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Tag: bacteria

Gut Flora Can Keep Species Apart

I’ve been fascinated by the scientific community’s growing understanding of the key role our gut flora plays in our health and wellbeing.

Interestingly, it seems that for some species, the gut flora may function as the type of reproductive barrier which drives speciation (the process by which new species arise from evolution). From this Nature News article (which is ironically about a Science paper)

Robert Brucker and Seth Bordenstein, biologists at Vanderbilt University in Nashville, Tennessee, have found that the gut bacteria of two recently diverged wasp species act as a living barrier that stops their evolutionary paths from reuniting. The wasps have subtly different collections of gut microbes, and when they cross-breed, the hybrids develop a distorted microbiome that causes their untimely deaths.

Why did this blow my mind? Three reasons:

  1. While I had been aware that our gut bacteria could have impacts on our health, other than traumatic cases like systematic inflammatory response syndrome, I had not been aware that they could directly cause death or serious reproductive impairment.
  2. That gut flora may be partly to blame for the unique health/reproductive problems that hybrids (i.e., like a mule [horse + donkey] or a liger [lion + tiger]) experience! Or, as the article puts it:

    “This is an important and potentially groundbreaking study,” says Jack Werren, an evolutionary geneticist at the University of Rochester in New York. “It reveals that problems in hybrids can be due not just to their genetic make-up, but to interactions between their genes and associated microbes.” The next step, he says, is to “determine which genes are involved in regulating which bacteria, and how this is disrupted in hybrids”.

  3. This also means that gut flora (and hence diet and all the other factors which affect our flora) may be a major driver of evolution & speciation!

Mind blown.

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Mosquitoes are Drawn to Your Skin Bacteria

There’s only two more days left in 2011, so time for my final paper a month post for 2011!

Like with the paper I blogged for last month, this month’s paper (from open access journal PLoS ONE) is yet again about the impact on our health of the bacteria which have decided to call our bodies home. But, instead of the bacteria living in our gut, this month is about the bacteria which live on our skin.

Its been known that the bacteria that live on our skin help give us our particular odors. So, the researchers wondered if the mosquitos responsible for passing malaria (Anopheles) were more or less drawn to different individuals based on the scent that our skin-borne bacteria impart upon us (also, for the record, before you freak out about bacteria on your skin, remember that like the bacteria in your gut, the bacteria on your skin are natural and play a key role in maintaining the health of your skin).

Looking at 48 individuals, they noticed a huge variation in terms of attractiveness to Anopheles mosquitos (measured by seeing how much mosquitos prefer to fly towards a chamber with a particular individual’s skin extract versus a control) which they were able to trace to two things. The first is the amount of bacteria on your skin. As shown in Figure 2 below, is that the more bacteria that you have on your skin (the higher your “log bacterial density”), the more attractive you seem to be to mosquitos (the higher your mean relative attractiveness).

Figure 2

The second thing they noticed was that the type of bacteria also seemed to be correlated with attractiveness to mosquitos. Using DNA sequencing technology, they were able to get a mini-census of what sort of bacteria were present on the skins of the different patients. Sadly, they didn’t show any pretty figures for the analysis they conducted on two common types of bacteria (Staphylococcus and Pseudomonas), but, to quote from the paper:

The abundance of Staphylococcus spp. was 2.62 times higher in the HA [Highly Attractive to mosquitoes] group than in the PA [Poorly Attractive to mosquitoes] group and the abundance of Pseudomonas spp. 3.11 times higher in the PA group than in the HA group.

Using further genetic analyses, they were also able to show a number of other types of bacteria that were correlated with one or the other.

So, what did I think? While I think there’s a lot of interesting data here, I think the story could’ve been tighter. First and foremost, for obvious reasons, correlation does not mean causation. This was not a true controlled experiment – we don’t know for a fact if more/specific types of bacteria cause mosquitos to be drawn to them or if there’s something else that explains both the amount/type of bacteria and the attractiveness of an individual’s skin scent to a mosquito. Secondly, Figure 2 leaves much to be desired in terms of establishing a strong trendline. Yes, if I  squint (and ignore their very leading trendline) I can see a positive correlation – but truth be told, the scatterplot looks like a giant mess, especially if you include the red squares that go with “Not HA or PA”. For a future study, I think it’d be great if they could get around this to show stronger causation with direct experimentation (i.e. extracting the odorants from Staphylococcus and/or Pseudomonas and adding them to a “clean” skin sample, etc)

With that said, I have to applaud the researchers for tackling a fascinating topic by taking a very different angle. I’ve blogged before about papers on dealing with malaria, but the subject matter is usually focused on how to directly kill or impede the parasite (Plasmodium falciparums). This is the first treatment of the “ecology” of malaria – specifically the ecology of the bacteria on your skin! While the authors don’t promise a “cure for malaria”, you can tell they are excited about what they’ve found and the potential to find ways other than killing parasites/mosquitos to help deal with malaria, and I look forward to seeing the other ways that our skin bacteria impact our lives.

(Figure 2 from paper)

Paper: Verhulst et al. “Composition of Human Skin Microbiota Affects Attractiveness to Malaria Mosquitoes.” PLoS ONE 6(12). 17 Nov 2011. doi:10.1371/journal.pone.0028991

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Fat Flora

intestines-microflora

November’s paper was published in Nature in 2006, and covers a topic I’ve become increasingly interested in: the impact of the bacteria that have colonized our bodies  on our health (something I’ve blogged about here and here).

The idea that our bodies are, in some ways, more bacteria than human (there are 10x more gut bacteria – or flora — than human cells on our bodies) and that those bacteria can play a key role on our health is not only mind-blowing, it opens up another potential area for medical/life sciences research and future medicines/treatments.

In the paper, a genetics team from Washington University in St. Louis explored a very basic question: are the gut bacteria from obese individuals different from those from non-obese individuals? To study the question, they performed two types of analyses on a set of mice with a genetic defect leading to an inability of the mice to “feel full” (and hence likely to become obese) and genetically similar mice lacking that defect (the s0-called “wild type” control).

The first was a series of genetic experiments comparing the bacteria found within the gut of obese mice with those from the gut of “wild-type” mice (this sort of comparison is something the field calls metagenomics). In doing so, the researchers noticed a number of key differences in the “genetic fingerprint” of the two sets of gut bacteria, especially in the genes involved in metabolism.

imageBut, what did that mean to the overall health of the animal? To answer that question, the researchers did a number of experiments, two of which I will talk about below. First, they did a very simple chemical analysis (see figure 3b to the left) comparing the “leftover energy” in the waste (aka poop) of the obese mice to the waste of wild-type mice (and, yes, all of this was controlled for the amount of waste/poop). Lo and behold, the obese mice (the white bar) seemed to have gut bacteria which were significantly better at pulling calories out of the food, leaving less “leftover energy”.

imageWhile an interesting result, especially when thinking about some of the causes and effects of obesity, a skeptic might look at that data and say that its inconclusive about the role of gut bacteria in obesity – after all, obese mice could have all sorts of other changes which make them more efficient at pulling energy out of food. To address that, the researchers did a very elegant experiment involving fecal transplant: that’s right, colonize one mouse with the bacteria from another mouse (by transferring poop). The figure to the right (figure 3c) shows the results of the experiment. After two weeks, despite starting out at about the same weight and eating similar amounts of the same food, wild type mice that received bacteria from other wild type mice showed an increase in body fat of about 27%, whereas the wild type mice that received bacteria from the obese mice showed an increase of about 47%! Clearly, gut bacteria in obese mice are playing a key role in calorie uptake!

In terms of areas of improvement, my main complaint about this study is just that it doesn’t go far enough. The paper never gets too deep on what exactly were the bacteria in each sample and we didn’t really get a sense of the real variation: how much do bacteria vary from mouse to mouse? Is it the completely different bacteria? Is it the same bacteria but different numbers? Is it the same bacteria but they’re each functioning differently? Do two obese mice have the same bacteria? What about a mouse that isn’t quite obese but not quite wild-type either? Furthermore, the paper doesn’t show us what happens if an obese mouse has its bacteria replaced with the bacteria from a wild-type mouse. These are all interesting questions that would really help researchers and doctors understand what is happening.

But, despite all of that, this was a very interesting finding and has major implications for doctors and researchers in thinking about how our complicated flora impact and are impacted by our health.

(Image credit) (Figure 3 from the paper)

Paper: Turnbaugh et al., “An obesity-associated gut microbiome with increased capacity for energy harvest.” Nature (444). 21/28 Dec 2006. doi:10.1038/nature05414

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Of Ticks and Bacteria

Another month, another paper to blog.

imageOne of the most fascinating things about studying biology is finding out the numerous techniques living things use to survive through adversity. This month’s paper digs into an alliance between a tick species Ixodes scapularis and a bacterium Anaplasma phagocytophilum to help the pair survive through long winter months.

In places where winters can get extremely cold, people will oftentimes use antifreeze to help protect their car engines. Many cold-blooded animals (ectotherms) survive harsh winters in the same way. They produce antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) which are believed to bind to ice crystals and limit their growth and ability to damage the organism.

As Ixodes ticks are fairly active during winter months and are a known carrier of Anaplasma phagocytophilum which is a cause of human granulocytic anaplasmosis, a team of researchers from Yale Medical decided to investigate whether or not Anaplasma had any impact on the ability of Ixodes to survive cold weather.

Panel A of Figure 1 (below) is a survival curve. It shows what % of ticks which have Anaplasma (in dark black circles) and which don’t (in white circles) survived being placed in –20 degrees (Celsius, of course, not Farenheit: this is science after all!) for a given amount of time. While all the ticks died after 45 minutes, at any given timepoint more ticks with Anaplasma survived than the ticks without. While only ~50% of ticks without Anaplasma survived after ~25 minutes in the cold, over 80% of ticks with the bacterium survived!

image

What could explain this difference? The researchers suspected some sort of antifreeze protein, and, after combing through the tick’s genome, they were able to locate a protein which they called IAFGP which bore a striking resemblance to other antifreeze glycoproteins.  But, was IAFGP the actual antifreeze mechanism which kept Ixodes alive? And did Anaplasma somehow increase its effectiveness?

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Panel C of Figure 4 (above) shows the key findings of the experiments designed to answer those two questions. Along the vertical axis, the researchers measured the amount of IAFGP gene expression (relative to the gene expression of a control, actin [a structural protein which shouldn’t vary]). Along the horizontal, the researchers tested four different temperature states (23, 10, 4, and 0 Celsius) with Ixodes ticks that were carrying Anaplasma (dark circles) and those that were not (white circles). Each individual circle is an individual tick and the line is the average value of all the ticks in the experimental group (the reason its not in the middle is because the vertical axis is a log scale). This sort of chart is one of my favorites, as it packs in a lot of information in one small area but without generating too much noise:

    • The lines get higher the further to the right we get: Translation: when temperatures go down, IAFGP levels go up – as you would expect if IAFGP was an antifreeze coping mechanism for Ixodes. (And if you could see Panel B of Figure 4, you’ll notice that IAFGP levels at 4 Celsius and 0 Celsius are statistically significantly higher than at 23 and 10)
    • The black dots on average are higher than the white dots: Translation: just carrying Anaplasma seems to push Ixodes’s “natural” levels of antifreeze protein up. And, judging from the P value comparisons, the differences we are seeing are statistically significant.

So, it would seem that IAFGP is somehow related to the affect of Anaplasma on Ixodes, but, is that the only link? To test that, the researchers used an experimental technique called RNA interference (RNAi) which allows a researcher to shut down the expression of a particular protein. In this case, the researchers shut down IAFGP to see what would happen.

imageimage

These results are interesting. Although, sadly, the charts (Panels B and F of Figure 5) are not on the same scale and are for different experiments, the numbers are striking. In Panel B, the researchers tested for the survival of ticks which were given a control RNAi (simulates the RNAi process except without what it takes to actually silence IAFGP, white circles) versus those which had IAFGP shut down via RNAi (white triangles). As you can see from the chart, after 25 min at –20 degrees Celsius, the control group hit 50% survival whereas the RNAi group’s survival rate plummeted to only 20%.

The researchers then repeated the experiment with Ixodes ticks which were given control RNAi (black circles) vs. the real thing (black triangles) and then allowed to feed on Anaplasma-infected mice for 48-hours. These ticks were then tested for survival after 50 min at –20 degrees Celsius. As you can see in Panel F, a 75% survival level amongst Anaplasma carrying ticks became less than 50% when IAFGP was shut down with RNAi.

All in all, a very simple positive-control, negative-control experiment showing a pretty clear linkage between Anaplasma, IAFGP gene expression levels, and the ability of Ixodes ticks to survive the cold. However, a few things still bug me about the study and stand out as clear next steps:

    • Panels B and F of Figure 5 are fundamentally different experiments, but presented as comparable. At face value, its hard to tell if IAFGP is the primary mechanism for how Anaplasma alters tick response to the cold. The survival levels of Anaplasma-carrying ticks when IAFGP is shut down is still higher than the survival levels of Anaplasma-free ticks which also undergo the RNAi – but this could be a result of the different experimental conditions (feeding conditions and time). The paper text also reveals that the –20 degrees for 50 min condition was selected because it was supposed to be the point at which there was 50% survival for that particular experimental condition – but clearly, the control group was experiencing 75% survival (and the group with IAFGP shut off was at 50%). Something is off here… but I’m not sure what.
    • Most of this research was conducted on a very abstract level – showing the impact of IAFGP expression levels on cold survival. While the RNAi experiments are very compelling, the lack of clear functional studies is problematic in my mind as I cannot tell from this data if IAFGP is directly responsible for cold survival or linked to other, potentially more important responses to cold.
    • No mechanism was proposed for how Anaplasma increases IAFPG levels in Ixodes. Understanding that would be very powerful and could unveil a whole world of cross-species gene regulation which we were previously unaware of (and could reveal new potential targets for medical treatments of diseases borne by insects).

Regardless of my criticisms, though, this was an interesting study with a very cool result. However, its probably of no comfort to people who have to deal with ticks which can survive cold winter months…

(Image credit – tick) (Figures 1, 4, and 5 from paper)

Paper: Neelakanta, Grisih et al. “Anaplasma phagocytophilum induces Ixodes scapularis ticks to express an antifreeze glycoprotein gene that enhances their survival in the cold.” Journal of Clinical Investigations 120:9, 3179-3190 (Sep 2010) — doi:10.1172/JCI42868

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Collateral damage by mitochondria

Another month, another paper to read and blog about.

This month, I read a paper (HT: my ex-college roommate Eric) by a group from Beth Israel about systemic inflammatory response syndrome (SIRS) following serious injury. SIRS, which is more commonly understood/found as sepsis, happens when the entire body is on high “immune alert.” In the case of sepsis, this is usually due to an infection of some sort. While an immune response may be needed to control an internal infection, SIRS is dangerous because the immune system can cause a great deal of collateral damage, resulting in potentially organ failure and death.

Whereas an infection has a clear link to sepsis, the logic for why injury would cause a similar immune response was less clear. In fact, for years, the best hypothesis from the medical community was that injury would somehow cause the bacteria which naturally live in your gut to appear where they’re not supposed to be. But this explanation was not especially convincing, especially in light of injuries like burns which could still lead to SIRS but which didn’t seem to directly affect gut bacteria.image

Zhang et al, instead of assuming that some type of  endogenous bacteria was being released following injury, came up with an interesting hypothesis: it’s not bacteria which is triggering SIRS, but mitochondria. A first year cell biology student will be able to tell you that mitochondria are the parts of eukaryotic cells (sophisticated cells with nuclei) which are responsible for keeping the cell supplied with energy. A long-standing theory in the life science community (pictured above) is that mitochondria, billions of years ago, were originally bacteria which other, larger bacteria swallowed whole. Over countless rounds of evolution, these smaller bacteria became symbiotic with their “neighbor” and eventually adapted to servicing the larger cell’s energy needs. Despite this evolution, mitochondria have not lost all of their (theorized) bacterial ancestry, and in fact still retain bacteria-like DNA and structures. Zhang et al’s guess was that serious injuries could expose a mitochondria’s hidden bacterial nature to the immune system, and cause the body to trigger SIRS as a response.

Interesting idea, but how do you prove it? The researchers were able to show that 15 major trauma patients with no open wounds or injuries to the gut had thousands of times more mitochondrial DNA  in their bloodstream than non-trauma victims. The researchers were then able to show that this mitochondrial DNA was capable of activating polymorphonuclear neutrophils, some of the body’s key “soldier” cells responsible for causing SIRS.

imageThe figure above shows the result of an experiments illustrating this effect looking at the levels of a protein called p38 MAPK which gets chemically modified into “p-p38” when neutrophils are activated. As you can see in the p-p38 row, adding more mitochondrial DNA (mtDNA, “-” columns) to a sample of neutrophils increases levels of p-p38 (bigger, darker splotch), but adding special DNA which blocks the neutrophil’s mtDNA “detectors” (ODN, “+” columns) seems to lower it again. Comparing this with the control p38 row right underneath shows that the increase in p-p38 is likely due to neutrophil activation from the cells detecting mitochondrial DNA, and not just because the sample had more neutrophils/more p38 (as the splotches in the second row are all roughly the same).

Cool, but does this mean that mitochondrial DNA actually causes a strong immune response outside of a test tube environment? To test this, the researchers injected mitochondrial DNA into rats and ran a full set of screens on them. While the paper showed numerous charts pointing out how the injected rats had strong immune response across multiple organs, the most striking are the pictures below which show a cross-section of a rat’s lungs comparing rats injected with a buffer solution (panel a, “Sham”) and rats injected with mitochondrial DNA (panel b, MTD). The cross-sections are stained with hematoxylin and eosin which highlight the presence of cells. The darker and “thicker” color on the right shows that there are many more cells in the lungs of rats injected with mitochondrial DNA – most likely from neutrophils and other “soldier cells” which have rushed in looking for bacteria to fight.

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Amazing isn’t it? Not only did they provide part of the solution to the puzzle of injury-mediated SIRS (what they used to call “sterile SIRS”), but lent some support to the endosymbiont hypothesis!

Paper: Zhang, Qin et al. “Circulating Mitochondrial DAMPs Cause Inflammatory Responses to Injury.” Nature 464, 104-108 (4 March 2010) – doi:10.1038/nature08780

(Image credit) (Figure 3 and 4 from paper)

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Bet on chance

When people think about strategy, they’re oftentimes looking for that one “silver bullet” which is the 100% correct and best answer. This is despite the fact that it is sometimes 100% valid to use random chance to make a decision.

Well, it turns out that bacteria have figured this out as well, as researchers have recently reported in Nature (HT: Wired Science). The researchers did a fascinating experiment where they forced bacteria to cope with a rapidly changing environment. Normally, you would expect that, if bacteria were forced into a different environment, the population as a whole would “evolve” to acquire the traits that are necessary to survive in that environment. And, at first, this is what the researchers observed – the shifts in environment “drove the successive evolution of novel phenotypes by mutation and selection.”

imageBut, after a while, something very interesting happened – some of the bacterial populations (roughly 1 in 12) “recognized” that they were being put through the ringer and evolved a “gambling” strategy (the researchers called it a “stochastic switching between phenotypic states”) whereby individual bacteria would actually pick a strategy at random! “Knowing” that they were in a constant state of environmental flux with little predictability, these populations of bacteria evolved an ability to have individual bacterium pick random strategies such that genetically identical bacterium would end up with very different traits!

Many people, let alone bacteria, find the idea of a random strategy as a winning one to be counter-intuitive. But, the ability of even the simplest creatures to re-capitulate proves that randomness can not only be effective, but its possibly how the earliest living things coped with a very strange and rapidly changing environment.

(Image credit)

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Snow from Bacteria

image Ice crystals (and sugar and other crystals for that matter) can only form through a process called nucleation. What this means is that snow does not form spontaneously, but instead must have something — could be a speck of dust, could be another ice crystal — from which the crystal can start building on.

The classic “kitchen chemistry” experiment that demonstrates this is the one used to make rock candy — if you boil a totally saturated sugar water solution such that the sugar completely dissolves in the boiled state, and you let the boiled solution cool without disturbing the liquid, no crystals jump out. But, if you stick something into the water (e.g. a popsicle stick), the crystals immediately form on the stick. The stick acts as the nucleator, letting the sugar crystals build onto something.

Tara C. Smith of Aetiology (hat tip: A. Phan) points out that the ice crystals which make up snow often use bacteria as nucleators:

The authors [of the Science paper] were looking at ice nucleators (IN) in snowfall. According to the Science paper, those IN are frequently bacteria, including, as the author notes in the news interview, some pathogens of plants (such as Pseudomonas syringae). Apparently (unbeknownst to me), P. syringae is already used to make fake snow (link), so the fact that it can serve as a seed for precipitation isn’t new. However, the authors note just how important these biological nucleators (including P. syringae) appear to be in the atmosphere:

“The samples analyzed were collected during seasons and in locations (e.g., Antarctica) devoid of deciduous plants, making it likely that the biological IN we observed were transported from long distances and maintained their ice-nucleating activity in the atmosphere… our results indicate that these particles are widely dispersed in the atmosphere, and, if present in clouds, they may have an important role in the initiation of ice formation, especially when minimum cloud temperatures are relatively warm.”

Bacteria… is there anything they *can’t* do?

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