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Disease surveillance systems are a cornerstone of public health tracking and prevention. This review addresses the use, promise, perils, and ethics of social media– and Internet-based data collection for public health surveillance. Our review highlights untapped opportunities for integrating digital surveillance in public health and current applications that could be improved through better integration, validation, and clarity on rules surrounding ethical considerations. Promising developments include hybrid systems that couple traditional surveillance data with data from search queries, social media posts, and crowdsourcing. In the future, it will be important to identify opportunities for public and private partnerships, train public health experts in data science, reduce biases related to digital data (gathered from Internet use, wearable devices, etc.), and address privacy. We are on the precipice of an unprecedented opportunity to track, predict, and prevent global disease burdens in the population using digital data.

The human microbiome has emerged as a key aspect of human biology and has been implicated in many etiologies. Shotgun metagenomic sequencing is the most high-resolution approach available to study taxonomic composition and functional potential of the human microbiome, and an increasing amount of published data are available for re-use. These public data resources allow the possibility of rapid, inexpensive hypothesis testing for specific diseases and environmental niches, and meta-analysis across multiple related studies. However, several factors prevent the research community from taking full advantage of these public resources. Barriers include the substantial investments of time, computational resources, and specialized bioinformatic expertise required to convert them to analyzable form, and inconsistencies in annotation and formatting between individual studies.To overcome these challenges, we developed the curatedMetagenomicData data package (described at https://waldronlab.github.io/curatedMetagenomicData/) for distribution through the Bioconductor 1 ExperimentHub platform (see Supplementary Methods). curatedMetagenomicData provides highly curated and uniformly processed human microbiome data including bacterial, fungal, archaeal, and viral taxonomic abundances, in addition to quantitative metabolic functional profiles and standardized per-participant metadata. Data resources are accessible with a minimum of bioinformatic knowledge, while integration with the R/Bioconductor environment allows full flexibility for biologists, clinicians, epidemiologists, or statisticians to perform novel analyses and methodological development. We produced these resources by (i) downloading the raw sequencing data, (ii) processing it through the MetaPhlAn2 2 and HUMAnN2 3 pipelines, (iii) manually curating sample and study information, (iv) creating a pipeline to document and represent the above results as integrative Bioconductor objects, and (v) working with the Bioconductor core . CC-BY-NC 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx

The U.S. Department of Health and Human Services' (HHS) Healthy People 2020 goals sought to improve health outcomes among sexual minorities; HHS acknowledged that a dearth of sexual orientation items in federal and state health surveys obscured a broad understanding of sexual minority-related health disparities. The HHS 2011 data progression plan aimed to advance sexual orientation data collection efforts at the national level. Sexual orientation is a complex, multidimensional construct often composed of sexual identity, sexual attraction, and sexual behavior, thus posing challenges to its quantitative and practical measurement and analysis. In this review, we (a) present existing sexual orientation constructs; (b) evaluate current HHS sexual orientation data collection efforts; (c) review post-2011 data progression plan research on sexual minority health disparities, drawing on HHS survey data; (d) highlight the importance of and (e) identify obstacles to multidimensional sexual orientation measurement and analysis; and (f) discuss methods for multidimensional sexual orientation analysis and propose a matrix for addressing discordance/branchedness within these analyses. Multidimensional sexual orientation data collection and analysis would elucidate sexual minority-related health disparities, guide related health policies, and enhance population-based estimates of sexual minority individuals to steer health care practices.

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Purpose of the ReviewAs the science of the microbiome advances, social epidemiologists can contribute to understanding how the broader social environment shapes the microbiome over the life course. This review summarizes current research and describes potential mechanisms of the social epidemiology of the microbiome.Recent FindingsMost existing literature linking the social environment and the microbiome comes from animal models, focused on the impact of social interactions and psychosocial stress. Suggestive evidence of the importance of early life exposures, health behaviors, and the built environment also point to the importance of the social environment for the microbiome in humans.SummarySocial epidemiology as a field is well poised to contribute expertise in theory and measurement of the broader social environment to this new area, and to consider both the upstream and downstream mechanisms by which this environment gets “under the skin” and “into the gut.” As population-level microbiome data becomes increasingly available, we encourage investigation of the multi-level determinants of the microbiome and how the microbiome may link the social environment and health.

Purpose:The effect of tobacco exposure on the oral microbiome has not been established. Methods:We 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.Results: Cigarette 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