…be prepared to take some disinfectants along for the ride.
One thing that is a total geek-out for me is reading about ecology. It’s one of the areas I wish I’d taken more coursework on back in college. At the time, it didn’t much interest me–studying species interactions was boring, and molecular biology was much more interesting. I’ve pretty much flipped 180 degrees on that one. (Well, molecular biology isn’t boring, but it’s moved off its rung as a top interest). My main interest as far as ecology is concerned is microbial ecology–especially of the ecosystem we like to call human beings. I’ve discussed bacterial ecology a bit previously (see here, here, and here, for instance), and a new study is once again making us reconsider what we know about our own personal microbial flora.
A new study published in PNAS examined microbial diversity in an unusual place–the human stomach. Though it’s now accepted that bacteria such as Helicobacter pylori can live in the stomach (and cause ulcers), the image of the stomach is still a pretty sterile place: too hostile to harbor much bacterial diversity.
Well, maybe not. In the new study:
A diverse community of 128 phylotypes was identified, featuring diversity at this site greater than previously described. The majority of sequences were assigned to the Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, andFusobacteria phyla. Ten percent of the phylotypes were previously uncharacterized, including a Deinococcus-related organism, relatives of which have been found in extreme environments but not reported before in humans.
The first few in that list had been identified before by culture, so to be fair, it was known that species besides Helicobacter could live in our stomachs. The problem with using culture to identify bacteria, though, is that there are so many out there that we simply can’t get to grow on agar plates or in nutrient broth–so we’re missing a huge chunk of the diversity out there when we rely on this technique. Therefore, iIn this study, the researchers used 16sRNA sequences–a conserved gene present in all bacteria, and one commonly used in these type of molecular ecology studies. And indeed, as they mention in their discussion, fully half of the types of bacteria they found were ones that had not been cultivated. There is a problem with this method, however. Culture is good in one way: the bacteria must be alive to find them. Regular PCR (polymerase chain reaction) isn’t so discriminatory. Therefore, the possibility exists that some of the bacteria they discovered weren’t growing, or had been killed by the stomach environment, or that they were just there as a result of being ingested in recently eaten food, etc. So, while the findings must be taken with a bit of a grain of salt, the fact that many of the species were found in multiple individuals makes it more likely that they can really live there and aren’t just transiently present. (Future studies can employ different techniques to confirm this).
Going back to the findings, they mention they identified a “Deinococcus-related organism.” As they note, Deinococcus has been previously found in “extreme environments,” including radioactive waste disposal sites (as well as more mundane locations, like animal feces). Indeed, this genus has the distinction of being the most radiation-resistant of vegetative cells. One species, Deinococcus radiodurans in particular is a fascinating organism:
Among the many characteristics of D. radiodurans, a few of the most noteworthy include an extreme resistance to genotoxic chemicals, oxidative damage, high levels of ionizing and ultraviolet radiation, and dehydration. The ability to survive such extreme environments is attributed to D. radiodurans ability to repair damaged chromosomes. It is known that heat, dehydration and radiation causes double-strand breaks in chromosomal DNA. D. radiodurans will repair these chromosome fragments, usually within 12-24 hours, using a two-system process with the latter being the most crucial method….To add to the list of radiation protective traits, D. radiodurans also possess carotenoid pigments [see this post for more on that topic–T], oxygen toxicity defense enzymes, and a distinctive outer membrane. First, carotenoids, which cause red pigmentation, are thought to act as free radical scavengers, thus increasing resistance to DNA damage by hydroxyl radicals. Next, high levels of enzymes such as superoxide dismutase and catalase both play a role in effective defense mechanisms against oxygen toxicity. Finally, a cell wall forming three or more layers with complex outer membrane lipids and a thick peptidoglycan layer containing the amino acid omithine also serves to protect D. radiodurans from lethal doses of radiation.
As they refer to the sequences they found as just “Deinococcus-related,” we don’t currently know if the species they found in the sample stomachs possess any of those properties or not, but it’s certainly worth further investigation to find out. Does that thick cell wall serve to make it more acid-resistant as well? Do any of the novel bacteria types they found play a role in human disease? It’s, um, food for thought. [/rimshot]