It’s an exciting time for ecologists who study microbes. DNA sequencing has grown so cheap and fast that they can run around identifying bacteria living just about anywhere they can reach with a cotton swab. Turns out, bacteria are everywhere, even in the cleanest houses, and scientists are starting to wonder: do those bacteria in the home reflect the bacteria that live inside the inhabitants?
And if so, can they travel from person to person?
A small insight into this question came at one of the presentations at the International Human Microbiome Congress (covered by New Scientist in a short piece here). James Scott, who studies molecular genetics at the University of Toronto, reported that the gut microbes of babies, as found in their poop, were also in the dust in the babies’ homes. It’s not clear whether this means that bacteria in the dust are colonizing the babies or vice versa—or both—but it’s still something of a surprise. Gut microbes don’t seem like the sort to thrive outside the body, as they tend to require an oxygen-free environment. But maybe the gut bacteria in the dust are in a dormant form, waiting to be absorbed into a new gut before flowering into life again.
The corollary of this finding is that perhaps the other inhabitants of that home might pick up those microbes. Your gut microbiome, thus, would be closer to your roommates’ than to a stranger’s, something that would be easy to test with modern sequencing techniques. There’s also room to speculate that as we learn more about the microbiome’s relationship to disease, the swapping of microbes within a household could reveal an infectious component to illnesses that we don’t currently think of that way. It’s just a speculation now, but an interesting one.
The scientists’ blood-sucking accomplices
What’s the News: Scientists searching for new and endangered species in tropical highlands face a Catch 22. Spotting shy creatures is the order of the day, but bushwhacking through forests is anything but subtle. How can you get a sense of what’s there when you can’t get close enough to see it?
Environmental DNA analysis is one of the answers—checking out the DNA in soil, for instance, can reveal what pooped there recently in amazing detail. But for a technique that can reach beyond a given patch of ground, scientists have been investigating using leeches from streamwater as their source of DNA. It turns out that blood from their last meal sticks around in their gut for a good long time, and they happen to be partial to human blood too—which makes them, in the scientists’ words, “easy to collect.” A new paper gives proof that the technique is valuable: blood in leeches collected from a Vietnamese rainforest reveals the presence of six mammalian species, some of them rare.
For years, the cutting edge technology for DNA sequencing has involved mincing DNA up into tiny pieces. Even as sequencing has gotten faster and cheaper, each new process has relied on chopping the DNA up to be analyzed, because, although this process can introduce errors in the readout and can be expensive, it was still the best we had. Now, technology unveiled at a recent conference in Florida could mean that the age of slicing and dicing is over, thanks to something called a nanopore.
A nanopore is a ring of proteins, made by a bacterium, through which DNA can be threaded, like a string through a bead. In the method of DNA sequencing just debuted by Oxford Nanopore Technologies, long, intact strands of DNA are shunted through nanopores on a chip, and the electrical conductivity of each nucleic acid as it comes through the pore lets scientists tell which DNA “letter” it is—A, T, G, or C. A long strand of DNA analyzed this way, importantly, isn’t destroyed, so it can be reanalyzed, and errors introduced in processes that use chopping are also avoided. Using such basic physical laws to deduce a DNA sequence is a simple, elegant solution to a tough problem. That’s perhaps why nanopore sequencing methods have attracted some significant investment in recent years: the UN National Human Genome Research Institute had, by 2008, given $40 million to groups pursuing nanopore sequencing.
Insight into long life is one of the new prize’s goals.
In 2006, the Genomics X Prize competition was announced: $10 million for sequencing 100 human genomes in 10 days for $10,000 apiece, to be kicked off in 2013. The idea was to spur innovation in technology by asking the (currently) impossible, the hallmark of the X Prize Foundation.
But while sequencing has gotten cheap, it hasn’t gotten all that much faster in the last five years, and none of the eight teams who signed up have ever gotten to the point where such a short time span could be feasible. So, Archon and Medco, the two companies funding the competition, have revamped the requirements. This week they’ve announced the new, improved Genomics X prize: $10 million for sequencing 100 human genomes in 30 days—but for $1,000 apiece. (Currently, getting your genome sequenced commercially runs about $5000 at the cheapest.) The new version of the competition, which will kick off on January 3, 2013, also has clearer standards for judging: the genomes have to be 98 percent complete and have no more than one error per million nucleotides.
Sequencing the DNA in a scoop of dirt can tell scientists what creatures are living nearby, a new study using soil from safari parks shows, and the amount of DNA present can even tell how many individuals of each species there are, which could allow field biologists to get preliminary surveys of species. But though the team managed to identify nearly all the species they had expected in the parks, from wildebeest to elephants, they are still addressing how to take samples that accurately represent the area’s biodiversity—one would have to avoid elephant latrines or wildebeest sleeping areas, for instance—and there is the additional problem that rare or small creatures, like insects, might easily be missed. That said, it’s still an unusual and interesting way to take a look at an area’s inhabitants without actually tracking them down.
Read more at Scientific American.
Image courtesy of malcyzk / flickr
If bacteria can’t grow in a Petri dish, sequencing them is difficult.
What’s the News: Want the genome of a bacterium you found in your belly button? Or, for that matter, of a bacterium producing a promising new antibiotic? Well, unless you can get it to thrive in a Petri dish and create a billion sister cells for analysis, you’re out of luck.
But sequencing the genomes of notoriously finicky bacteria, like those on skin, could be on the horizon with a new procedure that bypasses the Petri dish step. Pairing a new algorithm with an earlier technique, scientists from the Venter Institute and their collaborators can now get all that information from a single cell.
What’s the News: Scientists have been rooting around in the rice genome for years, and the same goes for wheat. But now the long-recalcitrant potato genome has finally been sequenced. Time for a celebration? Perhaps, but biologists can’t rest for long: in addition to the just-published genome, there are still three more to sequence in each commercial potato.