Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of citie

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities

The impact of cross-kingdom molecular forensics on genetic privacy

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual’s reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a “molecular echo” of an individual’s microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era. [MediaObject not available: see fulltext.

3-D OCT imaging of hyalocytes in partial posterior vitreous detachment and vaso-occlusive retinal disease

Purpose: To describe the spatial distribution and morphologic characteristics of macrophage-like cells called hyalocytes in the posterior vitreous cortex of a patient with unilateral partial posterior vitreous detachment (PVD) using coronal plane en face optical coherence tomography (OCT). Observations: A 54-year-old male with sickle cell disease (HbSC genotype) presented with a partial PVD in one eye. Rendered volumes of a slab extending from 600 μm to 3 μm anterior to the inner limiting membrane (ILM) revealed hyperreflective foci in the detached posterior vitreous cortex suspended anterior to the macula, likely representing hyalocytes. In the fellow eye without PVD, hyperreflective foci were located 3 μm anterior to the ILM. The morphology of the cells in the eye with PVD varied between a ramified state with multiple elongated processes and a more activated state characterized by a plump cell body with fewer retracted processes. In the same anatomical location, the hyperreflective foci were 10-fold more numerous in the patient with vaso-occlusive disease than in an unaffected, age-matched control. Conclusions and Importance: Direct, non-invasive, and label-free techniques of imaging cells at the vitreoretinal interface and within the vitreous body is an emerging field. The findings from this case report suggest that coronal plane en face OCT can be used to provide a detailed and quantitative characterization of cells at the human vitreo-retinal interface in vivo. Importantly, this case report demonstrates that 3D-OCT renderings can enhance visualization of these cells in relation to the ILM, which may provide clues concerning the identity and contribution of these cells to the pathogenesis of vitreo-retinal diseases

Imaging vitreous cortex hyalocyte response to paracentral acute middle maculopathy (PAMM) using OCT

INTRODUCTION: Vitreous cortex hyalocytes (VCH) are resident macrophage cells that provide immunosurveillance, respond to tissue injury and inflammation, and help maintain the transparency of the media. In this case report we demonstrate the use of optical coherence tomography (OCT) to image VCH in a patient presenting with PAMM secondary to antiphospholipid syndrome. CASE DESCRIPTION: A 38-year-old female with no known medical history presented with complaints of visual disturbances in the right eye. OCT revealed hyperreflective bands in the IPL and INL nasal to the fovea. A diagnosis of PAMM was made. Work-up revealed elevated titers of antiphospholipid antibodies. OCT revealed a decline in the inflammatory activation over a seven-month period as evidenced by changes in VCH distribution and morphology. CONCLUSIONS: Our findings suggest that monitoring changes in the distribution and morphology of VCH could have a potential clinical utility for assessing disease severity, predicting recovery, and early recognition of treatment response in various inflammatory ocular pathologies such as PAMM

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

Following publication of the original article [1], the authors would like to highlight the following two corrections

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Following publication of the original article [1], the authors would like to highlight the following two corrections

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.ISSN:0092-8674ISSN:1097-417

Francois Achard (1699-1782), Schweizer Rechtsgelehrter und Mathematiker

Publikationen: Réflexions sur l'infini mathématique, Berlin 1745/46. Chemisch-physikalischen Schriften, Berlin 1780. Quelle: Michaud, Biographie universelle ancienne et moderne. Historisches Lexikon der Schweiz: http://www.hls-dhs-dss.ch/textes/d/D31214. Vgl dazu: J.J. Littrow, Geschichte der Inductiven Wissenschaften, 2. Teil S. 557 Fußnote 30. Teilnachlass: Kurzbiographie Umfang: 1 S. Datum: undatiert Archiv-Signatur: Astr.-NL-4.25