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.
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.
Project description:Microbial sulfur cycling and chemoautotrophy are focal points of research in cold seeps. However, limited culture-dependent and in-situ studies have described the biological features and ecological significance of chemoautotrophic sulfur-oxidizing bacteria. In this study, we isolated Guyparkeria hydrothermalis SP2, a thiosulfate/sulfide-oxidizing chemoautotrophic bacterium, from cold-seep sediment. Electron microscopy, Raman spectroscopy, and stoichiometry confirmed the efficient production of zero-valent sulfur (ZVS) by G. hydrothermalis SP2. Genomic, transcriptomic, and qRT-PCR analyses revealed its utilization of the Sox pathway for thiosulfate oxidation and the fccB gene for sulfide oxidation. Its chemoautotrophic capability mediated by the Calvin-Benson-Bassham (CBB) cycle was identified through isotopic and qRT-PCR analyses. In-situ studies demonstrated its ability to produce ZVS by oxidizing sulfide in cold seeps, with a preference for different genes compared to those under laboratory conditions. Metagenomic and metatranscriptomic analyses indicated the ubiquity of its sulfur oxidation-based chemoautotrophic pathway in cold seep sediments. Therefore, this strain holds significance for investigating sulfur oxidation-based chemoautotrophic pathways in cold seeps.
Project description:We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.
