatment of malnutrition.


Assuntos
Apetite/fisiologia , Ingestão de Alimentos/fisiologia , Avaliação Geriátrica , Hospitalização , Inflamação/fisiopatologia , Idoso , Idoso de 80 Anos ou mais , Proteína C-Reativa/análise , Feminino , Humanos , Estudos Longitudinais , Masculino , Desnutrição/epidemiologia , Avaliação Nutricional , Fatores de Risco , Inquéritos e Questionários
10.
Preprint em Inglês | bioRxiv | ID: ppbiorxiv-182741

RESUMO

The current pandemic is caused by the SARS-CoV-2 virus and large progress in understanding the pathology of the virus has been made since its emergence in late 2019. Several reports indicate short lasting immunity against endemic coronaviruses, which contrasts repeated reports that biobanked venous blood contains SARS-CoV-2 reactive T cells even before the outbreak in Wuhan. This suggests there exists a preformed T cell memory in individuals not exposed to the pandemic virus. Given the similarity of SARS-CoV-2 to other members of the Coronaviridae family, the endemic coronaviruses appear likely candidates to generate this T cell memory. However, given the apparent poor immunological memory created by the endemic coronaviruses, other immunity against other common pathogens might offer an alternative explanation. Here, we utilize a combination of epitope prediction and similarity to common human pathogens to identify potential sources of the SARS-CoV-2 T cell memory. We find that no common human virus, other than beta-coronaviruses, can explain the pre-existing SARS-CoV-2 reactive T cells in uninfected individuals. Our study suggests OC43 and HKU1 are the most likely pathogens giving rise to SARS-CoV-2 preformed immunity.Competing Interest StatementThe authors have declared no competing interest.View Full Text

11.
Nutrients ; 11(9)2019 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-31443557

RESUMO

The effect of inflammation on appetite and food intake has been rarely studied in humans. In this study, we examined the association of C-reactive protein (CRP), as an inflammatory marker, with appetite and food intake among older hospitalized patients. A total of 200 older individuals, who were consecutively admitted to a geriatric acute care ward, participated in this prospective observational study. Appetite was evaluated using the Edmonton Symptom Assessment System (ESAS) and the Simplified Nutritional Appetite Questionnaire (SNAQ), respectively. Food intake was measured according to plate diagram method and participants were categorized as having food intake <75% and ≥75% of meals served. Nutritional status was evaluated using the Mini Nutritional Assessment Short Form (MNA-SF). In addition, serum CRP was analyzed and the levels >3.0 (mg/dL) were considered as moderate to severe inflammation. Of total population with mean age 81.4 ± 6.6 years (62.5% females), 51 (25.5%) had no inflammation and 88 (44.0%) and 61 (30.5%) had mild and moderate to severe inflammation, respectively. According to MNA-SF, 9.0% and 60.0% had normal nutritional status or a risk of malnutrition, respectively, whereas 31.0% were malnourished. Based on the SNAQ-appetite-question, 32.5% of the patients demonstrated poor and very poor appetite whereas 23.5% reported severe loss of appetite according to ESAS. Ninety-five (48.0%) of the participants had food intake <75% of the meals offered. Significant associations between SNAQ-appetite (p = 0.003) and ESAS-appetite (p = 0.013) scores and CRP levels were observed. In addition, significant differences were observed in CRP levels between intake ≥75% and <75% of meals served (p < 0.001). Furthermore, there were significant associations between appetite and nutritional status whereas malnourished older patients demonstrated a decreased appetite compared to those with normal nutritional status (p = 0.011). In a regression analysis, inflammation was the major independent risk factor for patients' appetite (p = 0.003) and food intake (p = 0.011) whereas other variables such as infection (p = 0.960), chronic inflammatory diseases (p = 0.371), age (p = 0.679) and gender (p = 0.447) do not show any impact on appetite. Our findings confirm that poor appetite and low food intake are associated with inflammation in older hospitalized patients, suggesting that inflammation may contribute an important aspect to the development of malnutrition in these patients.


Assuntos
Apetite , Ingestão de Alimentos , Comportamento Alimentar , Hospitalização , Inflamação/psicologia , Pacientes Internados/psicologia , Desnutrição/psicologia , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Biomarcadores/sangue , Proteína C-Reativa/análise , Feminino , Avaliação Geriátrica , Humanos , Inflamação/sangue , Inflamação/diagnóstico , Mediadores da Inflamação/sangue , Masculino , Desnutrição/sangue , Desnutrição/diagnóstico , Estado Nutricional , Estudos Prospectivos , Fatores de Risco
12.
J Vis Exp ; (149)2019 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-31355784

RESUMO

Polyomaviruses, like the BK-polyomavirus (BKPyV), can cause severe pathologies in immunocompromised patients. However, since highly effective antivirals are currently not available, methods measuring the impact of potential antiviral agents are required. Here, a dual fluorescence reporter that allows the analysis of the BKPyV non-coding control-region (NCCR) driven early and late promoter activity was constructed to quantify the impact of potential antiviral drugs on viral gene expression via tdTomato and eGFP expression. In addition, by cloning BKPyV-NCCR amplicons which in this protocol have been exemplarily obtained from the blood-derived DNA of immunocompromised renal transplanted patients, the impact of NCCR-rearrangements on viral gene expression can be determined. Following cloning of the patient derived amplicons, HEK293T cells were transfected with the reporter-plasmids, and treated with potential antiviral agents. Subsequently, cells were subjected to FACS-analysis for measuring mean fluorescence intensities 72 h post transfection. To also test the analysis of drugs that have a potential cell cycle inhibiting effect, only transfected and thus fluorescent cells are used. Since this assay is performed in large T Antigen expressing cells, the impact of early and late expression can be analyzed in a mutually independent manner.


Assuntos
Vírus BK/genética , Sequências Reguladoras de Ácido Nucleico/genética , Transcrição Gênica , Antivirais/farmacologia , Vírus BK/efeitos dos fármacos , Vírus BK/isolamento & purificação , Vírus BK/metabolismo , Citometria de Fluxo , Células HEK293 , Humanos , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Infecções por Polyomavirus/sangue , Infecções por Polyomavirus/virologia , Transcrição Gênica/efeitos dos fármacos , Infecções Tumorais por Vírus/sangue , Infecções Tumorais por Vírus/virologia
13.
Mol Ecol Resour ; 18(3): 681-690, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29194981

RESUMO

High-throughput sequencing makes it possible to evaluate thousands of genetic markers across genomes and populations. Reduced-representation sequencing approaches, like double-digest restriction site-associated DNA sequencing (ddRADseq), are frequently applied to screen for genetic variation. In particular in nonmodel organisms where whole-genome sequencing is not yet feasible, ddRADseq has become popular as it allows genomewide assessment of variation patterns even in the absence of other genomic resources. However, while many tools are available for the analysis of ddRADseq data, few options exist to simulate ddRADseq data in order to evaluate the accuracy of downstream tools. The available tools either focus on the optimization of ddRAD experiment design or do not provide the information necessary for a detailed evaluation of different ddRAD analysis tools. For this task, a ground truth, that is, the underlying information of all effects in the data set, is required. Therefore, we here present ddrage, the ddRAD Data Set Generator, that allows both developers and users to evaluate their ddRAD analysis software. ddrage allows the user to adjust many parameters such as coverage and rates of mutations, sequencing errors or allelic dropouts, in order to generate a realistic simulated ddRADseq data set for given experimental scenarios and organisms. The simulated reads can be easily processed with available analysis software such as stacks or pyrad and evaluated against the underlying parameters used to generate the data to gauge the impact of different parameter values used during downstream data processing.


Assuntos
Conjuntos de Dados como Assunto , Análise de Sequência/métodos , Software , Simulação por Computador , Modelos Genéticos , Modelos Teóricos
14.
BMC Genomics ; 18(1): 787, 2017 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-29037173

RESUMO

BACKGROUND: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task. RESULTS: From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample. CONCLUSIONS: TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapper and as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html .


Assuntos
Bases de Dados Genéticas , Eucariotos/genética , Metagenômica/normas , Sequenciamento de Nucleotídeos em Larga Escala , Padrões de Referência , Software
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