search

Humanitas-Danese-s-omics / ibd-meta-analysis-data

Creative Commons Zero v1.0 Universal
9 stars 5 forks source link

Eukaryotes - additional species of interests #2

Open RPHirt opened 2 years ago

RPHirt commented 2 years ago

Dear Colleagues,

I read with much interest your paper on the IBD Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) platform. However I was surprised that the eukaryotes did not include common symbiotic protists/parasites present in the gut and that are also potentially relevant in the context of IBD (in that respect it was great to see several listed Microsporidia!). The missing entries that would be great to see included are listed here:

1) Blastocystis spp. (a couple of genomes are available: e.g. GenBank: GCA_000151665.1 - subtype 7, but would be good to include most commons subtype found among humans). Potentially negatively associated with IBD

2) Cryptosporidium spp. (C. hominis e.g. GenBank GCA_000006425.2; C. parvum e.g. GenBank: GCA_001305335.1)

3) Toxoplasma gondii (genomes available: e.g. GenBank GCA_013099955.1)

4) Giardia lamblia (genomes available: e.g. GenBank GCA_000002435.2)

5) Gut trichomonads, including Dientamoeba fragilis and Pentatrichomonas hominis (no genomes but transcriptomics data are available). So could use contigs derived from the published transcriptomics data BioSample: SAMN05645745; Sample name: Pentatrichomonas hominis; SRA: SRS1644965 BioSample: SAMN03701404; Sample name: Dientamoeba fragilis; SRA: SRS944696

Also, a common Microsporidia in human infections is Enterocytozoon bieneusi. There is a genome sequence dataset but it has important bacterial contaminations, possibly why you did not include it? BioSample: SAMN00017218; Sample name: E. bieneusi 454; SRA: SRS065734

Looking forward to see what you think about the above suggestions as I plan to use the tools to investigate a number of questions made addressable thanks to the IBD TaMMA platform.

Kind regards,

Robert

Robert Hirt - Professor of Evolutionary Parasitology (PhD) Catherine Cookson Building (2nd floor, room M2.042A) Biosciences Institute, Faculty of Medical Sciences, Newcastle University Framlington Place, Newcastle upon Tyne, NE2 4HH, UK Tel. +44(0)191 208 6963 (direct) Home page: https://www.ncl.ac.uk/medical-sciences/people/profile/roberthirt.html

maximinio commented 2 years ago

Hi Robert, that is indeed a good point! We only recently realized we could also quantify protists and I assure you they will be available in the next version of IBD TaMMA! Best, L

RPHirt commented 2 years ago

Hi Luca,

Brilliant, thank you for the feedback, great to read that these data will be incorporated. If you are interested we could maybe put a paper together exploiting these microbial eukaryotes data?

All the best!

Robert

From: Luca Massimino @.***> Sent: 06 May 2022 16:36 To: Humanitas-Danese-s-omics/ibd-meta-analysis-data Cc: Robert Hirt; Author Subject: Re: [Humanitas-Danese-s-omics/ibd-meta-analysis-data] Eukaryotes - additional species of interests (Issue #2)

⚠ External sender. Take care when opening links or attachments. Do not provide your login details.

Hi Robert, that is indeed a good point! We only recently realized we could also quantify protists and I assure you they will be available in the next version of IBD TaMMA! Best, L

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHumanitas-Danese-s-omics%2Fibd-meta-analysis-data%2Fissues%2F2%23issuecomment-1119748599&data=05%7C01%7Crobert.hirt%40newcastle.ac.uk%7C1681f97b04bb4dde2ab508da2f76445b%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637874482238958058%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=f40mNOysubgQQeM7Xz%2BLxpfo30YQaBz9KzYXeSoJYjE%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYZRBH27U3RKXCDN3TK4IMLVIU4BVANCNFSM5TY2P2IA&data=05%7C01%7Crobert.hirt%40newcastle.ac.uk%7C1681f97b04bb4dde2ab508da2f76445b%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637874482238958058%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TCe5vlel8H%2FW8g0gHnGXEvxPJ1Gy2jJ0KbKVc9%2BThSg%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.***>