FAQ

Microbiome Search Engine is a search-able database of microbiome for in-depth data mining of microbial community studies by data integration and data selection. It contains large scale of microbial community samples with sequences, meta-data and analysis results. Based on the query sample(s), Microbiome Search Engine will provide the matched entry sample(s) in the database with very similar community structures in an ultra-fast speed. In addition, samples in the database can also be sorted, selected, exported and downloaded by their sampling meta-data information (meta-data).

This reference microbiome database is being constantly updated and will be released periodically.



Microbiome Search Engine accepts the query sample(s) that profiled by Parallel-META 3 for sequences. The latest Parallel-META 3 is available at http://bioinfo.single-cell.cn/parallel-meta.html

Sequence should be in FASTA/FASTQ format (eg, sample1.fa), then the command line for OTU profiling:

$parallel-meta -r sample1.fa -o sample1.out (for 16S rRNA sequences)

or

$parallel-meta -m sample1.fa -o sample1.out (for shotgun sequences)

Then in the output directory "sample1.out", the parsed taxonomy result file "classification.txt" is qualified for upload and search.This file contains two columns: the OTUs (greengene 13-8 on 97% level) and their sequence numbers.

Example:

#Database_OTU
Count
38922072
82487620
4414476830


Microbiome Search Engine accepts the samples in Parallel-META 31 results format. Sequences of samples should be analysed by Parallel-META 3. (See "Pre-process your query sample")

In "Query" secion, click the "Select" button choose the file you want to search, and then pressen press "Upload" button to submit. There are 2 advanced options:

  • Maximum matched sample number: The max matched sample number for visualization and download, default is 10;
  • Minimum similarity:The min similarity value between input query and matched sample(s), default is 0.85. The similarity varies from 0.0-1.0, and higher similarity indicates more community structure shared by 2 samples.


The similarity between the query sample and the matched samples is calculated by Meta-Storms2, which incorporated both the relative abundance of each individual organism and the phylogeny architecture among organisms in the community on OTU level. The similarity varies from 0.0-1.0, and higher similarity indicates more community structure shared by the samples. Then the shared community structure of your input query sample and the matched samples (s) can be illustrated in a bar chart on phylum level and displayed in the result page. In addition, the searching results can also be downloaded with full community information including OTU table and Multi-Sample-View1, which could be further analysed in Parallel-META 31.

Microbiome Novelty Score (MNS) is proposed to evaluate the compositional uniqueness of a microbiome sample when compared to all microbiomes in the database. A higher MNS means lower similarity to those microbiomes that have previously been sampled, suggesting higher novelty. MNS starts from 2010, and is not applicable for samples produced/published before 2010.

Microbiome Attention Score (MAS) is proposed to measures the connectivity of a given sample to all subsequent samples in the database. A higher MAS means more samples with similarity or samples with higher similarity had been sequenced, suggesting higher attention from the scientific community for this input sample.MAS starts from 2010, and is not applicable for samples produced/published before 2010.

If a microbiome has the two attributes of a) MNS ≥ 0.15 when first sequenced and b) MAS ≥ 14, then it is considered as “focus” samples. The combined MNS and MAS are quantitatively measured by Microbiome Focus Index (MFI):

MFI = MNS * MAS


Microbiome Novelty Score (MNS) is proposed to evaluate the compositional uniqueness of a microbiome sample when compared to all microbiomes in the database. A higher MNS means lower similarity to those microbiomes that have previously been sampled, suggesting higher novelty. MNS starts from 2010, and is not applicable for samples produced/published before 2010.

Microbiome Attention Score (MAS) is proposed to measures the connectivity of a given sample to all subsequent samples in the database. A higher MAS means more samples with similarity or samples with higher similarity had been sequenced, suggesting higher attention from the scientific community for this input sample.MAS starts from 2010, and is not applicable for samples produced/published before 2010.

If a microbiome has the two attributes of a) MNS ≥ 0.15 when first sequenced and b) MAS ≥ 14, then it is considered as “focus” samples. The combined MNS and MAS are quantitatively measured by Microbiome Focus Index (MFI):

MFI = MNS * MAS


In "View Sample", any samples can be tracked by the Sample ID in the database for quick access. User can also select samples with specified meta-data (such as Type, Habitat, Year, etc.) and export the detailed information in CVS format.

The Microbiome Search Engine online system also provides the complete database for download in "Download" including database index (.mdb file for Meta-Storms2), samples structure (Parallel-META 31 format), original sequences and meta-data of all samples in the database.





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