The detection problem of the anaerobic methane oxidation pathway

[king72858]

I encountered a problem while analyzing microbial methane oxidation pathways. In the pathway output results from the detection, I seem unable to find pathways for sulfate-dependent anaerobic oxidation of methane, nitrate-dependent anaerobic oxidation of methane, and metal-reduction-dependent anaerobic oxidation of methane. Among these dependent types, I can only find nitrite-dependent anaerobic oxidation of methane.

I have checked my input files, but these anaerobic methane metabolic pathways are still not detected. Could you provide suggestions on the appropriate search strategies or specific parameter configurations required to identify these pathways in the gapseq analysis pipeline?

[Waschina]

Hi @king72858

Could you please share links to the database entries (e.g., Metacyc or KEGG) for the pathways you mentioned?

[king72858]

Thank you for your reply! Apologies, I learned about these pathways from reviewing some literature on methane metabolism. After your response, I searched several databases but couldn't find any records of these pathways. Upon further examination of the literature, it appears these pathways remain only at the theoretical stage and have not been experimentally verified.

[jotech]

Hi, the sulfate, nitrate, and nitrite coupled variants of anaerobic methan oxidation should all have some experimental evidence!
As you mentioned, metacyc has only the nitrite variant
https://metacyc.org/pathway?orgid=META&id=PWY-6523
I think the problem is that those processes are often syntrophic and isolates are missing (https://en.wikipedia.org/wiki/Anaerobic_oxidation_of_methane). I think this is why the sulfate pathway, although it is known to happen, is less described enzymatically, which makes it challenging to include in metabolic models.

It would be interesting to know if the nitrite pathway is working in the models. Have you tried this @king72858 ?

[king72858]

I have tried, and it seems that the nitrite pathway does not function in the model.

After receiving your reply, I screened all the sequences of the NC10 phylum (currently, all nitrite pathways are classified under the NC10 phylum) based on key genes from UniPront, constructed a Hidden Markov Model using HMMER, and searched 107,008 species-level MAGs in the SPIRE database with "hmmsearch". However, no nitrite pathways were detected in the subsequent path detection.