Monthly Archives: May 2013

The Dirty Truth; Bacteria at Home

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.

Guts and Bugs; The Human Microbiome

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.

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.

Hard Rock and Hardrock

Road rash and cuts received during the fall in Bear Canyon, the worst of the accident isn't visible though.

Road rash and cuts received during the fall in Bear Canyon, the worst of the accident isn’t visible though.

Well, this wasn’t part of my training plan, I figured once I got out of the sling and cast in December I was done with that chapter of my life. After a great run up Fern Canyon to Bear Peak (47:03) then a quick run down Fern Canyon I hit the Bear Canyon Rd at pace. I decided to see what the legs had left, throwing down some nice sub 6min/mile as I pushed down the smooth wide gravel road. About half way down I looked up for a brief moment, in that moment my toe found a Hard Rock, the rock won, and I soon found myself skidding across the gravel. My initial reaction was to simply curse my stupidity and clumsiness, but as I got up I realized this fall was a little more than a couple scratches and some road rash. My left forearm and shoulder were dripping blood, I had a couple gashes in my knuckles, but worst of all, my left clavicle, the one I’d broken back in October, was very sore…F#@#T%.

The road rash/scratches on my legs as well. They run from the calf to the upper thigh.

The road rash/scratches on my legs as well. They run from the calf to the upper thigh.

As I jogged the last mile home the tenderness in my left clavicle quickly grew. When I hopped in the shower to clean off the blood and dirt the cuts on my shoulders and arms stung like crazy, but once again the worst part was that my left clavicle was extremely swollen. My first thought was, SHIT I broke it again, and my heart sunk as I heard myself say this. Why, why, why? After a day off of work to rest I went to see the good folks at CU Sports Medicine for a consult and some X-rays. To my dismay the diagnosis was a hairline fracture in the left clavicle, and several weeks of taking it ‘easy’. Meaning that the main break from October was still intact and the bones were still knitted together, so while broken the bones were stable.

I was initially crushed by the diagnosis, but as with many things, a good hike (no running) helps bring clarity. As I headed back into Bear Canyon on a sunny Thursday afternoon I happened to meet up with Joey and had a nice little discussion about his upcoming Bighorn 100. This really helped to take my mind off my own maladies for the moment. As we power hiked up the road my arm felt fine, so what if I couldn’t run for a few weeks, I was training for Hardrock (or Hardwalk). If I can hike, I can train for Hardrock! So things weren’t going as planned, but sometimes that’s how life is. The moments that define us aren’t the ones when things run smoothly, it’s the moments where life throws you a curve ball and you’re forced to persevere. So once again here I am, forced to readjusted training, but this time I can power hike to my hearts content and am hopeful to be back near full strength in a few weeks.

Giving Back

Crossing into the Shadow Canyon closure.

Crossing into the Shadow Canyon closure.

“It’s better to give than receive”, sometimes the age old clichés hit the nail on the head. In an attempt to keep myself from running too hard and too long his weekend I signed up with several other Boulder folks to head into Shadow Canyon for a day of trail work in the Flagstaff fire burn zone. After a quick tutorial we hopped in the trucks and drove right up to the base of Shadow Canyon, where we donned hard hats, shouldered various tools and began our long trek up to the saddle 1500ft above. Most of the trail is in very good shape, not being affected by the fire, but as we neared the saddle we could see some of the damage the combination of fire and erosion had caused.

Our work zone for the day, cutting a new switchback through the burn zone.

Our work zone for the day, cutting a new switchback through the burn zone.

We split into three groups; all working on different areas of the trail reroute and rebuild right near the saddle. The day’s tasks consisted of; moving logs/trees, building rock stairs, cutting out tread for the new trail, moving dirt, building log barriers and filling in the old trail with our dirt. I always forget how tough trail building is until I’m back out there lugging around 40lb bags of dirt and 12ft trees trunks.

Several of the OSMP staff hiked in Great Harvest sandwiches for lunch, so we all broke around 12:30pm to chow down! After devouring our sandwiches a few of us went for a short jog up South Boulder peak, only 0.2mi and 400ft from the saddle. This was one of the first times non-OPSMP employees had been up to the peak since last summer’s fire. South Boulder was a moonscape, the trees had been turned into burnt match sticks and the only signs of life were little bits of grass growing in the tread. Despite all this the trail was fairly easy to follow and we soon were atop South Boulder Peak staring off at the patch work of burned and unburned forest that adorned South Boulder Peak and Bear Peak.

Looking down the South Boulder Peak trail toward the saddle.

Looking down the South Boulder Peak trail toward the saddle.

The afternoon was much of the same, dig up some rocks, level out the tread, move the dirt. By day’s end we’d built 4 new stairs, filled in the old trail, and cut approximately 60-80ft of new trail through some pretty rocky terrain. It felt good to give back, especially since our efforts meant Shadow Canyon was even closer to reopening to the general public. Zack, Dave, Beau and John from the OSMP were great to work with and its too bad more of us trail runners/hikers/climbers don’t participate in giving back to the parks in this way. We constantly use and abuse our lands, but very seldom put in the hard work that’s required to upkeep and rebuild them.

Trail leading around the front side of Lumpy Ridge in RMNP.

Trail leading around the front side of Lumpy Ridge in RMNP.

With my sluggish run at Quadrock the previous weekend, and the fact that my legs came out feeling so strong, it was tough forcing myself to ‘rest’ this week. After a few early week short runs, Thursday I did a TT up Sanitas to test my legs, coming in just 12sec off my personal best of 19:06. This coupled with 1.5 laps of Green Mt on Saturday AM with Homie, a hike up Shadow Canyon, and a beautiful loop of Lumpy Ridge in RMNP put me at 13000ft of gain and 40miles, a rest week of sorts. It’s good that my legs are feeling strong again because I’ve got a lot of hard work ahead of me the next 4 weeks; with nearly 300miles and 90000ft of gain slated for the bulk of my Hardrock training. Still #4 on the Waitlist, so hopefully that June 1st deadline brings some good news.



Where Oh Where Has My Energy Gone?; Quadrock 50miler

Runners heading up Towers Rd near mile 5 of the Quadrock Trail Run.

Runners heading up Towers Rd near mile 5 of the Quadrock Trail Run.

My training wasn’t lacking (legs felt pretty good all day), it wasn’t for a lack of course knowledge (I knew the route well and where the difficulties were), or that I had forgotten gear (I was properly packed and stocked up). It was two much more minute details that led to my unraveling at the Quadrock 50miler this past weekend; lack of sleep and a little dehydration. One thing I learned long ago is that sometimes on race day you have it, and sometimes you don’t.

Making my way up the Howard Trail at mile 19, photo by Erin Bibeau.

Making my way up the Howard Trail at mile 19, photo by Erin Bibeau.

After crashing at a friend’s place in Fort Collins, Amanda and I woke at the crack of 4:30am, much earlier than I would like, but the latest possible time to get to the race start. It was a surprisingly pleasant morning, and promising to be a warm sunny spring day. The start line was bustling with all the runners and there was definitely a mix of excitement and anxiousness in the air. A few minutes after 5:30am we all lined up in the parking lot and off we went down the dirt road into Lory State Park. The climb up Sawmill/Towers went fairly uneventfully and I finally got to open up the pace heading down Spring Creek into Aid #2.

Heading up the Howard Trail with Arthur's Rock in the background around mile 20.

Heading up the Howard Trail with Arthur’s Rock in the background around mile 20.

The day was already warming and as I headed back up the Horsetooth Rock trail something wasn’t quite right, I couldn’t keep my heart rate under control, even at an easy hike and I was feeling very fatigued. While I made decent time back to the Tower’s Aid Station I had the feeling it was going to be a long day on the trail. Heading down Mill Creek I was terribly out of breath and my exertion did not match the pace and how my legs felt.

I was run down and sluggish the entire day and hit the 25mile turn around with thoughts of dropping to 25miles and just laying down to take a nap the rest of the day. Thankfully a little good spirit from the race volunteers brought me back to my senses. The internal monologue went as such…

Dark clouds looming ahead, thunder abounds as I climb up Spring Creek for the final time, mile 42.

Dark clouds looming ahead, thunder abounds as I climbed up Spring Creek for the final time, mile 42.

“I’m just wiped out and could just lay down in the sun and take a nice long nap and be done.”
“WTF are you saying? It’s a beautiful day out, you’re moving just fine and you have no legitimate reason to drop. Don’t worry about what your time is going to be, and suck it up and get back out on that trail”

So off I went back up the Timber trail on lap number two, trying to slow jog a little of the gentle uphill as my breathing would allow. The next lap went by fairly quickly thanks to some good company, despite how labored I felt on every uphill I was able to just let my legs flow downhill. As a group of us ascended the final climb up Spring Creek dark clouds began to roll overhead and the load boom of thunder continually echoed through the valley. Finally after 10 minutes a light rain started to fall, which soon turned to pea sized hail that pelted us with stinging force. Several of us donned jackets, but we all kept moving, soon arriving at the Towers Aid Station for the final time. Ahead lay several miles of downhill and flat, clearing skies and the home stretch. I headed off down the hill, legs still feeling pretty good I bombed the hill to the best of my ability. The final few rolling miles were not pretty, but I got through them and crossed the finish line in 10hours 23minutes, good enough for 40th place overall.

Yours truly running into the Arthur's Aid Station for the 4th and final time, mile 49.5, 2.5 to go. Photo by Jessie Wilburn.

Yours truly running into the Arthur’s Aid Station for the 4th and final time, mile 49.5, 2.5 to go. Photo by Jessie Wilburn.

I’d be lying if I said I wasn’t disappointed with my overall time at Quadrock, as I was hoping for a stronger run closer to 9-9.5hours, and my legs definitely felt up to that. I am happy that I stuck it out for the full 50miles even if the run did not feel good, I’m hopeful that these tough miles will pay dividends at Hardrock and UTMB. Pete and Nick put on a wonderful race, Fort Collins has some beautiful trails and the great spirit and support of all the spectators and volunteers really make this a fantastic overall event, one that I would highly recommend to anyone looking for a tough 50mile race. The course is truly unrelenting, and even if I was feeling better the constant ups and downs (total 11500ft gain/loss) will wear down even the strongest of runners. In all it was a good weekend, and I’m looking forward to catching up on my sleep and continuing to push the training forward toward the main goals; Hardrock and UTMB. Special thanks to my sponsors; Hind activewear for the comfy clothing and Vfuel Endurance for getting me through the day.

Keeping it Fun

After a nice mellow taper week (48mi/8500ft) I’m feeling fairly ready for Quadrock on May 11th, which will be a good indicator of my fitness moving forward to Hardrock and UTMB this summer. Hopefully we’ll also see some dry trails and melting snow in the high mountains after Quadrock, as I’m oh so ready to breath that high mountain air on a regular basis.

Untracked snow in Long Canyon on 5/4/13. After a 5th straight week of >1ft of snow.

Untracked snow in Long Canyon on 5/4/13. After a 5th straight week of >1ft of snow.

The past several weeks on the trails have been tough going, our weekly barrages of snow (1-2ft/week) has made for many wet and muddy miles in April. While I love stomping in puddles as much as the next 10yo trapped in a 30yo body, after a while one longs for clear dry trails to and to just be able to run. As I slop through the mud and moments of frustration boil to the surface I need to remind myself why I’m out in the first place. Sure running keeps me healthy, but I’m out on the trails because I enjoy it. If I just wanted to stay in shape there are many things I could do that didn’t involve mud, snow and puddles of cold water but the trails give me a freedom and enjoyment I don’t get on the roads or in a gym.

I’m sure every runner has had one of these moments of weakness; whether it be on a training run, at mile 2 of a 5k, mile 22 of a marathon or mile 90 of a 100. We are all human and are prone to ups and downs and rough patches while participating in our respective sports, the key is to remind yourself why you’re out there in the first place. For many of us its because we love the sport; the runners high, the feeling of successfully pushing yourself, the freedom of the run, the simplicity of the rhythmic motion, or the feeling of accomplishment after the run is completed. Whatever your reason, just remember that when you’ve hit that low or rough patch. “It can’t always get worse” and usually it’s much better, so remember the highs and all the good going forward.

Me as Spidey shredding some corduroy at Loveland on closing day, 5/5/13.

Me as Spidey shredding some corduroy at Loveland on closing day, 5/5/13.

Personally I like to give races and events a little more flair when possible with a good costume. A little color, a little flair and a little embarrassment for myself and everyone else I’m out there with seems to keep the mood light and to remind people we’re out here to have fun, regardless of the aches and pains we’re fighting through. So the next time you’re struggling through a rough patch while running, climbing, cycling or whatever your sport of choice, pause for a moment to remind yourself why you participate in the first place. Though if all else fails just think of me in a Spiderman suit, dressed up as wonder woman or throwing out jump kicks as a Teenage Mutant Ninja Turtle during a 100miler. Run fast, run healthy, but mostly run happy.

Me as TMNT Michelangelo executing a not-so-graceful jump kick during the 2012 IMTUF100.

Me as TMNT Michelangelo executing a not-so-graceful jump kick during the 2012 IMTUF100. Photo by

Rocking Dana's Wonder Woman outfit at the 2012 Leadville100 as a Pacer. Photo by Kelly Chadwick.

Rocking Dana’s Wonder Woman outfit at the 2012 Leadville100 as a Pacer. Photo by Kelly Chadwick.