| broad-scale environmental context | insect |
|---|
| collection date | 2013-10-01 |
|---|
| environmental medium | thorax and abdomen |
|---|
| geographic location | United Kingdom |
|---|
| investigation type | metagenome-assembled genome |
|---|
| isolation source | honeybee metagenome |
|---|
| project name | The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of Apicystis bombi, a parasitic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota. |
|---|
| sample name | SRR7986807_bin.3_metawrap_v1.3.0_MAG |
|---|
| ENA-CHECKLIST | ERC000047 |
|---|
| ENA-FIRST-PUBLIC | 2022-08-26 |
|---|
| ENA-LAST-UPDATE | 2022-08-26 |
|---|
| External Id | SAMEA110751597 |
|---|
| INSDC center alias | EMG |
|---|
| INSDC center name | EMG |
|---|
| INSDC first public | 2022-08-26T16:22:58Z |
|---|
| INSDC last update | 2022-08-26T16:22:58Z |
|---|
| INSDC status | public |
|---|
| Submitter Id | SRR7986807_bin.3_metawrap_v1.3.0_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 v1.3.0 |
|---|
| broker name | EMG broker account, EMBL-EBI |
|---|
| completeness score | 87.52 |
|---|
| completeness software | CheckM |
|---|
| contamination score | 1.2 |
|---|
| geographic location (latitude) | 55.9 |
|---|
| geographic location (longitude) | -3.67 |
|---|
| local environmental context | honeybee |
|---|
| metagenomic source | honeybee metagenome |
|---|
| sample derived from | SAMN10185825 |
|---|
| 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__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus apis |
|---|
| taxonomic identity marker | multi-marker approach |
|---|