Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Italy
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Not specified
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Space surrounding organism External to organism,Outside of body,Space surrounding organism,space surrounding organism
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Environmental factor environment factor,Environmental factor,environmental factor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No healthy samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2017 samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2017 samples are samples obtained from the three river depths(Meso, Secchi, and surface depth) during the cyanobacterial bloom in 2017.
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- non
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "depth" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.depth
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "depth" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.depth
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Needs review
Source: Figure 3
Description: Taxonomic analysis at the phylum level showed that, in most of the samples, Proteobacteria was the predominant taxonomic group followed by Actinobacteriota, Cyanobacteria and Bacteroidota .
Abundance in Group 1: increased abundance in 2017 samples
| NCBI | Quality Control | Links |
|---|---|---|
| ProteobacteriaProteobacteria |
Revision editor(s): Imaspecial
