Nanopore- and AI-empowered metagenomic viability inference
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ABSTRACT:
PROVIDER: PRJEB76420 | ENA |
REPOSITORIES: ENA
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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.
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Project description:Implantation is crucial for placental development which directly impacts fetal growth and pregnancy success with possible consequences on post-natal health. We postulated that early perturbations of the conceptus-maternal environment communication may alter the endometrium physiology that could account for the final reproductive outcome. Using cattle as an animal model, we compared gene expression profiles of the endometrial caruncular and intercaruncular areas during the critical period of implantation in three types of pregnancies: artificial insemination (AI), in vitro fertilization with embryo transfer (IVF-ET) or somatic cell nuclear transfer (SCNT). Less than 35% of the differentially expressed genes were found to be common between AI, IVF-ET, and SCNT conditions. Compared to AI, numerous biological functions and several canonical pathways and genes were found to be significantly affected in IVF-ET or SCNT, with a major impact on metabolism and immune function in SCNT. Our data show that the endometrium can fine-tune its physiology and could be considered as a biological sensor in response to pregnancy manipulations. Determining the limits of the endometrial plasticity should bring new insights on the contribution of the maternal compartment to the pregnancy outlet. Keywords: Fluorescence Microarray - Dye switch loop design 44 samples
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Project description:Autoinducer 2 (AI-2), a widespread by-product of the LuxS-catalyzed S-ribosylhomocysteine cleavage reaction in the activated methyl cycle, has been suggested to serve as an intra- and interspecies signaling molecule, but in many bacteria AI-2 control of gene expression is not completely understood. Particularly, we have a lack of knowledge about AI-2 signaling in the important human pathogens Staphylococcus aureus and S. epidermidis. Here, to determine the role of LuxS and AI-2 in S. epidermidis, we analyzed genome-wide changes in gene expression in an S. epidermidis luxS mutant and after addition of AI-2 synthesized by over-expressed S. epidermidis Pfs and LuxS enzymes. Genes under AI-2 control included mostly genes involved in sugar, nucleotide, amino acid, and nitrogen metabolism, but also virulence-associated genes coding for lipase and bacterial apoptosis proteins. In addition, we demonstrate by liquid chromatography/mass-spectrometry of culture filtrates that the pro-inflammatory phenol-soluble modulin (PSM) peptides, key virulence factors of S. epidermidis, are under luxS/AI-2 control. Our results provide a detailed molecular basis for the role of LuxS in S. epidermidis virulence and suggest a signaling function for AI-2 in this bacterium. Keywords: wild type without glucose control vs luxS mutant vs luxS mutant with auto-inducer II wild type without glucose control vs luxS mutant vs luxS mutant with auto-inducer II
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