Functional analysis with newer version of KEGG database

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Jessie HOU

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Oct 28, 2019, 12:28:11 AM10/28/19
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Hi,

I found one of the important bacteria (Dolosigranulum pigrum) in my data set contributes to several MetaCyc pathways. However, when I use the legacy KEGG database for the same data set, this bacterium does not contribute to any KEGG functional pathway shown in the resulting merged pathway abundance table. 

Since the NCBI genome assembly of this bacterium has just been published (2019/07/21), the legacy KEGG database did not include this bacteria. Does it mean I have to order the latest version of KEGG database, if I want to know this bacterium's KEGG functional potential with Humann2? If I obtain the KEGG license, how to use newest KEGG database with Humann2?

Any suggestions would be greatly appreciated. Thanks in advance.

Best regards,
Jessie

Eric Franzosa

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Oct 30, 2019, 3:01:01 PM10/30/19
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Dolosigranulum pigrum exists in the HUMAnN2's pangenome database, though that specific isolate genome is too new to have been included.

I'm not sure if updating the KEGG database would help to detect KEGG pathways from D. pigrum's HUMAnN2 pangenome. Doing so would require downloading the KEGG module/pathway definitions and reformatting them for use with HUMAnN2. Since this information is now available through KEGG's public API, we are exploring re-adding updated KEGG module/pathway definitions to HUMAnN2, but relying on UniProt for all other KEGG-centric annotations (e.g. KO mappings).

Thanks,
Eric



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