Antibiotic Resistance For Everyone!

Everyone should know what antibiotic resistance is. According to the World Health Organization, “this serious threat is no longer a prediction for the future, it is happening right now in every region of the world and has the potential to affect anyone, of any age, in any country.” So, I hope this short “comic” helps make it clear why we should all be thinking about antibiotic use…

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the OTHER microbiotas

The Body’s Ecosystem is a comprehensive – yet short enough to finish in a single sitting – review on current NON-GUT microbiota research, focusing on the mouth, lungs, swimsuit area, maternal microbiome and skin. It’s pretty interesting and pretty pretty – I really liked the accompanying artwork (including two hand-drawn, possibly NSFW genitalia pictures). It also features research from a couple UIdaho labs (m’ alma mater). In other words, a darn good read, in my opinion.
Altogether, the members of the human body’s microbial ecosystem make up anywhere from two to six pounds of a 200-pound adult’s total body weight, according to estimates from the Human Microbiome Project, launched in 2007 by the National Institutes of Health (NIH). The gastrointestinal tract is home to an overwhelming majority of these microbes, and, correspondingly, has attracted the most interest from the research community. But scientists are learning ever more about the microbiomes that inhabit parts of the body outside the gut, and they’re finding that these communities are likely just as important. Strong patterns, along with high diversity and variation across and within individuals, are recurring themes in microbiome research. While surveys of the body’s microbial communities continue, the field is also entering a second stage of inquiry: a quest to understand how the human microbiome promotes health or permits disease.

Just one of the pretty pretties in the article…

Pssst. Your holobiont is showing.

Here’s a sad story: Species A mates with Species B. They succeed in making a Hybrid Baby but their Hybrid Baby dies before it can fully develop. (I warned you it was sad.) Why did that happen? Sure, sometimes two genomes are just too different to successfully coexist – both the stars and the chromosomes must align to make a baby. Other times, as recently reported by Brucker and Bordenstein, the Hybrid Baby’s microbiota is the problem.

I think (or rather Google thinks) this is a Nasonia wasp.

In Nasonia wasps, there are three closely related species that all diverged less than one million years ago: Nasonia vitripennis (who I’m going to refer to as the V wasp), N. giraulti (the G wasp) and N. longicornis (the L wasp). When L and G mate and their LG offspring are mated to other LG offspring, 8% of the males die. When V and G mate and their VG offspring are mated to other VG offspring, 90% of the males die.

The phylogeny of the three Nasonia wasps (left) and the crosses that result in hybrid male lethality.

The phylogeny of the three Nasonia wasps (left) and the crosses that result in hybrid male lethality.

Brucker and Bordenstein hypothesized that microbes were responsible for the hybrid lethality of the the VG hybrids. Through DNA sequencing, they found that the gut microbes of the VGxVG wasps were unlike either parental type (in abundance or diversity), whereas the LGxLG wasps were. So, when a hybrid’s gut microbiota is like one of the parental species, the hybrid males live. When the gut microbiota is unlike a parent, the hybrid males die. They further found this could be boiled down to a change in the single dominant species: whereas a Providencia bacterium was most abundant in both V and G parents, a Proteus bacterium was most abundant in VGxVG wasps.

But that doesn’t conclusively show that microbes are responsible for the hybrid lethality. Brucker and Bordenstein then compare germ-free hyrbids to conventional hybrids – in other words, if we remove the germs (the microbiota, that is), do the hybrids still die? The short answer is no. Under normal conditions, about 80% of the pure Vs and pure Gs survive, whereas only 10% of the VGxVGs survive. Under the germ-free conditions, about 70% of the pure Vs and pure Gs survive and 60% of the VGxVGs survive. That’s a pretty significant increase in living hybrids! And to strengthen the case even more – when the germ-free wasps were fed a mixture of Providencia and Proteus bacteria, the hybrid survival rates went down to about 30%.

The authors perform other experiments for this study that include analysis of wasp genomic loci that were previously linked to hybrid lethality and a transcriptomic analysis, where they find immune genes to be a significant player. However, I’m going to switch gears a little bit and talk about the context the authors frame their discoveries in: the HOLOGENOME concept.

Most evolutionary biologists probably consider the individual as the fundamental unit of natural selection. We think about the genes of one mother or one father being passed on to one descendant. But is this view too constrained? The “hologenome” is all the genomes that belong to the “holobiont” – an organism and all its microbes. The Hologenome Theory of Evolution posits that the holobiont is the fundamental unit of natural selection, not just “the big organism”. Generally speaking, this makes a lot of intuitive sense, I think: we macros are pretty dependent on micros to get our genes to the next generation. But is the reverse true? To be THE fundamental unit of selection, the holobiont must pass its hologenome to its offspring – and I’m not sure this assumption universally holds. Certainly some macro-organisms always pass specific micro-organisms to their offspring (coprophagy in mammals might be a good example). But in most cases, where our microorganisms come from is a mix of vertical transmission (from our parents) and horizontal transmission (from the environment). I just can’t make this distinction make sense with what I think I know about heredity and selection. Natural selection depends on traits that make an organism more fit being passed on to its offspring and if some – or most? – of our microbiota is randomly acquired from the environment, natural selection can’t act on it. On the other hand, it’s very possible reality doesn’t abide by our definitions: perhaps only a few microbial taxa need to be passed directly from parent to offspring and these “founders” get microbial communities off on the right track and the rest of the communities fall into place from the environment.

Regardless – Brucker and Bordenstein pretty conclusively turned that sad story into a science story by showing that in Nasonia wasps, gut microbes play an integral role in hybrid survival. And if the Hologenome Theory of Evolution applies anywhere, I’d say it does here!

A healthy viable Nasonia holobiont (top) and an unhealthy, inviable Nasonia holobiont (bottom). From Brucker and Bordenstein (2013), figure 1B.

The sad story told in pictures: A healthy, viable Nasonia holobiont (top) and an unhealthy, inviable Nasonia holobiont (bottom). From Brucker and Bordenstein (2013), figure 1B.

Brucker, R. M. & Bordenstein, S. R. 2013. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science 341: 667-669.

Bacteria, Circumcision and HIV. Oh my!

Basically every place on our bodies is loaded with bacteria. All of these communities are important (I’ve written about some of the ways before) and more and more research seems to be finding that our microbes play an active role in fighting (or causing) disease.

So maybe it’s obvious that microbes in our swimsuit areas could be involved in sexually transmitted disease. OK, maybe not “obvious” but it may be the case with HIV and the penis microbiota. Did you know that circumcision reduces the rate of HIV transmission to men by 50 – 60%? That’s a pretty significant reduction (no pun intended). There are two major (and non-mutually exclusive) hypotheses as to how circumcision accomplishes this – morphological and bacterial. [SIDENOTE: if you are unfamiliar with the technical aspects of circumcision, I suggest Wikipedia – which has a lot of information but contains an image or two that may not be safe for work – or this Mayo Clinic site.]   

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@NothingInBio at #Evol2013: What we’re presenting

Cecret Lake - Alta Utah

The Evolution 2013 meetings are nearly upon us, and most of the team here at Nothing in Biology Makes Sense! are going to be in Snowbird, Utah for the joint annual meeting of the American Society of Naturalists, the Society of Systematic Biologists, and the Society for the Study of Evolution. Rather than make you hunt through the online program, here’s where we’ll be, and what we’re presenting:

  • Amy will present “The population genetics of rapidly evolving reproductive genes: How much variation should we expect to find?” on Sunday at 9:30, as part of the Evolutionary Genetics and/or Genomics section in Cotton D/Snowbird Center. [program link]
  • Look for some of CJ’s work in a lightning talk by her dissertation advisor, Mark Dybdahl, titled “Identifying the molecular basis of coevolution: merging models and mechanisms” on Monday at 11:45, in Superior B/Cliff Lodge. [program link]
  • Noah will present “What can we learn from sequence-based species discovery? An example using sky island fly communities” on Tuesday at 9:30, as part of the Community Ecology and Evolution section in Peruvian A/Snowbird Center. [program link]
  • Sarah will present “Nature, nurture and the gut microbiota in the brood parasitic Brown-headed Cowbird” on Tuesday at 10:30, as part of the Community Ecology and Evolution section in Peruvian A/Snowbird Center. [program link]
  • Jeremy will present “Evidence for recent adaptation in genome regions associated with ecological traits in Medicago truncatula” on Tuesday at 2:45, as part of the Genetics of Adaptation section in Rendezvous A/Snowbird Center. [program link]

Looks like we’re in for a busy Tuesday! But this year, you won’t have to choose between us.

Hey. Where’d you get that fungus?

Fungi are pretty. And the ones in your home are (hopefully) smaller than this.

I’m very excited to be going to this meeting in June that focuses on the microbiome (i.e., all the living microbes) of our built environment – our homes, work places, sewers, etc. I’m used to thinking about the genetics of much larger living things – like chipmunks – where large non-living things – like rivers – create barriers between populations within a species which allows the populations to evolve independently. It’s been surprisingly difficult for me to apply my background “macro” knowledge to my new “micro” interests. How do different microbial species arise? What is a microbial species, anyway? Specifically restricting my many questions to our homes – what barriers could cause divergence between seemingly connected individuals?

Bacteria abound on our skin and when we come in contact with items in our home, our bacteria are directly transmitted to the surface (think door knobs). Additionally, we shed skin cells – and their bacteria – in our homes resulting in a near constant snow of human-associated (and pet!) bacteria. These facts lead to human occupancy being a source of our indoor microbiome. But bacteria are not the only miniscule things sharing our living spaces. What about other microbes? And now for the question of the day: where does the fungi in your house comes from?

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Roller derby is like giant hug with every girl on the track: swapping microbes due to contact

Often I think we as scientist do a really good job of convincing ourselves that our work is important. However, our research rarely makes a big enough splash that a study is widely accepted by everyone as awesome. Trust me, I have recently tried to excitedly explain to a non scientist at a party why finding the recessive mutation behind disliking cilantro was sooooo cool. It didn’t work…

But this study is so cool that it has already blown up the blogosphere. So much so that I was considering posting on an awesome new review by two of my favorite researchers out of the UK (if you haven’t read this yet you should. Also check out Britt Koskella’s blog… it’s pretty awesome). But being a roller derby skater myself (Rolling Hills Derby Dames), I decided I couldn’t let such an awesome study go by without posting about it.

At the moment, the field of microbial ecology is going from big to huge. This is partially due to the inexpensive availability of genome data making it possible to asses the frequency and species of microbes within all sorts of environments. It could also be due to the immediate applicability to human health, as the composition of the microbiome has been linked to obesity, bacterial vaginosis and potentially irritable bowel syndrome.

These communities vary across different parts of the body and individuals, and change over time. And although we know quite a bit about how pathogens can be passed from person to person due to contact, not much is known about the effect contact has on the microbiome.

Lots of contact. Photo Credits to Scott Butner

Lots of contact.
Photo Credits to Scott Butner

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