Category Archives: Microbial coevolution

Perhaps it’s obvious in retrospect, but microbes rule the planet. They shape who we are, what we do, what infects us, and what we eat. And they do that for most other organisms too. The story of how important microbes are is only in its early chapters, so I will post here as I learn more about the role of microbes – and their coevolutionary interactions with us and other organisms – in shaping life on this planet.

Guest post by Sean Meaden

Do we need to watch what we spray? A summary of our recent review on the potential dangers of phage biopesticides.

Guest post by Sean Meaden, PhD student at University of Exeter working on phage-Pseudomonas syringae-plant host interactions.

It seems barely a week goes by without mention of the dangers of antibiotic resistance in popular news stories. Just last month the WHO called antibiotic resistance a ‘global threat’ in a well-publicized press release [1]. Whilst this might be slightly good news for those of us soon to be looking for post-doc positions in the field of microbiology, it certainly isn’t good for public health. The need for alternatives is pressing and it seems there just isn’t the financial incentive for large pharma companies to develop new drugs. Better stewardship of the compounds we already use is crucial, but so is exploring alternative options and exploiting our knowledge of microbial ecology and evolution.

One alternative strategy, known as ‘phage therapy,’ is the utilization of viruses that infect bacteria to decrease density of specific bacterial populations. In nature, phages have been estimated to kill as much as 20% of global bacterial populations each day [2]. As many reviews have noted, the use of phages is nothing new and has been a successful ongoing industry in Georgia and the former Soviet Union since the 1920s [3]. The aim of phage therapy is to find or create a phage that specifically infects a pathogenic strain of bacteria, culture it in the lab and turn it into a useable end product that can be ingested, applied topically or sprayed onto crops (as a biopesticide).

Phage cocktail production

Typical production of phage biopesticide. Reprinted from Meaden S and Koskella B (2013) Exploring the risks of phage application in the environment. Front. Microbiol. 4:358. doi: 10.3389/fmicb.2013.00358

The potential benefits of phage therapy are huge. However, given the negative consequences of improperly managed antibiotic use, we should be careful not to make the same mistakes again. It strikes me that a common theme in the phage therapy literature is ‘It’s OK, phages are naturally occurring,’ implying (in my mind at least) ‘What can go wrong?’ The same argument could have been made about antibiotics. After all, they too are naturally occurring compounds produced for microbial battles among themselves, and are likely to have been around for billions of years [4]. In our recent review [5] we explored the possible negative consequences of phage therapy to assess whether we are likely to make the same mistakes as we did with our often poor stewardship of antibiotics. Below is my summary of the main arguments we outline in the paper. On the whole I think the need for alternatives to antibiotics is huge, and by being prudent with our use of phages as a replacement (or synergistic treatment), and critically evaluating negative consequences, we will be better placed to use phage therapy successfully.

1) Implications of evolved resistance. This fairly obvious point is probably most comparable to antibiotic usage. We know that phages and bacteria undergo arms races of resistance and counter-resistance [6]. If the pathogens that are causing disease evolve resistance to the phages that we use as therapeutic agents, our cure becomes defunct and we have to go back to the drawing board. Finding new infective phages shouldn’t be too hard, but the process of turning them into a usable product that has passed regulatory hurdles is likely to be lengthy. This is a parallel problem to antibiotic production- there must be novel antibiotic compounds in the soil under our feet, but turning them into a lifesaving drug is the tricky part. A solution proposed by a group working on burn patients in Belgium is to create a reactive, cottage-industry style phage therapy centre that quickly screens for phage infectivity from a ready-made library, rather than a single product for widespread consumption (and most desirable to big pharma) [7]. Whilst this approach is great for pathogens that are readily culturable in the lab it might be more difficult for less tractable organisms.

2) Phage mediated attenuation of bacterial resistance. This argument seems to pop out of the literature as ‘OK, the bacteria might evolve resistance, but that won’t matter because resistance is costly so their virulence will be attenuated’. In a few cases this certainly does seem to be the case, for example Filippov et al. found reduced virulence of Yersinia pestis in mice (in other words mouse plague was less deadly when phage resistance had evolved; 8). In other cases, phage resistance actually had the opposite effect, making Pseudomonas aeruginosa more virulent in vitro, and rightly highlighting the need for caution in selecting phages for treatment [9]. Thus, for this argument to be used informatively we need much more data from a variety of systems and under more natural conditions or full-scale trials.

3) Agricultural cross-over. A consistent criticism of global policy on antibiotic stewardship is the use of antibiotics in agriculture. The addition of antibiotics at sub-therapeutic levels is great for feed efficiency and increasing yields. Given the increasing demand for protein in the global diet this issue isn’t trivial. However, it is likely that such practices increase levels of antibiotic resistance, and the bi-directional exchange of resistance genes from farm to community should be worrying. If phage therapy becomes more commonplace in agricultural settings could we see the same effect? Managed carefully, cross-resistance between agricultural and clinical phage therapeutics shouldn’t be a problem, especially given the typically (but not exclusively) high host specificity of phages. But I do think it’s worth acknowledging the potential for interference in order to prevent repeating mistakes of the past.

4) Horizontal gene flow from phage application. Phages are so good at transferring genes among bacterial cells that we use them in the lab to do just that. It’s certain that this horizontal exchange goes on in the environment, so we must ask: if we pump out unnaturally high volumes of phages (especially those with broader host ranges) into the environment, how likely are these phages to move genes around. This is especially problematic when the genes being swapped encode antibiotic resistance, toxins, or virulence factors. In this case, our attempt at a cure could actually make things much worse. We know that phage-mediated gene-transfer has played a part in cholera epidemics [10] and we should be careful about facilitating the spread of other unwanted bacterial traits.

5) Impacts on natural communities. The importance of a ‘healthy’ microbiome is constantly espoused (so much so that Jonathan Eisen has produced an award for ‘Overselling the Microbiome;’ 11). Although the direct effects of a healthy microbiota are still predominantly correlational, minimizing the disruption to a community whilst removing a pathogenic species must surely be the ultimate goal. Phages could hold great potential in this regard as they tend to be fairly specific in their host range (so could act more like snipers) relative to antibiotics (which act more like indiscriminate hand-grenades). On the other hand, artificially high volumes of phages could have unexpected effects on microbial processes, particularly in an agricultural environment. To my knowledge the effects of adding high titres of phages to microbial communities in the environment remains unexplored.

6)   Unpredictability of infection kinetics. This issue is an exciting one- the pioneer of phage therapy, Felix d’Herelle, is spuriously quoted as stating that immunity is contagious as well as the cure [12]. He might have been wrong about the biology but the premise that the cure is transmissible certainly seems possible with replicating phages. The downside is that it makes it hard to predict the persistence of phages in the environment. Unlike an antibiotic with a known half-life, a phage therapy product could continue to persist and replicate in the environment indefinitely. Even at low densities this raises an ethical question of something being uncontainable.

Recently, the ethical imperative of using phage therapy has been stated [13] and there is clearly a need for alternative strategies to antibiotic drugs. All of the concerns raised in our review are addressable and shouldn’t preclude the use of phage therapy in a clinical or agricultural setting. Moreover, all of the questions we have raised are readily answerable given the advances of microbial genomics over the last decade. We just need more data!!

If this summary piqued your interest, check out the whole article here, and open access: http://journal.frontiersin.org/Journal/10.3389/fmicb.2013.00358/full

References:

  1. http://www.who.int/drugresistance/documents/surveillancereport/en/
  2. Suttle, C. A. 1994 The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28, 237–43.
  3. Kutateladze, M. and Adamia, R. 2008 Phage therapy experience at the Eliava Institute. Med Mal Infect 38, 426–430.
  4. D’Costa, V. M. et al. 2011 Antibiotic resistance is ancient. Nature 477: 457–461.
  5. Meaden, S., & Koskella, B. (2013). Exploring the risks of phage application in the environment Frontiers in Microbiology, 4 DOI: 10.3389/fmicb.2013.00358
  6. Buckling, A. and Rainey, P.B. 2002. Antagonistic coevolution between a bacterium and a bacteriophage. Proc. R. Soc. Lond. Ser. B, 269: 931–936
  7. Pirnay, J.-P. et al. 2011. The phage therapy paradigm: pret-a-porter or sur-mesure? Pharmaceutical Research 28:934–937.
  8. Filippov, A. A. et al. 2011 Bacteriophage-resistant mutants in Yersinia pestis: identification of phage receptors and attenuation for mice. PLoS ONE 6, e25486
  9. Hosseinidoust, Z. et al 2013 Evolution of Pseudomonas aeruginosa virulence as a result of phage predation. Appl Environ Microbiol 79: 6110–6116
  10. Waldor, M. K. and Mekalanos, J. J. 1996 Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272:1910–1914.
  11. http://phylogenomics.blogspot.co.uk/2014/04/overselling-microbiome-award.html
  12. d’Herelle, F. 1924 Immunity in Natural Infectious Disease, Williams & Wilkins
  13. Verbeken, G. et al. 2014 Taking bacteriophage therapy seriously: a moral argument. BioMed Research Int. 2014: Article ID 621316, 8 pages.

Guest post over at Dynamic Ecology

Jeremy Fox, Meghan Duffy and Brian McGill recently invited me to write a guest post over at their fabulous blog, Dynamic Ecology.

If you’re interested in why I think microcosm experiments are so amazingly cool, go check out the post here.

Not drawn to scale.

Not drawn to scale.

Also, later this week I will finally be posting my review/recap of this year’s EEID meetings (first in London and then at Penn State). They were great!

Why I dropped out of psychology and became an evolutionary biologist, Part II: Evolution is happening, and it matters.

At about the same time that I was getting very frustrated by my psychology courses, I was taking an Evolution lab course (taught by the ingenious Janis Antonovics) where the theories I had been reading about first began to take shape. It was my first taste of why evolution mattered to me and also of how I could test it experimentally – yes, with controls!

chuck

Happy birthday to Charles Darwin. I wonder if he could have imagined how useful his work would be?

During one of our modules (or “labs” as I called them before becoming a Brit), Janis had each of us sample and test our own gut flora for antibiotic resistance. I won’t go into the details of how we did this (it is kind of gross), but instead explain why. When antibiotics are prescribed to kill off an infection caused by one pesky microbe, the entire microbial community is perturbed. What we are doing is imposing very strong selection against all sensitive bacteria in our body, and therefore selection for any bacteria that are able to survive. During treatment, replicating bacterial cells that do not carry resistance to the antibiotic you just took will be killed (want to know how?). This means you are left with much fewer, and a lower diversity of microbes; many of which positively influence your health. This was recently demonstrated using a multi-omic approach [1], where the researchers followed the microbial dynamics of a single patient taking antibiotics (for a nice synthesis of the work see here). They show that, as predicted, microbial diversity in the gut drops during the course of treatment and does not necessarily recover to its previous state after treatment.

One common way bacteria survive antibiotic treatment is by halting reproduction. This works because many antibiotics affect only replicating cells, and therefore any cells in the population that are just hanging about in stationary phase, the so-called “persister cells,” are temporarily resistant. However, just to emphasize how little we know about one of the most important evolutionary phenomena affecting human health: bacteria break even this rule. A recent study out this month in Science [2] has found that a bacterium closely related to the one that causes tuberculosis is able to reproduce, albeit slowly, in the presence of an antiobiotic to which it is not “resistant” (according to the current definition). The ability of this bacterial population to persist in the face of antibiotics is because identically genetic cells are in fact diverse in their behavior; specifically in production of an enzyme with which the antibiotic interacts. This means that some cells, just by chance, are able to survive and reproduce but that their future generations of offspring are just as likely to be killed by the antibiotic as any other cell in the population. In other words, in the absence of heritable genetic change, the population is unable to respond to selection and will not evolve resistance (at least using this mechanism). Unfortunately, this also means that the population will be able to persist and, if it gets lucky, a mutation conferring heritable resistance will pop up. A similar result, albeit without the amazing microfluidics, was found in 1997 [3].

If this result holds true for many more bacterial species, it would suggest yet another way in which our current army of antibiotics are likely to fail. So what does this mean in terms of finishing your course of antibiotics like all good children should? Well, we don’t know. We need data. I could rant about this, but instead I will refer you to a great talk by one of the experts, Andrew Read.

Okay, so evolution happens every time you take your antibiotics. But what about those microbes that aren’t picking fights with their human hosts? Are natural bacterial populations evolving as rapidly? Of course they are! I recently monitored changes in bacterial and bacteriophage populations living within horse chestnut tress in a park near Oxford and found that the bacteria were rapidly evolving resistance against their local phages, and the phages were responding by overcoming this resistance – all within the course of a single season (Paper in review now, so stay tuned). There are also many many examples of bacteria that have evolved incredible adaptations to changing or hostile environments. For example, bacteria are now known to thrive under the Antarctic ice, in thermal vents reaching up to 235°F, and in heavy metal environments. The resilience and adaptability of bacteria is staggering, and we are now learning how bacterial evolution can work in our favor, for example by turning toxic compounds into pure gold, storing our data, protecting against the spread of dengue fever, or making our food.

Rapid bacterial evolution also has major consequences for the fitness of macroscopic organisms with which they interact; our microbiota have important roles in our health (as I blogged about previously), plants associated with salt- and drought-tolerant Rhizobia can increase their fitness under harsh conditions, and emerging disease is often associated with bacterial acquisition of toxins or virulence genes. For example, the strain of Pseudomonas syringae that causes bleeding canker of horse chestnut trees acquired genes that allow it to thrive on woody tissue, presumably allowing for the host shift and subsequent spread.

Much of the great evidence for rapid evolution comes from microbes because of their short generation times and large population sizes, but this certainly does not mean the patterns we observe are restricted to microscopic beings. Indeed, one need look no further than the size of our watermelons and dogs to realize the speed at which an eukaryotic population can response to selection – especially when it is imposed artificially. During my PhD research with Curt Lively, I was able to show that trematode parasites can impose strong selection on populations of their snail hosts over only a few generations in the lab. We evolved experimental snail populations in tanks with and without the sterilizing trematodes and found that, over the five year experiment, trematodes adapted to specifically infect the most common snail genotypes in the tanks and subsequently drove the frequency of these types down [4]. And evidence for such rapid responses during experimental evolution is building. Rowan Barrett recently showed that stickleback populations can evolve cold-tolerance within three generations and Anurag Agrawal demonstrated rapid evolution (over only four years) of flowering time in experimental field populations that were affected by or protected from insect herbivores.

So whether it’s microbes, plants, or animals, there is no question as to whether populations evolve in response to the environment they are in and the species with which they are interacting. Evolution happened, is happening, and will continue to happen. I study evolutionary processes because I believe an understanding of how populations respond to selection is the only way we will be able to produce enough food, fight disease, and protect natural populations.

1 Pérez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, Otto W, Rojo D, Bargiela R, von Bergen M, Neulinger SC, Däumer C, Heinsen FA, Latorre A, Barbas C, Seifert J, Dos Santos VM, Ott SJ, Ferrer M, & Moya A (2012). Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut PMID: 23236009

2Wakamoto Y, Dhar N, Chait R, Schneider K, Signorino-Gelo F, Leibler S, & McKinney JD (2013). Dynamic persistence of antibiotic-stressed mycobacteria. Science (New York, N.Y.), 339 (6115), 91-5 PMID: 23288538

3 Thompson, J. K., et al. “Mutations to antibiotic resistance occur during the stationary phase in Lactobacillus plantarum ATCC 8014.” Microbiology 143.6 (1997): 1941-1949.

4 Koskella, B. and C.M. Lively. 2009. Evidence for negative frequency-dependent selection during experimental coevolution of a freshwater snail and a sterilizing trematode. Evolution, 63(9): 2213-2221.

Your body is a microbeland

Some people think of their bodies as a temple, others as a wonderland. Me, I think of mine as a petri dish. I am a long-term experiment on microbial community dynamics – with plenty of drama! Love stories, betrayal, war and peace. You name it; it’s going on in here somewhere.

We all think we’re special – and now science is corroborating that idea. My microbes are just as unique as I am. The bacterial community in my nasopharynx is vastly different from that of my gut, which is vastly different from that of my skin, which is vastly different from that of my mouth… and so on1. Furthermore, each of these microbial communities (called ‘microbiota’) is highly dissimilar to that of the person next to me. Although the current evidence suggests that human microbiota fall into three major types (termed ‘enterotypes’)2, the variation in exact microbial abundance and diversity among individuals is staggering; even identical twins harbor significantly different gut microbes than one another3!

I don’t always get along well with my microbiota. There are the odd days, like yesterday, where my microbial populations wreak havoc on my digestive system. Then others, where they cause me to break out in spots4. And still others, where they lend a helpful hand to intruding pathogens by conferring their acquired antibiotic resistances1. But most of the time, I am very happy with my pet microbes. They are constantly working away at alleviating my allergies5, protecting me from infection6, stabilizing my mood7, helping me repel or attract others, including pesky mosquitoes8, and allowing me to make the most of what I eat(even playing a key role in weight gain10).

I have never been particularly germ-conscious. As an evolutionary biologist, I know that a little immigration is good for the body population, fueling the fire of natural selection with a bit more additive genetic variation. So I don’t clean my counters with bleach, and I do let my dog share my bed. There are occasional consequences (I refer again to my illness yesterday), but for the most part I have a fairly healthy immune system. My philosophy is thanks in part to George Carlin’s sermon (http://www.youtube.com/watch?v=-Y-yH_Qyipc), and thanks in part to my studies. But it is also common sense – we are the result of millions of years of evolution. If we were hypersensitive to every bacterium that landed on our kitchen counters, natural selection would have taken us out a long time ago.

I may be weird, but the fact that I am more microbe than me – 10 times more! – is my motivation for taking good care of myself. A sense of responsibility for the health and welfare of all of those microbial cells that are working with me every day to keep us going. They are why I eat right, exercise (occasionally), drink in moderation, and get enough sleep.

So the next time you are scrubbing away at your sinks or dosing yourself with anti-microbials, take a moment to think about all of those commensal bacteria working away to make you… well, you. (and, on that note, keep them to yourself!)

Some food for thought:

1Ecology drives gene exchange within human microbiota: http://www.nature.com/nature/journal/v480/n7376/full/nature10571.html
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, & Alm EJ (2011). Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480 (7376), 241-4 PMID: 22037308

2Our microbiota fall into three main categories (with lots of variation!): http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html

3Microbiota of identical twins: http://www.pnas.org/content/107/16/7503.short

4Have acne? Use phage: http://www.businessweek.com/news/2012-10-10/good-viruses-will-fight-acne-as-1915-discovery-is-revived

5A potential link between microbiome diversity and allergies: http://www.pnas.org/content/early/2012/05/01/1205624109.abstract

6It seems the microbes on our skin help warn us about pathogen attack: http://www.nature.com/news/the-skin-s-secret-surveillance-system-1.11075

7Mind-altering microorganisms: http://www.nature.com/nrn/journal/v13/n10/abs/nrn3346.html

8Human skin microbiota affects attractiveness to malaria mosquitoes: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028991

 9A nice review on the role of our gut microbes and their recent evolution: http://www.annualreviews.org/doi/pdf/10.1146/annurev-micro-090110-102830

10A core gut microbiome in obese and lean twins: http://www.nature.com/nature/journal/v457/n7228/abs/nature07540.html

And a great piece about our microbiome’s in the Economist: http://www.economist.com/node/21560523