12276 results for ""statistically+reactive"+taxa+in+microbial+community"

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• Microbiome confounders and quantitative profiling challenge established microbial targets in colorectal cancer developmental stages

  Study EGAS00001007413

• Indonesian Microbiome Ecology and Evolution v1 (raw data)

  This dataset comprises 124 human faecal samples collected across Indonesia between 2015 and 2021, together with 6 controls. It was collected to study patterns of human microbiome variation across Indonesia’s diverse geography and lifestyles, and to generate the Indonesian Microbiome Ecology and Evolution (IndoMEE) metagenome-assembled genome (MAG) reference database. The dataset consists of 250 bp paired-end metagenomic reads from 124 faecal samples acquired from 116 individuals, at ca. 10.6 Gb / sample, together with 2 positive controls (ZymoBIOMICS Microbial Community DNA Standard by Zymo Research Cat# D6305), and 4 negative controls (for sampling: Blank, for extraction: Buffer EB by Qiagen Cat# 19086, for library prep: Nuclease Free Water by Ambion-Invitrogen Cat# AM9937). Library preparation was carried out using Illumina's TruSeq DNA Nano DNA kit, and sequencing was performed on the Illumina NovaSeq 6000 platform.

  Dataset EGAD50000001399

• Personalised Mapping of Tumour Development in Synchronous Colorectal Cancer Patients

  We performed an in-depth characterisation of 12 tumours from 3 syCRC patients by analysing histopathological, whole genome sequencing and RNA-sequencing data. We assessed the extent of genetic overlap between synchronous tumours and examined associations between clinicopathological information and the molecular, microbial and immune features of each tumour genome.

  Study EGAS00001004413

• Genome-wide associations of human gut microbiota variation and implications for causal inference analyses

  Here we use appropriate taxon-specific models along with support from independent cohorts to show association between human host genotype and gut microbiome variation. Using fecal derived 16S rRNA gene sequences and host genotype data from the Flemish Gut Flora Project (FGFP) we identify genetic associations involving multiple microbial traits. Mendelian randomization analysis was able to estimate associations between microbial traits and disease, however in the absence of clear microbiome driven effects, caution is needed in interpretation. This work marks a growing catalog of genetic associations which will provide insight into the contribution of host genotype to gut microbiome. Despite this, the uncertain origin of association signals will likely complicate future work looking to dissect function or use associations for causal inference analysis.

  Study EGAS00001004420

• Longitudinal Study of Vaginal Flora

  This prospective observational study aims to advance our knowledge of the natural history and abnormal alteration in vaginal microbial flora, and to identify risk factors that are associated with these changes. A total of 5500 healthy, non-pregnant women of reproductive age will be enrolled and followed up in Birmingham, Alabama, for one year (baseline visit plus once every three months afterwards, totaling 5 visits). Detailed information on sociodemographic status, medical history, hygiene practice, sexual behavior and psychosocial stress will be collected through in-person interviews. Routine gynecological and dental examinations will be carried out during the study visits. Samples of vaginal secretion and blood will be collected. Laboratory tests to quantify vaginal microbial flora and to identify infection of bacterial vaginosis as well as common sexually transmitted diseases will be conducted. Future submissions may contain metadata or molecular data from additional subjects.

  Study phs002367

• Diet driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome

  This study profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events. Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline.

  Study EGAS00001006982

• Longitudinal Multi'omics of the Human Microbiome in Inflammatory Bowel Disease (IBDMDB)

  Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of individuals worldwide. The Integrative Human Microbiome Project (HMP2) characterized a total of 132 CD, UC and non-IBD patients across a year to generate longitudinal molecular profiles of host and microbial activity during this time frame. A total of 2,965 stool, biopsy and blood specimens were produced and analyzed from this cohort. A comprehensive view of the gut microbiome's functional dysbiosis during IBD activity was derived from analyzed samples each providing a different window into disease activity. The study's resources, results and data are available through the Inflammatory Bowel Disease Multi'omics Database (IBDMDB) provide the most comprehensive description of host and microbial activities in IBD to date.

  Study phs001626

• Microbial infections in Alzheimer’s patients

  In the present study, we have examined fungal and bacterial infection in brain tissue from 10 AD patients and 16 control subjects by next-generation sequencing NGS using MiSeq sequencing platform (Illumina).

  Dataset EGAD00001003886

• Gut microbiome dynamics unravelled with metagenomics sequencing

  It has been already several years since we discovered that microbial therapeutics like Faecal Microbiota Transplantation can be used to treat Clostridium difficile infection (CDI) and Inflammatory bowel disease (IBD) with great success. The concept has challenged us to test the limits of our knowledge with the perspective to improve health in the most diverse conditions like Parkinson disease, depression, autism and obesity, just to mention a few. Note: the figure belongs to the original paper and is owned by the authors. Allyson L.Bird and colleagues from Genentech Inc. (San Francisco) recently published an interesting study building up on the key concept that “As microbial therapeutics are increasingly being tested in diverse patient populations, it is essential to understand the host and environmental factors influencing the microbiome.” The authors of this work analysed 1359 gut microbiome samples using shotgun metagenomics sequencing.  The results of the comparison done between microbiota composition across the different groups showed that biological sex is the strongest driver of diversity, while aging (age range studied: 20–69) appears to be the second factor. As smartly outlined in the authors’ own graphical abstract (figure to the left), Bacteroidota species consistently increased with donors' age while Actinobacteriota species, including Bifidobacterium, decreased. This study also integrated data from oncological patients to draw cancer-related evidences. After correcting the biases for technical and geographic differences, they found that cancer patients show significantly altered gut bacterial communities compared with their healthy counterparts. Eg. E.coli was found to be increased in cancer patients together with Bacteroidota/Firmicutes ratios. By comparing sequential samples taken from the same donors (413) within short-distance time points, the authors found that in the short term, intra-individual differences were less than the inter-individual ones, indicating a certain community stability being the norm. One of the pivotal points from this interesting study is that the data proceeds from extremely well-defined and selected donors. Specifically, the data for 949 selected healthy donors came from the Milieu Intérieur (MI) Consortium and extensive metadata, including demographic variables, serological measures, dietary information, and systemic immune profiles, are available. This precise stratification allowed for the robust detection of smaller changes, compared to former works. All sequencing data has been deposited in the EGA archive under the accession number EGAS00001004437. Enjoy this amazing open access paper published in the Experimental Journal of Medicine on January 2021.

  Blog gut-microbiome-dynamics-unravelled

• Genomic and ecologic characteristics of the airway microbial-mucosal complex

  Lung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide. Microbial communities at the airway mucosal barrier are conserved and highly ordered, reflecting symbiosis and co-evolution with human host factors. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species. We match the gene content of bacterial isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.

  Study EGAS00001006689