Frederick Bushman

Diet, genetic factors, and the gut microbiome in Crohn’s disease

COMBO: 97 subjects, diet questionaire, 454 of 16s. Found association between food groups and bacteria, lots of patterns and correlations.30-40 nutrients corelated with changes in bacterial populations. However there was a lot of variation so the moved on to the CAFE studies

CAFE studies: controlled studies of fat vs fibre. 10 healthy volunteers, 10 day with same meals each day with randomozed diets. Interpersonal varaition once again was very much dominant. Within 24 hours there was significant change in bacterial populations of diet initiation. High fat vs high fibre, and total calories all have a detactable effect. Considerable directional drift was consistant in all patients staying in the hospital regardless of diet, a complete mystery. Could be important about hospital enviroments, could just be drinking the same water or something like that.

Approachs to virome analysis. 10^10 phage particals were found per gram of stool in all samples. they used 454 titanium, with almost a million shotgun reads. Lots of phages, but no sequences that could be attributed to eukaryotic viruses in the entire study were found.  22 phage CRISPR arrays, including a CRISPR spacer on a phage found in a sample with the succesptible phage, suggesting that the phage recruited the CRISPR system to compete with other phages(?)

Lysogens: A type of viruses that can integrate into DNA, therefor potentially contribute new functionality to their host bacteria. A reasonable percentage of the phages may be lysogens

Bacterioides may have less phages, but Prof Weinstock can’t speculate why and the data is preliminary.

Subjects are more similar to themselves than others(As all these talks, inter personal variation dominates), but diets can make people more similar to eachother.

Procrustes analysis. I got lost here. PCA was done.

What determines the abundance of different phage? In some cases the abundance of the phage does not correlate with the abundance of the host.

Question: Is phage kinects in response to diet similair to bacterial? Answer: Possibly slower, not enough information

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