Project description:We used 16S V3/V4 region amplification to evaluate the composition of bacteria species in mouse fecal pellets after vehicle or ABX treatment and before and after fecal matter transplant.
Project description:Industrial anaerobic digestion (AD) represents a relevant energy source beyond today’s fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, mainly caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial- and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure . Here, we investigate the effect of microalgal organic loading rate (OLR) on the fermentation products profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics and metagenome-centric metaproteomics.
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:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:This study aimed to analyze changes in gut microbiota composition in mice after transplantation of fecal microbiota (FMT, N = 6) from the feces of NSCLC patients by analyzing fecal content using 16S rRNA sequencing, 10 days after transplantation. Specific-pathogen-free (SPF) mice were used for each experiments (N=4) as controls.
Project description:The study critically evaluate the results of 16S targeted amplicon sequencing performed on the total DNA collected from healthy donors’ blood samples in the light of specific negative controls.
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:Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue, and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers which could facilitate diagnosis, underlining the extreme necessity of basic research on this chronic disorder. The latest efforts by the researchers have focused on studying problems at the level of central nervous system sensitivity, inflammatory and oxidative disorders, and even imbalances related to the intestinal microbiota. A total of 892 women were initially enrolled in the study. For those fulfilling inclusion criteria, a plasma proteome analysis in blood samples was conducted. Briefly, blood was collected, centrifuged and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected, homogenized and processed for DNA extraction. Amplicon sequencing of V3–V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform Quality control procedures were implemented using thresholds set at 50,000 reads per sample, Q30 Phred Score and an average trimmed read length of 280bp. The statistical analysis was conducted using R v4.3.2 base packages. After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired healthy individuals) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and its integration into an algorithm allows to discriminate cases and controls. The multiomic approach for biomarker discovery in this study propose a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation. Plasma and fecal multiomics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.
