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1.
Microbiome Res Rep ; 2(2): 14, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38047277

RESUMO

Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare the composition of mock communities that are processed along with samples to their theoretical composition. A visual comparison between experimental and theoretical community composition and their correlation is provided for researchers to assess the quality of their sample processing workflows.

3.
Cir. Esp. (Ed. impr.) ; 101(9): 617-623, sep. 2023. tab, graf
Artigo em Inglês | IBECS | ID: ibc-225102

RESUMO

Introduction: To describe the design and implementation of a Crisis Resource Management (CRM) training program for the initial assessment of polytrauma patients. Methods: Prospectively implemented CRM training program in acute-care tertiary hospital by hospital personnel involved in the care of polytraumatisms. The program has a blended format and 23-h duration, including 11 h of online theoretical training followed by 12-h simulation modules and practical cases devoted to the roles of members of the trauma team, functioning of the polytrauma room, and key aspects of teamwork. The Human Factors Attitude Survey (HFAS) was used to assess attitudes related to non-technical skills, and the End-of-Course Critique (ECC) survey to evaluate satisfaction with training. We evaluated changes in the pre- and post-training assessments. Results: Eighty staff personnel (26% specialists, 16% residents, 29% nurses, 14% nursing assistant, 15% stretcher bearer) participated in three editions of the program. Theoretical knowledge improved from a mean (SD) of 5.95 (1.7) to 8.27 (2.1) (P < .0001). In the HFAS, statistically significant differences in 18 of 23 attitudinal markers were observed, with improvements in all items of “leadership” and “roles”, in 4 of 5 items of “situational awareness”, and in 4 of 8 items of “communication”. Mean values obtained in the ECC questionnaire were also very high. Conclusions: A CRM training model developed for the initial care of polytrauma patients improved theoretical knowledge and participants perceptions and attitudes regarding leadership, communication, roles, and situational awareness of members of the trauma team. (AU)


Introducción: Describir el diseño y la implementación de un programa de formación basado en Crisis Resource Management para la evaluación inicial de los pacientes con politraumatismos. Métodos: Implementación prospectiva de un programa CRM de formación en Hospital terciario con el personal del hospital involucrado en la asistencia de politraumatismos. El programa tenía un formato semipresencial de 23 horas de duración, incluyendo 11 horas de formación online de contenido teórico seguidas de 12 horas de módulos de simulación y casos prácticos referidos a los papeles de los miembros del equipo de trauma, funcionamiento del box de trauma y aspectos claves del trabajo en equipo. El Human Factors Attitude Survey (HFAS) se utilizó para evaluar las actitudes relacionadas con las habilidades no técnicas y el End-of-Course Critique (ECC) cuestionario para valorar la satisfacción con la formación. Se evaluaron los cambios antes y después de la formación. Resultados: Ochenta miembros del hospital (26% especialistas, 16% residentes, 29% enfermeras, 14% auxiliares de enfermería, 15% camilleros) participaron en tres ediciones del programa. El conocimiento teórico aumentó de una media (DE) de 5.95 (1.7) a 8.27 (2.1) (P < ,0001). En el HFAS, se observaron diferencias estadísticamente significativas en 18 de los 23 marcadores de actitud, con mejorías en todos los ítems de “liderazgo” y “roles”, en 4 de los 5 items de “consciencia situacional” y en 4 de los 8 ítems de “comunicación”. Los valores medios obtenidos en el cuestionario ECC tambien fueron muy altos. Conclusiones: Un modelo CRM de formación desarrollado para la atención inicial de los pacientes con politraumatismos mejoró el conocimiento teórico y las percepciones y actitudes de los participantes relacionadas con el liderazgo, la comunicación, los roles y la consciencia situacional de los miembros del equipo de trauma. (AU)


Assuntos
Humanos , Traumatismo Múltiplo , Educação em Saúde/métodos , 50230 , Inquéritos e Questionários , Hospitais
4.
Sci Rep ; 13(1): 8042, 2023 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-37198426

RESUMO

Human microbiome research is helped by the characterization of microbial networks, as these may reveal key microbes that can be targeted for beneficial health effects. Prevailing methods of microbial network characterization are based on measures of association, often applied to limited sampling points in time. Here, we demonstrate the potential of wavelet clustering, a technique that clusters time series based on similarities in their spectral characteristics. We illustrate this technique with synthetic time series and apply wavelet clustering to densely sampled human gut microbiome time series. We compare our results with hierarchical clustering based on temporal correlations in abundance, within and across individuals, and show that the cluster trees obtained by using either method are significantly different in terms of elements clustered together, branching structure and total branch length. By capitalizing on the dynamic nature of the human microbiome, wavelet clustering reveals community structures that remain obscured in correlation-based methods.


Assuntos
Microbioma Gastrointestinal , Microbiota , Humanos , Análise de Ondaletas , Consórcios Microbianos , Análise por Conglomerados
5.
Cir Esp (Engl Ed) ; 101(9): 617-623, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37085134

RESUMO

INTRODUCTION: To describe the design and implementation of a Crisis Resource Management (CRM) training program for the initial assessment of polytrauma patients. METHODS: Prospectively implemented CRM training program in acute-care tertiary hospital by hospital personnel involved in the care of polytraumatisms. The program has a blended format and 23-h duration, including 11 h of online theoretical training followed by 12-h simulation modules and practical cases devoted to the roles of members of the trauma team, functioning of the polytrauma room, and key aspects of teamwork. The Human Factors Attitude Survey (HFAS) was used to assess attitudes related to non-technical skills, and the End-of-Course Critique (ECC) survey to evaluate satisfaction with training. We evaluated changes in the pre- and post-training assessments. RESULTS: Eighty staff personnel (26% specialists, 16% residents, 29% nurses, 14% nursing assistant, 15% stretcher bearer) participated in three editions of the program. Theoretical knowledge improved from a mean (SD) of 5.95 (1.7) to 8.27 (2.1) (P < .0001). In the HFAS, statistically significant differences in 18 of 23 attitudinal markers were observed, with improvements in all items of "leadership" and "roles", in 4 of 5 items of "situational awareness", and in 4 of 8 items of "communication". Mean values obtained in the ECC questionnaire were also very high. CONCLUSIONS: A CRM training model developed for the initial care of polytrauma patients improved theoretical knowledge and participants perceptions and attitudes regarding leadership, communication, roles, and situational awareness of members of the trauma team.


Assuntos
Traumatismo Múltiplo , Humanos , Traumatismo Múltiplo/terapia , Currículo , Conscientização , Liderança , Competência Clínica
6.
Front Microbiol ; 14: 1094800, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37065158

RESUMO

Background: Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples. Methods: Human fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene·GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls. Results: Samples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs. Conclusion: Our study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.

7.
Nat Commun ; 13(1): 6638, 2022 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-36380002

RESUMO

The gut microbiota in early life, when critical immune maturation takes place, may influence the immunogenicity of childhood vaccinations. Here we assess the association between mode of delivery, gut microbiota development in the first year of life, and mucosal antigen-specific antibody responses against pneumococcal vaccination in 101 infants at age 12 months and against meningococcal vaccination in 66 infants at age 18 months. Birth by vaginal delivery is associated with higher antibody responses against both vaccines. Relative abundances of vaginal birth-associated Bifidobacterium and Escherichia coli in the first weeks of life are positively associated with anti-pneumococcal antibody responses, and relative abundance of E. coli in the same period is also positively associated with anti-meningococcal antibody responses. In this study, we show that mode of delivery-induced microbiota profiles of the gut are associated with subsequent antibody responses to routine childhood vaccines.


Assuntos
Microbioma Gastrointestinal , Vacinas Meningocócicas , Lactente , Gravidez , Feminino , Humanos , Escherichia coli , Bifidobacterium , Vacinação , Anticorpos Antibacterianos
8.
mSphere ; 7(6): e0051222, 2022 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-36394321

RESUMO

Diet is an important determinant of the human gut microbiome. Here, we analyzed fecal metagenomes of Dutch adults following omnivorous, pescatarian, vegan, and vegetarian diets. We compared the taxonomic composition of individuals from our study with publicly available gut metagenomes from westernized and non-westernized societies. We observed that, despite long-term transition to diets rich in plant fibers (vegan or vegetarian), the microbiomes of these were typical of westernized populations, and similar in composition to omnivores. Although there were no major differences in metabolic modules, we identified differences in the species that contributed to particular functions, such as carbohydrate degradation and short-chain fatty acid metabolism. Overall, this study shows functional redundancy of the microbiomes among westernized populations, which is independent of long-term individual dietary habits. IMPORTANCE Diet is an important modulator of the human gut microbiome, which is susceptible to increased consumption of plant fibers in vegan or vegetarian lifestyles. To investigate this, we compared the gut microbiome of Dutch adults following omnivorous, pescatarian, vegan and vegetarian diets. We did not observe major differences in the gut microbiome composition and function between individuals with different dietary habits. However, we observed differences in the species that contribute to the core functions of the gut microbiome. Our study thus emphasizes the need to better understand the species-specific functional changes associated with dietary habits in the human gut microbiome.


Assuntos
Dieta Vegetariana , Microbiota , Adulto , Humanos , Dieta , Dieta Vegana , Comportamento Alimentar
9.
Lancet Microbe ; 3(6): e443-e451, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35659906

RESUMO

BACKGROUND: Gut colonisation by extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli is a risk factor for developing overt infection. The gut microbiome can provide colonisation resistance against enteropathogens, but it remains unclear whether it confers resistance against ESBL-producing E coli. We aimed to identify a potential role of the microbiome in controlling colonisation by this antibiotic-resistant bacterium. METHODS: For this matched case-control study, we used faeces from 2751 individuals in a Dutch cross-sectional population study (PIENTER-3) to culture ESBL-producing bacteria. Of these, we selected 49 samples that were positive for an ESBL-producing E coli (ESBL-positive) and negative for several variables known to affect microbiome composition. These samples were matched 1:1 to ESBL-negative samples on the basis of individuals' age, sex, having been abroad or not in the past 6 months, and ethnicity. Shotgun metagenomic sequencing was done and taxonomic species composition and functional annotations (ie, microbial metabolism and carbohydrate-active enzymes) were determined. Targeted quantitative metabolic profiling (proton nuclear magnetic resonance spectroscopy) was done to investigate metabolomic profiles and combinations of univariate (t test and Wilcoxon test), multivariate (principal coordinates analysis, permutational multivariate analysis of variance, and partial least-squares discriminant analysis) and machine-learning approaches (least absolute shrinkage and selection operator and random forests) were used to analyse all the molecular data. FINDINGS: No differences in diversity parameters or in relative abundance were observed between ESBL-positive and ESBL-negative groups based on bacterial species-level composition. Machine-learning approaches using microbiota composition did not accurately predict ESBL status (area under the receiver operating characteristic curve [AUROC]=0·41) when using either microbiota composition or any of the functional profiles. The metabolome also did not differ between ESBL groups, as assessed by various methods including random forest (AUROC=0·61). INTERPRETATION: By combining multiomics and machine-learning approaches, we conclude that asymptomatic gut carriage of ESBL-producing E coli is not associated with an altered microbiome composition or function. This finding might suggest that microbiome-mediated colonisation resistance against ESBL-producing E coli is not as relevant as it is against other enteropathogens and antibiotic-resistant bacteria. FUNDING: None.


Assuntos
Escherichia coli , Microbioma Gastrointestinal , Adulto , Antibacterianos/farmacologia , Bactérias/metabolismo , Estudos de Casos e Controles , Estudos Transversais , Escherichia coli/genética , Etnicidade , Microbioma Gastrointestinal/genética , Humanos , Metaboloma , beta-Lactamases/genética
10.
Sci Rep ; 12(1): 1915, 2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-35115596

RESUMO

Influenza-like illness (ILI), a disease caused by respiratory pathogens including influenza virus, is a major health concern in older adults. There is little information on changes and recovery dynamics of the nasopharyngeal (NP) microbiota of older adults associated with an ILI. Here, we compared the NP microbiota in older adults reporting (n = 240) or not (n = 157) ILI during the 2014-2015 influenza season at different times of the ILI event. A small but significant effect of the ILI was observed on the microbiota community composition and structure when compared to controls and samples collected at recovery. Corynebacterium was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such as Haemophilus, Porphyromonas and Gemella had higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera, Corynebacterium, Moraxella and Dolosigranulum exhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery. Our findings demonstrate that acute-ILI is associated with alterations in the phylogenetic structure of the NP microbiota in older adults. The variation in the core microbiota suggests imbalances in the ecosystem, which could potentially play a role in the susceptibility and recovery of the NP microbiota after an ILI event.


Assuntos
Envelhecimento , Influenza Humana/microbiologia , Influenza Humana/virologia , Microbiota , Nasofaringe/microbiologia , Nasofaringe/virologia , Fatores Etários , Idoso , Carga Bacteriana , Disbiose , Feminino , Humanos , Influenza Humana/diagnóstico , Masculino , Pessoa de Meia-Idade , Filogenia , Dinâmica Populacional , Fatores de Tempo , Carga Viral
11.
Sci Rep ; 12(1): 1892, 2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-35115599

RESUMO

The human gut microbiome plays a central role in health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term dietary habits within a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.


Assuntos
Bactérias/genética , Dieta , Farmacorresistência Bacteriana/genética , Comportamento Alimentar , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Adulto , Bactérias/efeitos dos fármacos , Bactérias/crescimento & desenvolvimento , Dieta Vegana , Dieta Vegetariana , Fezes/microbiologia , Feminino , Humanos , Masculino , Carne , Metagenoma , Metagenômica , Pessoa de Meia-Idade , Países Baixos , Valor Nutritivo , Alimentos Marinhos , Fatores de Tempo , Verduras
12.
Otol Neurotol ; 43(2): e268-e273, 2022 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-34772881

RESUMO

OBJECTIVE: We developed a clinical sign that improves the sensitivity, specificity, and predictive values of the Head Impulse Paradigm (HIMP) Test by adding the Suppression Head Impulse Paradigm (SHIMP) Test using a diagnostic headband. METHODS: Prospective and descriptive study analyzing the function of 1,255 horizontal semicircular canals of subjects with differing vestibulo-ocular reflex (VOR) gains who showed-up with symptoms related to neurotology (Montevideo, Uruguay, March 2017 to March 2019). The clinical HIMP and SHIMP tests were assessed and the amplitudes of overt saccades were compared to each other. Clinical findings were contrasted against vHIT gains. CONCLUSION: The HIMP and SHIMP combined test using the H/S headband has high specificity and low sensibility. This test association can identify healthy individuals among individuals typically misdiagnosed as ill by the conventional HIT or HIMP maneuver of the HIMP test, as originally described by Halmagyi and Curthoys. Therefore, we recommend using the headband assisted HIMP/SHIMP test, instead of exclusively relying on positive HIMP results.


Assuntos
Teste do Impulso da Cabeça , Reflexo Vestíbulo-Ocular , Teste do Impulso da Cabeça/métodos , Humanos , Estudos Prospectivos , Movimentos Sacádicos , Canais Semicirculares
13.
J Adv Nurs ; 78(5): 1448-1460, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-34854496

RESUMO

AIMS: To explore the perceptions of nurses on the factors that influence their readiness to manage intimate partner violence (IPV) in Spain. DESIGN: Qualitative content analysis based on data from six different regions in Spain (Murcia, Region of Valencia, Castile and Leon, Cantabria, Catalonia, Aragon) collected between 2014 and 2016. METHODS: 37 personal interviews were carried out with nurses from 27 primary health care (PHC) centres and 10 hospitals. We followed the consolidated criteria for reporting qualitative research guidelines. Qualitative content analysis was supported by Atlas.ti and OpenCode. RESULTS: The results are organised into four categories corresponding to (1) acknowledging IPV as a health issue. An ongoing process; (2) the Spanish healthcare system and PHC service: a favourable space to address IPV although with some limitations; (3) nurses as a key figure for IPV in coordinated care and (4) factors involved in nurses' autonomy in their response to IPV, with their respective subcategories. CONCLUSION: In practice, nurses perceive responding to IPV as a personal choice, despite the institutional mandate to address IPV as a health issue. There is a need to increase continuous training and ensure IPV is included in the curriculum in university nursing undergraduate degrees, by disseminating the existing IPV protocols. Furthermore, coordination between healthcare professionals needs to be improved in terms of all levels of care and with other institutions.


Assuntos
Violência por Parceiro Íntimo , Enfermeiras e Enfermeiros , Currículo , Pessoal de Saúde/educação , Humanos , Pesquisa Qualitativa
14.
Sci Rep ; 11(1): 17148, 2021 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-34433845

RESUMO

The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray-Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.


Assuntos
Benchmarking/métodos , Microbiota , Kit de Reagentes para Diagnóstico/normas , Mucosa Respiratória/microbiologia , Biomassa , Humanos , Metagenômica/métodos , Metagenômica/normas , Reação em Cadeia da Polimerase/métodos , Reação em Cadeia da Polimerase/normas , RNA Ribossômico 16S/genética , Saliva/microbiologia
15.
Lancet Healthy Longev ; 2(1): e13-e23, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36098111

RESUMO

BACKGROUND: People aged 60 years or older are at high risk for respiratory infections, one of the leading causes of mortality worldwide. Vaccination is the main way to protect against these infections; however, vaccination is less effective in older adults than in younger adults due to ageing of the immune system, so innovative strategies that improve vaccine responses could provide a major public health benefit. The gut microbiota regulates host immune homoeostasis and response against pathogens, but human studies showing the effects of the gut microbiota on respiratory infections in older adults are sparse. We aimed to investigate the composition of the microbiota in relation to respiratory infections and local and systemic immune markers in older adults during an influenza season. METHODS: In this observational study, participants were selected from an influenza-like illness (ILI) prospective surveillance cohort in which community-dwelling adults aged 60 years and older in the Netherlands were recruited through their general practitioner or the Civil Registry. Inclusion criteria have been described elsewhere. Participants completed questionnaires and self-reported symptoms. To measure microbiota composition, faecal samples were collected from participants registering an ILI event, with a follow-up (recovery) sample collected 7-9 weeks after the ILI event, and from asymptomatic participants not reporting any event throughout the season. We tested associations between microbiota profiles and a set of health-related variables, patient characteristics, and local and systemic immune markers. We cultured identified bacterial biomarkers for ILI with CaCo-2 cells in an in vitro intestinal epithelial model and measured the induced immune response. This study is registered with http://www.trialregister.nl, NL4666. FINDINGS: Between Oct 1, 2014, and April 30, 2015, 2425 older adults were recruited into the ILI surveillance cohort. From Oct 1, 2014, to June 15, 2015, faecal samples were collected from 397 participants, of whom 213 (54%) reported an ILI event once throughout the season and 184 (46%) did not. 192 ILI participants recovered and provided follow-up samples. Microbiota composition was altered during an ILI event. The Bacteroidetes (mean relative abundance 17·51% [SD 11·41] in the ILI group and 14·19% [10·02] in the control group; adjusted p=0·014) and the Proteobacteria (3·40% [8·10] in the ILI group and 1·57% [3·69] in the control group; adjusted p=0·015) were more abundant in the ILI group than in the control group. The abundance of Ruminococcus torques was positively associated with ILI and the abundance of Escherichia/Shigella, negatively correlated with alpha diversity, and negatively co-occurred with beneficial taxa, including butyrate producers. R torques was associated with pro-inflammatory profiles, both locally in faeces and systemically in blood. ILI-associated taxa (R torques and Escherichia coli) had symbiotic effects on the cellular immune response when cultured together in an in vitro model. INTERPRETATION: The abundances of specific bacteria could be used as potential biomarkers for susceptibility to respiratory infections and as targets for intervention in the ageing population. FUNDING: The Dutch Ministry of Health, Welfare and Sport, and the Strategic Program of the National Institute for Public Health and the Environment.

16.
Nutrients ; 12(11)2020 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-33198235

RESUMO

Dietary modulation of the gastro-intestinal microbiota is a potential target in improving healthy ageing and age-related functional outcomes, including cognitive decline. We explored the association between diet, gastro-intestinal microbiota and cognition in Dutch healthy older adults of the 'New dietary strategies addressing the specific needs of the elderly population for healthy aging in Europe' (NU-AGE) study. The microbiota profile of 452 fecal samples from 226 subjects was determined using a 16S ribosomal RNA gene-targeted microarray. Dietary intake was assessed by 7-day food records. Cognitive functioning was measured with an extensive cognitive test battery. We observed a dietary and microbial pro- to anti-inflammatory gradient associated with diets richer in animal- or plant-based foods. Fresh fruits, nuts, seeds and peanuts, red and processed meat and grain products were most strongly associated to microbiota composition. Plant-rich diets containing fresh fruits, nuts, seeds and peanuts were positively correlated with alpha-diversity, various taxa from the Bacteroidetes phylum and anti-inflammatory species, including those related to Faecalibacterium prausnitzii and Eubacterium rectale and E. biforme. Animal product-rich diets associated with pro-inflammatory species, including those related to Ruminococcus gnavus and Collinsella spp.. Cognition was neither associated with microbiota composition nor alpha-diversity. In conclusion, diets richer in animal- and plant-based foods were related to a pro- and anti-inflammatory microbial profile, while cognition was associated with neither.


Assuntos
Cognição , Dieta Mediterrânea , Fezes/microbiologia , Microbioma Gastrointestinal , Idoso , Bactérias/isolamento & purificação , Feminino , Voluntários Saudáveis , Humanos , Masculino , Países Baixos , RNA Ribossômico 16S/genética
17.
Brief Bioinform ; 21(4): 1487-1494, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-31298267

RESUMO

This note complements and clarifies part of the work of Hawinkel et al. recently published in the journal and suggests some more or less standard tools and methods for carrying out association studies of the microbiome.


Assuntos
Microbiota , Modelos Estatísticos , Publicações
18.
19.
Nat Commun ; 10(1): 4997, 2019 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-31676793

RESUMO

The early-life microbiome appears to be affected by mode of delivery, but this effect may depend on intrapartum antibiotic exposure. Here, we assess the effect of delivery mode on gut microbiota, independent of intrapartum antibiotics, by postponing routine antibiotic administration to mothers until after cord clamping in 74 vaginally delivered and 46 caesarean section born infants. The microbiota differs between caesarean section born and vaginally delivered infants over the first year of life, showing enrichment of Bifidobacterium spp., and reduction of Enterococcus and Klebsiella spp. in vaginally delivered infants. The microbiota composition at one week of life is associated with the number of respiratory infections over the first year. The taxa driving this association are more abundant in caesarean section born children, providing a possible link between mode of delivery and susceptibility to infectious outcomes.


Assuntos
Bactérias/genética , DNA Bacteriano/genética , Parto Obstétrico , Microbioma Gastrointestinal/genética , Dinâmica Populacional , Bactérias/classificação , Cesárea/métodos , DNA Bacteriano/análise , Fezes/microbiologia , Feminino , Microbioma Gastrointestinal/fisiologia , Humanos , Lactente , Recém-Nascido , Gravidez , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vagina/microbiologia
20.
Actual. nutr ; 20(2): [34-42], Abril-Junio de 2019.
Artigo em Espanhol | LILACS | ID: biblio-1087630

RESUMO

Introducción: analizar la injerencia de la adherencia al tratamiento en la evaluación clínica optimiza el uso de pruebas y evita intensificar tratamientos que pueden aumentar riesgos en los pacientes. Conocer sobre las variables influyentes implica el conocimiento y el control de factores relativos al cuidado de la diabetes mellitus tipo 2 (DM2). Objetivos: analizar el efecto de la adherencia al tratamiento en adultos con DM2 en Argentina. Materiales y métodos: estudio transversal. Se incluyeron 1.520 pacientes adultos con DM2 con tres o más meses de antigüedad de enfermedad residentes en Argentina. Se aplicó un cuestionario validado autorreferido. Se evaluó el grado de adherencia reportada, las recomendaciones dadas por el equipo de salud, las formas de adhesión y los motivos de incumplimiento por medio del Summary of Diabetes Self-Care Activities (SDSCA). Resultados: representando diferentes regiones geográficas, la media de adherencia general para todas las características fue 4,32 (61,71%); los peores puntajes para la adherencia correspondieron a la actividad física, el monitoreo glucémico y la dieta en orden ascendente. Se observaron carencias en las recomendaciones por parte del equipo de salud al momento de indicar medidas higiénico dietéticas. Conclusiones: los resultados nacionales observados guardan similitud en la dieta, la actividad física y la disminución en el consumo de tabaco con respecto a los datos prevalentes proveniente de la Cuarta Encuesta Nacional de Factores de Riesgo


Introduction: analyzing the interference of adherence to treatment in clinical evaluation optimizes the use of tests and avoids intensifying treatments that may increase risks in patients. Knowing about the influential variables implies the knowledge and control of factors related to the care of diabetes mellitus type 2 (T2D). Objectives: to analyze the effect of adherence to treatment in adults with T2D in Argentina. Materials and methods: transversal study. We included 1.520 adult patients with T2D with 3 or more months of illness in Argentina. A validated self-reported questionnaire was applied. The degree of adherence reported, the recommendations given by the health team, the forms of adherence and the reasons for non-compliance through the Summary of Diabetes Self-Care Activities (SDSCA) were evaluated. Results: representing different geographical regions, the mean of general adherence for all the characteristics was 4.32 (61.71%); the worst scores for adherence corresponded to physical activity, glycemic monitoring and diet in ascending order. There were shortcomings in the recommendations by the health team when indicating hygienic dietary measures. Conclusions: the observed national results are similar in diet, physical activity and the decrease in tobacco consumption with respect to prevailing data from the Fourth National Survey of Risk Factors.


Assuntos
Diabetes Mellitus Tipo 2 , Cooperação e Adesão ao Tratamento
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