Biology subjects

Renson, A.

Publications and source records attributed to Renson, A..

6 recordsLinked to original sources

bioRxiv2020

Strengthening The Organizing and Reporting of Microbiome Studies (STORMS)

BackgroundHuman microbiome research is a growing field with the potential for improving our understanding and treatment of diseases and other conditions. The field is interdisciplinary, making concise organization and reporting of results across different styles of epidemiology, biology, bioinformatics, translational medicine, and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. MethodsA multidisciplinary group of microbiome epidemiology researchers reviewed elements of available reporting guidelines for observational and genetic studies and adapted these for application to culture-independent human microbiome studies. New reporting elements were developed for laboratory, bioinformatic, and statistical analyses tailored to microbiome studies, and other parts of these checklists were streamlined to keep reporting manageable. ResultsSTORMS is a 17-item checklist for reporting on human microbiome studies, organized into six sections covering typical sections of a scientific publication, presented as a table with space for author-provided details and intended for inclusion in supplementary materials. ConclusionsSTORMS provides guidance for authors and standardization for interdisciplinary microbiome studies, facilitating complete and concise reporting and augments information extraction for downstream applications. AvailabilityThe STORMS checklist is available as a versioned spreadsheet from https://www.stormsmicrobiome.org/.

genomics↗

bioRxiv2018

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study

PurposeThe effect of tobacco exposure on the oral microbiome has not been established. MethodsWe performed amplicon sequencing of the 16S ribosomal RNA gene V4 variable region to estimate bacterial community characteristics in 259 oral rinse samples, selected based on self-reported smoking and serum cotinine levels, from the 2013-14 New York City Health and Nutrition Examination Study. We identified differentially abundant operational taxonomic units (OTUs) by primary and secondhand tobacco exposure, and employed "microbe set enrichment analysis" to assess shifts in microbial oxygen utilization. ResultsCigarette smoking was associated with depletion of aerobic OTUs (Enrichment Score test statistic ES = -0.75, p = 0.002) with a minority (29%) of aerobic OTUs enriched in current smokers compared to never smokers. Consistent shifts in the microbiota were observed for current cigarette smokers as for non-smokers with secondhand exposure as measured by serum cotinine levels. Differential abundance findings were similar in crude and adjusted analyses. ConclusionResults support a plausible link between tobacco exposure and shifts in the oral microbiome at the population level through three lines of evidence: 1) a shift in microbiota oxygen utilization associated with primary tobacco smoke exposure, 2) consistency of abundance fold-changes associated with current smoking and shifts along the gradient of secondhand smoke exposure among non-smokers, and 3) consistency after adjusting for a priori hypothesized confounders. HighlightsO_LICigarette smoke was associated with microbial anaerobiosis in oral rinse specimens C_LIO_LIThe microbiome shifts associated with smoking and secondhand exposure were correlated C_LIO_LIShifts in oral bacterial oxygen utilization may mediate smoking and health outcomes C_LIO_LIWe propose "microbe set enrichment analysis" for interpreting shifts in the microbiome C_LI

epidemiology↗

bioRxiv2018

The Charlson Index is insufficient to control for comorbidities in a national trauma registry

BackgroundThe Charlson Comorbidity Index (CCI) is frequently used to control for confounding by comorbidities in observational studies, but its performance as such has not been studied. We evaluated the performance of CCI and an alternative summary method, logistic principal component analysis (LPCA), to adjust for comorbidities, using as an example the association between insurance and mortality.\n\nMaterials and MethodsUsing all admissions in the National Trauma Data Bank 2010-2015, we extracted mortality, payment method, and 36 ICD-9-derived comorbidities. We estimated ORs for the association between uninsured status and mortality before and after adjusting for CCI, LPCA, and separate covariates. We also calculated standardized mean differences (SMDs) of comorbidity variables before and after weighting the sample using inverse probability of treatment weights (IPTW) for CCI, LPCA, and separate covariates.\n\nResultsIn 4,936,880 admissions, most (68.3%) had at least one comorbidity. Considerable imbalance was observed in the unweighted sample (mean SMD=0.086, OR=1.17), which was almost entirely eliminated by IPTW on separate covariates (mean SMD=0.012, OR=1.36). The CCI performed similarly to the unweighted sample (mean SMD=0.080, OR=1.25), while 2 LPCA axes were better able to control for confounding (mean SMD=0.04, OR=1.31). Using covariate adjustment, the CCI accounted for 56.1% of observed confounding, whereas 2 LPCA axes accounted for 91.3%.\n\nConclusionsThe use of the CCI to adjust for confounding may result in residual confounding, and alternative strategies should be considered. LPCA may be a viable alternative to adjusting for each comorbidity when samples are small or positivity assumptions are violated.

epidemiology↗

bioRxiv2017

Lack of insurance is associated with lower probability of diagnostic imaging use among US trauma patients: An instrumental variable analysis and simulation

BackgroundUninsured trauma patients have higher mortality than their insured counterparts. One possible reason is disparities in utilization of appropriate diagnostic imaging, including computed tomography (CT), X-ray, ultrasound (US), and magnetic resonance imaging (MRI). We examined the association between lack of insurance and use of diagnostic imaging.\n\nMethodsData come from the National Trauma Databank 2010-2015. Patients were determined uninsured if payment mode was self-pay or missing. The primary outcome was any diagnostic imaging procedure, and secondary outcomes included CT, X-ray, US, or MRI. Risk ratios (RRs) were adjusted for demographics, comorbidities, injury characteristics, facility characteristics. We also used the 2010 Patient Protection and Affordable Care Act as an instrumental variable (IV), with linear terms for year to account for annual trends in imaging use. Monte carlo simulations to test effect of hypothetical violations to IV assumptions of relevance, no direct effect, and no confounding.\n\nResultsOf 4,373,554 patients, 953,281 (21.8%) were uninsured. After adjusting, uninsured patients had lower chance of any imaging (RR 0.98, 95% CI 0.98 to 0.98), x-ray (RR 0.99, 95% CI 0.99 to 1.00), and MRI (RR 0.82, 95% CI 0.81 to 0.83), and higher chance of ultrasound (RR 1.01, 95% CI 1.01 to 1.02). In IV analysis, uninsured status was associated with reduction in any imaging (RR 0.60, 95% CI 0.52 to 0.70), tomography (RR 0.52, 95% CI 0.44 to 0.62) ultrasound (RR 0.46, 95% CI 0.32 to 0.65), and MRI (RR 0.19, 95% CI 0.10 to 0.37) and increased likelihood of x-ray use (RR 1.74, 95% CI 1.31 to 2.32). Simulations indicated that a direct effect RD of -0.02 would be necessary to produce observed results under the null hypothesis.\n\nDiscussionOur study suggests an association between insurance status and use of imaging that is unlikely to be driven by confounding or violations of IV assumptions. Mechanisms for this remain unclear, but could include unconscious provider bias or institutional financial constraints. Further research is warranted to elucidate mechanisms and assess whether differences in diagnostic imaging use mediate the association between insurance and mortality.

epidemiology↗

bioRxiv2017

Sociodemographic patterning in the oral microbiome of a diverse sample of New Yorkers

11.1 PurposeVariations in the oral microbiome are potentially implicated in social inequalities in oral disease, cancers, and metabolic disease. We describe sociodemographic variation of oral microbiomes in a diverse sample.\n\n1.2 MethodsWe performed 16S rRNA sequencing on mouthwash specimens in a subsample (n=282) of the 2013-14 population-based New York City Health and Nutrition Examination Study (NYC-HANES). We examined differential abundance of 216 operational taxonomic units (OTUs), and alpha and beta diversity by age, sex, income, education, nativity, and race/ethnicity. For comparison, we also examined differential abundance by diet, smoking status, and oral health behaviors.\n\n1.3 Results69 OTUs were differentially abundant by any sociodemographic variable (false discovery rate < 0.01), including 27 by race/ethnicity, 21 by family income, 19 by education, three by sex. We also found 49 differentially abundant by smoking status, 23 by diet, 12 by oral health behaviors. Genera differing for multiple sociodemographic characteristics included Lactobacillus, Prevotella, Porphyromonas, Fusobacterium.\n\n1.4 ConclusionsWe identified oral microbiome variation consistent with health inequalities, with more taxa differing by race/ethnicity than diet, and more by SES variables than oral health behaviors. Investigation is warranted into possible mediating effects of the oral microbiome in social disparities in oral, metabolic and cancers.\n\nHighlightsO_LIMost microbiome studies to date have had minimal sociodemographic variability, limiting what is known about associations of social factors and the microbiome.\nC_LIO_LIWe examined the oral microbiome in a population-based sample of New Yorkers with wide sociodemographic variation.\nC_LIO_LINumerous taxa were differentially abundant by race/ethnicity, income, education, marital status, and nativity.\nC_LIO_LIFrequently differentially abundant taxa include Porphyromonas, Fusobacterium, Streptococcus, and Prevotella, which are associated with oral and systemic disease.\nC_LIO_LIMediation of health disparities by microbial factors may represent an important intervention site to reduce health disparities, and should be explored in prospective studies.\nC_LI

epidemiology↗

bioRxiv2017

Accessible, curated metagenomic data through ExperimentHub

We present curatedMetagenomicData, a Bioconductor and command-line interface to thousands of metagenomic profiles from the Human Microbiome Project and other publicly available datasets, and ExperimentHub, a platform for convenient cloud-based distribution of data to the R desktop. The resource provides standardized per-participant metadata linked to bacterial, fungal, archaeal, and viral taxonomic abundances, as well as quantitative metabolic functional profiles. The datasets can be immediately analyzed in R or other software with a minimum of bioinformatic expertise and no preprocessing of data. We demonstrate identification of taxonomic/functional correlations, an investigation of gut \"enterotypes\", and a comparison of the accuracy of disease classification from different data types. These documented analyses can be reproduced efficiently on a laptop, without the barriers of working with large-scale, raw sequencing data. The building and expansion of curatedMetagenomicData is based entirely on open source software and pipelines, to facilitate the addition of new microbiome datasets and methods.

bioinformatics↗