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.
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:We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.
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:The gut microbiota plays an important role in host health. Microbiota dysbiosis has been implicated in the global epidemic of Metabolic Syndrome (MetS) and could impair host metabolism by noxious metabolites. It has been well established that the gut microbiota is shaped by host immune factors. However, the effect of T cells on the gut microbiota is yet unknown. Here, we performed a metagenomic whole-genome shotgun sequencing (mWGS) study of the microbiota of TCRb-/- mice, which lack alpha/beta T cells.
Project description:Endocrine active substances pose risks to both human health and the environment, potentially impacting crucial endocrine-regulated functions like organism development and reproductive capability. However, current testing methods for chemical risk assessment are time-consuming, expensive, and involve extensive animal testing. In its current stance, the European Chemicals Agency (ECHA) advocates for advancing new approach methods (NAMs) to identify endocrine-acting substances (EAS) and non-EAS modalities for endocrine disruption assessment. One such NAM is the transcriptomic point of departure (tPOD) method, leveraging the fact that physiological effects stem from changes in gene expression, detectable through transcriptomic techniques. The tPOD method utilizes compound-induced, concentration-dependent alterations in gene expression to estimate benchmark doses (BMD) for responsive genes. In this study, we focused on determining a tPOD for androgenic activity of androstenedione in zebrafish embryos, correlating it with chronic effects observed in fish literature. Androstenedione, suspected as an endocrine disruptor in non-mammalian organisms, purportedly operates via an androgenic mode of action (MoA).
Project description:Smoking of combustible cigarettes has a major impact on human health, so the tobacco industry is developing modified risk tobacco products (MRTP) to reduce this health risk. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the potential of such a prototype (pMRTP) to reduce health risk. We investigated physiological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to conventional cigarette smoke (3R4F) or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure. The present manuscript describes the study design, setup, and implementation, as well as the generation, processing, and quality control analysis of the toxicology and "omics" datasets that are accessible in public repositories for further studies.
Project description:Smoking of combustible cigarettes has a major impact on human health, so the tobacco industry is developing modified risk tobacco products (MRTP) to reduce this health risk. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the potential of such a prototype (pMRTP) to reduce health risk. We investigated physiological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to conventional cigarette smoke (3R4F) or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure. The present manuscript describes the study design, setup, and implementation, as well as the generation, processing, and quality control analysis of the toxicology and 'omics' datasets that are accessible in public repositories for further studies.
Project description:Epigenetics may help understanding the molecular mechanisms of atherosclerosis as genetic predisposition explains only part of cardiovascular disease risk. In particular, DNA methylation, a reversible and highly regulative DNA modification could contribute to disease onset and progression as it functions as effector for environmental impacts, including dietary and life-style, similarly to risk factors for cardiovascular diseases. We addressed this issue by performing whole-genome shotgun bisulfite sequencing and high-resolution DNAmethylation array analysis of healthy and diseased donor-matched atherosclerotic DNA methylomes. Sequencing of bisulfite converted DNA and array based analysis of atherosclerotic lesions and normal carotid tissue.