We are not alone

Have you ever stared at one of those glossy photographs in National Geographic of the small birds riding on the head and back of a massive hippo partially submerged in some far away African pond and thought to your self “that’s got to be annoying.” Why doesn’t it shake them off? Why not submerge? Maybe, after dunking over and over only to have the birds return, has the hippo simply given into his avian hitchhikers, annoying, as they seem?

The African jacana bird is said to spend an average of five hours each day riding on the back of wading hippos – pecking at and ingesting flies, parasites, ticks, detritus and dead skin. Perched upon this floating buffet, the birds also feed upon the many small fish that can gather around the submerged hippo. Seems the fish feed on the same parasites, ticks, dead skin, and algae as do the birds. You would think the never ending pecking and nibbling would finally get to the hippo – and it does – often resulting in thrashing about in the water and fights with nearby hippo neighbours. But for much of the time, the hippo goes about daily water activities with pecking birds and nibbling fish in constant tow and just puts up with their intrusions. Stay with us, there is a point.

Researchers have observed that the hippo-bird-fish relationship may in fact be a symbiotic one, in that everyone benefits at some level – even the host. The hippo gets the ticks, parasites, dead skin, and flies efficiently removed on a dependable schedule, and the birds and fish benefit through nutrients derived from the regular cleansing. Interestingly, different species of fish have been observed targeting specific body parts of the hippo. Members of the carp family are known to be the main cleaner, mowing along the large surface of the hippos hide, removing everything indiscriminately. Species of cichlids prefer cleaning duties in the tail area, while other species clean between the many cracks in the soles of the hippo’s feet. While far from a passive recipient of these cleaning services, hippos have been observed splaying their toes and spreading their legs, affording easier access for the attendant fish. Being opportunists, hippos are known to visit places around the pond where large groups of fish are known to congregate, in effect pulling into “full service” cleaning stations. Life is good.

The health and nutritional dance played out on ponds throughout Africa between the hippo, its avian passengers, and the visiting nibbling fish has been going on for as long as hippos have been around – which is a long time. But is it necessary? Could the hippos do without the birds pecking them on the head throughout the day? Sure. But is the hippo healthier and better off with the parasites and ticks removed? Most likely, yes. The important point to take away from the pond hippo is the adaptability of the species involved – each enhancing its “lifestyle” through its relationship to the other. Such relationships in nature are often referred to as commensal – its Latin roots meaning “at table together.”

The symbiotic and beneficial arrangements between the hippo and his pond neighbours are not unique in nature – quite the opposite in fact. All around us, from the crustaceous barnacles and white lice that attach themselves to the underside of gray whales, to the spiders in our houses, powerful adaptive forces are forever driving these often necessary and sometimes odd relationships in nature. Many of these host-passenger relationships – though not all of them – can provide profound benefits to one or more of the participants, resulting in improved health/lifestyle and thus, better survivability. The hippo-bird-fish relationship may have already become so intertwined that subtle changes in this relationship may have negative health effects upon one or all partners. For example, if the hippo, for whatever reason, decides to spend more time on the shore and out of the water in the future, will that affect the species of fish that have come to depend on the submerged bounty to meet their nutrient needs? How will the hippo’s newfound terrestrial life affect the fishing success of the birds that enjoyed the ready access to fish as it sat perched on its multifunctional buffet-hunting stand? Will the parasites and ticks, not being removed on a regular schedule by the birds and fish, have a negative affect on the health of the newly land-based hippo, as they accumulate in number? It’s hard to know but easy to guess.

But what we can say with some certainty, is that if the symbiotic relationship between these pond dwellers has gone on sufficiently long enough to have physiologically conditioned the health and nutrient requirements of one of the participants, then we can expect some negative impact to its health, well-being and ultimately, its survivability if the action of one or more participant is removed or goes awol. Take our nibbling fish for example. Lets say a particular species, one that has evolved on a diet over eons that has always included significant nutrients garnered fromspecific algae growing on the under bellies of the pond hippo, is suddenly denied that food item with its specific nutrient profile that the fish has physiologically and metabolically become accustomed to. In other words, it has become a necessary part of the fish’s daily nutrient requirements and its overall health. Can the fish just do with out – and go about searching for replacement nutrients throughout the pond to make up the difference? Maybe. But if the nutrient profile of the hippo-algae contributed a significant portion of that particular species of fish’s diet, and the nutrient profile of that particular algae is not mimicked well in other resources in the pond available to the fish, then the fish has got a major problem on his hands/gills. Simply replacing hippo-algae with some run-of-the-pond low-grade algae might not do the trick. This would be like putting diesel in a car that runs on unleaded fuel – it stops.

Throughout our evolutionary march to mammalian dominance, humans have maintained a similar symbiotic relationship with an unlikely cast of characters. Though many people would be hard pressed to name any one of them, they are with us every minute of every day and it have been from the moment we entered this world.

We Are Not Alone – In Fact, We Are Well Outnumbered

Between 5 and 7 million years ago, a small group of primates stepped from the protective shadows of the tropical forest onto the open park-like settings of Africa and began a remarkable journey. The successes and failures of these early pioneers has been painstakingly reconstructed by paleoanthropologists and neatly filtered into the all-familiar and ever evolving “Family Tree.” From this, we can easily see the branches of early humanity as it pulsed into new forms, into uncharted lands, and only too often, into dead ends. From these earliest of evolutionary experiments, emerged modern humans. At over 6 billion strong, modern Homo sapiens sapiens stands as the ultimate expression of the success of those tentative steps by our earliest ancestors onto the open savannah. But we did not by any means do it alone and neither are we now.

It was in our early knuckle-walking days that we nurtured our symbiotic relationship with some evolutionary hitchhikers that would evolve and survive with us to this day – becoming so intertwined with our health and well-being that any affect on them, has an affect on us. You see, humans are host to a vast and complex community of microorganisms that have carved an ecological niche inside our bodies, on our skin, in our hair, under our nails, in our mouths, in our noses and, most relevantly, occupying every length of our gastrointestinal system (gut). At this very moment there are literally trillions of these gut microbes feeding on portions of your most recent meals. Like other living organisms, they live, multiply, and die based on access to quantities of sufficient quality food items – with variety being a plus. Well over 1,000 species of bacteria are present in a healthy human adult, with the vast majority living in the colon. In the stomach, acid keeps the bacteria at a relatively puny thousands of inhabitants. The small intestine has a quick transport time through its several metres in length, with the quick wash-through allowing “only” millions of bacteria to persist. At 1.5 m (5 ft) in length, the adult human colon contains at any given time about 1/4 kg (little over half a pound) of bacteria reaching 100,000,000,000,000 in total. This represents about 90-95% of all the cells in our body. Taken literally then, we are 20 times more microbe than mammalian. The typical adult has more bacteria in their colon than has ever been people living on Earth and ever will live on this Planet. We also excrete our own weight in faecal bacteria each year – try measuring it if you don’t believe us! If we live to about 75 years or higher then we should have excreted the equivalent weight of 12 elephants in faeces (African or Indian who knows?) and that’s a lot of hippos too. So who says humans aren’t full of s***?

Few people are aware that a significant portion of the stools (feces) we excrete on a daily basis are made up of these bacteria. In general, most of your daily stool is water – give or take – while the solids portion of the stool is about 65% bacteria, 20% undigested food items (fiber), and various other substances. That’s worth stating again: as much as 65% of your daily stool sample is comprised, not of undigested food items, but of bacteria. Most adults eating a Western-style diet will pass about 100 to 200 grams of stool a day, though this can vary greatly depending on gender, diet, menstrual cycles, mood, age and so forth. In some non-westernized countries, where high-fiber diets rule the day, it’s not uncommon for an adult to pass up to 300 to 400 grams of stool a day over multiple “sessions” and completed crossword puzzles.

The bacteria maintain their numbers and diversity in our colons based on the food they receive – i.e. mainly the food we, as the host, give them. This arrives in the colon as a number of substances, but in general, as dietary residues that escape digestion and absorption further up the line in the stomach and small intestine. We will return to this very important point in a moment.

Though a great number of species are present at any given time, over 99% of the billions of bacteria in our colon are represented by just a few genera (this means a group or family of bacteria that are related and called one group name e.g. for that well known bacterium E. coli, E. stands for Escherichia and is the genus name whereas coli is the species within that genus). We know that the vast majority of the bacteria found in the human gut are harmless, many are benign, and some are actually quite beneficial. Disease causing bacteria (pathogens) always are present in very small numbers, but they hog the press, giving bacteria their, vastly undeserved, negative public image. Their development is suppressed by the joined activity of the other intestinal bacteria, helped by the natural resistance of the host. It is only when the latter is weak or severely challenged, that harmful bacteria can develop and can cause disease. Throughout this book you will become very familiar with two groups (genera) of these good guys: Bifidobacterium or ‘bifidobacteria’ and Lactobacillus or lactobacilli. If you eat yoghurt (e.g. live-, bio-, bifidus, active, etc.), you may immediately recognize these names, as they have become very popular additives in a range of dairy products – as probiotics. Next time you are near the refrigerator or in the grocery store, check the label of some yoghurt products – the presence of “live cultures” is often prominently displayed. Don’t give too much thought as to where they came from in the first place though . . . . .

The idea of adding live strains of these healthful bacteria to your food comes from the observation of Elie Metchnikoff (1845-1916) a century ago that certain Bulgarian populations who consumed large amounts of fermented milk (yoghurt) generally had a better health condition than their counterparts who did not have access to the fermented milk. They also lived longer and happier than most. This took Metchnikoff away from his early observations that the colon was the site of ‘autotoxicity’ towards a more discerning health image, i.e. there were populations in there doing a great job for the host health, but they needed help.

Lactobacilli are present in very high numbers in fermented milk products. The human intestine however does all together not contain that many lactobacilli. Our intestines contain easily 1,000 times more bifidobacteria – and are very numerous in the gut human breast fed children. As much as 90% of the bacteria in the stools of breast-fed infant are bifidobacteria, with a much smaller amount seen in formula-fed infants. This is because components (glycoproteins) of human milk are able to stimulate them. High counts of bifidobacteria typically are associated with a good healthy condition. This is how bifidobacteria also entered into the picture of health food and almost certainly help explain the ‘breast is best’ argument. You will see later that bifidobacteria are powerful inhibitors of pathogens and this matches up with the lower infection rates of breast fed infants. Both lactobacilli and bifidobacteria can be grown in bioreactors on an industrial scale and added to the food (the probiotic concept). This aims to fortify the indigenous goodies that are lost after breast feeding finishes. Historically, probiotics in human use goes back centuries and was propelled by scientific observations that human and animal faeces contained ‘protective’ ingredients. These were the lactobacilli and bifidobacteria therein. Manufactures isolate them from such sources and use them as fortification in foods or to produce foods themselves – mainly fermented dairy products. Given the source of these strains, it is easy to understand how it is said that anything is usable or even saleable! Seriously, the concept is extremely worthwhile, the products taste good and some (not all) of them work. The peer reviewed scientific literature reports over 80 human trials that give a positive result in a variety of conditions ranging from gut problems like irritable bowel syndrome (IBS), travelers diarrhoea to cancers and genitor-urinary tract infections.

So, probiotics are successful and enjoy better scientific and media credibility than ever before. They are economically valuable too (several billion dollars worth are sold each year). Can things be even better however and what is the catch? Well, there are some issues that probiotic manufacturers need to get to grips with. The strains should be viable in the product, not alter the sensory quality of the food, be pure and maintain viability during bulk growth. This happens in only about half of the products sold in the US and UK daily and it is time that legislation moved towards routing out these less robust suppliers and removing their inefficient products – a crucial area of public health is being compromised otherwise. Some probiotic products are completely sterile – a major achievement in today’s food manufacture procedures! On the contrary, many good products do exist where suppliers exert the degree of rigor and quality control that is imperative. Having overcome that, the strains need to be strong enough to survive transit throughout the harsh conditions of the gastrointestinal tract. Again, some products do better than others. Technology such as microencapsulation has helped in some cases.

It is clear however ‘improving’ the composition of the intestinal bacteria can significantly contribute to good health. Everyone gets a gut problem sometime. If you are lucky it is an acute condition like gastroenteritis (a.k.a. food poisoning, gut ache, tummy rot, Montesuma’s revenge, Dehli belly, etc) whereby short term pathogens disturb the ecosystem and are usually transmitted in contaminated food or water. If you are unlucky a serious long term condition like IBS, inflammatory bowel disease (IBD) or colorectal cancer may arise – not to mention the systemic effects that the gut can exert. Few pharmaceuticals exist for these conditions and the approach is to attempt to repress rather than treat symptoms through an anti-inflammatory approach – with surgery too often being the resort taken. Can diet help? Well – yes: we are surrounded by a wealth of antioxidants, vitamins, nutraceuticals, functional foods, glucosinolates, carotenoids, lipid reducers and fibres. More on this later.

A major driver is modifying the composition of the intestinal flora in such a way that numbers of bifidobacteria or lactobacilli selectively are increased. Probiotics do so, but have drawbacks. However, the approach has too many positive medical and life quality implications not to proceed, e.g. microflora modulation is associated with increased resistance to invading pathogens (reduced risk for diarrhoea), increased absorption of calcium and magnesium (suppressing risk factors for osteoporosis), general stimulation of immune function (better protection against infection), reduced cholesterol and serum triglycerides (suppressing risk factors for cardiovascular disease), improvement of symptoms associated with IBS, counteraction of fat mass development, and increased bowel function (less constipation, ah yes!). Besides adding bacteria, there exist dietary means to selectively increase the beneficial bacteria that already are present in the colon, i.e. to selectively stimulate positive bacteria that already found a niche in the existing intestinal bacterial ecosystem. This can be done by feeding those bacteria selectively by means of ‘prebiotic’ food ingredients. This important and fast moving nutritional concept will be described in more detail further. Suffice to say that the concept is only a decade old but has attracted huge scientific, consumer and commercial interest worldwide.

Most folks are taken back when learning that gut microbes – or bacteria – have invaded our bodies in such large numbers and even more surprised when they find out that many of these bacteria play an important role in our health. How can this be? As youngsters we can remember our mothers saying “don’t touch that, you’ll get germs – put it down.” Seems some things are timeless. The message was simple – bacteria are bad and they will make you sick. Get rid of them. This is nonsense however. Our lives would be impossible, or decidedly uncomfortable, without them.

As a society, we are basically worried by bacteria. This phobia dates from a time where people did not have notion of the concept of hygiene – and today exists because of a febrile world where germ warfare is an issue. Death toll due to bad hygiene was very high and introduction of some basic rules of thumb was sufficient to reduce various infections and plagues in recent history. To get this message across to the general public, it had to be generalized to ‘bacteria are bad for you’. With the invention of antibiotics this general message was even strengthened. It was sufficient to kill bacteria in order to heal rapidly from various (infectious) diseases.  Today a lot more is known on the bacteria surrounding us. Public awareness is much more accessible and is also susceptible for more nuanced messages. A recent panel of independent experts organized as the Nonprescription Drugs Advisory Panel to the Food and Drug Administration concluded that “no significant difference in infections in households using antibacterial products and [than] those with regular soap and water.” The chairman of the panel, distinguished medical researcher Dr. Alastair Wood of Vanderbilt Medical School, went a step further and stated that “he saw no reason to purchase antibacterial products.”

The point here is not that antibacterial soap and gel companies are bad. They are not – but don’t be trapped into relaxing hygiene practice. Neither, was mom wrong. It is simply that not all bacteria in our environment are harmful – the vast majority in fact are not. In most cases where there is an interaction between bacteria and the human body at all, this interaction is benign. It is only some rare exceptions that are harmful, and during evolution the human body has developed various defense mechanisms against them.

Monkey See Monkey Do

Humans and other non human primates such as chimpanzees and gorillas are descended from a common plant-eating ancestor that once lived in the tropical forests of central Africa millions of years ago. Within these lush green regions, our earliest ancestors, like modern-day primates, lived on a diet of roots, leaves, fruits, bark, seeds, insects, and flowers – consuming very little or no meat. In other words, they foraged and ate what they found. Aside from the seasonal availability of high-energy dense fruits, with their significant concentrations of readably digested and absorbed sugars, the day-to-day diet was dominated by low-energy dense bulky plants, with lots of fiber. Diet of these early pre-humans was dominated by plants that provided the basics of fat, protein, carbohydrates and a vast array of essential vitamins and minerals extracted during digestion in the stomach and small intestine. However, a large portion of this bulky plant-based diet was not easily broken down by stomach acids or digestive enzymes of the small intestine, and therefore moved along to the colon for fermentation (by the bacteria therein). As mentioned above, the small intestine typically does not contain many bacteria (about 5 million could crowd onto a teaspoon – nothing compared to the colon!) In the colon the number of bacteria that could occupy just one fifth of a teaspoon is 1,000,000,000,000.

Indeed, any of the food items reaching the colon (the last compartment in the gastrointestinal system) meant they were not digested and absorbed in the small intestine, hence the term nondigestible. The vast majority of the food items that we consume are digested in the small intestine. The intestine itself but also the pancreas secretes digestive enzymes. Enzymes are tools that degrade food ingredients (proteins, carbohydrates, fats, . . .) into their composing units, which on their turn can be absorbed into the body – i.e., into the blood stream, in order to be converted into energy and building blocks of the body. Some ingredients that we consume however escape digestion because the enzymes that we secrete are not able to degrade them. These are the ‘non digestible’ food ingredients and they comprise about 100-200 grams entering the colon each day.  Nondigestible carbohydrates are represented by a complex set of compounds, but can conveniently be grouped under the category of fiber – or what your grandmother called “roughage.” The roughage would be the stringy and fibrous portions of the plants that give it shape and form. This is also known as insoluble fiber or, within scientific and nutritional circles, as non starch polysaccharides. The insoluble in insoluble fiber refers to the lack of dispersion of these compounds in water – i.e., none or very little. Just sits there – like a stick in a dish of water. But holding those fibers together, like cellular cement, are the soluble fibers. These are of the “non stringy” kind. In those same scientific circles, these are referred to as resistant starch, pectins, guar gum, and some oligosaccharides that are not digested due to their particular molecular construction, which cannot be attacked by our digestive enzymes. Soluble, if you haven’t guessed it, is the opposite of insoluble. When you drop these soluble fibers in a dish of water they disperse, mix with the water and become viscous and jelly-like (a.k.a. jell-forming). Like sugar and starch, soluble and insoluble fibers are carbohydrates. Not wanting to get bogged down in technical jargon, we will simply refer to all soluble and insoluble fibers as fiber for the time being and move on.

It is with this dietary fiber that has escaped digestion and absorption in the small intestine that our evolutionary hitchhikers earned their keep – and earn they did.

Due to the low-energy density of this bulky high fiber diet, our earliest ancestors had to eat lots of roots, leaves, flowers, bark, fruits, seeds and so forth to get enough fat, protein and carbohydrate to meet daily energy needs – often spending a large portion of their day just simply eating. This was primarily a function of the high water content of the available food the overall low density of fat, protein, and “digestible” carbohydrates. Imagine spending a couple of days in the woods or forest near your home and having to eat enough of the leaves, flowers, twigs and grass to get enough nutrients to keep going. During this back to nature adventure you would need to ingest large amounts of these items, spending much of your wilderness experience just eating. Consuming such a diet of leaves and bark all day, meant that a significant portion of the daily intake would be of the nondigestible fiber, and thus would end up in the colon for microbial fermentation. Time for our evolutionary hitchhikers to go to work.

Once in the colon, these meal parts – again, mainly nondigestible carbohydrates and fibers from the bulky plant-based diet – were rapidly fermented by the vast colony of bacteria living in our colon. The bacterial metabolic diversity in the colon is so to speak ‘omnipotent’. Considered as an organ (yes, you heard it here first, an organ!), it can eat or digest just about any kind of organic molecule. When bacteria ferment substrates they can develop and grow in numbers. As the bacteria grow in number, residual products called short chain fatty acids are produced through the fermentation. And here is the important part of this process and why evolutionary forces selected for the existence and maintenance of this metabolically active ecosystem of bacteria in the gut of our earliest ancestors. Energy.

As a byproduct of the fermentation process, like smoke generated from an open campfire, energy-rich, short-chain fatty acids were produced – along with a range of gases. The short-chain fatty acids, which are known by names like acetate, propionate, butyrate, are then easily absorbed into the bloodstream of the host and supplied a significant portion of the daily energy needs of our early ancestors. Using modern primates as a model, our earliest ancestors may have received between “30 to 50% of daily caloric needs” from the short-chain fatty acids generated by our evolutionary hitchhikers in the colon. This is astonishing when you consider that the gut bacteria generated that energy from food components that actually escaped our own digestive processes in the upper intestinal tract. they give us more than the birds give the hippos. As the undigested food came down the pipe every day, gut bacteria would efficiently go about their work extracting nutrient value (energy) from otherwise useless food items. That is, once the food had passed through the stomach and small intestine, it had been stripped of all of its nutrient value, and our early ancestors like us today, had no physiological mechanism for extracting any additional energy from the food – so down it went to the colon. For their service – which allowed our earliest ancestors to extract enough energy from the low-energy dense plant material of the rain forest to survive and multiply – gut bacteria were provided with a constant source of food (fermentable carbon sources) allowing them to maintain and proliferate in a safe and warm environment. Good for them, good for us. So important was this relationship to the health and nutritional status of our earliest ancestors living all those millions of years ago, that it is doubtful we would be here today in our current physical and cultural form were it not for our microscopic friends. Certainly, we would have shorter and much less comfortable lives.

As our early ancestors moved from the rain forest and open park settings to new environments, along went the gut bacteria. Over the next few million years, as our early ancestors evolved new forms and habits familiar to us today, they did it on an ever changing nutritional landscape that soon included higher-energy dense plant foods and ultimately greater and greater quantities of energy-dense animal protein and fat. This higher-energy dense diet meant that our early ancestors did not need to chew all day, they thus were free to spend more time on other activities – such as development of technologies like stone tools, ultimately fire, and so forth. During this period our brain size doubled, then tripled – reaching its modern size about 200,000 years ago. This time period marks the appearance of the first anatomically modern humans in the fossil record, pretty much looking as we do today. Interestingly, our gut proportions changed through this evolutionary period as well.

Since our newly evolving diet included more energy-dense foods – meaning more calories were being extracted and absorbed in the small intestine – the overall amount of nondigestible carbohydrates (fiber) reaching our colons became reduced. This in turn resulted in less energy needing to be generated in the colon by the bacterial co-workers. All of this resulted in an evolutionary reduction in the size of our colon – the fermentation factory – and a commensurate increase in the size of the small intestine. By volume, our current colon is more than half the size of the plant chomping-primates still living in those same rain forests we evolved from, whereas our small intestines – which reflect our higher-energy diet – are on average twice as long.

As humans underwent physical and nutritional evolution, gut bacteria evolved along with us – possibly quicker. Changes in our physical, physiological, and metabolic features were conditioned over millions of years of slow environmental change. This meant that changes in our diet as conditioned by regional climate variation and ultimately early technologies, never out-paced the ability of our intestinal bacteria to keep up and adapt – always standing ready to ferment and extract energy – for us and them – from anything sent down the pipe. In fact, the mere presence of the bacteria in our intestinal tract allowed us “flexibility” in our knack to adapt to shifts in diet, as brought about by changes in food availability and variation in new and ever-changing environments. Though our colon reduced in size, and thus marked a decrease in the total amount of low-energy dense undigestible foods in our diet, it did not decrease the importance and contribution of our evolutionary hitchhikers to overall health. In fact, the extraordinary chronological length of the relationship, with all the ups and downs that go with the evolutionary process, all but guarantees their seminal role in our metabolic and physiological health and well-being. Researchers are starting to learn just how important these tiny bacteria are, and always have been, to our overall health.

Evolutionary microbiologist Lora V. Hooper recently commented in the Annual Reviews of Nutrition that “Over our evolutionary history, components of the intestine’s microbiota [gut bacteria] have endured a stringent selection to become “master physiological chemists”: i.e., they have had to develop chemical strategies for regulating nutrient processing in ways that benefit themselves and us.” In a separate paper she further comments that “Recent results indicate that indigenous bacteria play a crucial inductive role in gut development during early postnatal life.” In other words, the gut bacteria that we have carried with us all these millions of years – and that have adapted to our ever-changing diet and accompanying physiological changes and demographic expansion – have become more than just a passive and convenient mechanism for extracting energy from undigested foods that reach our colons. They are now part of us in a very intimate and interactive way.

As we will soon see, the rapid pace at which humans accumulated technology and an ability to manipulate and control the nutritional landscape may have recently tinkered just enough with the good for them, good for us relationship with our evolutionary hitchhikers to be affecting our current overall health and well-being in not such good ways.


The Hippo Has Left the Water

Once our early ancestors stepped down from the tropical forest canopy 5 to 7 million years ago, it was not until about 2 million years ago that the first member of our genus Homo appeared in the fossil record – Homo erectus (a.k.a. Homo ergaster, best known for the near-complete skeleton of the Turkana Boy discovered in 1984 by Kimoya Kimeu and Richard Leakey). Up until the appearance of ‘erectus,’ our earliest ancestors were grouped under a mixed bag of characters known as Australopithecus and the more recently discovered Ardipithecus. The famed skeleton Lucy, discovered by Donald Johanson and colleagues in the Afar region of Ethiopia, was a three and half foot Australopithecus afarensis that lived over three million years ago.

For much of the 2 million year period of human (Homo) evolution, humans consumed a diet dominated by plants and animals that were foraged from the natural environment – wild plants, wild animals. It has been only within the last 10,000 to 5,000 years that cultivated grains and domesticated animals have been a measurable part of human diet. So, for over 99% of human history (last 2 million years of Homo) we were hunter-gatherers living on a diverse range of plants and animals (and varying amounts of fish). Given the quantity and diversity of plants in our diet over much of this 2 million year period, a steady flow of nondigestible food items were continually delivered down the digestive tract to the colon for fermentation. During this long period of time both host or at least intestinal tissue and the microbiota living in it have specialised so as to be optimally adapted to one another. This evolutionary stable strategy, as famed British Darwinist Richard Dawkins calls this process, resulted in a particular and complex set of bacteria or intestinal ecosystem. This interaction provided nutrients for the bacteria to grow and maintain their ecological niche in our colons. They would in turn provide energy from these otherwise unusable food materials. But this is not all that happened. As it is clear now that the intestinal bacteria co-evolved with their human hosts, some other evolutionary more important aspects than ‘you feed me I feed you’ mechanisms became established – and just as well. As mentioned, the intestinal bacterial ecosystem as we know it today is composed of well over 1.000 different species of bacteria (and these are just the ones that can be cultured in a laboratory). It is evident that it does not concern a random set of bacteria. No. The set of bacteria in this ecosystem are part of the results of the functioning of the evolutionary stable strategy. As the intestine is in direct contact with the external environment, all existing bacteria living in water, air, soil theoretically have physical access to our intestinal ecosystem. Hundreds not millions existing species however succeeded to find a niche in the colonic environment. This means that the established ecosystem is composed of a set of bacteria that can live in harmony (nutritional, ecological . . . ). All who are present are part of the club because for some reason they benefit from the others and the others benefit from them. A need to survive without oxygen probably ruled out the majority of others. Importantly, current members make it their evolutionary determined job to keep out new members. Together, then they set up a barrier preventing colonization by other bacteria (colonization resistance – more on this later). They do so by taking away food more efficiently than non adapted new-comers, by producing short-chain fatty acids that the new-comers do not like or even resist, by producing signalling molecules that genetically make life of newcomers impossible. But there is more.

During evolution there must have been combinations of intestinal microbes that were not beneficial for the host, our early ancestor in this case. Bacterial populations that even were harmful to the host (allowing the presence of high numbers of pathogens) resulted in the less ‘good’ development or even early death of the latter. Hominids having bad combinations of intestinal flora disappeared. With time – we are talking 100’s of millions of years as it is clear that even the ancestors of the hominids, having an intestine, also had an intestinal ecosystem of some kind – an intestinal flora allowing good viability and even good quality of life of the host established. Yes, dinosaurs had intestinal bacteria well.

A very important complementary part to this observation is that this microflora is in harmony not only within the bacterial ecosystem, but necessarily also with the host. Both have co-evoluted. The mechanism which the human intestine comes in first contact with intestinal flora is at the basis for this. The intestine of a fetus in the mother’s womb is sterile. It does not contain any microbiota at all. It does not have an intestinal ecosystem until the newborn comes in contact with vaginal and faecal matter from the mother. This cycle links the co-evolution of intestinal flora and host. As a direct consequence it can be stated that there is such a thing as a ‘good flora’. It is the flora that approaches the equilibrium flora that established according to the principles of the evolutionary stable strategy just described.

Such ecosystem co-evolution with the host took a long time to optimize. Changes in these patterns have occurred and still are occurring, but at a very slow pace. These changes have always been and will continue to be triggered by diet.

But as the early seeds of agriculture began to take hold about 10,000 years ago in what archaeologists call the Fertile Crescent – in today what is modern Iraq – significant changes in human diet were looming large on the nutritionally horizon with the coming of the Agricultural Revolution. Loren Cordain of Colorado State University refers to the grains of the Agriculture Revolution as “Humanity’s Double-Edged Sword.” In essence, he argues that while on the one hand agricultural grains – wheat, maize, rice, barley – gave us a reliable and abundant source of carbohydrate which to grow civilizations and nurture social and technological advances, on the other hand, the rapid increase of nutrient poor grains in diet marked a downturn in human nutrition that continues to this day. And he’s right.

Many Neolithic people who adopted agriculture throughout the world showed marked decrease in overall stature, poorer bone and dental health, shorter lifespan, and vitamin and mineral deficiencies. As more and more daily calories came from cultivated plants, we moved further and further away from our hunter-gatherer lifestyle and its diverse and nutrient-rich diet. This meant less greens, seeds, tubers, roots, nuts, fruits, berries, stalks, shoots, flowers, and pollen in the diet, to a reliance on a small number of cultivated grains. As the technology of farming and grain processing progressed over the millennia, the grains became more and more refined – with the end result being less and less undigested material reaching the colon as the outer bran or seed coat was removed (fiber) and the increasingly smaller size of the starchy particles were more readably digested in the small intestine. Not looking so good for the gut bacteria then.

The processing was initially accomplished by simply placing the grains on large flat stones and grinding them down with smaller hand-held stones. Though ground into smaller particle sizes, this early ‘flour’ still contained a significant portion of the ‘whole’ grain as the entire ground seed was consumed. This simple technology dominated the first few thousand of years of agricultural grain processing and examples of these early grind stones litter archaeological records throughout the world. As populations grew, the smaller grain processing systems were replaced by rotary stone mills around 1500 – 1000 B.C. throughout much of the Mediterranean region. With the advent of the stone mills came the popular use of sieves to separate the outer bran and seed coat from the purer starchy endosperm of the inside of the seed. In other words, the outer seed coating was isolated and discarded, much like peeling an orange and tossing the peel. The purer flour (more white-like, less brown) was coveted by the rich and ruling class, while the less pure flour – what we know today as brownish-looking whole grain flour – was associated with lower social class. With the introduction of the steel roller mills in the late 1800s, coupled with the widespread use of new fine silk sieves, true pure white flour was now available to the masses. Bakers and cooks were thrilled. We had arrived but had we considered the gut hitchhikers?


In the Blink of an Eye

In just 10,000 short years – and much shorter for many regions of the world – humans went from hunter-gatherers foraging about the landscape consuming a diverse diet of plants and animals to a world dependant on a handful of agricultural grains. With the dizzying number of products today made of these reliable, palatable, and relatively low-cost grains, it’s no wonder that two-thirds of the worlds caloric and protein intake is met with highly processed grain-based products. But, for over 99% of human history and nutrition, we never ate them. Zip. Zero. It is even doubtful those first Neolithic farmers would even recognize modern processed foods as foods at all. Nowadays, almost all food is processed in some way – how does a South African apple arrive “fresh” in a US supermarket?

Agricultural grains in and of themselves are not bad however. They are after all, just plants – and grass seeds at that. But it’s what we modern humans have done to them – processing them down to a mere nutrient-shadow of their former selves – and to the extent they have come to dominate modern diet at the expense of diverse vegetables and fruits, that makes their role in human health controversial. And dominate they do. On the medical front, highly processed grains have been fingered in the rapid rise and fall in blood-glucose and insulin levels following their ingestion, which in turn has been linked to a number of medical problems plaguing modern populations such as type 2 diabetes, obesity, and some aspects of heart disease – just to name a few. Just as a bad, a significant portion of these processed grains end up in snack-like foods that are notoriously rich in sugar and fat.

Even with the recent whole grain movement sweeping America, triggered in no small part by the mountains of scientific evidence pointing to the health benefits of increased whole grains and the release of the 2005 Dietary Guidelines for Americans and a snazzy, revamped US Food Pyramid (www.mypyramid.gov) recommending more whole grains over highly processed ones, the public is not changing its eating behaviour. In 1900, whole grain foods made up 36% of the daily calories for Americans. In 1970 this figure dropped to 15% and current levels are that Americans get about 1% of daily caloric needs from whole grain products. These whole grain foods were replaced by highly processed ones. Brown was out, white was in. Nutritional researcher Julie Miller Jones of the College of St. Paul Catherine and colleagues report that “Twenty percent of adults and forty percent of teens and children in a 2001 telephone survey reported that they never eat whole-grain bread [emphasis added].” The data are clear – whole grains are not on the consumer radar, though American consumers are literally swimming in a sea of highly processed grain products. Similarly, the messages about 5 (or even 8 now) good sized portions of fruit and vegetable are required daily are known, the advice is not used. In England records show that only 8% of the population ingest such a quantity. Presumably, the other 92% don’t care or don’t have time. They need a Trojan horse approach to nutrition and the gut bacteria are just waiting to help – see later (Note: we are not advocating any quick fix or replacement for a balanced healthy diet – whatever that is – just opening up options which for several reasons are needed).

The global dominance of nutrient- and fiber-poor processed grain products has been a double-whammy for our evolutionary hitchhikers. The processing of these perfectly nutritious and healthy seeds has removed the vast majority of the nutrients and even worse, the undigested portions (bran and germ [fiber]) that once reached our colons. The increase of processed grains in the diet has also meant that nutrient- and fiber-rich vegetables and fruits have assumed a minor role in diet. The decreasing role of nutrient- and fiber-rich fruits and vegetables in the diet has not been helped by the fact that they have become expensive. According to the US Department of Agriculture, during a period from 1985 to 2000 fresh fruits and vegetables increased in price by a whopping 120%. During this same period, sugary soft drinks increased by only 20% and fats and oils increased by about 30%. It’s no wonder the average American “derives almost 40% of daily energy (calories) from added sugars and fats.” These are a cheap and pervasive source of calories.

The reduction in fresh fruits and vegetables in our modern diets, and thus a reduction in the amount of nondigestible food items reaching our colons and the bacteria that have come to depend on them, and the increase in the consumption of fiber-poor processed grains, may be a function of economics and less about real choice. It simply costs more to eat healthy. And eating healthy means a diverse diet of vegetables and fruits and a reduced consumption of highly processed grain products and sugary /fat foods. It does little to have well-minded policy makers in the US recommend that we should eat 9 to 13 servings a day of fresh vegetables and fruit, when the “average low-income family can only spend an estimated $4 per person a day on food.” Put another way, a single father of three faced with the daily decision of feeding a family on a fixed budget would clearly like to have a platter of steamed, fresh vegetables with every dinner, but when you can buy three boxes of highly processed macaroni and cheese for just $1, the choice is already made. The socioeconomic factors affecting the amount of non digestible fiber reaching our colon are profound.

In the most recent 1% of human existence, an evolutionary blink of the eye, we have gone from a diet that once included 100, 200, and up to 400 grams a day of non digestible fiber – food items that escaped digestion and absorption in the small intestine and reached the colon for fermentation – to a diet that on average that might contain 5 to 50 grams of this material – maybe a little more for some of us. The average American adult is said to consume less than 15 to 20 grams of fiber a day. This low intake is similar throughout Europe. The outlook for our evolutionary hitchhikers is starting to look grim and we are not helping them to help us.

Throughout our history, changes in diet were subtle, although punctuated at times, and occurred over large spans of chronological time. Changes in diet moved at a glacial pace, nothing like the rapid development and acquisition of agricultural grains and the reduction of vegetables and fruit in the diet of our recent past. Lightning fast. This rapid change has no precedence in our evolutionary past and biologically speaking our bodies cannot adapt at this speed. The rapid advances in processing technology within the last 200 years that gave us fiber-free pure white flour coupled with the across-the-board reduction in vegetable and fruit consumption and increase of energy from sugar and fats, is wreaking havoc on our evolutionary hitchhikers.

Just when you thought it could not get any worse for our evolutionary hitchhiking friends, along come antibiotics. Hailed as a “magic bullet” for what ails you, antibiotics such as penicillin and tetracycline, revolutionized the treatment of infectious disease throughout the world. As the name implies, these are bacteria killers – and kill they do. Each and every year in America alone, doctors and health practitioners issue 150 million prescriptions for antibiotics to fight invading pathogens that seek to do us harm.  Most of us have taken an antibiotic at one time or another, or given them to our children, but have you ever had a doctor who prescribed them say to you “Oh, by the way, these antibiotics I am prescribing to you today may, in addition to killing the pathogenic bacteria that are making you sick, are likely wipe out a majority of the other bacteria in your body as well – the good ones, along with the benign ones.”  I doubt many of us have ever been provided with this small bit of critical information! Similarly, how many viral problems are “treated” with antibiotics – a complete waste of time and expense as they do not work.

But that is exactly what they do – kill indiscriminately most if not all of the good, the bad, and the benign. The simple fact is that there is no such thing as a truly selective antibiotic. Of course, antimicrobials have made crucial in roads into reducing the risk and symptoms of a plethora of disease but the friendly fire of this germ warfare between antibiotics and invading pathogens can potentially devastating affects on the population and health of our gut bacteria, requiring repopulation and growth. Their indiscriminate use (including on some farms where yield outweighs ecology) has not helped either. The next logical question you may be wondering is how you would go about repopulating the bacteria in ones colon? Aside from the negative impact and alteration of our resident bacteria, something is happening to the invading pathogens that are being targeted by antibiotics. They are, and have been, getting frighteningly wise to the ways of the exterminator.

So widespread is the use of ‘biocides’ (they are even spraying antibiotics on our food while it’s still in the field!) that bacteria have started to develop resistance. Just as the word implies, they are morphing into new strains and mutations that are out smarting the antibiotics, basically armor proof and unaffected by the antibiotics. When one considers the diverse hostile environments that bacteria can adapt to and grow in (volcanoes, ocean bed, deserts, high salt lakes, Mars . . .), its no wonder they can outsmart the antibiotics. These emerging mutant resistant super bugs have recently provoked the World Health Organization to acknowledge a global health crisis is looming if more care is not given to limited and more targeted use of antibiotics in the treatment of infection. These warnings are hardly new. In a 1945 interview in the New York Times, the British bacteriologist Alexander Fleming, who discovered penicillin, warned that the misuse of penicillin (read overuse) could lead to mutant forms that could resist the intended affects of the drug. Let’s hope it’s not too late.

*  *  *  *  *  *  *

Let us summarize where we are so far. Our early knuckle-dragging ancestors lived on a plant-based diet of leaves, roots, stalks, seeds, fruit, flowers and so forth. Similar to what non human primates living in tropical Africa are eating now. This bulky diet was high in non digestible carbohydrates (both soluble along with the particular oligosaccharides and insoluble fiber) and was of little use in the small intestine, so was sent quickly to the colon where waiting bacteria – billions of them – would quickly go about the task of breaking these materials down creating energy-rich, short-chain fatty acids and some gases (anti-social but necessary) in the process. These short-chain fatty acids were easily absorbed from the colon and used as energy by a number of organs including the liver, skeletal muscle, and brain. This cozy arrangement worked well for both parties: our early ancestors were able to extract much energy from otherwise nutritionally useless plant material and the bacteria received a steady flow of nutrients to live and thrive on, and a protected and warm place to live to boot.

Things went along fine for the next few million years as our early ancestors evolved into more human-like forms – the first being Homo erectus about 2 million years ago. As we evolved tool use, finally mastered fire, broadened our diet, and became more and more socially complex, the bacteria evolved right along with us. Our movements on the landscape and changes in our nutritional profile were slow, often occurring of hundreds of thousands of years. Never abrupt. Then about 10,000 years ago we started trading in our hunter-gatherer lifestyle for farm tools. Initially, this transition would not have been a significant shock to the food supply (non digestible carbohydrates) to the bacteria in our colons and our health, but it sounded the toll for what was about to come: finely ground flour and settled towns, villages, and cities. As population grew and more and more people came to depend on the annual harvest, they hunted and gathered less and less. This meant a decrease in the diversity of plants in our diet and a reduction in the amount of non digestible carbohydrates being sent down the pipe to our colons to the ever-awaiting bacteria. These were necessary changes largely – socially and ecologically.

It is thought that a particular group of non digestible carbohydrates called the prebiotic oligosaccharides (prebiotics) played a central role in this. They are particular in the group of the soluble dietary fibre. Just like them they are not digested, and hence are completely available for fermentation by intestinal bacteria. But there is one particular aspect to it that completely distinguishes them from the fibre fraction : they are fermented in a selective way. It was shown that they promote the growth of certain groups of bacteria that themselves outcompete other bacteria. It was observed that the bacteria whose growth is promoted .. fit with a set of bacteria related to the evolutionary stable strategy- established flora. The bacteria whose growth is selectively promoted are associated with good health and are the probiotics already present therein. So, what we are doing here is fortifying the ecosystem, by targeting its beneficial inhabitants, rather than adding new ones to them. As such, prebiotics when added to our modern highly processed western type diet offer means to approach a diet with which we and our intestinal flora have co-emerged.


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