Archive for the ‘Interesting Articles’ Category

By Ann Gibbons

The Khoisan hunter-gatherers of Namibia offer a glimpse of our ancestors’ great genetic diversity.

The famous Kalahari Bushmen of southern Africa have long been in decline. For more than a century, the people, who speak Khoisan languages, have been pushed off their land by farmers and brutalized by colonialists.

Yet for tens of thousands of years, the Khoisan’s ancestors were members of “the largest population” on the planet, according to a new study.

The Khoisan have long stood apart from other groups within Africa. They look distinct, speak in “click” languages, and have also maintained the greatest genetic diversity known among human populations. Usually, big populations harbor the most diversity. But census counts show that the 100,000 Khoisan speakers in Africa today are far outnumbered by other groups, such as the 45 million Bantu speakers and their 180 million descendants who now speak Swahili and other languages. Researchers have thought that the Khoisan inherited their genetic diversity from a large ancestral population, an idea supported by a single Khoisan genome published in 2012. But scientists couldn’t rule out that the variation in Khoisan DNA arose from more recent interbreeding with other diverse Africans.

In the new study, published online today in Nature Communications, biochemist Stephan Schuster of Nanyang Technological University in Singapore and colleagues sequenced the complete genomes of five Khoisan hunter-gatherers from Namibia and compared them with the DNA from 1462 genomes of people from around the world. Schuster’s team found that two of the Khoisan, members of the Ju/’hoansi population in Namibia, inherited their DNA only from Khoisan ancestors in the northern Kalahari region and showed no sign of interbreeding with non-Khoisan speakers. These two Ju/’hoansi genomes preserve ancient diversity inherited entirely from their direct ancestors, the authors say.

Using several different methods of analysis, the team reconstructed population sizes for the ancestors of the Khoisan, as well as for Europeans, Asians, and another African group, the Yoruba. They found that all four groups declined in effective population size (the number of breeding adults) between 120,000 and 30,000 years ago. The non-Khoisan groups’ numbers plunged precipitously—by 30,000 years ago, European and Asian populations had plummeted by 90% from their peak, thanks to population bottlenecks caused by the migration of small groups out of Africa. But the Khoisan population declined by only 26%. (Yoruba populations dropped by 69%).

The researchers uncovered declines in population in all four groups, likely tied into periods of dry climate in Africa. But the Khoisan suffered the least, perhaps because their huge ancestral population was buffered from droughts that winnowed other groups, such as the Yoruba and the African ancestors of Europeans and Asians, because the Khoisan lived farther south in Africa where rainfall actually increased. The Khoisan then began a more drastic decline in the past 20,000 years or so, with a major blow when the Bantu farmers spread through Africa 4000 years ago. “This shows us how much climate can influence populations,” says genomicist Webb Miller of Pennsylvania State University, University Park, a co-author.

Other researchers agree that it’s likely that the Khoisan descend from a large population. But because sampling of African genomes is still so spotty, not everyone is yet convinced that the Khoisan “was the largest population on Earth at some point,” says evolutionary geneticist Pontus Skoglund of Harvard University. “Many African populations are not included for comparison,” he says, so it is possible that some of the diversity seen in the Khoisan was inherited from recent interbreeding that cannot yet be detected.

Either way, the study makes it clear that even though the Khoisan are genetically diverse by today’s standards, even they carry just a fraction of our ancestors’ genetic legacy over the past 120,000 years. “It is quite staggering how much extraordinary genetic variation and ethnic diversity was present but is now lost,” Skoglund says. The Khoisan, retaining more than the rest of us, offer a rare window to look back in time at some of that diversity.


By Dan John (web)


If I could summarize smart training I would say this: Train your whole body daily with enough work and appropriate load. Let me give you two words to aid in your understanding of training the movements with appropriate work and load: Integrity and Environment.
Integrity is a word I use often in my work. I use it to talk about “being the same person in every situation,” being true to one’s values and system, and, the key for this section, “being one piece.”
“The body is one piece” has been a teaching truth of mine for decades, but it can be simplified to “Integrity.” As you train and pursue your goals, you must think of your body (mind and soul) as one piece. Your feet, even if you don’t realize it, are searching for clues from the ground to protect you from making a life changing or life altering error. You inner ear is helping out your feet by providing feedback on what is upright, and the rest of your body is sharing information to help your decision making process.

As for environment, it’s “everything out there.” It can be water, ground, trees, rocks, falling rocks, and everybody else. It can be as controlled as a cement floor and an air-conditioned room, or as chaotic as the breakers hitting a tidal pool. We are constantly waging a full scan on everything around us and reacting to all this input.

We can use integrity and environment to help understand the fundamental human movements and how they can be seen over the lifetime of training.

Let’s just discuss the upper body and how your local playground might be the best toolkit for training you know.

The “Push” is an attempt to separate from the environment. Babies strive to push the floor away to begin moving on their own, the bench press is an attempt to separate the bar from the chest, and we spend much of our life pushing away mom and dad so we can grow up. Not surprisingly, pushing muscles tend to be the muscles of youth. As you review Janda’s Phasics—a group of muscles classified by Dr. Vladamir Janda as extensors, or essentially “pushers,”—you will note that these are the ones that weaken with age or illness.

The “Pull” is how we unite or embrace our environment. When we try to bring things closer to ourselves, like during a pullup, row, or embrace, we are attempting to close the gap between our integrity (our body) and the environment. Sports naturally flow between push and pull as we try to leverage an opponent or nature. As we age, we wish everyone we know were just a bit closer either due to hearing loss or just distance. Janda’s Tonics—classified as your flexors or “pullers”—are the muscles that tighten with age or illness.

If you wish to do both the Push and Pull in the healthiest, safest manner, go look for some Monkey Bars. If you ever want a full upper body workout in about a minute, swing from hand to hand across the Monkey Bars.

Hold on. Why do we call them Monkey Bars? In Wikipedia’s definition of “Brachiation,” there is a very interesting description of the traits of brachiators: “Some traits that allow primates to brachiate include short fingernails (instead of claws), inward-closing hook-like fingers, opposable thumbs, long forelimbs, and freely rotating wrists.”

Sound familiar? Yeah, well, look in the mirror! Go find a park and rename them “Human Bars” and take back our equipment! Like Charleton Heston warned us: “Take your paws of me, you damn dirty ape!” My friends, let me warn you: First the playgrounds, then the world. Seriously, there are movies about this!

No. Really.

There is a beach in California with rings set up so that one can “fly” back and forth and back and forth. Now, by the time you read this, some group interested in safety will have banned them, but if you want to look fantastic in the upper body, start brachiating. The beachcombers who do these big swings look amazing. Now, the chicken or the egg question: Does swinging build this physique or does a certain physique allow “flying rings.”

Either way, it doesn’t matter. Your upper body is made to do it. Its job is to both separate and embrace the environment.

Traditionally, I have gathered a bunch of our typical training drills into something I call “The Sixth Movement.” I am never sure what to call this, but basically it is everything besides push, pull, hinge, squat and loaded carries (the five foundational movements). It is groundwork. It is rolling. It is literally “everything else.”

Generally, though, the Sixth Movements seems to encourage this: Integrity with the Environment.

Rolling on the ground makes falling seem safer. Turkish getups simplify popping up off the ground to get some more beer during the Super Bowl. Rolling on the floor with a grandchild makes everyone happier. (That last one isn’t scientific, but it is true.)

The Sixth Movement(s) bring you back to the early days of sitting around a fire and listening to a story. We are reminded of sliding in and out to spark the embers, sliding back into the earth to hear the story, and rolling over on the ground to fall asleep.

Our relationship with the earth shouldn’t be “me and it,” it should be “I and Thou.” Yes, it might be a bit heavy for a lifting audience, but just roll around for a while and trust this point.

Crawling can be seen as simply “engaging the horizontal environment.” Brachiating can be summed with “engaging the vertical environment.” You don’t need to swing from limb to limb to engage the vertical environment as you can do that simply through Monkey Bars or Rope Climbing. The recent popularity of rock climbing reflects this basic truth of the human person: We like to explore what is around us and hidden behind that next curve, tree, or mountain.

I was lucky to be educated in the last wave of the classic Physical Education programs. We began the year with marching. Can you even imagine the number of phone calls to the principal if today you had kids marching around the schoolyard following the commands “To your left, to your left, to your left, right, left?” We learned sports and games, but we also spent quality time on climbing ropes, high bars, dipping bars and Monkey bars.

In most P.E. classes today, you simply see pick-up basketball games and dodgeball. In many states, it has all but vanished for the scholastic curriculum. If you don’t learn certain skills as a child, bicycling and swimming quickly come to mind, it is going to be difficult to pick them up in your adult years. Learning to ride a bike involves some falling and tumbling and this isn’t always the best for adults.

Let’s rediscover the great tradition of physical training.

by Jeff Leach (source)

AS THE SUN set over Lake Eyasi in Tanzania, nearly thirty minutes had passed since I had inserted a turkey baster into my bum and injected the feces of a Hadza man – a member of one of the last remaining hunter-gatherers tribes in the world – into the nether regions of my distal colon. I struggled to keep my legs in the air with my toes pointing towards what I thought was the faint outline of the Southern Cross rising in the evening sky. With my hands under my hips – and butt perched against a large rock for support – I peddled an imaginary upside down bicycle in the air to pass the time as I struggled to make sure my new gut ecosystem stayed put inside me.

With my butt cheeks flexed and my, you know what puckered, I wondered if I had just made a terrible mistake. Could I really displace my western gut microbial ecosystem with that of a man, who, days before had dined on animals as diverse as zebra and monkey, possessed one of the most diverse gut microbiomes of any person in the world? Would my immune system soon freak out at the presence of what should be some familiar Old (microbial) Friends now setting up shop throughout the slimy vastness of my gastrointestinal tract? Or had I just unwittingly infected myself with some lethal bacteria or virus? The pros and cons – mostly cons – of my evening turkey basting activities raced through my anxious mind as I peddled my way into the evening.

Hadza hunter-gatherer

My colleagues and I have been working and living amongst the Hadza hunter-gatherers of Tanzania for over a year now. Over the course of several field sessions, we’ve collected nearly 2,000 human and environmental samples in an attempt to characterize the microbes on and within the Hadza and the microbes in their environment. The human samples have mostly included stool (feces), but also swabs of hands, foreheads, bottoms of feet, tongues (some spit), breast milk from mothers, and so on. Environmental sampling has included swabs of the plants and other foods they consume – like berries, roots, honey, etc. – and a dizzying number of animals ranging from Greater Kudu, Impala, Dik Dik, Zebra, various monkeys and birds, and so on. For the animals, we collect feces and when possible swabs of the stomach contents of larger animals – all of which end up covering the Hadza sooner or later during butchering (see little blurb in Nature titled Please Pass the Microbes). We also swab their homes – inside and out – along with the various water sources. In short, we swab everything including the researchers while in the field.

The official title of our little project is The Effect of Seasonality and Transculturation on the Human Microbiome: a Pilot Study in Tanzania and includes a talented team of collaborators from New York University, University of Colorado-Boulder, Stanford, Mount Sinai School of Medicine, Western University & Lawson Health Research Center in Canada, and several researchers from the National Institute of Medical Research in Tanzania. Additional collaborators working on various analysis are scattered at universities in the US and Europe.

Twenty years of rainfall in Hadza Land taken at Kisema Ngeda.

As the clunky title of our study implies, we are interested in how Hadza microbes – along with their environmental microbes (water, homes, plants and animals) – shift between the wet and dry seasons. Due to some unique geography and global weather patterns, East Africa experiences a striking wet and dry season – essentially 6 months of rain, followed by almost none (see figure). This reality means that during the dry season, as water holes dry up, the Hadza kill a lot more animals as dwindling water sources make the animals more predictable and easier to shoot with their poison arrows from hunting blinds (aka ambush hunting). An increase in protein and fat from animals means a drop off in other caloric resources, mainly plants, as the Hadza will often binge of meat when possible (note they have no storage so everything is eaten in a short period of time). During the wet season when Hadza Land is awash in greenery and flowers, the Hadza enjoy an abundance of wild honey (gooey fat of the larvae included) and massive stands of sugary berries. With the coming of the rains larger animals are more scattered and thus harder to kill, so make up less of the daily calories (though its highly variable from day-to-day and week-to-week and from camp-to-camp). No matter the season, fibrous baobab fruit and subsurface tubers are a daily constant for the Hadza. Yes, they consume lots and lots of dietary fiber!

The impact of seasonality on the Hadza and their microbial environment is an interesting and possibly important question as it relates to what a normal or healthy microbiome might have looked like before the niceties and medications of late whacked the crap out of our gut bugs in the so-called modern world. It’s not a stretch to say that nearly all of us in the western world are a hot microbial mess due to, well, just about every aspect of our daily lives – hence the emerging microbial connection to a staggering number of diseases and ailments in the twenty-first century including IBD, autoimmune disease, obesity, type 2 diabetes, and so on.

Should we really strive for a certain composition of gut microbes as many modern buggy-like products infer – such as those found in over the counter probiotics, various drinks and foods? Or does the reality of our seasonal past reveal that our gut microbiome is a shape shifting metabolic organ pulling the strings on our health and well being in a bi- or even tri-annual circadianlike rhythm? Said differently, and with all due respect to the brilliant Harvard researcher Richard Wrangham of fire made us human fame, is seasonality and its impact on our symbiotic microbes more responsible for what makes us human? I like to think it might – plus, Seasonal Homo is kind of catchy.

The Hadza are particularly (microbially) interesting over, say, remote groups in South America, as they still live in a part of Africa that purportedly gave rise to our genus Homo. However, Lee Berger and his colleagues working new fossil sites in South Africa are giving East Africa a run for its money for the prize for which part of Africa holds the honor to the geographical cradle of humanity. Regardless, being only a stones throw from famous paleontological sites like Olduvai Gorge of Leakey fame, the Hadza literally hunt and gather many of the same animals and plants that humans and our ilk have subsisted on for millions of years – not too mention they are literally covered in the same dirt, drink the same water (save the occasional cow turd floating about), and practice the same central-based foraging that has brought people together in microbial-sharing camps/communities for the better part of the Pleistocene.

While the Hadza are not living fossils, nor in anyway represent a perfect referent population for early human evolution (but close), their hunting and foraging lifestyle and constant contact with the natural microbial world, natural births, extended breast feeding and limited to access to western medications, makes them one of the best – if not the best – population in the world for trying to understand what our ancestral microbes may have once looked like, where we got them and at what point in our life history we acquired them, before the rest of us ran gut first into the buzz saw of globalization.


On the original question of whether or not the gut microbiome composition of the Hadza changes between wet and dry seasons, our initial – though unpublished data – suggest yes (see graph). To our knowledge this is the first study in the world to document this pattern among rural and remote populations. Ecologically speaking, this suggests there may not be one steady state – or equilibrium – for the human gut. It’s moving target with multiple steady states.

Though we see seasonal shifts in the composition of the Hadza gut microbes across the same individuals, we are currently trying to determine if there exists any functional shifts as well (via shotgun metagenomics). In other words, even if the members shift around from season to season, are the metabolic capabilities – or ecosystem services – of the entire community conserved between seasons or do they change as well? We should know this in the near future.

If we squint for a moment and consider the Hadza and the seasonality of our ancestral past and its impact on our shape shifting gut microbiota as relevant to populations in the western world – and no reason we shouldn’t, though some may argue otherwise over hair splitting details – then we might need to start rethinking an entire industry of probiotics and the like that suggest we need a certain set of bugs in this drink or that slimy yogurt.  And since we are on the subject of probiotics, some significant and dominant players on the market today include characters with names like bifidobacterium and lactobacillus. Interestingly, while the Hadza harbor bifidobacterium and lactobacillus while still breast-feeding, these bugs are essentially absent in Hadza post-weaning (i.e., more or less absent after age 5).

This begs the question: should we really consider these groups of bacteria as essential and necessary to human health despite what a multi-billion dollar industry tells us? Clearly, mountains of research suggest these lactic acid bacteria are good for us, but are there other – more ancestral – groups of bugs that may be more in tune with our seasonal gut post-weaning? More importantly, does the persistence of bifidobacterium and similar bugs in our western gut – mainly due to continued consumption of cow’s milk, ingestion of some probiotic/prebiotic foods, and so on into adult life – nudge out or blunt down other members of our gut ecosystem that would otherwise flourish and provide important ecosystem services? We are currently trying to understand this as we perform various co-occurrence analyses of the Hadza data. Stay tuned.

It’s also interesting to note that while the most dominant group of bacteria in the American Gut is thegenus Bacteroides – by a country mile – this group of bacteria is a minor, minor player in the Hadza gut. Almost non-existent. The prevailing wisdom is that these bacteria are driven by our high protein-fat and sugary diet. However, I think it has a lot more to do with our absence of dietary fiber and resulting alkaline guts (see Going Feral). As my own self-experiments have shown, I can turn my Bacteroides up or down with the amount of fiber in my diet irrespective of the amount of other macronutrients like fat. To me at least, I think the dominance of Bacteroides in the western gut has to do with pH levels, which is “mainly” driven by fermentation of dietary fiber (fermentation of fiber equals more SCFAs and thus a more acidic colonic environment which strains of Bacteroides don’t like). So with the average American eating less than 20g of fiber a day – pitiful – we are likely lugging around the most alkaline guts in human history which in turn is allowing certain species of Bacteroides (and some opportunistic pathogens) to flourish. Again, if we squint for a moment and lean on the gut of the Hadza, then maybe we shouldn’t let Bacteroides dominant our gut – and by doing so, who else is getting nudged out or down and potentially dragging us closer to ill health? I suspect the Hadza keeo Bacteroides levels low with their high, daily levels of dietary fiber which keeps their colonic environment very acidic. In addition the high protein-fat and sugary argument doesn’t hold with the Hadza either as they will often gorge on meat-fat and eat piles of sugary honey for weeks on end during the wet season – and we see no blooms in Bacteroides when we sample during these periods. It’s the Fiber Stupid!

Some of our initial sequencing data on the Hadza reveal extraordinary diversity of certain groups of bacteria – one that sticks out, among many – is the genus Prevotella. Currently there are only two described/sequenced species of Prevotella derived from the human gut: P. copri and P. stercorea.Strikingly, the Hadza appear to harbor dozens of species! This is interesting as Prevotella have been linked/correlated to enhanced susceptibility to arthritis and some other issues. So, is the diversity of Prevotella species in the ancestral Hadza beneficial, benign, or possibly even problematic? It’s exciting to think that we all once harbored this diversity of Prevotella but have lost it through our western diet and lifestyle. At the moment we don’t know what to make of the Hadza diversity of this important genus, but we are working on it. Stay tuned.

Oxalobacter formigenes is another species of bacteria that most of the Hadza carry and that the rest of us in the western world have more or less lost. Oxalobacter, as an oxalate-degrading gut microbe, hasgained attention in recent years for its ability for preventing calcium oxalate kidney stones. Graduate students Amanda PeBenito and Lama Nazza in Marty Blasers lab at NYU have been looking at Oxalobacter levels in our Hadza samples and have found that most of the Hadza still carry this important microbe – and acquire it at a young age. Conversely, Oxalobacter seems to be disappearing from our western guts and may be at the root of rising levels of kidney stones. Less the 15% of Americans still carry this important microbe and almost no kids are acquiring now – according Amanda and Lama’s research. Since Oxalobacter is sensitive to penicillin’s, our overuse of some western medications may be the problem.

As the examples of Prevotella and Oxalobacter reveal – and note there are lots of others emerging in the Hadza samples – we have potentially lost an extraordinary diversity of microbes that may have once contributed to our proper functioning and the reason I found myself peddling an imaginary bicycle under a Baobab tree this past August.

When we started working with the Hadza during the summer of 2013, we would live near them but not in their camps. And though I lived in their environment while working with them, I continued eating western food all the while collecting my stool samples as well as theirs. Other than the occasional taste of wild meat and some baobab fruit, my diet consisted of pasta, some canned meats, fruits, veggies, booze, etc. I was interested in seeing whether or not simply being in their environment would change my gut microbes in any meaningful way. And it did – but only so slightly. The next field session I not only lived in their environment, but drank their water and ate their food – giving up my normal, western camp food. But I did smoke weed on occasion as the Hadza are big pot smokers (they trade honey and meat for weed with the local Datoga). As with my previous experience, the combination of environment plus Hadza food altered my gut microbe composition as well. However, my gut bugs still did not match that of an age-matched Hadza male. Granted, I did not stay on the Hadza diet long – only 6-8 days at a time. The experiment of “going Hadza” was to see if I could catch or acquire their consortium of microbes through diet and lifestyle changes. Clearly my changing microbiota suggested yes. Since I did not have the time to live amongst the Hadza for months on end – a time I felt would be necessary to make my gut look more Hadza-like – I thought something more radical was needed.

Fecal microbiota transplants – or FMT – have become all the rage. And as the name implies, it entails taking a small amount of fecal matter from one person and putting it another. While the promise of this therapy is hard to overstate, the science is still a long way down the road from being a simple thing for everything that ails us in the western world. FMT has been proven again and again as a successful treatment for C. Diff infections – where antibiotics have been unable to clear the infection and in many cases, only make matters worse – its use in IBD and other issues is still a work-in-progress. But everyone – including me – is hopeful that the idea that you can restore microbial diversity or otherwise improve dysbiosis in a sick gut with a donor stool is breathtaking.

When I first considered the idea of doing a fecal transplant between a Hadza hunter-gatherer and myself, I ran the idea pass a number of colleagues working in various areas of microbiology and medicine. If memory serves, one hundred percent of the experts I consulted said don’t do it. Concerns ran from it’s too risky or you’re not sick so why do it, and so on. But it was comical to hear more than a handful of experts warn against doing it, but if I did, it sure would be interesting to see the data! So I carefully weighed the advice and jumped in with both butt cheeks.

While for ethical reasons I cannot disclose the donor, I can say it’s a Hadza male, in his mid 30s, with a wife and handful of kids. Before the poo swap took place, I knew more or less what microbes he carried as we had sampled him several times over the months prior and that he harbored at least twice the amount of species (OTUs) that I carried – including all those crazy Prevotella and those oxalate eating Oxalobacter. We also took the donor to a small hospital in the town of Haydom and had him tested for Hep A-C and a few other things. For HIV, we used rapid field test strips and repeated the test multiple times over several days. While it’s not possible to catch everything, we were being cautious. However, I had no data on the parasites he might carrying at the time of the transplant as those analysis were still ongoing at Jack Gilbert’s lab at the University of Chicago. Oh well, parasites be damned, onward with the science!

Since I wasn’t sick and in need of a transplant for those reasons, why was I taking the risk? To that advice – which I greatly appreciated from my colleagues – I responded that while I don’t technically have a diagnosed disease like a refractory C. diff infection for which a fecal transplant was the best cure, I did have a western gut microbiota – one I was given when I passed through my mother’s vaginal canal and that I had spent a lifetime of knocking the crap out of with chlorinated tap water, the occasional antibiotic, mountains of shitty (and good) food, living more or less the sterile life of an American male – devoid of the kind of microbes my donor had grown up with – and last but not least, a semi truck load of booze I had consumed as an average American male (I’m 47 so I have seen the bottom of my share of tequila bottles). Therefore I did consider myself gut sick even if I had not been diagnosed as such. But that’s not the whole reason.

The bigger reason or hypothesis I wanted to test was one of microbial extinction, something I believe we all suffer from in the western world and may be at the root of what’s making us sick. My colleagues and Hadza collaborators Maria Gloria Dominguez-Bello and Marty Blaser at NYU estimate from their decades of work in the US and among Amerindian populations in South America, that us modern humans have lost a third (or more) of the microbial diversity we once enjoyed. The Hadza data thus far suggest this number could be as high as half. So for me, and my little transplant experiment with a Hadza hunter gatherer still living at microbial ground zero for all humans, I wanted to know if my western diet and lifestyle could rapidly destroy this newly acquired diversity in a short period of time. Since the human genome contains ~23,000 genes and our whole-body microbiome accounts for another staggering 5-10 million genes – most of which our deep in our gut – my distal gut ecosystem restoration project attempted to replace 99% of the genes in my body.

Again, if you squint with me for a minute, could I simulate 10,000 years of human history – from the transition of hunter-gatherer to agriculturalists, to crowded conditions of civilizations, to indoor plumbing, to the introduction of antibiotics and antimicrobial soaps, to Lady Gaga – all in a short few months with my fecal transplant?

So once the fecal transplant had been completed that warm, August night – with the aid of a turkey baster (note also I’m pretty sure my colleagues who brought me the turkey baster purchased the largest one made and sold at Walmart) – I immediately went back to camp and started back on my western diet (note I had been on a pure Hadza diet for a few days leading up to the transplant).

Before and after the transplant I took stool, blood, and urine samples (note I’m still taking stool samples weeks after the experiment). We also took several samples of the donor stool. At the writing of this blog post I’m not sure if the fecal transplant took – that is, whether my body successfully took the transplant and if so, what percentage of my donors bugs populated my distal colon. I was able to “hold in” the donors sample until 11AM the next morning, a period of 16 hours, before having my first bowel movement. So I am hopeful. I should know by early November, when all the samples are sequenced, whether or not the procedure took.

So, if I was able to acquire and keep a portion on my donors ancestral microbial ecosystem, how much of it could I wipe out as I transitioned back to the US and then back to Tanzania this coming November? When I arrive back in Tanzania in mid November, I will go back on the Hadza diet – and of course, live in their environment – to see how much of the original donors samples I can get to spring back to life. If my transition back to the US results in a loss of my newly acquired diversity, then essence – if you squint with me for a moment – I was able to recreate the epidemiological transitions we’ve all experienced in the last 10,000 years in a few short months. Regardless of the outcome, it will be interesting. I will also do another transplant or two when I return in November, but this time I will stay on the Hadza diet to see if I can hold onto whatever ecosystem I acquire at transplant.

So how did I feel after the transplant? Not that much different other than – as it was pointed out to me by my girlfriend – I seemed to be farting a lot less – a lot less! Didn’t really notice any change in my mood or my bow hunting skills either! But it is interesting that I started shedding a few pounds for no apparent reason. Interesting. Stay tuned.

Don’t try this at home!

by Christian Thibaudeau web

July, 2013 CrossFit Marathon

You want to hear something crazier than Christian Thibaudeau doing CrossFit? How about Christian Thibaudeau doing a 24-hour CrossFit marathon?

By now you might realize that I have an “all-out” attitude. Moderation isn’t in my nature. So after less than two months of this type of training my wife and I decided to sign up for a 24-hour CrossFit marathon organized to raise funds for a city that got hit by a huge train explosion that devastated half the downtown area. The event lasted 24 straight hours, one workout being performed every hour. We were divided into teams of four, so we all had to do six workouts, one every four hours or so. My wife and I stayed at the gym the whole time, except for two brief periods when we went back home to feed the dogs. It would be a lie to tell you that we slept, as sleeping was a physical impossibility.

When I got to the gym, I quickly noticed that a ton of people knew me; some knew me because I had coached them in Olympic lifting and many others knew me by reputation. All were surprised to see me there as they didn’t know anything about my “shift in training.”

So when the first workout came up I felt an amazing amount of pressure. In fact, my heart rate was close to a fatal level before the workout even started. Plus, the workouts were picked at random so we couldn’t really assign specific workouts to the team members because we didn’t know the order of the workouts in advance. That made things even worse.

It turns out that I had to do the workout named “Fran,” which is 21 thrusters (95 pounds), 21 pull-ups, 15 thrusters, 15 pull-ups, 9 thrusters, 9 pull-ups for time. It looks quite innocent, but the thing is that you basically can’t breathe during that workout. The thrusters are the absolute worst exercise when it comes to breathing, and then you have to do pull-ups where deep breathing is almost impossible because you can’t elevate your chest.

I made the mistake of really blasting through the first 21 thrusters. While I was the first one done, I gassed out bad when I walked toward the pull-up rack. This was due to lack of breathing plus the elevated heart rate at the start. I was able to pull through but I promised never to do that workout again.

My second workout was even worse:

18 toes-to-bar
16 hand release push-ups (a push-up where, after your chest touches the floor, you momentarily pull your hands off the floor)
14 pull-ups, chest to bar
12 ring dips
10 chin-ups
8 handstand push-ups
6 pull-ups, chest to bar
4 clean & jerk with 155 pounds
60m walking lunges while carrying 45 pounds overhead

It actually went fairly well, except for falling down three times while doing the handstand push-ups (it’s not something I’d practiced), but I was really disappointed when I saw that the next workout (the one a teammate got to do instead of me) was testing your deadlift 1RM. I would have cleaned up on that one!

I did fairly well in my third workout, which consisted of five rounds of the following:

200m farmer’s walk while holding one 45-pound bumper plate in each hand (held by the hole)
20m bear crawl (running on all fours)
10 high box jumps (36″)

Again, the next workout consisted of 5-4-3-2-1 in the power clean and kettlebell snatch. I would’ve done very well at that one, too, but my wife got to do it and I’m proud to say that her cleans looked very solid. Finally, in the next round, I drew one that was designed for me: “Isabelle,” which is 30 snatches with 135 pounds. All eyes were on me and I was expecting a very solid performance.

Sadly, when luck is not on your side, it’s really not on your side. After the first 10 reps, where it felt like I was snatching an empty bar, my left quad started to cramp bad. In fact I was unable to put any weight on my leg at all without experiencing severe cramps. So I stopped, took two servings of Plazma and 3000ml of water, waited 10 minutes and did it again. Sadly, most people were finished and getting some rest by then.

The rest of the experience is a haze. I’m someone who normally wakes up at 4:30 AM and goes to sleep at 8 PM. That day I still woke up at 4:30 AM but I finished my fourth workout at roughly 3 AM. I do not respond well to sleep deprivation. I finished with a workout that was tailored to me, but at that point I was fighting to stay alive and awake so I can’t say that I killed it.

The main thing I learned during these four weeks was the value of loaded carries. I was reminded about them when I had to do a workout at CrossFit Levis that included 5 rounds of a 400m farmer’s walk while carrying 24kg kettlebells. Then, two days later, I did the farmer’s walk at the CrossFit marathon. My forearms and traps might have doubled in size. Okay, I’m exaggerating, but the farmer’s walk did have a profound impact. And I also found that they can teach you to breathe properly during intense effort. When doing conditioning/strength-capacity type work, breathing is something that’s highly underrated, yet is of supreme importance for optimal performance. I’ll make sure to include more farmer’s walks in my training for their effects on body composition, muscle mass, and breathing skills.

It Was Going So Well..

Back to the present… My CrossFit experience ended soon after my third month passed. That’s when my health issues started. I don’t want to cover them all over again since they were detailed in theMicro-PA forum, but suffice it to say they stopped my momentum.

What Now?

I spent some time rebuilding some of the muscle mass I lost when I was hospitalized. To do that, I went back to regular heavy lifting. Now that my base is coming back, I’m focusing on the Olympic lifts again. I’m doing plenty of strength work, too. I have the two Olympic lifts every day and I do pulling strength-movements on day 1, pushing on day 2, and legs (squats) on day 3. I then take a day off and repeat.

I’m using the tried and true 5 x 5 for my strength lifts. My goal is to get 5 sets of 5 reps with the same weight, and when I can do that I increase the load. I never decrease the weight. On some sets I might only make it to 3 or 4 reps, but that’s fine and it means I won’t increase the weight for the next workout.

Will I do CrossFit again? Probably. Not to the same extent as I did last summer but when my strength levels are back up where I want them to be, I’ll start hitting CrossFit Levis with my wife once or twice a week. I’ll have to be ready to have my ass kicked, though, since, unlike me, she didn’t stop!

by Christian Thibaudeau web

June, 2013 Second Month Observations

Shredded-Physique1. A hard month of training is now behind me. I can say that this form of training is addictive and I certainly see why CrossFit is popular. I mean, it really sucks when you’re doing it, but the amount of pride you feel and the sense of accomplishment is hard to beat. As for my own training and results, I love what I’m seeing and how I’m feeling.

2. During my second month of training I observed and learned a few more things that I want to share with you. I always felt that I am the average T Nation reader. I want what they want and like what they like. I like to be strong and muscular, but I love to be lean and feel athletic. I said that my ideal physique is that of Georges St. Pierre with 10-15 pounds more of muscle, but considering what’s happening to my body I might as well change that to 20 pounds more muscle!

3. While I expected to get leaner with this type of training, I was afraid of losing some muscle mass.After all, my lowered volume of overall strength work and increase in metabolic conditioning work would surely lead to some loss in size. I was actually willing to live with this, but so far I’m shocked by the results. I certainly haven’t lost any size, and quite possibly gained some size, as evidenced by the fact that I’m a lot leaner while my bodyweight remains fairly stable. This tells me two things: 1) the amount of strength/heavy lifting necessary to build strength and size is much lower than I thought and 2) lighter resistance work can actually become a muscle growth stimulus if you push it hard enough.

4. After some deep introspection I realized that I value being super lean more than being super big.Don’t get me wrong, I want big muscles and you really can’t get the look I want without a good amount of muscle tissue, but being a walking anatomy chart has always been my main goal. The problem is that every time I tried to get that lean in the past, I felt like crap throughout the process. I had no energy and lost a lot of strength. Why? Because with the type of training I was doing, I achieved fat loss by food/carbs reduction (sometimes quite drastic) and I’m now doing it while eating just as much food, if not more, than during a muscle gain phase.

5. My back, shoulders, and legs are definitely improving the most. What freaks me out (in a good way) is seeing my back get lean! As I mentioned, it would normally take extreme dieting to get back definition, but I’m now seeing tons of separation. The shoulders are much rounder, which is cool because in the past when I was “dieting down,” shoulder roundness was the first thing I’d lose. My legs are bigger, but of course that’s not surprising since I’m doing four squatting workouts per week, plus the Olympic lifts and complexes.

6. I decided to add daily ring dips and chins to improve my relative strength. I find that with the daily ring dips I’m able to maintain chest mass despite dropping bench pressing almost completely. This led me to the conclusion that dips can be a superior chest builder to the bench press.

7. This is the first time in my life that I really like the way I look. I think that most of us who get serious about training do so because we’re not satisfied with the way we look. I’m no different. Even when I did bodybuilding I never liked the way I looked. This could’ve been because when I finally reached the degree of leanness and muscularity I felt so bad that I had a negative outlook on everything. I can safely say that this is the first time I ever looked and felt great at the same time.

8. The more I experience it, the more I believe that submaximal lifting that focuses more on speed and density of work is a great way to build muscle. This is especially true of the Olympic lifts, so I decided to go a bit lighter on my Olympic lift days (I’m building overall strength with the strength days anyway) and focus more on complexes and EMOM loading (every minute on the minute). I feel that this will give me more overall muscle gains while also solidifying my technique while preserving the nervous system.

9. You really need to up the carbs! Not only will you not get fat on this program, the carbs (the right ones) will actually help you get leaner because you’ll be able to train harder. I ran out of Finibars at one point and it hit me really hard. I didn’t realize how much they helped me recover from these workouts.

by Christian Thibaudeau web

May, 2013 Stuff I Learned From My First Month of CrossFit

1. I’d become lazy with my own training. I’d stayed in my comfort zone way too much, turning up the heat only when I really had to improve fast (e.g., before a T Nation video session).

2. My cardiovascular system is both better and worse than I thought it was. Better because I found I was able to keep going way past the point where I thought that I’d actually die, and worse because I think that dying would have felt better!

3. Some of the workouts used are very conducive to my own physique goals (my ideal physique is Georges St. Pierre with 10-15 pounds of added muscle mass). However, some are also very counterproductive and will make reaching my goals harder.

4. Training to be good at CrossFit will do more to build the body I want than just doing CrossFit. I think that’s one of the reasons why the top-level guys and girls have such great bodies – they do CrossFit sessions but they also do plenty of strength work.

5. I know that my strength-building methods are more effective than those used by even the top CrossFit athletes. I also know that the type of work done in the productive (for my goals) CrossFit workouts will do a lot to help me build quality muscle and get me leaner. A combination will give me everything I want from my training.

6. It’s fun to finally learn hard skills like handstand push-ups, muscle-ups, and the like, but you don’t need them to build the ultimate physique. If there’s one thing I don’t really like about CrossFit is the complexity of some of the skills. I understand that “being prepared for everything” is their driving concept, but if your goal is just to be more muscular, leaner, and stronger, the advanced skills aren’t necessary.

7. There’s something magical about being able to perform an explosive lift when you’re metabolically fatigued and your heart rate is running at 200 bpm. Being in that kind of distressed physical state activates a powerful survival mechanism. When you do strength and power work in that state you create a very powerful growth stimulus that cannot be achieved any other way.

8. My lats got sore for the first time ever and grew significantly. I always hated pull-ups and because of that I avoided them. I found that practicing them every day by doing strict pull-ups, kipping, butterfly, and rings at a non-maximal level worked like nothing else to build my lats. The weird thing is that I didn’t feel my lats that much while doing them, but I sure felt them the next day! This made me reconsider several things that I believed were immutable truths.

9. CrossFit indeed has a fairly high injury risk potential. Even as somebody who’s a student of lifting technique, I tended to cut the corners during a WOD. As such, it’s important to train the big basic lifts used in CrossFit during regular strength sessions to make proper technique as automatic as possible.

10. During a CrossFit workout, you get in a state of deep focus that allows you to do things you wouldn’t expect. For example, at one point I was having a hard time breathing and was very close to passing out, but I ended up doing one of my most technically solid snatches ever, with about 10 pounds less than my current max at the time. Experiencing that type of tunnel vision-like focus is something that you can learn to transfer to strength workouts and make them a lot more productive. I can also use my wife as an example. During regular strength workouts you couldn’t force her to deadlift 135 (because of the “big plate” on each side), yet during a WOD she went up to 225 pounds.

11. My capacity to do a high workload even in a state of metabolic distress has improved dramatically and much faster than expected. Along with my own training, I’m doing two workouts at the Levis CrossFit box/gym along with my wife. I’ll be honest, the first week I really thought that there was no way I’d be able to finish, or even survive. I felt a deep sense of panic about two-thirds of the way into each workout. By the second week I was actually able to finish strong instead of just surviving, and by the third week I felt so much better that after one workout I questioned whether I did the workout right because I actually felt good at the end!

12. I got lean fast! I’m the leanest I’ve been in the past five years and that’s with zero emphasis on nutrition. In fact I’m eating a lot more carbs now. After the first week I even jacked up my carb intake a lot to make sure I was recovering. Here’s what my daily food intake looks like. Keep in mind that this is not a dietary recommendation. I really didn’t plan anything and I’m certainly not among the gluten haters!

• 6 sirloin hamburgers (150g of carbs)
• 3-4 scoops of Plazma™ (roughly 114-152g of carbs)
• 6 scoops of Mag-10® (30g of carbs)
• 14 rice cakes (112g of carbs)
• 2 Finibars (80g of carbs)
• Some berries (roughly 20-30g of carbs)

That’s between 520 and 540g of carbs per day, and sometimes I even get to 600. Not bad for someone who used to fear ever going above 50 grams per day.

13. Despite my biggest fear, not only did I not lose any strength, I actually got stronger on many movements including pull-ups, dips, overhead presses, and deadlifts. My power snatch also improved. My power clean stayed the same, though, mostly because I couldn’t train it hard due to an elbow injury dating back two years ago when I went overboard on ring work.

14. I’m almost unbreakable with weights in the 60-75% range. Before that I could do tons of sets of 1-2 reps with 90% and not break. But I couldn’t handle higher reps or workloads. To give you an idea, after three weeks I tested myself on the deadlift and was able to perform 60 deadlift reps in less than 8 minutes with loads ranging from 70 to 75%. That might not seem humongous, but that’s one rep every 8 seconds. And honestly, I could have kept on going. I also did 60 behind-the-neck push presses, all over 225 pounds, in a tad under 9 minutes.

15. My lats and shoulders have improved the most. I used to have very good rounded delts, but for some reason I lost some size, roundness, and strength in those muscles over the past two years or so. My guess is that it was caused by a significant decrease in overhead pressing work (in favor of the bench press) and some chronic shoulder inflammation. To be good at CrossFit, you need to be super efficient and strong overhead, so I really had to shift my focus more on overhead pressing strength than the bench press. It paid off. I also did a lot of high-rep overhead work, which seems to be more effective than maximal loads to build the delts. Growing the lats was a given since I had to become good at pull-ups since they were basically present in all the workouts I did at the CrossFit box.

16. I lost fat in the upper and lower back, areas normally super stubborn for me.

17. I feel much better. I used to have energy crashes and even “borderline depressive” episodes. I attributed that to a messed up brain chemistry. Turns out that I was just out of shape! I find myself more energetic, happy to do chores. I’m not yet at the point of enjoying visiting my in-laws, but it will come I’m sure.

18. I feel athletic. I walk differently. I look more fluid and am more confident. I look like a different person when you see me approaching and it’s not even from the physical changes!

19. My bodyweight hasn’t changed much despite being a lot leaner. I started out at 215 pounds, which is pretty much my normal weight, and after four weeks I’m 213 pounds, but I’ve lost a lot more fat than just two pounds. So much for the fear of whittling away to 180 pounds in weeks!

20. The sport that will benefit the most from Plazma™ is training for CrossFit, no contest. Not only was I able to easily recover from some brutal metcon sessions and still lift big during my strength sessions, but I never felt physically out of it. I actually only got really sore once and that was after a workout where I did 64 power cleans with 185 pounds at the CrossFit gym and then push-pressed 295 pounds an hour later during a regular strength workout. My traps got sore, but that’s about it.


Here’s what you need to know…

•  While the thinking used to be that CrossFit made guys weak, the average competitor in the CrossFit Games is very impressive.

•  Quite a few CrossFit girls have better physiques than some figure competitors, even without dieting.

•  There’s something magical about being able to perform an explosive lift when you’re metabolically fatigued and your heart rate is skyrocketing.

•  Doing submaximal lifting that focuses more on speed and density of work, like you do in CrossFit, is a great way to build muscle.

•  CrossFit can also get you lean fast, even with zero emphasis on nutrition.

I have a secret. I did CrossFit almost exclusively last summer. I’ve competed in Olympic lifting, powerlifting, and I’ve been a competitive bodybuilder… and now I can say I’ve been a CrossFitter too. I went to CrossFit Levis three times a week and then trained on my own to work on strength and my Olympic lifts. I actually kept a kind of CrossFit journal back then. So, one year later, here it is: my CrossFit diary, along with some current-day observations.

Why I Decided to Try CrossFit

1. I’ve worked with a lot of CrossFit athletes this year, helping several prepare for the Canada East regionals. I helped some with their Olympic lifting and others with their entire training. I’ll tell you this: I’ve trained figure competitors who go to extreme lengths in their dieting, cardio, and training, and quite a few of the CrossFit girls I’m working with have better physiques than the figure girls… and that’s without dieting. Similarly, a former Canadian national bodybuilding champion I know started training for CrossFit and she looks better – not just better, but also more muscular and stronger – than when she was bodybuilding!

2. I always believed that CrossFit made girls look great and guys look small, in addition to making them lose strength. I don’t believe the latter anymore because some of the competitive CrossFit athletes are quite strong. The average competitor in the CrossFit games can do a 245-pound snatch, 335-pound clean & jerk, 550-pound deadlift, and a 450-pound back squat. And several overhead squat in the 300s and front squat in the 400s. Four of the guys I’m coaching can snatch over 225 pounds, which is pretty darn strong!

And just take a look at the top CrossFit competitors: Dan Bailey, Neil Maddox, Rich Froning, Jason Khalipa. These guys look badass – big muscles, athletic look, and lean. The average height/weight ratio of the top guys is 5’10”, 195 pounds at 8% body fat or under. I know that on the internets if you’re under 200 pounds you’re considered a weakling, but in reality a very lean 200 on an average-height body is very muscular. Heck, when I last competed in bodybuilding I weighed 188 pounds!

3. CrossFit has done more for Olympic lifting than Olympic lifting itself has ever done! Any sport/training model that’s based heavily on the snatch, clean, jerk, and push press can’t be all that bad.

4. I’m doing some workouts with my wife and there’s something very sexy about a girl doing deadlifts, clean & jerks, and snatches that really help re-ignite the passion in a marriage!

5. I hate not being good at something, especially when it’s training-related!

6. I always believed in the maxim, “Leaders lead from the front, not from the back.” And I always lived by the credo of never asking a client to do something that I can’t do myself. You might not be at the same level, but you should be physically capable of doing what you ask of them. Since I’m working with a lot of CrossFit athletes, I felt bad not being able to “lead from the front.”

7. Five years ago, I suffered from a viral myocardiopathy that led to heart failure. For two years my heart was functioning at 20-30% efficacy. This was hard to accept for someone who used to be athletic. It really affected my training and quality of life. Because of that I realized the importance of a strong cardiovascular system. I also believe that my CV health (or lack thereof) greatly diminished my capacity to gain muscle. Every time I went above 220 pounds I felt really bad and had to come down in weight.

8. I always believed that training density is one of the most important factors to stimulate a maximal response from your sessions. In CrossFit, density is the most important element. Every workout is either based on doing a certain amount of work as fast as possible or doing as much work as possible in a certain time frame. The sense of urgency this gives you can be as powerful as a shot of adrenalin.

That’s why I decided to give it a try.