Friday, April 19, 2013

Canine Cooties

Yup, they exist. And you've probably got them. No worries, though-- while you're training your dog, your dog's bacteria are training your immune system not to freak out. Read more about it on NPR!

Wednesday, April 3, 2013

Extremophiles in the Belly Button Forest!


Not only are the microbiota in our navels proving to be unique from human to human (i.e., no enterotypes like in the gut), almost 1.5K new species have been discovered there! A recent study conducted by the Belly Button Biodiversity project (BBB) found over 2.5K species in all, some of which included extremophiles that typically live in ice caps, volcanos, or glaciers.

Ah, the microcosm and the macrocosm! More closely connected than you might think....

Thursday, February 28, 2013

THEY'RE ALIVE!!!!!!!!!!

Whoa!!! The push has begun... for viruses to be classified as living organisms!

Why? Because they have immune systems! And by that, I mean they've begun to steal genes that code for restriction enzymes from bacteria. See, the single-celled have a lot on the line. With them, it's all or nothing. Consequently, most of the battles evolution has prepared them to fight are on the molecular level: most bacteria contain genes for enzymes that protect them from an invading virus' foreign DNA by snipping it into pieces. Some viruses have acquired this simple yet effective defense system, found in most prokaryotes as a means of protecting their DNA from being modified.

Let's be friends!

Does that make them living? I mean, they still need host organisms to reproduce... but they certainly do manage to multiply regardless. And the fact that they have immune systems now (whaaaat) means they're evolving. Looks like I need to start reading and writing more about the human virome. It's amazing!

Sadly, no word yet on the vagina virus forest. I will temper my disappointment by listening to Bjork's Virus- apparently, it was inspired in part by her experience with chronic Candida overgrowth!*

tl;dr? Viruses are close to being alive! They're evolving! With prokaryotic immune systems! Inside of us! Bjork is awesome!

*disclaimer: Candida is a yeast, btw/obv. the song is about symbiosis between hosts and parasites (i.e., the microbiota!)

Saturday, February 23, 2013

Malnutrition and the Gut Microbiota

Here's an interesting case of malnourished identical twins who present with two distinct types of malnutrition: one's got kwashiorkor, and the other has marasmus. Kwashiorkor is characterized by edema (swelling) and a distended belly (actually a compromised liver) and associated with protein-poor diets; marasmus is more of a wasting disease associated with starvation. Kwashiorkor is a bit more mysterious as a disorder and difficult to treat, for it doesn't always respond to protein supplementation.

Both brothers had identical genomes and were fed the same diet. Researchers found 13 other cases similar to this one, where one twin had kwashiorkor and the other didn't. By transplanting gut microbes from both healthy and kwashiorkor kids into germ-free mice, they found that "a child with kwashiorkor can effectively transmit their symptoms to a mouse by donating their gut microbes." However, mice with the kwashiorkor microbes were fine when fed a normal diet. Only when they ate a starchy diet low in protein did they begin to develop symptoms.

The sample size was small, but I think this is a really interesting development in our understanding of the disorder. I wouldn't be surprised if we started to see enterotypes associated with kwashiorkor in the next couple of years. Fecal transplantation, rather than dietary supplementation with nutrient-dense food packets, might become the norm. Maybe we'll even see the best of both worlds: calorie rich probiotic supplements with specific bacteria added to confer stability to the microbiota and maximize nutrient absorption. Surprisingly enough, that kind of technology might also be applicable to treating obesity, another metabolic disorder with its own set of associated microbes.

Saturday, February 2, 2013

Where did all these creatures come from!?!?

So, we've established the basic principle that human beings and other animals (with rare exception) are basically walking petri dishes, and that this is a necessary/good thing. When does this all happen, though? Are we born with microbial zoos in our intestines? Does a newborn's mouth have the same variety in bacterial species as that of a five year old?

Not quite. The womb is a pretty sterile place, so fetuses aren't generally privy to the many wonders of having a microbiota. The magic happens at birth: whether C-section or vaginal delivery, a newborn's first exposure to the world outside its mother is also its body's first encounter with microbes. Birth is a pretty important event in microbiota development. Prego ladies' vagina forest populations actually evolve during the course of pregnancy to include milk-digesting species of bacteria. On the way out, newborns ingest some of those microbes and are colonized, giving them a leg up in the whole digesting lactose game.

sweet, sweet victory.

Breastfeeding kids also have a head start in the grand scheme of colonization, as their intestines become home to Bifidobacterium faster than their formula-quaffing buddies. C-section kids tend to have it the worst. First off, that's how scientists breed gnobiotic mice, or mice with limited or no microbiota... so right away, it's kind of a free-for-all in terms of colonization. Instead of harboring vaginal microbiota-associated creatures like Lactobax et al., C-section kiddos' first experience with bacteria tend to be more on the skin microbiota side (think Stapholococcus, etc). Of course, young humans' tendency to put everything in their mouth levels out the playing field eventually-- or does it?

"That looks like it needs to be licked. Please, allow me."

It depends. Genetics plays a big role, but C-section babies may have an increased risk of allergies, autoimmunity and other inflammatory conditions later down the line. Of course, it's not a given that all C-section babies will have issues -- it's just a possible consequence of the all-at-once colonization they're subjected to at birth. Babies who made their way through the vaginal canal tend to have slower, steadier rates of colonization, which is a bit easier on a newly forming immune system. If you think about dogs, there are some you'd call "well-socialized," and others not so much. The ones who weren't introduced to other dogs when they were young can be more aggressive and unsure of how to act around their peers. The same goes for immune systems and bacteria: tolerance of others is an important attribute among the single-celled, as well.

It's also important to realize that as we get older, our microbiotas differentiate more. Newborns generally have the same bacteria EVERYWHERE-- so the microbiota of their genitals, skin, guts, mouths, and other orifices all look about the same in terms of microbial diversity. It's not until everything has the chance to mature that certain kinds of bacteria become more popular in different parts of the body.

So, that's the story. Once we leave our mamas' bellies, our bodies become hosts to all kinds of microbes, which form cliques in different parts of our bodies. In most cases, everybody lives happily ever after.


Saturday, January 26, 2013

Some Budding Yeast I Used To Grow

Pure genius. This video makes me seriously question why we don't replace textbooks with stop-motion animation. Found here.

10 Ways the Human Microbiome* Project Could Change the Future

Check it out! Understanding the nature of the ecosystems within us is changing our whole view of medicine as we know it. Pretty crazy stuff! You might also want to read about the awesomeness that is the Human Microbiome Project. Or, if that's a bit to narrow of a scope for you, take a look at the Earth Microbiome Project.

*This blog post nicely outlines the theoretical difference between a microbiota and a microbiome. Although it's been nearly four years since its publication, people are still confused about which term to use. Personally, I think microbiome has a nicer ring to it, but out of habit and, um, correctness, I use the word microbiota to refer to the populations of microcritters inhabiting our various orifices. Technically, a microbiome is the collection of genomes associated with the little critters in your body. Just sayin'.