Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v2 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4943 viral probes for the detection of 416 viruses (112 viruses transmitted by small mammals and 304 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v1 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4209 viral probes for the detection of 409 viruses (109 viruses transmitted by small mammals and 300 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

Project description:The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts. These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination. Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated. In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content. Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains. Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins. Many of these differences occurred in regions of the E. coli chromosome previously shown to be M-bM-^@M-^\hot spotsM-bM-^@M-^] for the integration of horizontally-acquired DNA. PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay. The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers. Twelve isolates of E. coli ( 3 from bear, 3 from cattle, 3 from deer and 3 from humans) were isolated from feces and/or raw sewage. Genome content for each strain was assessed in duplicate using comparative genome hybridization with E. coli K12 MG1655 as the reference for a total of 24 arrays.

Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods.

Project description:The gut microbiota is closely associated with the health and production performance of livestock. Partial studies on ruminant microbiota are already in progress in the Qinghai-Tibetan Plateau Area (QTPA) in China, but large-scale and representative profiles for the QTPA are still lacking. Here, 16S rRNA sequencing was used to analyze 340 samples from yak, cattle, yak-cattle hybrids, and Tibetan sheep, which lived in a shared environment from 4 eco-regions of the QTPA during the same season, and aimed to investigate the fecal microbiota community composition, diversity, and potential function. All samples were clustered into 2 enterotypes, which were derived from the genera Ruminococcaceae UCG-005 and Acinetobacter, respectively. Environment, human activity, species, and parasitization all affected the fecal microbiota. By assessing the relationship between the fecal microbiota and the above variables, we identified a scattered pattern of fecal microbiota dissimilarity based more significantly on diet over other factors. Additionally, gastrointestinal nematode infection could reduce the capacity of the bacterial community for biosynthesis of other secondary metabolites, carbohydrate metabolism, and nucleotide metabolism. Ultimately, this study provided a fecal microbiota profile for ruminants living in 4 eco-regions of the QTPA and its potential future applications in developing animal husbandry regimes. IMPORTANCE Cattle, yak, and sheep reside as the main ruminants distributed throughout most regions of Qinghai-Tibetan Plateau Area (QTPA) in China. However, there is a lack of large-scale research in the QTPA on their fecal microbiota, which can regulate and reflect host health as an internalized "microbial organ." Our study depicted the fecal microbiota community composition and diversity of yak, cattle, yak-cattle hybrids, and Tibetan sheep from 4 eco-regions of the QTPA. Additionally, our results demonstrated here that the ruminant samples could be clustered into 2 enterotypes and that diet outweighed other factors in shaping fecal microbiota in the QTPA. This study provided a basis for understanding the microbiota characteristic of ruminants and its possible applications for livestock production in the QTPA.

			Action	DRS
	SRR28342100_1.fastq.gz	Fastqsanger.gz
	SRR28342100_2.fastq.gz	Fastqsanger.gz
	SRR28342200_1.fastq.gz	Fastqsanger.gz
	SRR28342200_2.fastq.gz	Fastqsanger.gz
	SRR28342300_1.fastq.gz	Fastqsanger.gz

Dataset Information

Arthropods from sheep and cattle fecal samples

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