The explanation and importance of N50 (or lack there of)

It’s pretty hard to quantify how “good” a genome or transcriptome assembly is. How do you tell you got it right? How complete is it?

One way to determine if it’s a good is N50, which is kind of a confusing concept. It’s not quite the mean, or the median length, but it is well explained in a new post over at the Molecular Ecologist!

And they promise that the importance/misinterpretation of this well used standard for genome/transcriptome assembly will be explained in future posts.

I’m looking forward to the rest of the series!



Now that’s a mouthful

A new study released in the journal Microbiome (it’s open-access!) has concluded that “intimate kissing” that lasts at least 10 seconds can transfer 80,000,000 bacteria between the participants’ mouths. So many microbes sloshing around – it’s a little bit gross, a little bit cool, and 100% science.

NPR wrote a short piece about it here.

A Conversation about High Throughput Sequencing and General Biology

In a recent keynote address at the High Throughput Sequencing for Neuroscience meetings, Sean Eddy from the Howard Hughes Medical Institute addresses the need for biologist to do their own sequence analysis. Although this talk was given by a neuroscience rather than an evolutionary biologist, the conversation is generally applicable to the entire biological community.

Favorite quotes:

“But if you’re a biologist pursuing a hypothesis-driven biological problem, and you’re using using a sequencing-based assay to ask part of your question, generically expecting a bioinformatician in your sequencing core to analyze your data is like handing all your gels over to some guy in the basement who uses a ruler and a lightbox really well.”

“If you learned to implement it in Perl — and you could do this in an afternoon, with a few lines of Perl code — I think you would find yourself endowed with a superpower, like Wonder Woman with her golden lasso of truth, and it’s a superpower that a biologist can use with surprising effectiveness on large data sets.”

Find the whole article here.



What’s lurking on your glabella

Figure 1 from Grice and Segre (2011), showing the distribution of viruses, bacteria, fungi and mites on our skin and where glands and hair follicles originate.

Figure 1 from Grice and Segre (2011), showing the distribution of viruses, bacteria, fungi and mites on our skin and where glands and hair follicles originate.

Our skin is an amazing organ – it keeps our guts in and intruders out. We have an average of 1.8 m2 and this area contains many distinct regions that vary in pH, temperature, moisture, exposure, etc. Your forearm is dry, your cheeks are oily and your elbow crease is considered “moist”. Hair follicles, pores, glands, nails – if we think of our bodies as planets, there are a lot of different habitats. And it turns out our habitats are home to many, many things.

Oh et al. (2014) analyzed 263 samples from 15 human beings at 18 habitats (anatomical skin sites). They were interested in the biogeography of skin – and how it varies between people and across habitats. Do all forearms look alike? Do all “dry” habitats have similar function? It was already known that there are large scale microbial diversity patterns in the skin microbiome. For example, oily sites contain relatively low taxonomic diversity, perhaps because these sites are most selective when it comes to who is able to live there. At the other end of the diversity spectrum are dry sites, which tend to have high diversity.

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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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