I have list of bacterial species with names and taxonomy id. I want to know their habitats for e.g. human gut, environment, mud etc etc. I don't have any clue how to move on. Any help would be appreciated.
Thanks
Do you have the NGS reads with you corresponding to these set of bacteria? If yes, then you can use SourceTracker
It will be rather difficult with only the bacterial names, until you stumble upon a habitat database.
A long time ago NCBI hosted a file that included such info. However, as far as I know, said file has not been available for years already. I think MEGAN still uses it, or rather some old version of it (at least a few years ago when I used it last time). Anyway, what do you hope to gain by connecting your taxonomy ids to habitats? I recall reading a paper (many years ago) where the author was showing how basically every metagenome gave a very similar habitat profile, no matter where it was from (grassland, bottom of the sea, Antarctic lake, etc.).
Hi,
I have some blast results of protein from yeast. I got some significant blast hits from the bacteria. I suspect those are probably horizontally transffered genes (HTG) from bacteria to yeast. I quickly want to check habitats of those bacteria to see if yeast habitats and bacterial habitats are similar. If so, I suspect somewhere they lived together and so HTG event happened.
Anyway, thanks for your suggestion. I found a source which can give me exactly the information which I want. JGI has very rich microbiome annotations. I can easily map taxonomy to ecosystem and habitats.
Cheers.
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version 2.3.6
Hi Vijay,
Good to know this new tool. I don't have NGS reads from bacteria. But I found a very useful resource which can fulfil my purpose. JGI has very rich microbiome annotations. I can easily map taxonomy to ecosystem and habitats.
Cheers
Thanks for sharing Chirag! Good Luck.