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ABSTRACT:
PROVIDER: PRJNA1235503 | ENA |
REPOSITORIES: ENA
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Project description:Microbial diversity (multi-primer) analysis Metagenome
| PRJNA1209712 | ENA
Project description:Circadian clocks are important for gut health. This experiment aimed to determine the role of core clock gene Bmal1 in regulating microbial rhythmicity in health and dextran sulphate sodium induced colitis. Mice were generated with Bmal1 selectively deleted in Villin-expressing cells (predominantly IECs).Microbial DNA was extracted from fecal pellets collected from IEC-Bmal1-/- and Bmal1flox mice (aged 8-19 weeks) at zeitgeber time 0, 4, 8, 12, 16, 20 across the 24h day with the DNeasy PowerSoil Pro Kit (Qiagen), as per manufacturer’s instructions. Pre-amplification of the V4 region of 16S rRNA was performed using forward primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGAT-CTNNNNNGTGCCAGCMGCCGCGGTAA-3' (annealing sites in bold) and reverse primer 5'-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGACTACHVGGGTWTCTAAT-3'. Sequencing was performed by the University of Liverpool Centre for genomics Research, using the Illumina MiSeq v2 platform (Illumina), generating 250bp paired-end reads. PhiX control v3 library (PhiX) was spiked into samples to balance low base diversity often found in microbiome samples. Quality control was performed and OTU tables were generated using a pipeline provided by the University of Manchester Bioinformatics Core Facility local Galaxy service. Briefly, VSEARCH clustered OTUs and removed chimeras. The OTU database was mapped to the SILVA (v138) reference database with >97% homology threshold. All samples passed quality checks and had sequence depth >45,000. The OTU table was analysed using R packages phyloseq, vegan, limma and ALDEx2. JTK_CYCLE 93 was used to identify rhythmic OTUs with a period of 24 h and an adjusted P value < 0.05.
2025-07-04 | E-MTAB-15306 | biostudies-arrayexpress
Project description:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them. This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).
2011-03-08 | E-GEOD-27542 | biostudies-arrayexpress
Project description:Samples of oil and production water were collected from five wells of the Qinghai Oilfield, China, and subjected to GeoChip hybridization experiments for microbial functional diversity profiling. Unexpectedly, a remarkable microbial diversity in oil samples, which was higher than that in the corresponding water samples, was observed, thus challenging previously believed assumptions about the microbial diversity in this ecosystem. Hierarchical clustering separated oil and water samples, thereby indicating distinct functional structures in the samples. Genes involved in the degradation of hydrocarbons, organic remediation, stress response, and carbon cycling were significantly abundant in crude oil, which is consistent with their important roles in residing in oil. Association analysis with environmental variables suggested that oil components comprising aromatic hydrocarbons, aliphatic hydrocarbons, and a polar fraction with nitrogen-, sulfur-, and oxygen-containing compounds were mainly influential on the structure of the microbial community. Furthermore, a comparison of microbial communities in oil samples indicated that the structures were depth/temperature-dependent. To our knowledge, this is the first thorough study to profile microbial functional diversity in crude oil samples. From the Qinghai Oilfield located in the Tibetan Plateau, northwest China, oil production mixtures were taken from four oil production wells (No. 813, 516, 48 and 27) and one injection well (No. 517) in the Yue-II block. The floating oil and water phases of the production mixtures were separated overnight by gravitational separation. Subsequently, the microbial community and the characteristics of the water solution (W813, W516, W48, and W27) and floating crude oil (O813, O516, O48, and O27) samples were analyzed. A similar analysis was performed with the injection water solution (W517).
2016-04-01 | E-GEOD-55293 | biostudies-arrayexpress