Difficulties in built a correlation network after using q2-SCNIC

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Thanks @joaomiranda,

Do you mean is it a coincidence that Ae. aegypti and Ae. taeniorhynchus are both connected to exactly three bacterial species? Yes, that's a coincidence.

As for why they're not connected to more, FlashWeave tries to only associate nodes of the network that are directly dependent on one another. It doesn't mean that a mosquito node only affects its neighbours, it just suggests that the effects that it has on the broader community might be through its neighbours.

To try to visualise that, here is an illustration of where the mosquito nodes fall in their Louvain communities.

network (13)
network (13)787×612 41.3 KB

In this plot, the mosquito nodes are in an "undefined" community. This is a result of a QIIME 2 issue (but it's also convenient, because it means you can see where they are). They are not actually in undefined communities, they're in the communities that they're surrounded by, as you can see by visualising the Louvain communities directly (mozzies-louvain.qzv (1.2 MB)).

You might notice that this network looks slightly different to the last one. That's because I changed the FlashWeave parameters slightly to stop it ignoring features that didn't occur in at least 20 samples (which is almost all your samples). I also removed the location data from your metadata to focus on the mosquito species.

When performing any bioinformatics it is important to vary the input parameters to demonstrate that your conclusions are robust to parameter choices.

If you're seeing corroborating evidence in your ANCOM results, that's great. I would like to see the results if you publish them.

Here are the commands that I used to generate the above results.

Remove the locations from the metadata.

cut -f1,2 -d$'\t' Metadata.txt > mozzies-only.tsv

Generate the network with looser observations constraints and using only mosquito metadata.

qiime makarsa flashweave \
    --i-table filtered-bacteria-table.qza \
    --m-metadata-file mozzies-only.tsv \
    --p-n-obs-min 2 \
    --o-network mozzies-network.qza

Infer the Louvain communities.

qiime makarsa louvain-communities \
    --i-network mozzies-network.qza \
    --o-community mozzies-louvain.qza

Visualise the Louvain communities (as attached above).

qiime metadata tabulate \
    --m-input-file mozzies-louvain.qza \
    --o-visualization mozzies-louvain.qzv

Visualise the resulting network, with Louvain communities and taxonomic classifications

qiime makarsa visualise-network \
    --i-network mozzies-network.qza \
    --m-metadata-file corrected_taxonomy.qza \
    --m-metadata-file mozzies-louvain.qza \
    --o-visualization mozzies-network.qzv

Here is the resulting visualisation: mozzies-network.qzv (223.4 KB).

Hope that helps. Feel free to follow up if you have any more questions.

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