Project description:Purpose: This study aims to compare and analyze the differences in bacterial community composition in fecal samples from mice treated with Control(DW), Vancomycin (VAN), Ampicillin (AMP), Neomycin (NEO), Metronidazole (MET), and a combination of all antibiotics (ALL, VANM) using 16S rRNA sequencing. Methods: Each antibiotics treated mice's fecal samples were collected and stored -80'c until analyzation. DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol. Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. PCR products were purified using AMPure XP beads, and sequencing adapters were added using the Nextera XT Index Kit (Illumina). The library was further purified with AMPure XP beads and quantified using automated electrophoresis with the TapeStation System (Agilent). Sequencing was performed using the MiSeq v3 reagent kit (Illumina), following the manufacturer’s protocol. Results: QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data, from sequence preprocessing to taxonomic classification. Paired-end sequences were merged and quality-filtered using Deblur. The resulting amplicon sequence variants (ASVs) were used for downstream analyses. Conclusions: Our study presents a comparative analysis of bacterial community composition in fecal samples from antibiotic-treated mice. We observed that microbiota composition varied distinctly depending on the type of antibiotic administered.
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
Project description:Sample multiplexed scRNA-seq is a promising strategy to overcome current barriers in high cost and potential technical variations by multiple scRNA-seq tests. In this study, we developed a highly efficienct novel sample barcode labeling method using DNA-encoded Lipid Nanoparticles ('Nanocoding') that could label cells with minimal dependence on their type or sample conditions. This method provids a roubust and general protocol for sample barcoding and multiplexing in scRNA-seq. We demonstrated the performance of Nanocoding through three scRNA-seq studies, which include: 1. mouse spleen cells mix (one dataset including 6 mouse spleen tissues samples); 2. HeLa-mouse Stromal Vascular Fraction(SVF) cells mix (one dataset containing mixed HeLa cell and SVF cell); 3. Aged-Young SVF cells mix (one dataset containing two SVF samples) tests. These studies showcased the biomodal distribution of barcode counts in different models with high signal-to-background ratio, as well as pan-cell labeling activity for efficient and accurate sample-multiplexing. By using Nanocoding, we profiled obsity and age related change in lipid metabolism associated genes or inflammatory related features, in various cell types from spleen or adipose tissues.
Project description:This sample is part of a study that compares small sample amplification technologies. The analysis looks at differential gene expression when compared to one round of T7 amplification. A tumor cell line was used in comparison to a human reference RNA in this study. Keywords = amplification Keywords = small sample Keywords = Affymetrix Keywords: other