bacteria – Page 4 – Jonathan Eisen's Lab

#PLoSOne paper keywords revealing: (#Penis #Microbiome #Circumcision #HIV); press release misleading

UPDATE – READ COMMENTS – LEAD AUTHOR HAS GOTTEN PRESS RELEASE CHANGED

A new paper just showed up on PLoS One and it has some serious potential to be important The paper (PLoS ONE: The Effects of Circumcision on the Penis Microbiome) reports on analyses that show differences in the microbiota (which they call the microbiome – basically what bacterial species were present) in men before and after circumcision. And they found some significant differences. It is a nice study of a relatively poorly examined subject – the bacteria found on the penis w/ and w/o circumcision. This is a particularly important topic in light of other studies that have shown that circumcision may provide some protection against HIV infection.

In summary here is what they did – take samples from men before and after circumcision. Isolate DNA. Run PCR amplification reactions to amplify variable regions of rRNA genes from these samples. Then conduct 454 sequencing of these amplified products. And then analyze the sequences to look at the types and #s of different kinds of bacteria.

What they found is basically summarized in their last paragraph

“This study is the first molecular assessment of the bacterial diversity in the male genital mucosa. The observed decrease in anaerobic bacteria after circumcision may be related to the elimination of anoxic microenvironments under the foreskin. Detection of these anaerobic genera in other human infectious and inflammatory pathologies suggests that they may mediate genital mucosal inflammation or co-infections in the uncircumcised state. Hence, the decrease in these anaerobic bacteria after circumcision may complement the loss of the foreskin inner mucosa to reduce the number of activated Langerhans cells near the genital mucosal surface and possibly the risk of HIV acquisition in circumcised men.”

And this all sounds interesting and the work seems solid. I note that some friends / colleagues of mine were involved in this including Jacques Ravel who used to be at TIGR and now is at U MD and Paul Kiem who is associated with TGen in Arizona. For anyone interested in HIV, the human microbiome, circumcision, etc, it is probably worth looking at.

However, the press release I just saw from TGen really ticked me off. The title alone did me in “Study suggests why circumcised men are less likely to become infected with HIV”. Sure the study did suggest a possible explanation for why circumcised men are less likely to get HIV infections – the paper was justifiably VERY cautious about this inference. They basically state that there are some correlations worth following up.

The press release goes on to say “The study … could lead to new non-surgical HIV preventative strategies for the estimated 70 percent of men worldwide (more than 2 billion) who, because of religious or cultural beliefs, or logistic or financial barriers, are not likely to become circumcised.” Well sure, I guess you could say that. I think they are iplying you could change the microbiome somehow and therefore protect from HIV but that implies (1) that there really is a causal relationship between the microbial differences in HIV protection and (2) that one could change the microbiome easily, which is a big big stretch given how little we know right now.

Anyway – the science seems fine and not over-reaching. But the press release is annoying and misleading. Shocking I know. But this one got to me.

UPDATE – SEE COMMENTS HERE AND IN FRIENDFEED. LEAD AUTHOR GOT PRESS RELEASE CHANGED.

Price, L., Liu, C., Johnson, K., Aziz, M., Lau, M., Bowers, J., Ravel, J., Keim, P., Serwadda, D., Wawer, M., & Gray, R. (2010). The Effects of Circumcision on the Penis Microbiome PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008422

Undercooked meat does not kill people, E. coli O157:H7 does

Which would you prefer? A clean meat supply, where the meat you eat is generally free of nasty pathogenic bacteria? Or a meat supply that has to be irradiated and cooked in order to make it safe?

Check out the article in Newsweek for a sort of discussion of this issue relating to the E. coli O157:H7 strain found in ground beef recently, and more frequently all the time.

Why is E. coli O157:H7 in ground beef in the first place? The answer to this depends on at what point in the life cycle of the meat processing you want to track the E. coli to. Meat processors would like to say it just comes from a little bit of “contamination” during making ground beef. But the real question to me is, why is there so much E. coli O157:H7 around for it to contaminate the ground beef? Well, I like the explanations of Michael Pollan and Eric Schlosser given in the Newsweek article:

Schlosser says

we have a systemic problem here starting in the feedlots, spreading in the slaughterhouses, and winding up in the ground beef at plants that make frozen patties. Putting Topps out of business isn’t going to solve that fundamental problem.”

Pollan says

This particular bug was not a problem before the industrialization of the meat supply,” says Michael Pollan, an investigative journalist and food writer. “It’s an adaptation to the feedlot diet [which is composed of corn, ethanol byproducts and other grain feed]. Animals who get a proper diet and are outside eating grass don’t get much of it. Even if you give the animals fresh hay in the last days of their lives, the E. coli burden drops 80 percent. But it would just screw up the workings of the [industry]. The other way [to reduce risk] is to slow down the lines, if you could butcher with more care.”

A meat industry consultant counters this by saying

When you pack people together in cities, diseases pass between them easier. If you’re living in the plains with five miles between households, you’re less likely to get sick. I think it’s the nature of the world. The reality is if you cook the meat you’ll never have a problem. I eat beef a lot and I may get indigestion from time to time, but I don’t get sick. No one will ever get sick if you fully cook the meat. This isn’t rocket science.

Not the most ringing endorsement in the first place (is indigestion supposed to be a good thing?). But Pollan wraps up my feeling on this:

if there is indeed manure in the meat, however microscopic, you’re still eating cooked manure.

So – yes, getting cheap meat will require us to industrialize the process somewhat. But do we really want the meat to be as cheap as possible? I do not think so. I think quality of the environment, quality of the meat, and reducing the spread of nasty pathogens should also be part of the equation. I am not going to start eating raw meat, but just because you can kill the bacteria in contaminated meat does not mean I want to eat it.

Metagenomics Based Discovery Highlight: Novel Photosynthetic Organism Discovered

Normally I avoid writing about discoveries in non Open Access journals. But I cannot help myself here. On Friday a wickedly cool paper was published in a journal that I will not name here. In this paper they describe a new bacterium: “Candidatus Chloracidobacterium thermophilum.” It is REALLY rare for a new bacteria to be described in a journal like this one. How did they get it in this journal? Well this organism represents the first new photosynthetic lineage of organisms discovered in many many many years. The bacterium is in the phylum Acidobacteria and can carry out aerobic photosynthesis. Prior to this discovery, photosynthesis was only known in five evolutionary lineages – all of them bacteria: Cyanobacteria, Chlorobi, Chloroflexi, Proteobacteria and Firmicutes. Photosynthesis in plants, algae and other eukaryotes all came from symbioses with cyanobacteria to these five groups represented the only “primary” photosynthetic lineages. Thus it is a big deal to find a sixth lineage having photosynthesis.

And – here is the fun part. How did they find this? With the help of metagenomics.

Only five bacterial phyla with members capable of chlorophyll(Chl)–based phototrophy are presently known. Metagenomicdata from the phototrophic microbial mats of alkaline siliceoushot springs in Yellowstone National Park revealed the existenceof a distinctive bacteriochlorophyll (BChl)–synthesizing,phototrophic bacterium. A highly enriched culture of this bacteriumgrew photoheterotrophically, synthesized BChls a and c underoxic conditions, and had chlorosomes and type 1 reaction centers.“Candidatus Chloracidobacterium thermophilum” is a BChl-producingmember of the poorly characterized phylum Acidobacteria.

That is, they saw the first hints of this through analysis of metagenomic data which was generated by isolating DNA from a Yellowstone hot spring and sequencing the snot out of it. Anyway – as some might have guessed – my only lament about this paper is that it is in a non Open Access journal (I tried to convince the lead author to submit elsewhere but was not convincing enough I guess). It really is too bad – it would be nice to post some of their figures here for others to look at and it this paper would make a great one to use for educating the public about metagenomics. But alas the public cannot get this from Science for at least 1 year and bloggers and other news sources cannot really run with the story because of the copyright limitations. So – great science and great example of the power of metagenomics but restricted public use.