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VSL#3

ABSTRACT: Metagenomic shotgun analysis on VSL#3 manufactured at Nutrilinea(Italy)

PROVIDER: PRJEB31428 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3181827_1.fastq.gz	Fastqsanger.gz
	ERR3181827_2.fastq.gz	Fastqsanger.gz

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VSL#3 Meta

Project description:Metagenomic analysis of a VSL#3 samples manufactured at CSL lot n° 805095

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

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.

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Zearalenone-induced aberration in gut microbiome composition and function are associated with degeneration in ovary reserve

Project description:We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.

2019-11-09 | GSE140149 | GEO

Project description:Shotgun metagenomic analysis

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Project description:ZVI Metagenomic shotgun sequencing analysis

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mWGS analysis of the fecal microbiota of WT and TCRb-/- mice

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.

2024-05-06 | GSE262397 | GEO

VSL#3 protects against development of visceral pain in the neonatal maternal separation model: A whole genome microarray study

Project description:Background & Aims: Irritable bowel syndrome (IBS) is a disorder characterized by chronic abdominal pain and is linked to post-inflammatory and stress-correlated factors that cause changes in the perception of visceral events. Increased evidence indicates that probiotic bacteria may be useful in treating IBS. Our aims were to evaluate the efficacy of treatment with VSL#3, a mixture of 8 probiotic bacteria strains, in the neonatal maternal separation (NMS)-induced visceral hypersensitivity rat model and to determine whether it modulates the colonic expression of pain-related genes. Methods: Male NMS pups were treated orally with placebo or VSL#3 at days 3-60, while normal, not separated rats were used as control. After 60 days from birth, perception of painful sensation induced by colorectal distension (CRD) was measured by assessing the abdominal withdrawal reflex (score 0-4). The colonic gene expression analysis was assessed by using Agilent Whole Rat Genome Oligo Microarrays. Results: NMS rats exhibited both hyperalgesia and allodynia when compared with controls. VSL#3 showed a potent analgesic effect on CRD-induced pain without modifying colorectal compliance. The microarray analysis demonstrated that NMS rats had both over- and downregulation of several genes involved in inflammatory and painful processes and VSL#3 was able to counteract these alterations. Conclusions: This study indicates that VSL#3 is effective in reducing visceral pain in an experimental model of IBS by induction or suppression of pain-modulating genes. These observations provide support for the use of VSL#3 in the treatment of painful conditions related to IBS.

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Identification of pathways and transcription factors relevant to gut inflammation and anti-inflammatory probiotics

Project description:Using Affymetrix data analysis, important signalling pathways and transcription factors relevant to gut inflammation and anti-inflammatory action of probiotics were identified using the clinically validated probiotic VSL#3 and the IL10-knockout mouse, an animal model for inflammatory bowel disease. VSL#3 increased expression of genes involved in PPAR signalling and metabolism of xenobiotics and decreased expression of genes involved in immune response/inflammatory response.

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Project description:Metagenomic shotgun sequencing of Irritable bowel syndrome patients and matched controls

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