Field of Science

Thursday afternoon sessions at IHMC11

Rob Holt: colorectal carcinoma metagenomics.  (His tone of voice makes this sound dull...)  Nearly 20% of global cancer burden known to be due to infectious agents.  They're doing a systematic search for additional agents and factors.

Pipeline:  Start with tumor samples, get RNA, subtract host rRNA, RNA-seq.  (I'm not quite sure what his strategy is...).  Human genome and transcriptome subtracted.  Now look for known viral and bacterial sequences.  What aligns to known bacteria etc, and what potentially novel-organism sequences don't align?

Reconstruction:  could detect 0.1 pg of viral RNA (8 kb) per 2 µg human RNA.  Recovery about 33& of input.  Dull dull...

Why look in colorectal carcinoma? Lots of exposure to microbes, precedent of H. pylori, the guy in the next lab had some we could use.  Has 669 candidate seq (no, candidate bacterial species )from control, 492 from tumor, 250 common to both?  Most reads from the known gut bacteria, some phages.  (Different from Meta HIT (INRA intestinal tract).

High abundance of Fusobacterium nucleatum (anaerobe, Gram-neg, periodontal, appendicitis) in tumors but not controls (86-fold overrep), but no other significant correlations.  Mostly two of the eleven patients, and mostly rRNA sequences of the bacteria.  Look at other tumors, see commonly overrep of Fusobacterium.

"This is quite exciting" (said in monotone).  No clinical correlations found with presence/absence of Fusobacterium, even though this species known to be pathogenic.

Question about tumor site (different types of tumors in different places in the colon and rectum) and about the patients not having their gut 'cleansed' before the tumors are excised (so the tumors could have a lot of surface bacterial contamination).

Heather Maughan:  Ecology and evolution of the cystic fibrosis lung microbiome.  Healthy lungs are not completely sterile, but we can get rid of the bacteria we breathe in.  But in CF lungs the bacteria are like unwelcome house guests, very hard to get rid of.  Follow bacteria in CF lungs through childhood and adults.  See changes in prevalence of the common bacteria.  (H. influenzae important in young patients but not adults.)

Get 'explants' (= lungs removed from CF patients receiving lung transplants) plus hundreds of sputum samples from baseline and exacerbation patients.  Sequencing 16S rDNA.  Also whole-genome microbiome sequencing (includes host DNA, viruses and phage).  Now lots of info about methods of analyzing the data - how many reads, how efficient, appropriate cutoffs, false-positive rates, worst is still good 0.08%.

Individual patiets differ in their microbial diversities.  All have Burkholderia, most Haemophilus, Pseudomonas.  Peptostreptococcus (anaerobic),  Some reads mapped to chloroplast relatives - patients may be breathing in pollen.. 

Kristine Wylie: Human virome in children and adults.  (Oh-oh, nasty audio problem.  There's an echo from the rear speakers, making it very hard to understand what she's saying.  At the question period, discover the same problem with audience microphones audio.)

Children with fevers have more viruses in the nasopharynx, only febrile children have viruses circulating in plasma (except anello?).  Anello virus in plasma only in afebrile children.  These viruses have only recently been discovered,  they're common and genetically diverse, and have not yet been associated with disease.  Bocavirus.  RSV.  Human rhinovirus QPM.  Human parainfluenza virus.

Human microbiome project samples:  Two times from same person, from multiple body sites.  Find the same kinds of viruses at many sites.  Find papillomaviruses in various sites.

Frederick Bushman:  The virome of the human gut: metagenomic analysis of changes associated with diet.

Cross-sectional study of diet and stool microbiome (COMBO)  See strong associations between certain bacteria and certain dietary components.  Patterns of phyla of bacteria with high-fat or high-fiber, and of specific bacteria.  But dietary effects accounted for only a small fraction of total variation between individuals.

Controlled feeding experiment (CAFE)  10 healthy volunteers, captive feeding in a hospital for 10 days; low fat or high calorie diets.  Variation much lower between individuals, except on day 1.

VIROME:  Goal is to characterize the whole viral population.  (Lambda control gave quantitative recovery.)  10^10 phage per gram of stool!  Circular contigs (genomes?) all about 5-6 kb.  Linear ones very diverse lengths.  7000 new virus genomes!  19-785 per individual sample.  Lots of 'unknown'!  No contigs of eukaryotic viruses at all, but bits of eukaryotic viral genomes in phage genomes.  He thinks there has been lots of misidentification - what appears to be DNA indicating presence of a eukaryotic virus is really jsut a bit of phage genome.  See CRISPR system used to compete with other phage (I forget what CRISPR does).

Lysogeny:  He thinks they found lots of evidence, but the audio problems mean that I'm not sure what he said.

Interpersonal variation in virome:  Most variation is accounted for by who is being examined.  Subjects on different days are more similar to themselves than they are to other subjects on the same day.  But subjects on the same diet do get more similar than they were before.

What determines phage abundance?  Abundance of host?  Lysogenic induction?  No evidence for consistent relationships to putative host abundance.

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