Turned up to eleven: Fair and Balanced

Posted 11:51 AM by Paul

Archaea and disease
Archaea (or archaebacteria) are a large and difficult to study group of microorganisms that are similar in appearance to bacteria, but biochemically very different. Based on the pioneering work of Carl Woese of the Univ. of Illinois, Champaign-Urbana, a method for studying the phylogenetic distribution of bacterial, eukaryotic, and archaeal species was determined. The method relies on a so-called "molecular clock" using the sequence of the ribosomal RNA.

So what is ribosomal RNA? The ribosome is the cell's protein factory, that converts mRNA sequences into amino acid sequences (the central dogma of molecular biology is DNA to RNA to protein) that fold into 3 dimensional proteins that do the cell's business. Clearly, a cell that doesn't have functional ribosomes isn't going to last long (or at all!). So the ribosomes, made of ribonucleic acid molecules (rRNA or ribosomal RNA) and proteins arranged in a complex 3D structure, have two very important features wrt "molecular clock" applications. 1) they are absolutely critical, so any mutation that alters their function is big trouble, and 2) they have been around a very long time, so the evolutionary tree can be rooted at the very beginning of life. Bacteria have them, eukaryotes have them, archaea have them. Some parts of the ribosome cannot be changed at all without destroying the function. These are called conserved regions. Other parts can mutate relatively freely, and are called variable regions. These variable regions form the basis for the molecular clock.

Based on this method, microorganisms (and macroorganisms!) can be identified and placed into a phylogenetic tree. Now, even in the time that Woese was first looking at this, it was clear that microbes were literally everywhere, doing literally everything. So as time passed, and the technology grew cheaper and faster, many microbes were placed in the tree. It became clear that there was much more phylogenetic (read, evolutionary) distance between microbes than there is between eukaryotes. It is clear, for example, that the last common ancestor between people and nematodes is much more recent than between Escherichia coli and Methanococcus. In fact, a whole deep evolutionary branch of microbes was identified, called the Archaea.

Archaea look similar to bacteria, but are fundamentally physiologically different. They use ether rather than ester linked lipids in their cell membranes, they used different compounds in their cell walls, and they use fundamentally distinct mechanisms for acquisition of nutrients from the environment. (here is a nice overview of Archaea)

Most Archaea fall into two categories, extremophiles andmethanogens. Extremophiles are microbes found in extreme enviroments, such as sulfur springs and deep sea vents, or in the Dead Sea. They not only tolerate but thrive on very high salt contents, high temperatures, or high pressures. These organisms have been isolated by their lifestyle for eons, and this explains, to some extent, the evolutionary distance. The other physiological type of Archaea, however, methanogens, are not nearly so geographically isolated. In fact, there are methanogenic Archaea in your body right now! The are in seawater, sediment, the intestinal tracts of many animals, and can be said, in biological terms, to be "ubiquitous".

This brings up a conundrum for microbiologists. Typically, when a broad category of microbes is known, there exists within that category a pathogen, that is, a species or strain that causes disease. Of course, microbes that haven't come into contact with other living things for billions of years are unlikely to be pathogenic, but those in our guts and soils may find a good evolutionary strategy in pathogenesis. The consensus, I think, has been that we will eventually find an Archaea that causes disease, but because they are difficult to work with (cultivation and genetics of Archaea is significant challenge, it might take a while.

Well, no more! David Relman at Stanford and his associates have shown that abundant Archaea in the oral cavity is well correlated with periodontitis, which can lead to atherosclerosis, stroke, and other health issues. An excerpt from the press release.

Relman and members of his lab embarked on a comprehensive, controlled study of the archaea found in the subgingival crevice - the deep gap between the gums and teeth - where periodontitis begins. They rigorously analyzed samples from 58 patients' mouths taken by their collaborator, Gary Armitage, DDS, at the UC-San Francisco School of Dentistry, and found that more than one-third of the periodontitis patients had archaea in their diseased subgingival spaces, but nowhere else in their mouths. In addition, the relative abundance of archaea correlated with disease severity. Their findings are published in this week's issue of the Proceedings of the National Academy of Sciences.

"Of course we'd ultimately like to say archaea caused disease, but it's a horse-and-cart problem right now because we haven't shown that the archaea come before the disease," Relman said. In the future, he noted, they will collect specimens repeatedly from the same spot in the subgingival pocket in hopes of being able to pinpoint the moment when the archaea start to increase in number and then determine whether that predicts the later development of the disease.

The paper's first author, Paul Lepp, PhD, research associate in microbiology and immunology, explained that while a third of the periodontitis sufferers harbored archaea, many of the others had high levels of bacteria that - like archaea - consume hydrogen. Hydrogen consumption creates a more hospitable environment for bacteria long known to play a role in gum disease.

The group speculates that archaea may not directly cause periodontal disease. Rather, the microbes may indirectly contribute to it by helping other organisms - in this case, gum-damaging bacteria - grow more productively. Lepp said they are now looking for other hydrogen consumers to test their theory.

"In my mind, it's increasingly clear that the disease may be the result of a community disturbance rather than the presence or absence of a particular organism," Relman said.

Relman also sees a potentially broader side to this research. "Maybe we should look a little harder for evidence of archaea as promoting or causing other diseases. We certainly have them in our bodies and we are exposed to them, so the archaea have the opportunity to cause disease if they are capable of doing so. We haven't been looking for them so we wouldn't know."

As the quote says, the Archaea are probably not the single causative agents of the disease, but probably contribute to a polymicrobial etiology, or as Dr. Relman puts it, community disturbance. Later this week I will post some more material on biofilms, microbial communities, ecology, and disease. Cheers.

Posted 8:23 PM by Paul

A vaccine-disease theory put to rest
I have been interested in the "vaccine as cause of disease" notion for some time, the most immediately relevant ones being thimerosal/autism and MMR/autism. Without getting to deep into those ones, I will say that there is valid cause for concern about the level of thimerosal that was in childhood vaccines (it was removed in 1997, IIRC), but the jury is still out. If it turns out that autism rates fall dramatically over the next 5-10 years, then that would be solid potential evidence (with proper epidemiological analysis, of course). However, one of the more outlandish but persistent theories was the HIV in polio vaccine hypothesis. A recent issue of The Scientist cites a report in Nature putting the final nail in the coffin of this theory. An excerpt;

The final nail is in the coffin for the now largely refuted theory that the human immunodeficiency virus type 1 (HIV-1) crossed into humans as a result of contamination of oral polio vaccine (OPV), according to a new study. In the April 22 Nature, Michael Worobey and colleagues report that the chimpanzees claimed to be the source of simian immunodeficiency virus (SIVcpz) that crossed over actually contain a SIVcpz unrelated to HIV-1.

“Scientifically, this paper spells the end of the OPV theory,” said Edward Holmes, from the University of Oxford, who was not involved in the study.

The OPV/AIDS theory holds that chimpanzees from the Kisangani (previously Stanleyville) area in the Democratic Republic of Congo that were purportedly used in the preparation of OPV transmitted a SIVcpz to humans. Evidence against this has been piling up, first with the absence of SIVcpz or chimpanzee DNA in old OPV stocks and then with data suggesting HIV originated 30 years before the OPV trails.

By the way, while I am glad to find that this theory has been discredited, I in no way mean to imply that anything wrt thimerosal/autism has similarly been discredited. However, it is worth noting that vaccination is the single most effective public health tool in existence, and has been responsible for a tremendous improvement in the quality of life over the last century or so. It is nice to see that good science is winning out in the search for answers in this arena.