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dib-lab / sourmash-slainte

Project template for sourmash-based characterization of genomes and metagenomes
BSD 3-Clause "New" or "Revised" License
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identify an example data set #12

Open ctb opened 9 months ago

ctb commented 9 months ago

iHMP? or something else?

it'd be nice if it had a specific set of genome(s)... could do the hu et al one

ctb commented 9 months ago

suggestions from a post on bluesky -

https://bsky.app/profile/rossbenjamind.bsky.social/post/3ki3jws62pd2g

https://bsky.app/profile/sieravirus.bsky.social/post/3ki3iomo2x22b

https://bsky.app/profile/contaminatedsci.bsky.social/post/3ki3btz24li2x

ctb commented 9 months ago

Poyet et al., Alm sr author, 2019 A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research https://www.nature.com/articles/s41591-019-0559-3

a comprehensive collection of 7,758 gut bacterial isolates paired with 3,632 genome sequences and longitudinal multi-omics data.

Sharon et al,, Banfield sr author. 2013. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization https://pubmed.ncbi.nlm.nih.gov/22936250/

We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (∼99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%.

Aggarwala et al, Faith sr author. 2021. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

We assembled a collection of >1,000 different bacterial strains that were cultured from the fecal samples of 22 FMT donors and recipients. We sequenced 85 metagenomes from the 7 donor fecal samples used for FMT and recipient samples taken before and for up to 5 years after FMT.

ctb commented 8 months ago

https://bsky.app/profile/contaminatedsci.bsky.social/post/3kipls72or22o

https://www.biorxiv.org/content/10.1101/2024.01.10.575018v1

Here, we use 4,055 isolate genomes and 360 metagenomes to trace the dynamics of strains on individuals and their transmission.

pretty tractable actually...