The talk was very well attended, a testament to the interest in this new field. Dr. Gordon, as seems to be the custom nowadays, introduced the concept that we are more bacterial than eukaryotic, at least by sheer number of cells. I think he mentioned we are 90% microbial and 10% “us” and referred to the collective organism as a supra-organism.

The largest diversity of microorganisms living in our body are located in our gastrointestinal tract. Dr. Gordon alluded to the fact that the modern world with the ability to travel from one place to another, the exposure to many different kinds of foods and the 60 years in which humans have been regularly using antibiotics can really affect the diversity of bacteria in our gut.

2 out of the 100 phyla of bacteria known dominate. These are the firmicutes and the bacteroidetes. There are 8 others in smaller proportion. There is at least one Archaeon. There might be more phages than bacteria in our gut!

There are many unknowns like what is the geography lengthwise and depthwise. What things affect diversity? How robust are the communities to new bacteria introduced and how much functional redundancy is there in the supra-organism?

Are these bacteria passed down from parents to kids? It seems from his work with mice that yes. Siblings share a much more common bacterial signature.

Testing feces in humans shows bacterial diversity is controlled by at least two effects which are the legacy effect (bacteria are passed down by families, so you can track these movements) and the host-gut environment (shown by moving zebrafish microbes into germfree mice and moving mouse bacteria into germfree zebrafish. In the first case the mouse had a mouselike microbiome even though very different proportions were originally introduced. The zebrafish also had very zebrafish-like microbiomes even though they had mouse bacteria put into them!).

Another interesting vignette I remember from the talk dealt with the Archaeon, a methane consuming bacteria, that lives in the gut. It somehow interacts with B. theta and a microbial food web is set up. B. theta alters its foraging habits in the presence of the Archaeon. I think B. theta consumes a completely different set of polysaccharides from mucus creating a different environment in the host. The application? Instead of trying to alter the delicate balance of firmicutes and bacteroidetes, Gordon suggested that in the absence of the Archaeon the body would not have the same metabolites to pick up and could make a big difference in weight loss! I think the details are a bit fuzzy but I’m sure you can read more about it on his site!

From this week’s Nature and Nature alert:

1) The platypus genome was just published. It was very interesting to see that the genome in a way reflected the major physical characteristics of the platypus. There were conserved genome regions that are similar to reptiles, birds and mammals. This isn’t something I’m normally too interested in, as I don’t have the resources to look at all this data or the knowledge to reasonably interpret it, but platypuses are just so weird, I thought it would be worth mentioning.

2) An interesting PNAS article dealing with bacterial symbionts of surgeonfish that belong to the Epulopiscium spp. The unique characteristic that really distinguishes these bacteria is their size, with individual bacterium measuring up to 600 microns (not the record holder though, that distinction goes to the “Sulfur Pearl of Namibia,” aka Thiomargarita namibiensis). This PNAS article focuses on how polyploidy, that is having multiple copies of the genome within the same organism (we’re normally diploid because we have two sets of chromosomes), correlates with the size of the bacterium.

The size of these Epulopiscium spp. is particularly interesting because bacteria are normally believed to be small due to the constraints imposed by nutrition and metabolism on organisms that don’t have specialized pathways to better exploit the environment, causing them to be smaller in order to maximize diffusion to the organism by increasing their surface to volume ratio. The authors propose that perhaps the many copies of the genome can allow compartmentalization and different functions on different regions of the cell, making it more capable of responding to complexity like eukaryotes do.

This article from Zhen et al. in Cellular Microbiology is talking about IGTP (Interferon-gamma-inducible GTPase) being able to inhibit apoptosis by signaling through FAK, which once it’s phosphorylated can bind to the SH2 domain of PI3K, then activating the PI3K/Akt pathway causing NFKB mediated expression of caspase inhibitors, etc. Interesting as I think of interferon-gamma being present in most proinflammatory contexts, so are cells actively trying not to apoptose in these environments?

I am so utterly tired.  Every 15-20 minutes… beep, beep, beep.  Growing bacteria, incubating this or that, shaking bugs, checking the autoclave, washing blots, etc.  Tuesdays on a gpt week are tough.  I was so tired I couldn’t even think of multitasking!  The very thought was incapacitating, and I had to do things one step at a time!

Anyway, on better news, I think my Southern blots finally worked.  ECL kits are so much easier to use than the Pierce North2South!

Well this post has seen the light of day, perhaps not so much for its relevance to microbes (oops), but because it’s something I have to deal with. Anyway, if you are familiar with Big Blue, you’ll understand exactly how this works. Otherwise it’s convoluted and I normally have to recur to many diagrams to get it across. The gist of it is a rodent that has had bacteriophage genomes knocked in at a certain intron. The bacteriophage are not actively used by the rodent but are present in every cell of its body. It’s believed that the phage genome can be used as a reporter of the background levels of mutations perceived by the rodent.

The DNA from the phage can be separated from the mouse DNA and it carries 2 sets of reporters. The first set, consisting of the gpt gene [similar to the HPRT gene in humans] and CAT cassette, is on a plasmid transfected into E. coli [microbes, yay!]. Since gpt incorporates the toxic 6-thioguanine, only bacteria with a mutated gpt gene survive, so it’s useful for looking at small mutations that inactivate the gene. There’s also a set of genes, red/gam, used by bacteriophage to transfect bacteria. E. coli previoulsy transfected by another phage target red/gam products and prevent the entrance of other phages. If the DNA recovered from the mouse suffered a large deletion that excised red/gam then plaques form in a lawn of E. coli telling you about the existence of mutants (The ability to measure larger deletions is gpt delta’s claim to fame). If you are really interested in how this works and what people do with it, here’s a review written by Nohmi himself.

People who really buy into these models use them to determine how carcinogenic compounds are when given to a mouse. People who don’t buy into these models, raise a whole host of problems concerning the relevance of untranscribed, unrepaired, highly methylated, phage DNA in telling us about the levels of DNA damage in the host.

Anyway, I won’t get into that right now, but I actually wrote this entry to mention an interesting paper, where the treatment was given as smaller doses over several days (as opposed to the normal bolus approach) and the gpt delta mice were looked at 1- and 4-weeks after the end of treatment. The normal spike in MF seen is pretty normal when you give a putative chemical carcinogen to a rodent, but the interesting thing was the follow-up where they saw that at 4-weeks the levels were back to normal. It was surprising to see the follow-up as it’s not common practice in many of these gpt delta rodent/chemical carcinogenesis experiments. I had the naive impression that the spike in MF set up the mice for a lots of mutations, but maybe a lot are repaired or occur in cells that are going to be destroyed anyway.

PS here’s Nohmi’s official site with protocols

The paper showed how ischemia-reperfusion injury can activate PA. The temporary loss of oxygen to an organ [ischemia] causes some damage, but after prolonged loss of oxygen, reoxygenation can be more damaging as reactive oxygen species [ROS] are released [reperfusion injury]. During ischemia (and a lot of other processes, including some considered oncogenic), hypoxia-inducible factors (HIF) is released setting of a chain of events. As a brief summary, HIF-1a causes the release of lots of adenosine (I think by breaking down ATP), which is supposed to help protect the epithelium by making tight junctions tighter and not allowing neutrophils to get by (source of ROS which may be damaging the host?). It’s been reported that PA-I lectin in addition to its binding of galactose, could bind N-acyl homoserine lactones (quorum sensing molecules) and adenine. Patel et al. demonstrated that adenosine is processed by PA using an adenosine deaminase, causing the activation of PA-I lectin.

Being my first entry, I got a bit carried away with the length. The main take home message from the discussion was that bacteria are capable of not only reacting to the consequences of host responses but that they can at times respond to the mediators/signals used by the body to activate the responses. This gives them a slight edge as they can anticipate and adapt to the host’s next move.

There are interesting reviews by Mark Lyte (who coined the words “microbial endocrinology” for this reemerging field [reemerging according to Moselio Schaechter from "Small Things Considered"]) or Vanessa Sperandio (who coined “inter-kingdom signaling“). They’ve separately worked a lot on how catecholamines (epinephrine and norepinephrine AKA aderenaline and noradrenaline) can induce growth, adhesion, etc. on E. coli. There are cool papers out there about how IL-2, IL-1B, TNFa and others are being shown to have an effect on many bugs like E. coli, P. aeruginosa, Vibrio, etc. so check out the links below.

Global Effects of the Cell-to-Cell Signaling Molecules Autoinducer-2, Autoinducer-3, and Epinephrine in a luxS Mutant of Enterohemorrhagic Escherichia coli

Catecholamine induced growth of gram negative bacteria

Enhancement of growth of virulent strains of Escherichia coli by IL-1

IL-2 and GM-CSF stimulate growth of a virulent strain of Escherichia coli

Modulation of Bacterial Growth by TNFa In Vitro and In Vivo

Blocking catecholamine-induced growth in E. coli O157:H7, Salmonella enterica and Yersinia enterocolitica