Project description:Analysis of breast cancer survivors' gut microbiota after lifestyle intervention, during the COVID-19 lockdown, by 16S sequencing of fecal samples.
Project description:FastQ files from 16S sequencing of fecal samples from pancreatic cancer xenografted mice not treated (CTRL) and treated with chemotherapy (GEM+nab-PTX), probiotics (PRO) and chemotherapy + probiotics (GEM+nab-PTX+PRO)
Project description:Mammalian feces can be collected non-invasively during field research and provides valuable information on the ecology and evolution of the host individuals. Undigested food objects, genome/metagenome, steroid hormones, and stable isotopes obtained from fecal samples provide evidence on diet, host/symbiont genetics, and physiological status of the individuals. However, proteins in mammalian feces have hardly been studied, which hampers the molecular investigations into the behavior and physiology of the host individuals. Here, we apply mass spectrometry-based proteomics to fecal samples (n = 10) that were collected from infant, juvenile, and adult captive Japanese macaques (Macaca fuscata) to describe the proteomes of the host, food, and intestinal microbes. The results show that fecal proteomics is a useful method to investigate dietary changes along with breastfeeding and weaning, to reveal the organ/tissue and taxonomy of dietary items, and to estimate physiological status inside intestinal tracts. These types of insights are difficult or impossible to obtain through other molecular approaches. Most mammalian species are facing extinction risk and there is an urgent need to obtain knowledge on their ecology and evolution for better conservation strategy. The fecal proteomics framework we present here is easily applicable to wild settings and other mammalian species, and provides direct evidence of their behavior and physiology.
Project description:Purpose: The goal of this study is to compare colonic transcriptional responses following ex-vivo colonization with fecal samples collected from multiple sclerosis patients, before and after Propionic acid treatment and between the patients that responded or not to the therapy. Methods: Bulk whole-tissue mRNA profiles of 13-day-old wild-type mice colons were generated by deep sequencing, in triplicate, using Illumina NextSeq platform.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:A subset of post-infection irritable bowel syndrome (PI-IBS) patients have elevated, or high fecal proteolytic activity (PA). Fecal PA has been shown to correlate with increased symptom severity as well as lower quality of life scores, increased fecal output and increased intestinal permeability. To address the underlying mechanisms of barrier disruption as a consequence of high fecal PA, colonic biopsies were collected from healthy individuals PI-IBS patients (n=11). Individuals diagnosed with PI-IBS were further divided in to 2 subgroups, high PA and low PA as defined by the PA in matched fecal samples. RNA was extracted from the biopsies for bulk RNA sequencing to understand transcriptional differences between healthy and high PA PI-IBS patients as well as high PA and Low PA PI-IBS patients.
Project description:We found that low protein diet consumption resulted in decrease in the percentage of normal Paneth cell population in wild type mice, indicating that low protein diet could negatively affect Paneth cell function. We performed fecal microbiota composition profiling. Male mice were used at 4-5 weeks of age. Fecal samples were collected for microbiome analysis.
Project description:We found that western diet consumption resulted in decrease in the percentage of normal Paneth cell population in wild type mice, indicating that western diet could negatively affect Paneth cell function. Subsequent generations of western diet consumption further reduced percentages of normal Paneth cell population. We performed fecal microbiota composition profiling. Male mice were used at 4-5 weeks of age. Fecal samples were collected for microbiome analysis.
