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!

Extremophiles in the Belly Button Forest!

WHOA.

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....

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!)

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.

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.

Hooray!

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'.

Seasons in the (Vaginal) Microbiota

Do me a favor and click on that picture. It's one of the first images I've ever seen that illustrates the ("average") human microbiota! I'm really loving the Lactobacilli section-- check out all that pink! One drawback of this graphic is that it doesn't show changes and cycles of local microbiota-- though to be honest, a 3D animation would be necessary to depict that AND the variety of species listed. It's true: like all ecosystems, the local microbiotas in our skin, mouth, gut, and genitals go through seasons.

It's crazy to think of how our local microbiotas change as we age, let alone the cycles they go through on a regular basis. The best example I can give is of the vagina and its veritable forest of Lactobacilli. A healthy vaginal microbiota is associated with a lot of Lactobax, but most women experience an increase of anaerobic bacteria during their periods. These anaerobic bacteria aren't exaaactly pathogenic, but many are associated with bacterial vaginosis and that weird fishy smell (good morning, ladies!). The chart below shows the changes in the microbiota of two ladies' vaginas at different points in their menstrual cycles.

I'd be interested to know how the vag forest would be affected by, or whether it might have an effect on, irregular periods. On a side note, I found this seed supplement regimen today that's supposed to help balance hormones for ladies with irregular cycles. It's simple and seems really effective.

Anyway, here's the gem of a study I got the above chart from. Happy Saturday!

Classy Colonization

Living the good life-- the well-colonized one, that is. Ginger kefir with lime and plenty of organisms.

On Epigenetics

When I was in seventh grade, I learned that our genes can't be changed, ever. Once we go from gamete to fertilized egg, that's it. Stuck for life. They even mentioned some poor schmuck who thought that genetic evolution due to behaviors (i.e., changes that didn't involve actual gene mutations) could be passed onto later generations. Ha! Hahaha!

Fast forward four years. I'm in high school now, and my AP Bio teacher is telling me that yeah, we have these genes, but some of them can get turned on and off, kinda like light switches. That the genes themselves are recipes, and the ribosome is the kitchen-- but who controls which meals are created, and when?

I didn't learn the word epigenetics until college, but by the time I did, I understood exactly what it meant. Epigenetics is the concept of the chef in the cooking metaphor-- it's the factors that control gene expression. Things like histone modification and DNA methylation, markers that promote or downregulate the use of those recipes. These physical modifications that surround DNA send messages like, "hey guys, let's, like, never transcribe this POKEMON gene." (Yes, there was a cancer gene that was called POKEMON... until Nintendo threatened to sue.)

The ways in which epigenetics manifests, or has the potential to do so, are nuts. Things like grandchildren of famine survivors being more susceptible to diabetes; chemical exposure resulting in disorders that persist through generations; and maybe even sexual preference.

Epigenetics is interesting to me because it's super relevant to the interactions between the microbiota and the human immune system. Certain microbes have the ability to flip genes on and off (for better or for worse) in susceptible individuals. Sometimes this is good: many people take probiotic supplements because they promote anti-inflammatory pathways and a tolerant immune system. On the other hand, some pathogenic bugs cause inflammation and sickness, even cancer.

It also makes our diet seem that much more important, like a drug we feed ourselves constantly. I think of the many stories I've heard of autoimmunity or cancer being reversed or vastly tempered through dietary modifications*, and I am amazed. It's both heartening and terrifying to know that we have the power to influence our biological makeup, simply by adjusting our everyday habits. It puts the onus on the individual to act in her best interests: eat right for your body, sleep enough, exercise, brush your teefs. Sometimes it isn't enough, but sometimes that's all it takes. Epigenetics is the bridge connecting the duality of nature vs. nurture; it's a clear demonstration of the capability of our environment to influence our phenotype (genetic output) and those of our progeny.

Personally, I think RuPaul says it the most eloquently.

*obv this is not par for the course, but I think we can all agree that it happens and is amazing, right?

Healing Leaky Gut Syndrome with Ecoimmunonutrition

Leaky guts happen, and they happen for a variety of potential reasons. They're associated with chronic inflammatory conditions including(but not limited to, obv) Candida overgrowth, psoriasis, autism, type 1 diabetes, and IBS. Although these disorders manifest differently on the outside, their pathophysiologies all have leaky gut in common.

So why does it matter if your gut permability is increased? Well, a few reasons. First, leaky gut is associated with an imbalanced gut forest. That means that pathogenic bacteria and yeasts are dominating the microbial population and generally being jerks. Second, if those nasty microbes escape the holding cell of your intestines and make it into your bloodstream, that pisses off your immune system, which has to deal with the mess. Lastly, in your immune system's smothering rage, it will stop being able to tell what is you and what is not you, and you could end up with an autoimmune disorder. Don't believe me? Take a closer look at this quote from that Wikipedia article:

"Together with the gut-associated lymphoid tissue and the neuroendocrine network, the intestinal epithelial barrier, with its intercellular tight junctions, controls the equilibrium between tolerance and immunity to nonself-antigens. When the finely tuned trafficking of macromolecules is dysregulated in genetically susceptible individuals, both intestinal and extraintestinal autoimmune disorders can occur." (Fasano and Shea-Donohue, 2005)

Now, this is all very depressing, of course. Nobody wants a leaky gut, and nobody wants autoimmunity going on in their bodies. But wait! What's that on the horizon? A bird? A plane?

IT'S ECOIMMUNONUTRITION!

This study, published in China in 2009, found that "Application of ecoimmunonutrition can protect intestinal mucosal barrier in rats with operative stress, increase the expression of occludin, maintain the gut epithelial tight junction, and eliminate gut bacterial translocation." Epigenetics FTW!

So what is ecoimmunonutrition, exactly? From my understanding, it's basically supplementation with probiotics and maybe some other immunomodulatory functional foods. I like the word, though. It looks like it was coined in Sweden all the way back in 1998 (!!!), when Will Smith was gettin' jiggy and Palmolive still made dish soap with antibiotics in it. Go Swedes!

Of course, there are other ways to treat a leaky gut: Candida diets, specific carb diets, blah blah blah. This method is by far the coolest and most integral, though, because neither of those diets work as efficiently or as well without probiotic supplementation. Also because it involves eating bacteria... duh.

L

PS The kefir is freaking delicious.

Ingesting Ecosystems: Grow and Eat Your Own Self-Propagating Probiotics!

No, but for real. This study came out about a week ago, and it's one of the first to use non-culturing methods to identify microbial populations in water kefir grains. Super important-- when researchers did that to ladies' coochie snorchers, they discovered organisms that they never imagined were part of the vagina forest. Besides the obvs (Lactobacilli), they found a heck of a lot of Bifidobacterium strains in kefir samples, which is promising for those with digestive issues.

I ordered some kefir grains from a random seller on etsy. By chance, he lives less than 20 minutes away from me, so the kefir grains pictured above contain fairly local microbes. I reconstituted them earlier this week, and now I'm making my first batch of kefir.

Anyway, I am super excited for the microbial revolution to start in my digestive tract. Will let you know how it goes.

L