At Last! A Poop Museum!

Ok, we've examined my borderline-deranged fascination with poop before ( see "How About a Fecal Transplant?," "Fabulous, Synthetic Poop" and "Cleaning Up Poop In Paradise"), so you'll understand why I was so thrilled recently when I learned that somebody has at last created a fitting tribute to this stupendous substance in the form of a museum.  Yes, a museum dedicated to excrement!

It's on the Isle of Wright, U.K., where apparently people are as enlightened (or deranged) about poop as I am.  I learned about the museum recently while scanning one of my routine online news sources, BBC.Com. This story was in their Earth section, a collection of brilliantly-written science articles, many of which are not only informative but also very, very funny. The author of this one is Katie Silver, whose enthusiasm for the topic is quite clearly conveyed in her entertaining and informative writing style -- I highly recommend  that you read the entire article, "Five Surprising Uses of Poo."  [Note -- "Poo" is the British translation of "poop."  The two terms will be used interchangeably henceforth.]

Zoo Poo

The museum is in the local zoo, where the curators have displayed 20 samples of animal droppings from crows to lions. Only one is from a human -- a sample of baby's poop -- but I could offer some real eye-catchers if the museum wants to expand their collection.  The National Poo Museum, as it is ambitiously called, even has its own website, https://www.poomuseum.org/, which provides a number of interesting details about the zoo and even includes an animated rendition of its catchy theme song, "They've Got An Awful Lot Of Poo At The Zoo."  Take a listen -- it's very cute.

How, you might ask, does the museum actually display specimens that are so...ah, delicate and aromatic?

Encapsulated Pigeon Poop

The answer is their invention of a clever process of drying and encapsulating them in plastic resin:

"...the [drying] machine [is] a long pipe with ‘poo hammocks’ that go into a poo dryer. Depending on the size of the faeces it will stay in the dryer for anything from a day to a couple of weeks. It’s then covered in resin and encapsulated, with vacuum chambers used to remove the air bubbles. The end result looks a little like a crystal ball. Except it has a poo in the centre." (Silver, 2016)

Somehow I find the mental picture of "poo hammocks" quite amusing.

Anyway, there is a great deal of serious information that can be gleaned from poop. My wife and I are very familiar with this from spending many hours on African safaris and nature walks in other parts of the world, during which our guides/trackers gave us many poop lessons. For example we now know the difference between male versus female giraffe droppings (females are tapered), between white rhino and black rhino poop (the nature of the cuts on undigested twigs), what a hyena had for dinner (smell and nature of bone fragments), and why wombat do-dos are cubes (the wombat pats them into that shape so rivals can't roll them off the trail). A good tracker can tell the approximate age and health of the animal, how long ago the nugget was deposited, how fast the animal was traveling, and even where it might be headed next, based on various telltale signs. A poop-pile is an open book, so to speak.

Of course, from past blogs we know that it's not just what you see in poop that counts, but sometimes what you can't see -- i.e., the trillions of microbes that live in our gut and ultimately reside in our poop as well. The microbial signature of different species can provide useful information as to what kind of animal made a deposit even when other indicators are long lost.  For example, Katie Silver documents how microbial poop signatures have recently provided evidence of the exact route Hannibal's army took when crossing the Alps 2000 years ago, which up until now had been mainly conjecture.  Hannibal took with him some 15,000 horses, which are prodigious poopers.  Archeologists located one spot along the most likely route where that many animals might have been kept during the crossing. When then dug down to the 2000-year level they found a high concentration of both organic material and Clostridia bacteria, a microbe common to horse droppings. The magnitude of the deposit and its microbial signature provide solid evidence that this was the actual route.

Fossilized Dino Dropping

A preserved bit of horse droppings from Hannibal's campaign would make a great exhibit in the Poo Museum, but as far as I can tell there isn't one. Nor does the Museum have an example of the ultimate in preserved poop -- a coprolite, or fossilized dinosaur dropping. These dino nuggets can be up to two feet long and are highly prized by paleontologists for the information they provide about diet, feeding behavior, and even health of animals that are now extinct. A recent Smithsonian Magazine article reports on an even rarer find -- a 150 million-year-old pterosaur fossil that seems to show the contents of its digestive tract still inside. What an exhibit that would make!

Despite the shortcomings of not having specimens from Hannibal's Crossing or from any dinosaurs, the National Poo Museum is quite active in promoting beneficial educational programs. For example, the museum's website lists this year's events as:

• Continuous Program, Summer, 2016:  "Poo At The Zoo" featuring the resin-sphere exhibits.
• May 30-June 15, 2016:  "Love Your Poo Week," focusing on waste treatment and disposal.
• July 6, 2016:  My personal favorite, "Brighton Turd Nerd Night" featuring expert speakers on topics such as "Tackling dog shit in postwar Paris" and "Dirty dogs, worms and the politics of shit in 1970s Britain." 

The last one sounds particularly interesting.  However, the connection between poop and politics seems a bit obvious, and not just in 1970's Britain......

A Traveler's Tales of Tummy Troubles

Betty the Bat made another circle through the latrine, this time dipping a wing in friendly recognition (or so I imagined).  I had been there four times already and the night was still young. The open-pit latrine was down a walkway lit by kerosene lamps, the smell of which brings a touch of nausea to this day. Another smell that haunts me is the disinfectant/deodorizer the lodge used in the latrine, because this night effluvia was coming out both ends of me, meaning at times my head was disturbingly close to the source of the odor.  The latrine was about 100 feet from the rooms in our lodge on the Amazon River in Peru, where earlier in the day we had arrived for a few days of exploring flora and fauna of the jungle.  In the afternoon we had gone fishing for piranha and the chef had prepared them for us to taste at dinner.  I, however, never got that far -- before I could take my first bite my intestines told me in no uncertain terms to make that first trip to the latrine.  Probably something I ate for lunch, but it was never clear. Whatever the exact cause, after a day in a hammock watching the Amazon flow by (while my wife had a great adventure trekking through the jungle),  I rejoined the living.

Over the 40+ years my wife and I have been traveling, we have both had a number of incidences of traveler's tummy troubles. When we relate stories like the one above to other people (usually in a bout of "competitive complaining") they often assume our intestinal problems occur more often in third-world countries and exotic locales within them.  Actually, our experience doesn't offer strong support for this.  A counter example to my upchucking along the Amazon occurred recently in Sweden, undoubtedly one of the most developed, squeaky clean places on the planet.  In this case some "Toast Scoggen" cleaned me out better than a colonoscopy prep. On the other hand, a trip to Zambia, Africa a few years ago included a meal cooked for us by local village women in open pots on the ground  -- no problems at all. And yes, it happens in the good old USA.  I once ran back to our motel after dinner at a restaurant in Maine, nearly leaving a trail of DNA as I went. 

Timid travelers also assume that if they stick to eating in upscale places they will be less likely to encounter problems.  Again, not our experience.  Many years ago I remember having lunch at the very posh Acapulco Princess hotel and then waiting outside a bathroom shortly afterwards for my wife's bipolar evacuation of it.  On the same trip, however, we ate a fish dinner at a local beach restaurant, selected from several as being the most upscale and clean-looking.  But as we left we discovered the food had actually come from the restaurant next door, prepared in a tiny shack where cockroaches seemed to be the dishwashing staff.  No intestinal distress at all.

Another of our observations is that there are definitely individual differences in susceptibility -- some people are just plain more prone to traveler's tummy than others.  Many years ago my wife and I started sharing our food in restaurants -- two or more dishes which we split between us. Since then we have discovered that even when exposed to exactly same food we have different intestinal reactions.  Perhaps the first time this was apparent was on our first trip to France, where I spent a good portion of time in the bathroom but my wife never had any problems. On this trip I did a very good imitation of a Bulimic, because even though I was sick a lot I kept on eating because the food was so good.  We later figured out that part of the difficulty was that in those days my stomach was pre-loaded with a high amount of acid from many cups of coffee, vitamin C supplements, and routine ingestion of aspirin for various aches and pains. Mixing all that acid with rather rich food was like a recipe for a volcano science project.  After cutting down on the supplemental acid, the next trip to France was much more pleasant, though far more fattening.

Although my problems in France were likely due to stomach acid, the most common cause of traveler stomach troubles is exposure to microbes.  About 80% of all cases are caused by bacteria of several kinds (mostly of the E. coli variety) and 10% or so by viruses (like the infamous Norovirus) and various protozoa (see Wikipedia). According to the CDC, intestinal problems are the most common travel affliction (other than walletus depletiosis) hitting 30-70% of all travelers, usually within the first week or so of their trip.  Although visitors to developing countries are at higher risk, all destinations have a significant risk level, even the most highly developed (as my personal experience attests).  Also, travelers from developed countries get sick more often than those from developing regions (Medicinet), and all visitors have a higher incidence than locals because the residents have developed resistance to the most common pathogens (Wikipedia) . Note, this often makes terms for traveler's tummy troubles like "Montezuma's Revenge" rather appropriate -- it is payback for germs invaders brought from Europe that infected the natives who had no natural immunity.

Traveler's intestinal problems nearly always last only a few days and go away on their own, though many people like to take antibiotics and anti-motility drugs like Lomotil.  (I love the double meaning of "anti-motility").  These treatments have their downsides, however.  Popping antibiotics may kill the offending bad microbes but it will also kill the beneficial ones that live in your gut and help protect you from other kinds of infections (see How About a Fecal Transplant?, Microbes for Breakfast!, and Fabulous Synthetic Poop!).  And male geezers with prostrate problems should be wary of the side effects of some anti-motility medications -- you may become plugged up in more ways than you wish (I speak from experience on this one).

So, is there any way to prevent this unpleasantness?  Being very careful in what you eat and drink is certainly good advice, but as the CDC notes, "Traditionally, it was thought that TD [Traveler's Diarrhea] could be prevented by following simple recommendations such as 'boil it, cook it, peel it, or forget it,' but studies have found that people who follow these rules may still become ill."  It is also the case that often a traveler can't follow these recommendations for practical reasons (like when traveling with a group or as a guest of a local resident).  The CDC is pretty blunt and realistic about this: "Although food and water precautions continue to be recommended, travelers may not always be able to adhere to the advice. Furthermore, many of the factors that ensure food safety, such as restaurant hygiene, are out of the traveler’s control."  My own experience, as illustrated by the examples above, is certainly in line with the CDC's conclusion -- being careful is prudent but hardly guarantees you won't still get sick at some point and predicting when or where is very difficult.

Besides trying to watch what you eat and drink, there is evidence that taking daily doses of bismuth subsalicylate, the active ingredient in Pepto Bismol, can cut the incidence of stomach illness by up to 50%. But there are a number of side effects and interactions that make its use questionable for many people:  "BSS commonly causes blackening of the tongue and stool and may cause nausea, constipation, and rarely tinnitus. BSS should be avoided by travelers with aspirin allergy, renal insufficiency, and gout and by those taking anticoagulants, probenecid, or methotrexate. In travelers taking aspirin or salicylates for other reasons, the use of BSS may result in salicylate toxicity" (CDC ). Sounds like the cure may be as bad as the problem. Likewise, preventative doses of antibiotics do seem to work, but they may lead to greater stomach problems down the road by encouraging bad microbes that are resistant to antibiotics and therefore very difficult to treat. Also, good microbes aid in digestion and help fight a wide range of diseases -- killing them may not be a very wise thing to do.  Speaking of good microbes, one preventative measure which seems to me like it should work is to ingest probiotics (like yogurt, kefir, and soft cheese), but so far the research is inconclusive (even so, I try to keep up my input of yogurt while traveling).

It seems to me we are left with two choices.  One is to buy some virtual reality goggles and experience travel electronically, without the messiness and risk of actually doing it. This certainly avoids traveler tummy troubles, but also removes some of the most rewarding aspects of real travel, like unplanned interactions with real people.  As you might guess, I heartily reject this option. The second is to accept that occasional tummy troubles are a small cost to pay for the life-enriching experiences that come from being exposed to cultures other than your own.  Traveling in total comfort and safety is not possible and even if it were, I don't think it would be desirable because the most beneficial aspects of travel involve a certain degree of challenge and adventure that can lead to surprisingly positive experiences.  Like making friends with Betty the Bat.

Whose Mind Is This, Anyway?

"....we are not unitary individuals but superorganisms, built out of both human and nonhuman elements; it is their interaction that determines who we are."  (Kramer & Bressan, 2015)

One of the illusions most of us hold with great conviction is that we are separate and distinct from the rest of the world.  "I am here. You (and everything else) are there."  "I am this.  I am not that." This belief in separateness and in the essence of our self identity seems so clearly true that we tend not to question it.  However, once we begin to examine closely what is meant by "here" and "there," "I" and "you," "this" and "that," things start to get a bit fuzzy.

My somewhat deranged fascination with (a) microbes (aka "germs") and (b) excrement (aka "poop") has led me to discover that there is a lot of scientific evidence supporting the idea that our belief in separateness is simply not correct. I've written about some of this before (see Fabulous Synthetic Poop!, Microbes for Breakfast!, and How About A Fecal Transplant?).  Research has shown that each of us is host to more than 100 trillion microbes that live in, on, and around us. Some microbes have been with us since before birth, influencing our development in the womb, and others joined us as we traveled through the birth canal and when our mothers nursed us. The interdependency between their lives and ours is so complete that for the first year of life our immune systems are switched to low so that more microbes can colonize our bodies -- it seems that the evolutionary advantage of having beneficial strains of these critters become part of us is so strong that it outweighs the risk of early childhood infection from "bad" microbes or other pathogens. In fact, we are dependent on them to the point that we could not survive for long without them. They are essential in digesting food, mounting successful immune defenses against diseases, and synthesizing certain vitamins.

In adulthood there are 10 times more microbes in us than there are human cells. Together they are our "microbiome," a community of creatures that interact with each other and with us in complex ways throughout our lives.  The relative number of different strains of bacteria in our microbiomes is unique to each person -- a kind of microbial fingerprint. In fact, some recent preliminary research has shown that we leave microbial traces in our environments that are as identifiable as fingerprints even without touching anything (Meadow et al., 2015).  It seems each of us has a "cloud" of bacteria that surrounds us and which leaves our unique signature wherever we go. If we could make the cloud visible (a "microbiomic aura") it would be very difficult to discern where our microbes end and "we" begin.
 
"I" and "Me" most definitely do not refer to a single, unitary organism that exists separately from all other organisms.  As I suggested with the opening quote above, it is more appropriate to regard ourselves as "superorganisms" -- beings composed of many organisms whose lives are intimately and inextricably intertwined. This integration goes beyond just physical interactions, however.  There is now considerable evidence that even our thoughts, feelings, and behaviors are influenced by nonhuman elements within us -- our minds, in other words, may also be those of superorganisms.

The current state of our knowledge about humans as superorganisms was recently presented by Peter Kramer and Paola Bressan of the University of Padua in an excellent article published in the journal Perspectives on Psychological Science (Kramer & Bressan, 2015). Kramer and Bressan review the data on the microbiome and also research that has investigated other foreign components of our makeup, including viral DNA, cells from other human beings, and microbes that reside in the brain. Their conclusion is quite different from our usual self-view:

...our emotions, cognition, behavior, and mental health are influenced by a large number of entities that reside in our bodies while pursuing their own interests, which need not coincide with ours. Such selfish entities include microbes, viruses, foreign human cells, and imprinted genes regulated by viruslike  elements.......we are not unitary individuals in control of ourselves but rather ... collections of human and nonhuman elements that are to varying degrees integrated and, in an incessant struggle, jointly define who we are.

I'll focus on just two examples to illustrate the psychological influences of our nonhuman residents: gut microbes and brain microbes.  If you want to explore other sources of influence, see Kramer & Bressan's paper, or a less technical partial treatment from BBC.Com, "Is There Another Human Being Living Inside You?"

Effects of Gut Microbes on Behavior, Personality & Mood

Certain strains of microbes in our microbiome have been shown to alter a number of neurotransmitter chemicals, for example by manufacturing and releasing GABA and other neuroactive substances, including noradrenaline, acetylcholine,serotonin, and dopamine. These chemicals are involved in mood regulation (eg., euphoria, anxiety and depression), risk-taking behavior, memory formation, sociability, responsiveness to stress, and they likely play a role in certain mental disorders, such as schizophrenia and autism.

The link between specific patterns of gut microbes and behavior has been clearly shown in animal studies where normally timid strains of mice become adventurous and adventurous mice become timid when colonized with the microbiome of the other strain through fecal transplants. In other studies, mice raised with minimal gut microbes showed lower levels of anxiety under calm conditions, but stronger than normal reactions when stressed.  These effects could be eliminated if the germ free mice were given fecal implants from normal mice, but only up to a certain age: "Thus, early exposure to (healthy) gut flora is required for normal development of the stress response ...[and] neonatal infection with pathological bacteria may permanently alter such response, predisposing the individual to stress-related disorders later in life" (Kramer & Bressan, 2015).  Increasing certain microbe strains commonly found in yogurt reduced despair-like behaviors (eg., passivity, not attempting to escape stressful stimuli) in rats, and feeding mice a microbe-laced broth improved their memory and reduced anxiety and depression-like behaviors.

Studying the psychological influences of microbes in humans is more challenging because our experiences can be unwittingly influenced by expectations and prior beliefs  -- the so-called placebo effect, or just plain "wishful thinking."  Relying on self-reports of mood, for example, is not scientifically convincing, but several studies of the effects of altering microbial concentrations of certain gut microbes have also included more objective measures.  For instance, in one study healthy individuals ingested daily doses of lactobacilli, the same microbe found in yogurt and other "probiotic" products.  After one month there was a significant reduction of self-reported anxiety and depression, but more importantly there was also a measurable reduction in stress-related cortisol levels, showing the same effectiveness as benzodiazepines (eg. Valium). In another study these same bacteria modified healthy women’s brain activity in regions that control processing of emotion and sensation, dampening reactions to facial expressions of anger and fear ... these same regions are involved in anxiety disorders (Kramer & Bressan, 2015).

Microbes on My Brain

Most of us are hosts not only to gut microbes but also to strains of microbes that colonize our brains. Residing in the brain gives them the opportunity to directly manipulate neurotransmitters and to influence behavior. Particularly interesting, however, is evidence that they do not simply influence mental processes, they also manipulate the brain in ways that increase their own survival and genetic viability.

Unlike gut microbes, brain microbes are almost always parasites, in that they exploit us while simultaneously doing us harm. They are surprisingly (and disturbingly) common. We usually think of parasites as prevalent only in poorer, less developed countries, but in the case of certain brain microbes the rate of infection is uncorrelated with poverty or level of development. For instance, toxoplasma gondii infects about 22% of the U.S. population (CDC data), 50% of those in the U.K and continental Europe, and as high as 70-80% is some South American and African countries, but as low as 10% in parts of Asia (Hill & Dubey, 2002,  Kramer & Bressan, 2015). It is generally believed that toxoplasma evolved as an animal parasite and humans are an incidental host that has occurred in modern times because of close contact with certain animals.

Toxoplasma is a particularly good example of a microbe that manipulates the brain activity and behavior of its host. Toxoplasma eggs are usually found in the poop of animals that have eaten intermediary hosts of the microbe. Animals that ingest the poop become infected and the microbe is spread more widely.  A common example is when domestic cats eat infected mice or rats, then excrete poop with toxoplasma eggs. Rodents, not known to be picky about their food, eat the cat poop and complete the cycle. Humans who come into contact with infected cat feces (say through gardening or cleaning a litter box) can also become hosts by unwittingly ingesting eggs they have accidentally transferred to their food. Another source of infection for humans has been found to be commercially available food, particularly under-cooked meat or fish that has somehow been tainted with Toxoplasma eggs.

Now for the really interesting part. Rats and mice that are infected with Toxoplasma lose their fear of cats and even become sexually attracted to cat urine (see Berdoy, Webster, & Macdonald, 2000).  This, of course, is very bad for the rodents but very good for Toxoplasma because only in the intestines of cats or other intermediary hosts can the microbes produce eggs.  "Toxoplasma manipulates the brain of the rat so as to increase the probability that its otherwise uncertain transfer to the cat’s intestines actually takes place" (Kramer & Bressan, 2015).  The mechanism for this seems to be an increase of the neuroactive chemical dopamine, which in humans is known to be associated with recklessness and sensation-seeking behavior and greater susceptibility to schizophrenia.  This may also be a cause of higher workplace and traffic accidents among infected humans.  Aside from the neurological effects on behavior, Toxoplasma doesn't usually pose serious physical problems for its host unless the victim's immune system is weakened.  Humans with other health problems, young children, and elderly are at risk and in infants neurological damage can be quite severe.  For this reason pregnant women (who can be infected but asymptomatic) are often advised to avoid contact with cats in order to prevent passing Toxoplasma eggs to their offspring.

Conclusion

Besides Toxoplasma there are a number of other microbes that often colonize the brain, and there are several non-microbial life forms that also influence behavior and cognition. The bottom line for me is that "knowing thyself" requires assessing the contribution 100's of trillions of other organisms to our sense of who we are.  The old adage, "we are not alone," applies not only to things that are external to us but also to things that are deeply embedded within our bodies. Perhaps, as Kramer & Bressan put it: "It is time to change the very concept we have of ourselves and to realize that one human individual is neither just human nor just one individual. "
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Sources & Resources
Kramer, P., & Bressan, P. (2015). Perspectives on Psychological Science, Vol. 10(4) 464–481
You're Surrounded by a Cloud of Bacteria as Unique as a Fingerprint: Washington Post, 9/22/15
CDC - Toxoplasmosis - Epidemiology & Risk Factors 
CDC -Toxoplasma gondii Infection in the United States
Berdoy M., Webster, J. P. and Macdonald, D. W. (2000) Fatal attraction in rats infected with Toxoplasma gondi. Proc. R. Soc. Lond. B, 267, 1591-1594
Is There Another Human Being Living Inside You?:  BBC.com, 9/18/15 

Fabulous Synthetic Poop!

Last year I wrote about important scientific breakthroughs being made in understanding our microbiomes, the collection of trillions of bacteria that live on and in our bodies  -- see How About A Fecal Transplant?

One conclusion from this research is that our general cultural attitude that "the only good microbe is a dead microbe" is emphatically wrong.  We are very dependent for our health and well-being on these little critters, and in fact we can't exist without them.

The bacteria that colonize our guts are particularly noteworthy -- they enable us to digest food, synthesize certain vitamins, and fight off many infectious diseases. Normally the thousands of bacterial strains in our intestines form a complex ecological community in which competition among them is in balance. Of course, certain intestinal bacteria are quite harmful to us if they overwhelm the good guys, which can happen because of changes in diet, physical trauma, encounters with environmental toxins, or illness that weakens the immune system. One example is Clostridium Difficile, a strain of bacteria which can cause chronic severe diarrhea and other intestinal problems and is linked to 14,000 deaths each year in the United States. It is notoriously hard to treat.

In the past we have responded to Clostridium Difficile and other intestinal infections with a "nuke'm all" strategy of giving patients broad-spectrum antibiotics that kill both bad and good bacteria, not unlike a gardener spraying the entire garden with herbicide to get rid of weeds.  This has two unfortunate consequences.  First, the harmful bacteria become resistant to the antibiotics, requiring ever more powerful forms of treatments.  Second, wiping out the good bacteria destroys the normal ecological balance in the microbiome that can help keep the bad bacteria in check.

One very promising approach to these problems has been the fecal transplant, an "interesting" procedure in which the stool from a healthy donor is implanted in the intestinal tract of a patient with a bacterial infection, for example through fecal suppositories. The idea is that the healthy stool contains the complex collection of microbes needed to restart a depleted microbiome in another person. Despite what researcher Dr. Alexander Khoruts calls the "ick" factor, the procedure seems to work, particularly in Clostridium Difficile infections.

And now the really good news for those of us who have trouble with the concept of fecal suppositories, or in general with the idea that somebody else's poop can be good for us. A group of British and Canadian researchers reported just this month in the journal Microbiome that they have developed a successful new procedure that removes much of the "ickiness."  Their report has a catchy title:

"Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut."

Who says scientists don't have a sense of humor?

The procedure is to take poop from a healthy donor, but instead of transplanting it directly to a recipient (thence the "ickiness), the bacteria in the poop are cultured in a laboratory and about 30 of the purified beneficial strains are combined to make "synthetic poop" that contains the bacteria but not the "ick."  The researchers call this material "RePOOPulate." Seriously.

The RePoopulate procedure has the advantage of allowing a high degree of control over the kinds and numbers of bacteria in the transplant.  This means the exact same treatment can be re-administered if necessary, and it also reduces the chances of inadvertently transferring diseases from the donor.  And once the bacteria have been cultured new RePoopulate can be concocted without a new poop donor.

This seems like a great advance to me, and you really have to give the researchers credit.  There is, however, just one teensy problem left to work on.  The transplant is performed during a colonoscopy.  For those unfamiliar with this procedure, see Dave Barry's famous essay on the subject.

Of course, I suspect if you are someone suffering from a Clostridium difficile infection you wouldn't think twice if a colonoscopy would end your suffering.

As for myself, I'm still hoping for a synthetic poop pill.
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Additional links for the scatologically inclined:

"How About A Fecal Transplant?"  My blog last year on this general topic.
"Stool substitute transplant therapy...."  The Microbiome journal article on synthetic poop.
"Artificial Poop Transplant May Fight Bacterial Infection:"  A somewhat more readable article in LiveScience about the procedure.
 "Microbes For Breakfast"  My previous blog on why eating microbes is good for you.

Microbes for Breakfast!

On the breakfast buffet table was a big bowl of white stuff the consistency of thick whipped cream.  The little sign beside it said "Yogurt." Normally I would have moved right on to the real food, since at that time I placed yogurt in the same "not-past-my-lips" category as cottage cheese (what are all those lumps, anyway?) and buttermilk (anything that leaves scum that thick on the empty glass can't be good).

This was in 2003, on our third trip to France. Previous visits had introduced me to some fabulous French food and although for most of my life I've not been very adventurous when it comes to eating I tend to throw caution to the wind when traveling there.  And so I tasted it.

Well, as has happened a few other times in France, I thought I had died and gone to heaven (two other occasions were when I tried my first chocolate croissant and when I took my first bite of Roquefort cheese).  This homemade yogurt stuff was rich and creamy and smooth and not quite like anything I had ever tasted before -- I loved it.  Wow, me eating yogurt -- wonders will never cease!

Since then I have become a real yogurt fan, and now I have it for breakfast (usually with granola my wife makes) almost every day, and when we travel I seek it out whenever possible. But those who know me will understand that I don't just eat it -- I've had to investigate it and research it so I can justify my recent passion for something I rejected for most of my life.  And what I've learned is that (a) yogurt is one of nature's most perfect foods and (b) many of its beneficial qualities come from a most unlikely source -- microbes, aka "germs."

Webster's defines yogurt as "a fermented slightly acid often flavored semisolid food made of milk and milk solids to which cultures of two bacteria (Lactobacillus bulgaricus and Streptococcus thermophilus) have been added."  Sometimes other strains of bacteria are also added.  Sounds yummy, right?  Fermented....semi-solid...bacteria...... Had I read this first I would never have tried it.

Yogurt can be made from the milk of cows (most common in the U.S. and Europe), sheep or goats (common in Turkey, where yogurt probably originated), and water buffalo (India & Egypt). Each of these has a different flavor and texture.  Greek style yogurt is strained to remove some of the liquid and is therefore thicker and a bit more tart.  Yogurt can be made from whole milk or from reduced-fat milk.  When the source is low-fat or non-fat milk the resulting yogurt has almost no cholesterol and the calories it contains are nearly all from protein, a very good thing from a health viewpoint (though there is some loss of flavor -- let's face it, fat tastes goooood).  Assuming the yogurt hasn't been adulterated by adding sweeteners, the nutritional qualities are remarkable.  It is a food that is high in protein, calcium, and several vitamins but low in fat and cholesterol.

But that's not all.  What about those bacteria?  It may be obvious that they are responsible for the fermentation process that results in yogurt, just like microbes are used to make beer, cheese, and wine.  However, in those cases the bacteria are pretty much finished once the job is done and they convey no particular health benefits of their own.  In yogurt, though, they continue to produce benefits even after the yogurt is consumed, assuming they are still alive (some manufacturers heat the finished yogurt, which kills the bacteria).  That's right, it is healthier to eat live germs than dead ones.  Here are some of the health benefits that research has shown derive directly from the live bacteria, excerpted from a summary by the Dr. Sears Health Group:

• Yogurt is easier to digest than milk. Many people who cannot tolerate milk, either because of a protein allergy or lactose intolerance, can enjoy yogurt. The culturing process makes yogurt more digestible than milk. The live active cultures create lactase, the enzyme lactose-intolerant people lack, and another enzyme contained in some yogurts (beta-galactosidase) also helps improve lactose absorption in lactase-deficient persons. Bacterial enzymes created by the culturing process, partially digest the milk protein casein, making it easier to absorb and less allergenic.
• Yogurt contributes to colon health.  ... yogurt contains lactobacteria, intestines-friendly bacterial cultures that foster a healthy colon, and even lower the risk of colon cancer. Lactobacteria, especially acidophilus, promotes the growth of healthy bacteria in the colon and reduces the conversion of bile into carcinogenic bile acids. The more of these intestines-friendly bacteria that are present in your colon, the lower the chance of colon diseases. Basically, the friendly bacteria in yogurt seems to deactivate harmful substances (such as nitrates and nitrites before they are converted to nitrosamines) before they can become carcinogenic...For senior citizens, who usually have more sensitive colons or whose intestines have run out of lactase, yogurt is also a valuable food. Elderly intestines showed declining levels of bifidus bacteria, which allow the growth of toxin-producing and, perhaps, cancer-causing bacteria. [my italics]
• Yogurt improves the bioavailability of other nutrients. Culturing of yogurt increases the absorption of calcium and B-vitamins. The lactic acid in the yogurt aids in the digestion of the milk calcium, making it easier to absorb.  
• Yogurt can boost immunity. Researchers who studied 68 people who ate two cups of live-culture yogurt daily for three months found that these persons produced higher levels of immunity boosting interferon. The bacterial cultures in yogurt have also been shown to stimulate infection-fighting white cells in the bloodstream. Some studies have shown yogurt cultures to contain a factor that has anti-tumor effects in experimental animals.
• Yogurt is a rich source of calcium. An 8-ounce serving of most yogurts provides 450 mg. of calcium, one-half of a child's RDA and 30 to 40 percent of the adult RDA for calcium. Because the live-active cultures in yogurt increase the absorption of calcium, an 8-ounce serving of yogurt gets more calcium into the body than the same volume of milk can.  [my italics]
• Yogurt is an excellent source of protein. ...Besides being a rich source of proteins, the culturing of the milk proteins during fermentation makes these proteins easier to digest. For this reason, the proteins in yogurt are often called "predigested." 
• Yogurt can lower cholesterol. There are a few studies that have shown that yogurt can reduce the blood cholesterol. This may be because the live cultures in yogurt can assimilate the cholesterol or because yogurt binds bile acids, (which has also been shown to lower cholesterol), or both. 

So the lesson here is that although there are plenty of nasty microbes out there that will kill us or make us very sick, there are many that do the opposite.  In fact, as detailed in my blog "How About A Fecal Transplant?"  we apparently can't live without some of them residing in our guts.

And of course the additional lesson of yogurt is that these little critters can be very tasty, too.

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Some additional info:
A summary of research studies on the benefits of yogurt from the National Yogurt Association.

WebMD's summary of yogurt benefits.

How About A Fecal Transplant?

Yes, you read correctly.  A fecal transplant.  "Fecal" as in "poop."  "Transplant" as in "from one person to another."

This new medical procedure makes the idea of using leeches, maggots, and flesh-nibbling fish seem appetizingly appealing by comparison.  I recently learned about it from a couple of New York Times science articles by Carl Zimmer and Gina Kolata, and it was so interesting I did some followup investigating of my own. The transplant is one promising development in the treatment of all kinds of health problems that has emerged from the field of medical ecology, a branch of microbiology which studies the complex interactions between health and a person's microbiota (or microbiome), the collection of 100 trillion microbes that live on and in each human body.

The two to five pounds of complex microbial communities that inhabit our bodies are apparently essential to not just our health but to our very existence.  Without them we would be unable to digest food, synthesize certain vitamins, and fight off many infectious diseases.  While it is certainly true that quite a few bacteria are harmful to us, many more are beneficial to the point that we can't live without them.  Our microbiome is as essential to us as our heart or our brain.

A microbiome is a true ecosystem in the sense that it involves a complex balance among the many different species of bacteria, viruses and fungi that comprise it.  In fact, one difficulty in studying these organisms has been that they are so adapted to living surrounded by other microbes and are so dependent on their host body that many can't be isolated and grown in the lab, and even if they do survive outside of the body they often behave differently than in their natural environment. However, a recent five-year federally funded research program has begun to give a clearer picture of our microbial communities and their impact on our health by using DNA analysis that doesn't require laboratory cultures. Called the Human Microbiome Project, the study involves 200 scientists at 80 institutions who have sequenced the genetic material of bacteria taken from nearly 250 healthy people, an immense effort that has led to some surprising findings.

For one thing, the researchers discovered more strains than they had ever imagined — as many as a thousand bacterial strains on each person. And each person’s collection of microbes was different from the next person’s, a kind of microbial fingerprint that uniquely identifies each individual.  Also surprising was that there were genetic signatures of disease-causing bacteria and viruses lurking in the microbiome of every one of these healthy individuals.  Instead of making people ill, or even infectious, the disease-causing microbes were simply living peacefully among their neighbors, held in check by the complex interactions of the microbiome community.

Another finding is that a person's microbiome changes throughout life in response to environmental and biological influences.  This process begins at birth, when certain key bacteria are transferred from mother to child during delivery and afterward during nursing. In pregnancy the relative concentrations of certain bacteria change in a women's birth canal in response to hormonal shifts.  One species of bacteria that is normally rare but becomes dominant is lactobacillus johnsonii. It is usually found in the gut, where it produces enzymes that digest milk. It’s an odd species to find proliferating in the vagina, to say the least. Dr. Aagaard-Tillery, one of the scientists who made this discovery, speculates that during delivery a baby will be coated by lactobacillus johnsonii and ingest some of it, an inoculation that prepares the infant to digest breast milk. The milk, it turns out, contains some 600 species of beneficial bacteria and also certain sugars that the baby can't digest but which nourish the bacteria. It seems the mother is not only feeding the child but also the child's bacteria and thereby promoting the development of the child's microbiome.

Our cultural attitude toward microbes is decidedly negative and non-selective:  "The only good microbe is a dead microbe."  However, the more we learn about the microbiome the clearer it becomes that this is not really justified and may be very harmful to us in the end.  For example, the use of broad-spectrum antibiotics to treat infections, while effective in the short run, wipes out not only the bad bacteria but also many of the the ones that are necessary to restore and maintain health.  We have generally assumed that the microbiome would return to normal on its own, but scientists are now realizing that assumption isn't justified -- it would be like assuming that lettuce and tomatoes would spontaneously return after spraying the whole garden with herbicide to kill the weeds.  In fact, there appear to be certain strains of harmful bacteria that thrive in disrupted or diminished microbiomes following broad-spectrum antibiotic treatments, like the antibiotic-resistant Clostridium difficile.  Re-establishing a healthy microbiome is very difficult in these circumstances.

Enter the fecal transplant.

According to Lita Proctor, program director for the Human Microbiome Project, "Half of your stool is not leftover food. It is microbial biomass.”  Assuming the donor is healthy, this means stool contains the complex collection of microbes needed to restart a depleted microbiome in another person.  And it seems to work.  Initial studies using fecal suppositories to treat Clostridium difficile infections have been very promising, and larger clinical trials are underway.  Fecal transplants are also being studied as a way to treat obesity by transplanting fecal samples from lean donors to obese patients. Researchers at the Academic Medical Center in Amsterdam are running a clinical trial to see if fecal transplants can help treat obesity. They have recruited 45 obese men; some are getting transplants from their own stool, while others get transplants from lean donors. The scientists are finding that the transplants from lean donors are changing how the obese subjects metabolize sugar.

Efforts are also underway to isolate the bacteria from the poop, to remove the "ick" factor, as researcher Dr. Alexander Khoruts puts it.  He would eventually like to develop probiotic pills that contain just a few key species required to build the intestinal ecosystem  -- Poop Pills, so to speak.

I certainly learned a lot from researching this topic, and the information has changed my outlook about who and what I am. For one thing, I realize how wrong my belief is that I am separate and independent from my environment.  "I" am composed of trillions of other organisms without which I could not exist.  They are as much "me" as any other part of my body.  As Dr. Barnett Kramer of the National Cancer Institute has said,  "humans in some sense are made mostly of microbes. From the standpoint of our microbiome, we may just serve as packaging.”

Certainly a humbling thought.