Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1304876 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microbial diversity after inoculation with RP01
| PRJNA940313 | ENA
Project description:Interventions: Open label Phase 1b proof of concept study to test for dysbiosis in small cohort of people identified as at risk for developing colorectal cancer (CRC) based on the background of conventional adenomatous polyps, and the potential of a light infection with hookworm to improve microbial richness and diversity.
All participants will receive in total 20 hookworm larvae (L3) to be applied by the study nurse as two doses of 10x L3 to the skin approximately 4 weeks apart. The L3 will be applied to a non-adherent dressing which will be placed on the forearm of the participant. The dressing will need to remain in place for the remainder of the day, and disposed of at night.
Analyses of blood and rectal mucosal immune responses, mucosal and faecal microbiomes will be undertaken pre and 12 months post hookworm infection.
The fidelity of the hookworm intervention will be monitored by participant reported incidence of a rash at the inoculation site (the first week after inoculation) and laboratory tests for the typical immune response (eosinophilia) and the presence of parasite eggs in faecal samples taken at the post-inoculation clinic visits.
Primary outcome(s): A composite primary outcome including measurements of bacterial species richness (number of observed operational taxonomic units, OTUs) and bacterial species diversity (Shannon Index) in faecal and colon biopsy specimens, determined by shotgun metagenomic sequencing[Week 52 post hookworm inoculation]
Study Design: Purpose: Prevention; Allocation: Non-randomised trial; Masking: Open (masking not used);Assignment: Single group;Type of endpoint: Efficacy
| 2469531 | ecrin-mdr-crc
Project description:A three-stage continuous fermentative system was developed to simulate and control physicochemical factors of the gut biology. Inoculation was of each reactor was performed from a human fecal sample which was initially amplified with a batch procedure. Samples from the initial feces, the batch and from the bioreactors media were collected to extract bacterial DNA. 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. Amplified DNA was purified and labelled with either Cy3 or Cy5 dye and hybridized on the microarray.
2013-05-07 | GSE46677 | GEO
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:Desulfuromonas acetexigens is capable of extracellular electron transfer (EET) and can generate high peak current densities >9 A/m2 in a very short period (~20 h after inoculation) under potential induced growth (–0.1 V vs. Ag/AgCl) and acetate as the electron donor. Despite its high electrochemical activity in microbial electrochemical systems, the proteome and EET mechanisms of D. acetexigens are still unknown. Here, the proteome of D. acetexigens was characterized and a stimulus-induced comparative analysis was performed to elucidate its putative EET mechanism. Proteome analysis indicates that D. acetexigens is a versatile bacterium with a high diversity of accessory genes that allow it to adapt to diverse environments.
2025-06-09 | PXD034195 | Pride
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
2016-08-02 | E-GEOD-85064 | 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