Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.

2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress

Comparative Microbial Metagenomic Analysis of Drinking Water Plants and Wastewater Treatment Plants in Istanbul

Project description:Wastewater treatment plants (WWTPs) and Drinking water treatment plants (DWTPs) are critical points for public health for persistently remaining microorganisms after treatment may pose a risk. This study aimed to conduct microbial metagenomic analyses on waters from both DWTPs and WWTPs under the Istanbul Water and Sewerage Administration (ISKI). In this study a total of 52 samples were included, comprising 18 samples from DWTPs and 34 from WWTPs. All water samples underwent pre-isolation filtration. DNA isolation was conducted using filter material, followed by library preparation and sequencing on a NovaSeq 6000 instrument following the manufacturer's guidelines.

2025-01-09 | E-MTAB-14353 | biostudies-arrayexpress

Metagenomic sequencing of mice with different treatments / 16S rRNA sequencing of mice before and after the use antibiotics

Project description:Metagenomic sequencing of mice with different treatments: Mice were randomly divided into donor control group (Donor + MRS), constipation model group (STC + MRS), or a Lactobacillus acidophilus treated group (STC + La): A humanized mouse model was established by intragastric administration of fecal bacterial liquid from healthy donors or STC patients on alternate days, followed by continuous administration of Lactobacillus acidophilus in treatment group. Finally, the feces of each group of mice were collected, and the intestinal microbial communities of the mice were analyzed through metagenomic sequencing. 16S rRNA sequencing of mice before and after the use antibiotics: Before and after treating the mice with antibiotics, the mice's feces were collected for 16s rRNA sequencing respectively.

2026-03-11 | E-MTAB-16505 | biostudies-arrayexpress

Metagenomic Shotgun of microorganisms cultivated with EPS

Project description:Metagenomic Shotgun of EPS-cultivated microorganisms

| PRJEB24069 | ENA