Posts tagged: bacteria

Germ DIY: Infecting yourself for fun and profit (updated)

A while back I said I had “microbiomes on the brain”. I meant that metaphorically. But now, two surgeons at UC Davis are in big trouble for deliberately putting bacteria in their patients’ brains.

Thing is, they say the patients requested it. “If I come down with a glioblastoma, I will demand that it be done on myself,” one of the surgeons told the Sacramento Bee.

Glioblastoma is a nasty, nasty brain cancer.  According to the SacBee article – I haven’t been able to track down any other information on this therapy – there are accounts of glioblastoma patients surviving years after contracting infections, leading to a hypothesis that introducing bacteria into head wounds might be an effective therapy. [UPDATE: lots and lots of info here, both on the UC Davis situation and on the idea of treating cancer with bacteria]

How did the UC Davis patients fare? One died of sepsis (infection), one died from the tumor but also had sepsis, and one lived for at least ten months after the treatment, with a reduction in the tumor but also suffering a wound infection. The surgeons then asked for permission from an ethics committee to infect five more patients.

The university said no way, launched an investigation, and ultimately told the surgeons not to do any more experimentation on humans. The surgeons say they weren’t experimenting, just applying an admittedly rare treatment.

Going rogue: DIY germ transfers

Bacterial transfers occupy a weird gray area in medicine They’re not exactly a drug, or a tissue, or a device (the categories the FDA considers for regulation). You can get bacteria from anywhere, especially if the source you’re looking for is the human microbiome: everyone you know is a potential donor.

Fecal transplants, which have a 90% success rate at curing debilitating C. diff infections, are so cheap, easy, and effective that they should be a first treatment, not a last resort; but few doctors offer them. One is working on a home enema protocol so sufferers can DIY the treatment with their donor (often a spouse or close relative).

It’s not so different from the situation with sperm donors: almost half the earth’s population possesses the little swimmers, and can churn them out on demand,  so why should the expense and red tape of a sperm bank be necessary for conception without sex? Controversially, it’s not; a lesbian couple can meet their donor for coffee and perform the transfer in a two-step process simple enough it can be done in a Starbucks bathroom.With sources of human microbiota all around us, there’s no need to limit probiotic treatments and research to species you can grow industrially and stuff into a pill, that must then make their way through the patient’s digestive tract before eventually finding their home (although, miraculously, that often works.) Why not try a more direct route?

Babies born by c-section miss out on their mothers’ vaginal microbiota, possibly leading to health problems. Probiotics and even fecal transplants have been tried, with mixed success, but the simple technique of smearing mom’s vaginal secretions onto the baby “has been proposed … but to date there are no published studies.”

Who knows what other bacterial “transplants” might be therapeutically important? For skin infections, vaginal infections, perhaps even transfer of mouth bacteria to prevent cavities? I’m not endorsing brain bacteria, but I bet there are some promising disease treatments growing in you, and on you, right now.

Highlights from #germchat

hashtagI had a fun time today on twitter #germchat discussing the human microbiome. Check out a Storify transcript here.  Here are some of my favorite things I learned:

How do oral probiotics affect health in places other than the gut? According to @DrJamesVersalov, they provide molecules that circulate through the bloodstream and “act like hormones”: vitamins, amino acids, etc.

Is it bad to be sanitizing our hands all the time? @DrJamesVersalov says handwashing avoids spreading infections, but established skin microbiota survives washing. @JATetro adds that sanitizer (as tested in his lab) actually does kill all the bacteria.

Is our idea of beneficial probiotics skewed toward certain species? @JATetro says most are fermenters (as found in kimchee, kombucha, sauerkraut) and their byproducts, like sugars and amino acids, are “buffers” between bugs and our immune system. @peterdilaura  agrees with my suspicion that there is “big potential impact from low abundant harder-to-culture bugs”. @JATetro says he found a microbe in the subway that he was asked to culture for probiotic potential.

Here’s an intriguing idea: @peterdilaura suggests we get “sub-therapeutic dosing” of antibiotics from food.

The concentration of probiotics matters, says @JATetro, and it may not be as simple as eating yogurt, as in the case of Danone’s health claims.

We are only 10% us: where did that count come from, that established bacterial cells outnumber our own cells 10-to-one? @bernat_olle says to check out Savage, 1977.

The nasty critters that live in a komodo dragon’s mouth

Imagine not knowing whether an animal is venomous.

I don’t mean some shadowy creature that bit you and then slithered off into the night before you could identify it. I mean a well-known species, represented in zoos worldwide, beloved of young zoology nerds (disclaimer: yes, I was one of those children). I mean the komodo dragon.

Komodo Dragon
I won’t keep you waiting. The current thinking is that yes, the komodo is venomous, based on studies done just a few years ago by Australian venom expert Bryan Fry. The previous theory had been that the komodo just has a nasty bacteria-filled bite: toxic microbes grow on bits of rotten meat in the lizard’s teeth, causing deadly infections.What brings this to mind, today: a Nature News article on Rob Knight, who collects and sequences microbiomes from all corners of the world. (Heard of the Earth Microbiome Project?) The lede finds Knight sampling komodo dragon spit; ingeniously, he just holds the swab while the lizard gets curious and licks it. Then he takes samples from its head, belly, and enclosure.

He’s planning on comparing the microbiomes of komodos in zoos and in the wild, looking at questions relating to the animals’ own survival – although I wonder if the work will confirm (or refute) any of the old factoids about deadly bacteria in komodo saliva.

The komodo’s saliva “teems with over 50 strains of bacteria,” says a typical fact sheet. It’s not that impressive a number – really, my or your mouth has more than that. Actually, the komodo’s probably does, too. The relevant study here is Aerobic salivary bacteria in wild and captive Komodo dragons (2002), which cultured 57 species; cultures don’t always give the full picture, as we know, and the researchers say their techniques disregarded any anaerobic species.

Pasteurella multocida on Columbia Horse Blood AgarThose researchers injected komodo saliva into mice (and plain saline into controls) and waited a few days to see which mice died. Then they cultured blood from the dead or dying mice, and found a bug called Pasteurella multocida, which the komodo dragons happened to have antibodies to.

Case closed? Well, Pasteurella is found in a variety of animals, where it is sometimes a part of normal respiratory flora. And, as the authors of a human oral microbiome paper wrote,  “the oral cavity is an open system where exogenous microorganisms from the environment are continually introduced by eating, drinking, and breathing.” Their point was that it’s hard to get a good count of species, but the same caveat can apply to the search for a single toxic bacterium. That’s what Fry thinks the deal was with Pasteurella – it was a bystander in the swampy water the komodo hunts in.

Tracking down the animal’s venom glands was a beautifully multifaceted approach, involving field observations like the one above, as well as anatomy studies (he put a komodo through an MRI machine to look for venom glands), modeling of the skull based on CT scans (to show that it doesn’t have a powerful enough bite to kill on its own – later confirmed by another researcher’s tests with live dragons) and tests of the contents of the venom glands (revealing two proteins that dilate the prey’s blood vessels and keep its blood from clotting). Phylogenetic studies also show that komodo dragons – plus a lot of other reptile species that you wouldn’t expect, like iguanas – come from venom-producing ancestors.

Microbiomes with surprising effects

I’ve got microbiomes on the brain lately. It all started with this Scientific American article I read while half-watching my kid run amok in the library with a toy lawnmower – but I’m getting ahead of myself.

That’s “microbiome” in the sense of an ecosystem. Living on you, and in you. When I teach nutrition I tell my students about how poop is 50% bacteria, and 90% of the cells in your body are bacterial. “We are only ten percent us,” I say, although I still don’t know where that number comes from.

The fascinating thing is, these bacteria (and other microbes) aren’t just hitchhiking; they interact with our own body functions in ways we are only just beginning to understand. Take that SciAm article – it blew my mind with a few paragraphs about Helicobacter pylori.

Pathogens to commensals

Helicobacter pyloriThis is the bacterium that causes stomach ulcers; it gets its name because it is actually corkscrew-shaped, and burrows into our stomach lining. Just a few decades ago, ulcers were thought to be caused by stress and bad food. Then, in the 1980s, we found that H. pylori was the cause. However, the plot thickens: 80% of people who have H. pylori living inside them don’t have a problem with ulcers.

But it gets even better: not only is H. pylori a normal part of gut flora, it seems to help our body regulate acid levels in the stomach. AND, it regulates the amount of ghrelin (think of it as a hunger hormone) released after meals. People who have taken antibiotics to kill off H. pylori have trouble with both aspects; they tend to gain weight after treatment, presumably because their stomachs don’t send a strong signal to the brain to stop being hungry.

Like the other, more familiar ecosystems in our world, the human microbiome is changing with time and technology. According to that article, 80% of people used to have H. pylori; now only 6% of children have it, presumably because of heavy use of antibiotics.

I’m not saying they cause obesity, but once we have a better understanding of our microbiomes, we may look back on antibiotics as barbaric: effective, but at what cost?

The same article mentioned a bacterium that seems to regulate inflammation via T-cells (causing less inflammation in our bodies, which we think is a good thing). That bacteria help us digest our food is old news. What else do our microbes do for us?

Why we’re learning all this now

The journey of H. pylori (in human minds) seems kind of classic: first unknown, then considered a pathogen, then a harmless bystander, now a good guy. I think we’ll see a lot of other microbes follow its path. We used to think E. coli was the predominant species in the human intestine; then we realized it’s just the one that grows best in the lab. Swab some poop on a petri dish, and the E. coli takes over while its buddies die off.

That’s why a metagenomic approach is turning up such neat findings lately: no need to culture the critters in the lab, just throw it all in a blender and sort out the DNA. A 2010 publication described almost 30,000 proteins that were previously unknown. The most recent census from the Human Microbiome Project supposedly shows that there are 8 million genes in the microbiome, to add to the 22,000 or so that we can properly call human.

(Is it just me, or are scientists and reporters a little over-sensitive about our “small” number of genes? Hey, we do more alternative splicing than other organisms, ok? We have bacteria helping us out so we get to count all of those! Can’t we just be happy with what we’ve got? Can’t we come to terms with the idea that, just maybe, 22,000 is plenty?)

But you don’t have to take my word for it…

Anyway, if this stuff sounds interesting, the Human Microbiome Project website is a big ol candy jar, full of projects like “Metagenomic study of the human skin microbiome associated with acne” and ” The human virome in children and its relationship to febrile illness“. I’ll be busy over here for a while, OK?

If this is your first time trying to wrap your head around this stuff, maybe you’d like to start with a TED talk: try Jonathan Eisen talking about how the microbiome is like an organ we never noticed we had. “We are a teeming ecosystem,” he says.  You could also read this week’s newsy articles that seem shocked that “Even healthy humans” can host 10,000 microbe species. (Even? I’d be willing to bet that we have fewer species when we’re sick. Just my guess though.)

Now, when we talk about microbes, that usually means bacteria. (If you hear anybody saying “bugs,” that doesn’t mean insects, like I thought when my dad described yogurt as being “full of bugs” when I was a kid … I stopped eating yogurt for years). Microbes can include fungi and viruses, and yes, there is a population of fungus among us, and even a normal healthy virome. That virome article talks about the friendly viruses as preying on the bacteria inside us, which surely happens – if we are an ecosystem, it would have to be multi-layered, like the rainforest – but why not friendly viruses that hop into and out of our own, human cells?

There’s lots more to explore here. I’ll leave you with just a few of the things I stumbled across this week:

News bits: Bacteria are team players; your brain-controlling helmet is on its way.


Great news, everybody! The brain can be stimulated, without implanting electrodes, by a new ultrasound technique. Who is working on this? Military scientists! Why? So they can make brain-controlling helmets. Um, OK!


Antibiotic-resistant bacteria send chemical signals to their neighbors that help them fight the antibiotic’s effects. Some are calling it altruism. As a player of a team sport, I know the feeling. If you’re the strongest blocker in the pack, you can’t do everything yourself; you communicate with your teammates, tell them where to go and what to do, because you’re nothing without your team. Heck, you can’t even block if you’re 20 feet out of the pack. Unless you’re the, uh, jammer bacterium. (Clearly more research is needed on microbial roller derby.)


5 myths about the female brain: Empathy, multitasking, playing with dolls, sucking at math – Do women have an advantage in those areas? Not that we know of. These excerpts come from a new book called Delusions of Gender. I haven’t read it, but one review says: “Instead of a ‘male brain’ and a ‘female brain,’ Fine gives us a glimpse of plastic, mutable minds that are continuously influenced by cultural assumptions about gender.”

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