| broad-scale environmental context | human digestive system |
|---|
| collection date | 2018-01 |
|---|
| environmental medium | saliva |
|---|
| geographic location | Denmark |
|---|
| investigation type | metagenome-assembled genome |
|---|
| isolation source | oral metagenome |
|---|
| project name | The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterisation of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA. |
|---|
| sample name | SRR13061518_bin.5_MetaWRAP_v1.3_MAG |
|---|
| ENA-CHECKLIST | ERC000047 |
|---|
| INSDC center name | EMG |
|---|
| Submitter Id | SRR13061518_bin.5_MetaWRAP_v1.3_MAG |
|---|
| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
|---|
| assembly software | metaspades v3.15.3 |
|---|
| binning parameters | MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. |
|---|
| binning software | MetaWRAP v1.3 |
|---|
| broker name | EBI-EMG |
|---|
| completeness score | 88.79 |
|---|
| completeness software | CheckM |
|---|
| contamination score | 0.33 |
|---|
| geographic location (latitude) | 55.67 |
|---|
| geographic location (longitude) | 12.57 |
|---|
| local environmental context | oral cavity |
|---|
| metagenomic source | oral metagenome |
|---|
| sample derived from | SAMN16796875 |
|---|
| scientific_name | uncultured Capnocytophaga sp. |
|---|
| sequencing method | Illumina HiSeq 2500 |
|---|
| taxonomic classification | The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga;s__ |
|---|
| taxonomic identity marker | multi-marker approach |
|---|