New Insights into the Intrinsic and Extrinsic Factors That Shape the Human Skin Microbiome.

Despite recognition that biogeography and individuality shape the function and composition of the human skin microbiome, we know little about how extrinsic and intrinsic host factors influence its composition. To explore the contributions of these factors to skin microbiome variation, we profiled the bacterial microbiomes of 495 North American subjects (ages, 9 to 78 years) at four skin surfaces plus the oral epithelium using 16S rRNA gene amplicon sequencing. We collected subject metadata, including host physiological parameters, through standardized questionnaires and noninvasive biophysical methods.

Genetic Analysis of Norovirus Strains that Caused Gastroenteritis Outbreaks Among River Rafters in the Grand Canyon, Arizona.

Toilet solid waste samples collected from five outbreaks among rafters in the Grand Canyon were subjected to sequencing analysis of norovirus partial capsid gene. The results revealed that a GI.3 strain was associated with one outbreak, whereas the other outbreaks were caused by GII.

Genetically distinct genogroup IV norovirus strains identified in wastewater.

We investigated the prevalence and genetic diversity of genogroup IV norovirus (GIV NoV) strains in wastewater in Arizona, United States, over a 13-month period. Among 50 wastewater samples tested, GIV NoVs were identified in 13 (26 %) of the samples. A total of 47 different GIV NoV strains were identified, which were classified into two genetically distinct clusters: the GIV.

Occurrence and genetic diversity of human cosavirus in influent and effluent of wastewater treatment plants in Arizona, United States.

Human cosavirus (HCoSV) is a novel member of the family Picornaviridae. We investigated the prevalence and genetic diversity of HCoSV in influent and effluent wastewater in Arizona over a 12-month period, from August 2011 to July 2012. HCoSV sequences were identified in six (25%) influent samples and one (4%) effluent sample, with the highest concentration of 3.

Norovirus Outbreaks Among Colorado River Rafters in the Grand Canyon, Summer 2012.

Objective: To investigate the incidence and causative agent of the recurrent outbreaks of acute gastrointestinal illness (AGI) among different rafting groups on the Colorado River in the Grand Canyon National Park during the 2012 summer season.

Methods: Confidential illness reports were completed by all individuals with symptoms of AGI, and samples of fecal matter and vomitus, surface swabs of rafting equipment, and environmental swabs at stops along the hiking corridor were collected and tested for the presence of norovirus using reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

Results: During the active outbreak period between May 9 and July 9, 2012, 97 rafters (1.

Quantification and genetic analysis of salivirus/klassevirus in wastewater in Arizona, USA.

Salivirus/klassevirus sequences were identified in 7 (15%) wastewater samples collected in Arizona monthly for a year, with the highest concentration of 2.28 × 10(5) and 2.46 × 10(4) copies/L in influent and effluent, respectively.

Relative abundance and treatment reduction of viruses during wastewater treatment processes--identification of potential viral indicators.

Waterborne pathogenic viruses discharged from wastewater treatment plants (WWTPs) pose potential public health risks. In the present study, we investigated the relative abundance, occurrence, and reduction of eleven different viruses at two WWTPs in southern Arizona over a 12-month period, from August 2011 to July 2012. Influent and effluent samples from the two WWTPs were collected monthly.

Occurrence of Cryptosporidium, Giardia, and Cyclospora in influent and effluent water at wastewater treatment plants in Arizona.

We investigated the occurrence of Cryptosporidium, Giardia, and Cyclospora at two wastewater treatment plants (WWTPs) in Arizona over a 12-month period, from August 2011 to July 2012. Influent and effluent wastewater samples were collected monthly, and protozoan (oo)cysts were concentrated using an electronegative filter, followed by the detection of protozoa using fluorescent microscopy (Cryptosporidium oocysts and Giardia cysts) and PCR-based methods (Cryptosporidium spp., Giardia intestinalis, and Cyclospora cayetanensis).

Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples.

The extraction and purification of nucleic acids is a critical step in the molecular detection of enteric viruses from environmental or fecal samples. In the present study, the performance of three commercially available kits was assessed: the MO BIO PowerViral Environmental DNA/RNA Isolation kit, the Qiagen QIAamp Viral RNA Mini kit, and the Zymo ZR Virus DNA/RNA Extraction kit. Viral particles of adenovirus 2 (AdV), murine norovirus (MNV), and poliovirus type 1 (PV1) were spiked in molecular grade water and three different types of sample matrices (i.

Molecular survey of concrete sewer biofilm microbial communities.

The microbial composition of concrete biofilms within wastewater collection systems was studied using molecular assays. SSU rDNA clone libraries were generated from 16 concrete surfaces of manholes, a combined sewer overflow, and sections of a corroded sewer pipe. Of the 2457 sequences analyzed, α-, β-, γ-, and δ-Proteobacteria represented 15%, 22%, 11%, and 4% of the clones, respectively.

Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers.

In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined in sewage spiked samples and environmental waters using different group-specific and host-specific PCR assays. Bacteroidales DNA recovery ranged from 59 to 71% for aliquots of supernatant collected after the elution step.

Microbial atrazine breakdown in a karst groundwater system and its effect on ecosystem energetics.

In the absence of sunlight energy, microbial community survival in subterranean aquifers depends on integrated mechanisms of energy and nutrient scavenging. Because karst aquifers are particularly sensitive to agricultural land use impacts due to rapid and direct hydrologic connections for pollutants to enter the groundwater, we examined the fate of an exogenous pesticide (atrazine) into such an aquifer and its impact on microbial ecosystem function. Atrazine and its degradation product deethylatrazine (DEA) were detected in a fast-flowing karst aquifer underlying atrazine-impacted agricultural land.

Identification of bacterial populations in drinking water using 16S rRNA-based sequence analyses.

Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populations in drinking water by analyzing 16S rRNA-based clone libraries.