It seems the NY Times has been on a microbiome binge the last several weeks. Two articles on the topic is more than I’ve seen in the public forum in several years, but it’s a good thing. This past weekend I wrote about the human microbiome and commented on the role our internal biodiversity  plays in a host of things; from digestion, to overall immune health, to how we tolerate different foods. See “Guts and Bugs” for more on that. On May 27th the NY Times post an article about the house hold microbiome. Not just the bacteria that colonize your internal personal compartments, but those that colonize all the surfaces and every little nook and cranny around your house, “Getting to Know Our Microbial Roommates”.

Another interesting topic for those germaphobes out there, and the sciencey folk. I found this article to be a much simpler and less comprehensive discussion than the previous article I mentioned, but none the less a good topic for discussion. It’s fairly common knowledge that within our homes reside hundreds of different microscopic species (bacteria, fungi, virus, phages…) that we interact with on a day to day basis. A common misconception is that all of these are evil and need to be bleached to high heaven. I think what the article relays and what the early results coming out show (data from another CU Boulder lab!) is that most of these household microbes are what is commonly found on our skin, in our noses, in the soil and within the inhabitants of the household. Basically, most of them are nothing to be scared of and a little bacteria never hurt anyone (well most of us).

Of course there are the exceptions, don’t eat that raw chicken (and clean up after) or lick that mold growing on the old cantaloupe in your fridge, but for the most part we can relax a little bit. The one thing that scares me a lot more than the home is the hospital. The author briefly touches on this, a topic that is becoming increasing problematic in the healthcare industry and is most prominently seen in the rise of MRSA infections (Methicillin-resistant Staphylococcus aureus). These places are breeding grounds for microorganisms, and with the constant flow of sick patients in and out, combined with the use of anti-microbial agents and antibiotics, we’re selecting for only the strongest of all these bugs. I’m not saying don’t go to a hospital if you’re injured or sick, but I am saying that its a real rising danger that everyone should be aware of. The health care industry is doing its best to understand the issue and how to deal with it long term, but its still a work in progress. Fresh air, sunshine and a strong immune system are always the best ways to circumvent this possible danger.

A topic I’ve often brushed aside or been very curt on to date is what my lab research deals with, there is more to me than just running 🙂  The overall focus of my group is mucosal and intestinal HIV infection, but one of the largest areas of focus is the relationship between bacteria and HIV infection, specifically one’s commensal bacteria. Within each and every one of us lives a diverse microbiome, consisting of hundreds of different bacterial species. Each one colonizing a specific niche within us, many having beneficial and symbiotic roles, and yes some pathogenic species we’d be better off without. In the past several years technological advancements have allowed for rapid and very thorough analysis of these bacterial species that reside within the various compartments of the human body; leading to a better understanding of the complexity of the human microbiome and many more questions yet to be answered. In the past several months I’ve received a flurry of questions from friends about the human microbiome, personal microbiome sequencing and fecal transplants. I’ll avoid the latter for now, but know that I am familiar with them and I do know Dr’s that I can recommend if people want a recommendation.

In the past year I’ve read dozens of articles about the human microbiome and probiotics and attended several talks on the subjects as well, but most of these have been in science papers relegated to the small community of scientist who study the topic. This past week I was sent a link to an article published in the New York Times on May 15th by Michael Pollan entitled “Some of My Best Friends are Germs” (click link for the article). It was one of the first articles on the Human Microbiome I’ve read that was not only written for the general audience, but where the author not only did his homework, but did a very comprehensive job discussing many of the reasons why we should ALL care about our microbiome just as much as we do our diet. In fact you’ll see that in many instances these two items (diet and the microbiome) are very intimately related.

In the article Pollan participates in a microbiome sequencing project based at CU Boulder and interviews some of the biggest players in the microbiome world, people at CU Boulder and CU Denver with whom I’ve worked, collaborated and interacted with. I won’t summarize the article, as I strongly encourage all readers to take 15-20min to read it on their own, but I will respond to and comment about a few of the points made in the article. If you want to discuss the specifics or have science questions feel free to ask me and I’ll do my best to answer.

Humane Microbiome sequencing data generated by Eric Lee.

I think one of the most critical discussions the article brings up is the ongoing ‘cleansing’ of the Western microbiome. Through our diet and daily practice we’re slowly killing off much of the diversity within our microbiome, something that may be associated with a lot of our immune disorders, obesity issues and digestive troubles that ail an increasing number of people in the ‘developed’ world. The shift in our diets away from a more plant based diet toward large amounts of meat consumption and our overuse of antibiotics and antimicrobial agents may be slowly depleting our guts of the diversity that is hypothesized to be necessary for optimal gut health.

In addition to the affects one’s microbiome has on digestive health is the lesser known idea that all the bacteria that make up our gut microbiome also play a key role in creating and modulating our immune system. Bacteria from the gut are constantly translocating across the gut wall and into our circulatory system, I can corroborate this from my personal studies looking at human gut tissue. As these bacteria move from your intestine into your body, the body is forced to respond and either identify the microbe as ‘friend’ or ‘foe’. One might think, ‘well if I have bacteria inside me, isn’t that a bad thing?’, not necessarily. Many of the commensal bacteria that live in our gut want nothing to do with colonizing the rest of us, thus simply die off and do no harm to the rest of the body, it’s our immune system’s job to recognize these and to realize that they pose no threat. Then there are the pathogenic bacteria that once they are released into our tissue want to colonize, reproduce and spread, here it’s the immune system’s job to recognize these and kill them off before one get’s a full blown infection (ie salmonella and pathogenic E.coli).

If the body isn’t trained properly and simply tries to attack EVERY BACTERIA that enters the tissue we’d be in a constant state of inflammation, ie many of the autoimmune and inflammatory bowel disorders seen in the Western world today. Alternatively if our gut isn’t properly colonized by the good comensals this creates a niche for all those bad bacteria and pathogenic bacteria (the weeds) to grow up and do damage to our body, without the benefits of good bacteria. Just like the “Hygeine Hypothesis” that was made popular in the 90s and early 2000s, we’re starting to realize that bacteria might not be so bad, in fact it appears they are necessary for us to live a healthy life.

As Pollan says in the article we are no where near having a complete understanding of all the nuances of the Human Microbiome, and what a healthy microbiome might be. Every bacterial species plays a unique role, but what these roles are is not fully understood. Probiotics and Prebiotics may be beneficial, but we don’t yet know enough to say there is a ‘best’ formula for people to take for optimum gut health. What we as scientist do know is that the health and diversity of our microbiomes is critical for many aspects of our lives, not just digestion and these are affected by many factors starting as early as birth. The goal of my ramblings isn’t to tell you to eat less meat, to go guzzle gallons and gallons of probiotic yougart or to stop sanitizing your house. All I want is for you to think about the consequences that many of your actions have on the health of those little microscopic organisisms that colonize the various niches of our body, you know, the one’s that outnumber your human cells 10 to 1. Next time you are thinking about taking antibiotics because you just don’t feel well, rub that hand sanitizer all over your child because she/he was crawling on the floor or the you pick up that big steak for dinner; remember the bacteria.