Protist metagenomics in New York City
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB26690 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2581730_1.fastq.gz | Fastqsanger.gz | |||
| ERR2581730_2.fastq.gz | Fastqsanger.gz | |||
| ERR2581740_1.fastq.gz | Fastqsanger.gz | |||
| ERR2581740_2.fastq.gz | Fastqsanger.gz | |||
| ERR2581750_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 328 |
Similar Datasets
Project description:18S rRNA gene V4 region amplicon sequencing of protists in NYC environmental samples
| PRJEB23950 | ENA
Project description:Shotgun metagenomic sequencing of NYC raw sewage samples
| PRJEB28033 | ENA
Project description:Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.
| S-EPMC6794324 | biostudies-literature
Project description:Protists targeted sequencing of 18S rRNA HV 9
| PRJNA305513 | ENA
Project description:Cryptosporidiosis is a parasitic diarrheal infection that is transmitted by the fecal-oral route. We assessed trends in incidence and demographic characteristics for the 3,984 cases diagnosed during 1995-2018 in New York City, New York, USA, and reported to the New York City Department of Health and Mental Hygiene. Reported cryptosporidiosis incidence decreased with HIV/AIDS treatment rollout in the mid-1990s, but the introduction of syndromic multiplex diagnostic panels in 2015 led to a major increase in incidence and to a shift in the demographic profile of reported patients. Incidence was highest among men 20-59 years of age, who consistently represented most (54%) reported patients. In addition, 30% of interviewed patients reported recent international travel. The burden of cryptosporidiosis in New York City is probably highest among men who have sex with men. Prevention messaging is warranted for men who have sex with men and their healthcare providers, as well as for international travelers.
| S-EPMC7045836 | biostudies-literature
Project description:The incidence of Legionnaires' disease in the United States has been increasing since 2000. Outbreaks and clusters are associated with decorative, recreational, domestic, and industrial water systems, with the largest outbreaks being caused by cooling towers. Since 2006, 6 community-associated Legionnaires' disease outbreaks have occurred in New York City, resulting in 213 cases and 18 deaths. Three outbreaks occurred in 2015, including the largest on record (138 cases). Three outbreaks were linked to cooling towers by molecular comparison of human and environmental Legionella isolates, and the sources for the other 3 outbreaks were undetermined. The evolution of investigation methods and lessons learned from these outbreaks prompted enactment of a new comprehensive law governing the operation and maintenance of New York City cooling towers. Ongoing surveillance and program evaluation will determine if enforcement of the new cooling tower law reduces Legionnaires' disease incidence in New York City.
| S-EPMC5652439 | biostudies-literature
Project description:Neighborhood physical disorder, or the deterioration of urban environments, is associated with negative mental and physical health outcomes. Eleven trained raters used CANVAS, a web-based system for conducting reliable virtual street audits, to collect data on nine indicators of physical disorder using Google Street View imagery of 532 block faces in New York City, New York, USA. We combined the block face indicator data into a disorder scale using item response theory; indicators ranged in severity from presence of litter, a weak indicator of disorder, to abandoned cars, a strong indicator. Using this scale, we estimated disorder at the center point of each sampled block. We then used ordinary kriging to interpolate estimates of disorder levels throughout the city. The resulting map condenses a complex estimation process into an interpretable visualization of the spatial distribution of physical disorder in New York City.
| S-EPMC4963033 | biostudies-literature
Project description:Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for genetic signatures of adaptation. We tested for (i) high-frequency, extended haplotypes that could indicate selective sweeps and (ii) loci of extreme genetic differentiation between the NYC sample and a sample from the presumed ancestral range of brown rats in northeast China. We found candidate selective sweeps near or inside genes associated with metabolism, diet, the nervous system and locomotory behavior. Patterns of differentiation between NYC and Chinese rats at putative sweep loci suggest that many sweeps began after the split from the ancestral population. Together, our results suggest several hypotheses on adaptation in rats living in close proximity to humans.
| S-EPMC7851592 | biostudies-literature
Project description:Each day, the New York City Department of Health and Mental Hygiene uses the free SaTScan software to apply prospective space-time permutation scan statistics to strengthen early outbreak detection for 35 reportable diseases. This method prompted early detection of outbreaks of community-acquired legionellosis and shigellosis.
| S-EPMC5038417 | biostudies-literature