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Belly Button Wonderland
July 5, 2011 11:35 AM   Subscribe

"Out of 53 species [of bacteria found in my belly button], 35 were present in only 10 or fewer other volunteers. And 17 species in my navel didn’t show up in anyone else. In the column for notes in Dunn’s spreadsheet, he’s annotated these species with scientific descriptions like “weird one” and “totally crazy.” Several species I’ve got, such as Marimonas, have only been found in the ocean before. I am particular baffled that I carry a species called Georgenia. Before me, scientists had only found it living in the soil. In Japan." (via Sullivan)
posted by LarryC (74 comments total) 33 users marked this as a favorite

 
Man, I am seriously disappointed that there is no clicky option on that site to send in my own sample. I MUST KNOW.
posted by elizardbits at 11:39 AM on July 5, 2011 [12 favorites]


I have 87 species of bacteria in my belly button, but most of them are just ironic.
posted by It's Raining Florence Henderson at 11:45 AM on July 5, 2011 [2 favorites]


How long should I let the bleach sit in my belly button this evening?
posted by Mick at 11:47 AM on July 5, 2011 [13 favorites]


I'm no microbiologist, but is this really surprising? Are there not at least 53 species of bacteria creeping, crawling, burrowing, mating, feeding, dying and otherwise carrying on within any navel-sized region of the human skin?
posted by swift at 11:50 AM on July 5, 2011 [5 favorites]


When Whitman said that we contain multitudes I do not think this is what he meant.

Or maybe it was....
posted by cmyk at 11:52 AM on July 5, 2011 [11 favorites]


I recall reading a study about swabs taken from folks' backs. They showed dozens of species of microbes, including bacteria, viruses and fungi, many of which had never before been discovered. Amazing to think that all that biodiversity is just sitting right there on our skin.
posted by darkstar at 11:53 AM on July 5, 2011


I've heard of navel-gazing, but this is ridiculous!
posted by codacorolla at 12:00 PM on July 5, 2011 [12 favorites]


"Your bacteria.. and you. Working together to ensure a smoother, softer, healthier skin."
posted by seanmpuckett at 12:04 PM on July 5, 2011


Freemasons rule the country!
posted by griphus at 12:07 PM on July 5, 2011 [5 favorites]


Stupid joke aside, it's amazing how the Japanese microbe was able to get into this dude's belly button. Does anyone know how something like that would even happen?
posted by codacorolla at 12:08 PM on July 5, 2011 [2 favorites]


Belly Button Wonderland

That's the name of my John Mayer cover band.
posted by Faint of Butt at 12:09 PM on July 5, 2011 [9 favorites]


Stupid joke aside, it's amazing how the Japanese microbe was able to get into this dude's belly button. Does anyone know how something like that would even happen?

He was naked on a bean bag chair, watching pirated kung fu movies, eating some sushi and got overzealous in his watching, did a mid-air karate chop and dropped some wasabi on his belly.

This is completely feasible. Wasabi is a root and a lot of it is grown in Japan.
posted by Mister Fabulous at 12:15 PM on July 5, 2011 [5 favorites]


codacorolla: "it's amazing how the Japanese microbe was able to get into this dude's belly button. Does anyone know how something like that would even happen"

Genetic surveying of bacteria varieties is still at a very rudimentary stage. There are likely many common species left to be discovered. For all we know it is a common bellybutton bacteria that was once found in Japanese soil samples.
posted by idiopath at 12:17 PM on July 5, 2011 [10 favorites]


I've heard of navel-gazing, but this is ridiculous!

Just wait 'til they start bean-plating!
posted by The 10th Regiment of Foot at 12:22 PM on July 5, 2011 [1 favorite]


For all we know it is a common bellybutton bacteria that was once found in Japanese soil samples.
And this would explain how it got into a guy in North Carolina's navel how?
posted by tizzie at 12:27 PM on July 5, 2011 [1 favorite]


Virtually none of the "wasabi" consumed in the US (or the UK, or pretty much anywhere else that isn't Japan) has any actual wasabi in it. It's instead composed of the much more common horseradish root. I once went to the only sushi restaurant in Washington DC that claimed that it served the real thing. But on that particular day, the proprietor didn't serve it, because he felt that it didn't withstand the trip from Japan well.

So, anyway, my personal theory for the moment is "Japanese girlfriend". I could be wrong. :)
posted by Citrus at 12:29 PM on July 5, 2011 [3 favorites]


My belly-button is an evolutionary cage match for some of the most lethal bacterial microfauna this world has ever seen. One day they will swarm forth and devour everything, but for the time being, I can still keep them in place with a small bit of lint.

It's not an absence of reasonable hygiene, it's my efforts to keep you all alive, just a little bit longer.
posted by quin at 12:30 PM on July 5, 2011 [2 favorites]


tizzie: "And this would explain how it got into a guy in North Carolina's navel how?"

Probably from someone else's bellybutton? We mostly have the same bacteria in our guts worldwide as well. Maybe someone touched their navel, then touched a door handle.
posted by idiopath at 12:35 PM on July 5, 2011


Two silly points.

- If this becomes commonly measured, people will unquestionably make the number of different bacterial species in their belly-button a point of pride. They will start to get together with the specific goal of gaining an exotic species and increasing their number (compare with birdwatchers). I see these parties where people will lift the front of their shirts, rub the exposed skin with a bacteria-friendly medium, and smoosh their bellies together. Their pale, paunchy, middle-aged bellies.

- “You, my friend, are a wonderland” is a line that will appear in the next Zach Braff film.
posted by benito.strauss at 12:38 PM on July 5, 2011 [4 favorites]


Wildlife of Your Body is the Belly Button Biodiversity website, wherein collections of bacteria grown on agar media plates are displayed, to bring attention to the multitude of microorganisms living on people. (Sadly, they don't do much more than display the plates with growth. There is no indication of what is growing on them.)

"Your navel may well be one of the last biological frontiers. It is time then, to explore."
Why begin with the belly button?

Because no one volunteers when we ask for armpit samples. Because our belly buttons are relatively isolated, a place where microbes are safe. Because everybody has one, its what once connected us to our past. Yet, we barely notice it in our daily lives, to the point that few people actually wash theirs. Which is great for the bacteria! They are well protected, and provide a refuge of our wild nature. We can ask many questions about the microbes on our bodies (what controls which live where, whether the species on men and women are different, whether innies and outies sport different fancies, etc…) but a first step is to simply see who is there, the way the first explorers, upon arriving at new continents, simply wrote home to describe what they found.
I think most of the sampling was done at past live events, so you can't send in cotton swabs of your belly button buddies.
posted by filthy light thief at 12:39 PM on July 5, 2011 [1 favorite]


Anyone thinking back to Sweet Movie and the gallon jug of isopropyl alcohol?
posted by adipocere at 12:40 PM on July 5, 2011


I'm waiting for the underarm deodorant which contains beneficial species in stasis along with nutrients to help them get established-- then the toothpaste.

(And after that the eyedrops.)
posted by jamjam at 12:41 PM on July 5, 2011 [3 favorites]


This Washington Post article does a much better job of conveying the real point of the research.

"The project was conceived as a lighthearted exercise in science communication, but it is making a serious contribution to the understanding of microbial diversity."

"The results reflect our ignorance of microbial diversity, Hulcr suggests: The inhabitants of our navels seem weird because biologists haven’t sampled extensively enough to document the full diversity of microbial life in a variety of habitats. He likens the reactions to the first round of belly button results to the astonishment of the first European explorers seeing African big game"
posted by idiopath at 12:41 PM on July 5, 2011 [3 favorites]


Maybe he bought pants or underwear that came from Japan, were handled by someone with Japanese dirt under their fingernails, or were in a container next to one full of Japanese plants.

I know we'll never know, but I'm having fun thinking up all these hypothetical transmission methods.
posted by subbes at 12:41 PM on July 5, 2011


Did the Japanese soil bacteria have tentacles?
posted by Mister Fabulous at 12:42 PM on July 5, 2011 [1 favorite]


How long before the special "99.9% of bacteria killed" Dettol branded belly button bleach launches on the market?
posted by Augenblick at 12:42 PM on July 5, 2011


subbes: "I know we'll never know"

I am standing firm on my theory that it is a bacteria that all humans have in our bellybuttons, but just happened to first be found in a Japanese soil sample, because that is the first place we happened to look.
posted by idiopath at 12:44 PM on July 5, 2011 [8 favorites]


I once went to the only sushi restaurant in Washington DC that claimed that it served the real thing. But on that particular day, the proprietor didn't serve it, because he felt that it didn't withstand the trip from Japan well.

Must have been all the bacteria. I hope it didn't spread anywhere.
posted by eykal at 12:44 PM on July 5, 2011


Think of all the plants and animals you've ever seen. Now think of all the plants and animals you've identified via genetic testing. Divide the second number by the first and multipy by the number of countries on the Earth.

Did you get a really small number?

That's how it happens.
posted by Kid Charlemagne at 12:53 PM on July 5, 2011 [1 favorite]


Think of all the plants and animals you've ever seen. Now think of all the plants and animals you've identified via genetic testing. Divide the second number by the first and multipy by the number of countries on the Earth.

Did you get a really small number?


No. But then, cataloguing your earth species is what I was sent here to do.
posted by It's Raining Florence Henderson at 12:54 PM on July 5, 2011 [14 favorites]


What do I feed my belly button pets?
posted by TwelveTwo at 12:59 PM on July 5, 2011 [5 favorites]


Belly Button Wonderland Beanbag Plastic World (Ren & Stimpy)
posted by MrFTBN at 1:23 PM on July 5, 2011


" The inhabitants of our navels seem weird because biologists haven’t sampled extensively enough to document the full diversity of microbial life in a variety of habitats. "

The inhabitants of our navels seem weird because they live in our belly buttons. I mean, who does that? WEIRD THINGS. If they weren't weird before they decamped to Innie Manor, they certainly became weird after.
posted by louche mustachio at 1:26 PM on July 5, 2011


Hey, what's up kids? So I just finished watching Friedkin's Bug and . . . [reading] . . . uh oh.
posted by FelliniBlank at 1:32 PM on July 5, 2011 [2 favorites]


This must really be why we invented microscopes: so that we could take navel gazing to a whole new level.
posted by Net Prophet at 1:41 PM on July 5, 2011 [1 favorite]


Another Japanese soil to navel vector: as the nori was drying out it was trampled by some peasant in his wooden clogs. Nori went to sushi, sushi was eaten by hand, hand scratched navel.

Or Japanese soil bacteria were catapulted into the atmosphere by the tsunami, travelled around the world, was collected by a flying plane, ground caterer touched aircraft door, said caterer touched researcher's stomach.

Also, I once read somewhere that each of us has about 10 atoms of Shakespeare in us.
posted by Laotic at 1:49 PM on July 5, 2011


Where does it come from though? I think studying this will help us figure out a lot of interesting things. Gut bacteria is primarily transferred from mother to child, but since the advent of the C-section, it seems like babies are getting more of their gut bacteria elsewhere. It's hard for bacteria to establish itself in the gut after a certain age, but scientists aren't sure what that window is, and anyway, bacteria can steal genes from other bacteria! Normal species of gut bacteria common all over the world were found to have genes that produce porphyranases, enzymes used to digest porphyrans, a carbohydrate type only found in seaweed. But only in Japanese individuals. The only other place porphyranase is found is in marine bacteria, so the hypothesized source was that gut bacteria used horizontal transfer to acquire the genes from bacteria present in seaweed in the diet, but it must have happened some time ago since even unweaned infants had the gene in their bacteria.
posted by melissam at 2:03 PM on July 5, 2011


One of the atoms of Shakespeare wound up in Japan, and another wound up in this guy's navel, thus transmitting bacteria by the Laws of Contagion or Similarity. Or maybe quantum tunneling. Or Lint Theory.
posted by hattifattener at 2:03 PM on July 5, 2011 [1 favorite]


my navel is encrusted with Midi-chlorians
posted by Fupped Duck at 2:55 PM on July 5, 2011


My world is the wild west of biology.

So, I did my Ph.D. dissertation on this topic -- not bacteria on belly buttons, but where bacteria live. Basically, are there separate 'Japanese' and 'German' species of bacteria that act the same way? The answer is becoming quite clear-- the same species appear everywhere where there are identical environments. We are constantly under a rain of different bacteria from every habitat imaginable. There are no (or very, very few) geographic variations in bacteria. So, the fact that there are 'Japanese' bacteria on the author is not very surprising. This is completely different than most plants and animals, where different species have evolved in different areas. (Example: why are there kangaroos only in Austrailia, when they play the same ecological role as deer in the United States?) Bacteria are really good at moving around the globe, even without human help. Other fun facts about this article:

-Only 53 species in his belly button???? I would estimate the number of species would instead be in the hundreds or thousands. I am shocked that it is this low. Probably, this is due to how the study was done (not to fault the scientists! Every technique has limitations.) Sequencing all of the DNA in the sample leads to a drastic underestimation of the diversity because of an initial amplification step (PCR). Culturing these bacteria on petri dishes would be crazy -- only 0.1% to 5% of bacteria have been cultured. Think about this proportion. Imagine a zoo with 99% of species that you have never heard of before, and that are as distantly related to each other as mushrooms and dolphins. (This is probably an underestimation of how different these species are.)

-There are estimates of 1 million to 10 million bacteria species. About 10000 have been named and cultured. Many cultured species have only been officially cultured once. A species might seem to be found in soil from Japan that first time, and no one has tried to culture it from anywhere else. Hence, the author has bacteria from 'Japanese soil'.

-Culturing and naming bacteria is a dying science (possibly overly dramatic but fewer people are trying, and there is less grant money to do it). Instead, the field has turned towards sequencing the entire sample instead (which I bet this study did). We get lots of data this way, and it has uncovered hundreds of new groups in bacteria that we did not know existed. But, people are expecting to learn everything from a sequence of A, T, C, and Gs, instead of interacting with the orgamisms. There is a gold mine of new and exciting biology here that we cannot predict from genomes, if anyone is interested in it.... and if there is money for it.

This is the state of bacterial ecology.
-We just got tools to detect most of these bacteria
-Everytime a new tool or technique is invented, we discover even more diversity and species.
-Diversity is not geographically based, as in plants and animals. Instead, it is environmentally based, so a change of 1 degrees in temperature in otherwise identical habitats might lead to an entire different community of species.
-Everyone is moving to DNA-based techniques, which gets lots of great data (yea!) but at the expense of culture-based methods, where novel bacteria functions can be studied (boo!)
posted by Peter Petridish at 3:14 PM on July 5, 2011 [138 favorites]


There are estimates of 1 million to 10 million bacteria species. About 10000 have been named and cultured. Many cultured species have only been officially cultured once. A species might seem to be found in soil from Japan that first time, and no one has tried to culture it from anywhere else. Hence, the author has bacteria from 'Japanese soil'.

Aha! That explains something about one of my junior high school science projects from ages ago. My project was to take different types of soil samples from around town and try to culture bacteria from those soil samples on petri dishes - and then to identify as many as I could. I got soil samples from 5 places around town, including one where there has been a recent fire (that turned out to have very few bacteria species). As you mention, there were a bazillion different types of bacteria (I could only identify a handful). Thanks to an incompetent biology teacher, I was under the impression that I had somehow messed up the cultures. The teacher let it be known that he only expected about 5-10 species from each dish and that many of them would be common to all. He was right about the latter, but so, so wrong about the former.

Thanks for clearing that up for me!
posted by vidur at 4:12 PM on July 5, 2011 [2 favorites]


So, I did my Ph.D. dissertation on this topic . . .

God I love Metafilter.
posted by LarryC at 4:37 PM on July 5, 2011 [14 favorites]


I wonder what kind of bacteria live in my ----

whoa what the heck

when did I eat peanuts?
posted by Ambrosia Voyeur at 4:40 PM on July 5, 2011 [1 favorite]


This piece of news is about to send o-c self-cleaners into a cleaning binge! Or maybe make them come to terms to the fact we have bacteria even INSIDE us! And that's ok.
posted by elpapacito at 5:03 PM on July 5, 2011


So, I did my Ph.D. dissertation on this topic , by Peter Petridish - Omen Nomen
posted by elpapacito at 5:04 PM on July 5, 2011


[...] Because our belly buttons are relatively isolated, a place where microbes are safe. Because everybody has one, its what once connected us to our past. Yet, we barely notice it in our daily lives, to the point that few people actually wash theirs. [...]

My emphasis. Really?! Okay. Now I really have to know. Hands up everybody who doesn't wash their belly buttons.
posted by likeso at 5:06 PM on July 5, 2011


Really?! Okay. Now I really have to know. Can you see our hands?
posted by It's Raining Florence Henderson at 5:08 PM on July 5, 2011 [1 favorite]


Why, yes.

You mean you can't?
posted by likeso at 5:15 PM on July 5, 2011 [2 favorites]


He didn't get the invite?
/query cabal

posted by likeso at 5:17 PM on July 5, 2011 [1 favorite]


I don't often wash my belly button because putting my finger in there feels so WEIRD. What's that about, anyway?
posted by Ambrosia Voyeur at 5:24 PM on July 5, 2011 [7 favorites]


Stupid joke aside, it's amazing how the Japanese microbe was able to get into this dude's belly button. Does anyone know how something like that would even happen?

The microbe was first identified in Japan. It could live in a bunch of other places just as happily as far as we can tell.
posted by c13 at 5:26 PM on July 5, 2011


Much like spanish or swine flu...
posted by c13 at 5:27 PM on July 5, 2011


posted by Peter Petridish at 6:14 PM on July 5 [20 favorites +] [!]

Eponyrrific!
posted by FelliniBlank at 5:29 PM on July 5, 2011


What's that about, anyway?

It feels totally weird. Maybe because it's a kind of scar tissue? We need someone with anatomical knowledge.

Is there a doctor in the house? Or a Dr. House?
posted by likeso at 5:34 PM on July 5, 2011


This is a wonderful way to get people interested in science. Niches love species. Very cool.

At swift and others, we know very few bacteria. I learned in a bio book (this is definitely out of date info, by the way) that we only know 10,000 species of bacteria. Maybe now it's 100,000, but that's still nothing. We know 15,000 ants. There are definitely more bacteria than ants. It'll take some time to sort it all out.

Petrified Peter, it's only an estimated 1-10 million bacteria? That's so much lower than I expected. Do you know that we have an estimated 1-10 million beetles, and very possibly we have that many (tiny, parasitic) wasps too? We already know 350,000 of the beetles and 100,000 of the wasps and there's no sign of slowing in either.

Second question: can you teach me something about genetic identification? My ecology friends are a) scared of it and b) think it overrepresents species numbers. I don't necessarily believe these things, but it doesn't seem a bit queer at times. Should we really be calling bacteria species, anyway, considering their asexual shenanigans?

I bet those guys are having a blast.
posted by Buckt at 5:51 PM on July 5, 2011


Oompa Loompa doompadee dah,
Giving a swab you will go far.
You will live in happiness too,
Like the guys that thrive in my Omphalos do.
posted by unliteral at 5:53 PM on July 5, 2011 [2 favorites]


Hey biology guys, what exactly makes a species in bacteria land? I always thought that in sexual animals the ability to create offspring that was fertile was the key. (I'm sure you'll laugh at that standard as horribly outdated.) But bacteria reproduce asexually, right? So we can't even use that.
posted by benito.strauss at 6:04 PM on July 5, 2011 [1 favorite]


benito, I actually asked the same question a few above you, but I'll crack at it anyway. I think in bacteria it's mostly about how closely related things are.Literally, how much of their DNA is the same? In most animals, while reproduction is still the gold standard, most species are identified by looks alone (and recently, looks and genetics and sometimes genetics alone). If it's different enough, we'll call it a species. In 50 years some tenured taxonomist who focuses on a single small group will sort the rest out. This leads to things like ole Linnaeus calling male and female ducks different species.

People almost never go to the trouble of trying to breed things or anything like that. Especially not with arthropods, which are most of everything anyway.
posted by Buckt at 6:35 PM on July 5, 2011


This is totally great! Microbiome studies are really ramping up and I'll bet there are going to be a lot of weird and wonderful surprises along the way.

Bonnie Bassler gave a delightful TED talk with lots of great bacteriariffic factoids (more Bassler previously, also previously in this list) including the stunner that there are more bacterial cells in your body than cells of your own organism, IIRC.

There is a lot more to the story about how microbes interact with the human body and influence human health. Lest we forget, our gut flora produce vitamin K....but farther along the intestinal tract than where it could be proximally absorbed....
posted by Sublimity at 6:38 PM on July 5, 2011 [4 favorites]


Because everybody has one, its what once connected us to our past.
Yes but what about the Outies??
posted by etaoin at 6:40 PM on July 5, 2011


Super cool. But the story and this discussion are making my belly button pucker.

Honest, I am totally squicked out by belly buttons. Having to deal with them on three newborns was TORTURE. BAH.
posted by Lulu's Pink Converse at 7:08 PM on July 5, 2011


Sublimity, not only are there more bacterial cells in your body than human cells, they also comprise ~1/5 of your mass. Finally, since each of those puppies has a (somewhat unique) genome, that means only like 1% of the genes in your body codes for being a human.
posted by Buckt at 7:33 PM on July 5, 2011


And they didn't find any salt or ketchup from when he'd been eating chips?
posted by arcticseal at 8:43 PM on July 5, 2011


People in Japan are scratching their heads, wondering how this guy's belly-button bacteria ended up in their soil.
posted by eye of newt at 9:05 PM on July 5, 2011 [4 favorites]


Buckt --

No one has a good estimation of bacteria species, so these estimates of 1-10 million are blind guesses. Geographic isolation is common in ants and beetles so much that many islands in the Pacific have ant species only found on that island. This type of isolation does not appear to occur in bacteria; the thought is that wind carries all bacteria everywhere around the globe, so these is no development of 'Japanese' species versus 'German' species. Hence, the true number of bacteria species may be less than the number of insect species.

Most people are taught about the biological species concept, in which organisms that can produce viable offspring are considered the same species. This works great for animals, just ok for plants (many plant species will form hybrids with other, closely-related species), and horribly for any type of non-obligate sexual species -- any type of asexual species that might have the option of having sex. There are debates on the best speculation concepts for these species.


Currently, bacteria species are determined by percent similarity in a key gene, the 16S ribosomal rna. Scientists use this as a barcode to identify species. Yes, this is quite arbitrary, and no one is happy about it. There is a lack of biological theory to determine what is a species and what explains the following observation -- bacteria genomes are clustered together by similarity. Put another way, there is not a smear of bacteria genomes, in which every possible genome is found. This clustering could be because of natural selection choosing some groups of bacteria over others -- basically, ecology sorting out which bacteria survive in a given habitat. These clusters are still important and need to be named and studied; hence, microbiologists call them species. Because of the role of ecology in this process, this is called an ecological species concept. (Ecology and evolution work really closely on microbial size and time scales.)
posted by Peter Petridish at 12:23 AM on July 6, 2011 [7 favorites]


Jokes on them, I swabbed my bellybutton with bacteria from fifty seven countries and some nutrients a week beforehand. Look for me on the news.
posted by Dillonlikescookies at 4:33 AM on July 6, 2011


Peter Petridish, thanks so much. I was wondering if it was just through genetic assay, and was preparing an objection that setting the cut-off for declaring a species would make it pretty arbitrary. But you do observe clustering! Mind blowing, and I can't wait to see what explanations arise.
posted by benito.strauss at 9:10 AM on July 6, 2011


"Hey biology guys, what exactly makes a species in bacteria land?"

I'm doing my thesis related to this topic! The short answer is: its complicated, but one can only really understand where we are with it by knowing roughly where we've been.

Back in the day bacteria were named according to as close an approximation of the traditional Linnaean system as they could create, carving out what was considered either a separate tree or an absolute basal branch of the tree of life for microbiologists. Naming species worked roughly the same way as it did in macro biology where researchers would look at the physiology of two strains and reason that the two critters were either too similar or roughly different enough. (Whether the two organisms could successfully mate with fertile offspring has only ever really been a rough guide at the macro level, generally not been available to test, and useless for determining higher taxa anyway) This meant things like looking at the cell shape and colony morphology, seeing if it stains differently, and checking out its cardinal temperatures, as well as growing it on different media to see what kinds of sugars it can eat, what salt concentrations it likes, what pH it likes, and plenty more.

This all started to change in the 30s or so with the introduction of bacteriophages, or the viruses of bacteria. With a library of different phages one can test them on large collections of strains to see which bacteria are sensitive to which phages generating a big table. In your excel spreadsheet, or with one's razor back in the day, you can then separate strains into different groups with distinct patterns. There was a significant push to make co-sensitivity to at least some phages the same kind of rough general guide for forming genera that functional reproduction is for species in sexual macro-organisms.*

By far the biggest change in how microbial taxonomy works, and Norman Pace calls it a bigger revolution than Darwin, happened with this paper (PDF) Essentially Carl Woese figured that it was a much better idea to define microbial diversity genomically and so started to sequence 16s RNA subunit DNA from different strains to compare them, he went with that gene because it is essential for all life as we know it and is incredibly resistant to horizontal gene transfer. What he found was the basis for the three domains tree of life (PDF), (wiki). Nowadays to name a new bacteria you've got to at least do something like this paper (PDF), which is a combination of the first and third methods. (Phage typing is still done in some clinically relevant stains where the other options are just that much worse but its a pain in the ass and requires training and a library)

If you guys want to see what its like to isolate a new strain and try to figure out what it is here is a PCR sequence that has not been published made from universal 16s ribosome primers from a strain one of my students isolated from soil.

attgaacgctggcggcaggcctaacacatgcaagtcgagcggatgagaagagcttgctcttcgattcagcggcggacgggtga
gtaatgcctaggaatctgcctggtagtgggggacaacgtttcgaaaggnnnnnnnaccgcatacgtcctacgggagaaagcaggggac
cttcgggccttgcgctatcagatgagcctaggtcggattagctagttggtgaggtaatggctcaccaaggcgacgatccgtaactggtctgag
agggtgatcagtcacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattggacaatgggcgaaagcctga
tccagccatgccgcgtgtgtgaagaaggtcnnnnnnnnnnnnnnnnnnnnnnngaagggcattaacctaatacgttagtgttttga
cgttaccgacagaataagcaccggctaactctgtgccagcagccgcggtaatacagagggtgcaagcgttaatcggaattactgggcgtaa
agcgcgcgtaggtggtttgttaagttggatgtgaaagccccaggctcaacctgggaactgcatccaaaactggcaagctagagtacggtag
agggtggtggaatttcctgtgtagcggtgaaatgcgtagatataggaaggaacaccagtggcgaaggcgaccacctggactgatactgac
actgaggtgcgaaagcgtggggagcaaacaggattagataccctggtagtccacgccgtaaacgatgtcaactagccgttggaatccttga
gattttagtgnnnngctaacgcattaagttgaccgcctggggagtacgnccgcaaggttaaaactcaaatgaattgacgggggcccgcac
aagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaggccttgacatgcagagaactttccagagatggattggtgc
cttcgggaactctgacacaggtgctgcatggctgtcgtcagctcgtgtcgnagatgttgggttaagtcccgtaacgagcgcaacccttgtcct
tagttaccagcacgttatggtgggcactctaaggagactgccggtgacaaaccggaggaaggtggggatgacgtcaagtcatcatggccct
tacggcctgggctacacacgtgctacaatggtcggtacagagggttgccaagccgcgaggtggagctaatctcacaaaaccgatcgtagtc
cggatcgcagtctgcaactcgactgcgtgaagtcggaatcgctagtaatcgcgaatcagaatgtcgcggtgaatacgttcccgggcct


The student had already used Pseudomonas Isolation Agar to select for pseudomonads and grown it on a whole bunch of selective and differential medias to get a pretty good idea of what it was. You can compare it to all of the other 16s ribosomal RNA sequences that have been published as of less than a month ago here, just like they did. Just paste the sequence into the box and hit submit. For reference, about a third of the students who got decent sequences ended up with matches that were as close to one species as another one or more.

If anyone wants me to have this done with soil from your garden or something, and lives in the continental United States as intercontinental/international shipping of soil is a bad plan, I'd be happy to, just MeMail me and I'll send you an address. Some students always forget to bring their own and are usually much happier with a unique sample from someplace weird.

*This is also where folks started to regret putting Escerichia, Klebsiella, and Shigella into separate genera as a phage isolated against E. coli is almost as likely to infect a strain of Shigella as another strain of E. coli and we now know that they really are much more different within themselves than among themselves.
posted by Blasdelb at 10:07 AM on July 6, 2011 [16 favorites]


Thanks so much, Blasdelb. If you're feeling bored I've got some follow-ups.

- Do you even bother trying to construct/infer higher levels than genera for bacteria, or are Family, Order, Class etc. mostly meaningless for them?

- In that 16s sequence you posted, what does 'n' stand for?

- Am I weird for finding the Woese paper sweetly old-school? All the collected data was published in the paper, in a table that took up two pages.
posted by benito.strauss at 2:29 PM on July 6, 2011


I've got the day off!

-YES! If anything they tend to be more meaningful in assigning external difference and internal similarity, though how to arrange them and what that all means turns into decades long pitched battles. For some context check out the links in the box on the right of the wikipedia article for E. coli, which is nicely filled in being that its for E. coli. Here is a scan of the tree of life how I see it that I made when drunk at a party a little while ago*. I see the endosymbiotic events that shaped life as we know it as being more than worth distorting some of the objectivity of statistical genomics in showing the truth, but most disagree. This is one of the most widely published ones.

-"n" stands for nucleotide which could mean an A, T G, or C and represents an error in the sequencing. It is still information that is valuable to the mystical algorithms that programs use.

-I hope not! Though I totally see how it would feel that way. For example, I only really interact with say astronomy at the level of review (Someone big in the specific field writing up a summary of current work for people outside of that specific field) if that and don't ever interact with the data if only because I wouldn't understand it anyway even if I love astronomy. Big research articles that change everything are still being published all the time, they're just, for most people, worth glancing over until the review of the work and what follows is written.

*Note the beer stains as well as the references in the comments
posted by Blasdelb at 4:57 PM on July 6, 2011 [1 favorite]


The thing that struck me about the Woese article is that it looked like the bulk of the results generated were published in the body of the article (unless I'm reading it wrong -- I'm not an academic). The last bio article I looked at (it was less than five years old) had a 40 page .pdf annex to contain all the tables and diagrams.

I think you missed the link on your beer-stained tree of life. If you're ever in Boston I will contribute the beer required to make a fresh copy.
posted by benito.strauss at 7:18 PM on July 6, 2011


Awesome conversation, benito and Blasdelb. Also, thanks for the response Petriarch. I didn't expect to hear about the 'clustering,' either, although from an evolutionary stance it makes perfect sense. Things might tend to have a number of similar genes and functions. If one of those genes changes to modify the function, then the other genes might rapidly change as it better matches the new niche, a la punctuated equilibrium. Coool. Stuff.
posted by Buckt at 8:07 PM on July 6, 2011


Whoops, thats embarrassing, this is the link, I've always wanted more excuses to visit New England.

Easily the biggest paper of the last century was only a page long, no bullshit, no fluff, mountains of snark, and complicated issues to kvetch about. Come to think about it, someone should probably make it a post.
posted by Blasdelb at 9:14 PM on July 6, 2011 [3 favorites]


as excellent beer and science filled excuses are the best kind
posted by Blasdelb at 1:08 AM on July 7, 2011


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