The Essential Book of Fermentation (8 page)

In a rare instance of the demonstration of the transfer of genes from bacteria outside the gut to bacteria inside the gut in connection with food, scientists have found that bacteria in the guts of some Japanese people can digest porphyran, a polysaccharide compound in seaweed that is normally indigestible. This was discovered after a team of French scientists found the genes for a pair of porphyran-digesting enzymes in
Zobellia galactanivorans
, a marine bacterium. They then started looking for these genes in other species and found them in gut bacteria of Japanese folks who ate a lot of seaweed, but not in the gut bacteria of Westerners. They theorized that the human gut bacteria probably acquired the genes centuries ago in a gene transfer from marine microbes hitchhiking through the human gut on the seaweed so abundant in the Japanese diet.

Similarly, Westerners who eat land plants that contain polysaccharides can break down these compounds because of enzymes in their gut bacteria. “When you eat a salad, it’s not you that breaks down the vegetables, it’s the bacteria in your gut,” said Gurvan Michel, one of the French scientists who found the seaweed-digesting bacteria. And maybe our gut bacteria acquired this ability from the microbes that had been breaking down land plants into their constituent nutrients for the past billion years: the soil bacteria that coat the plants we eat.

The intestinal flora as a whole consists of about 90 percent beneficial bacteria and 10 percent pathogenic organisms—not enough pathogens to overcome the advantage of beneficials in nutrient competition, gut wall attachment site availability, or the beneficials’ production of compounds like bacteriocins that keep the pathogens disarmed or reduce their numbers. It’s the same situation in the organic garden or farm, or in any healthy wild ecosystem, where there are always organisms with opposite functions that naturally form a healthy balance. In the microbial world, there are beneficial gut bacteria and pathogenic disease-causing bacteria, in the insect sphere there are plant-eating bugs and bug-eating bugs, and in the larger world there are chickens that eat grain and foxes that eat chickens. However, the range of illnesses caused by gluten intolerance—from full-blown celiac disease to simple gluten sensitivity—seems to upset this delicate balance of competing microbes in our gut, giving the pathogens more advantages and leading to conditions as uncomfortable as bloating to as life-threatening as colon cancer. While the intestinal flora doesn’t cause gluten intolerance as far as we know, the health of the intestinal ecosystem can be thrown off balance by the condition. Such imbalance, which is called dysbiosis, is, at least in current medical thinking, caused by faults in the gut’s secretions of peptide enzymes.

While we are focusing on these effects in humans, be aware that gut bacteria have all sorts of functions in the guts of other animals. For instance, it has long been thought that resistance to pesticides is always the result of an evolutionary leap encoded in the genome of certain insects. But according to a recent study reported in the
Proceedings of the National Academy of Sciences,
it’s the presence of Burkholderia bacteria in the guts of
Riptortus pedestris
, a common bean bug, that is responsible. Burkholderia break down the insecticide fenitrothion, and 100 million of these soil-borne bacteria can inhabit the gut of a single bean bug. Bean bugs that harbored the bacteria survived doses of fenitrothion that killed 80 percent or more of undefended bean bugs within five days.

Within the intestinal tracts of all animals and within the living soil system that covers the earth’s land are myriad processes that sustain life or digest life and that we are just beginning to understand. And such interactions don’t just affect animals. It has recently been discovered by scientists at the University of Delaware that when disease organisms try to invade
Arabidopsis thaliana
plants through their stomata—those tiny pores on the undersides of leaves that open and close in response to environmental conditions—soil bacteria called
Bacillus subtilis
at the plants’ roots signal the pores to close, shutting the door on the pathogens. The research involved inoculating three thousand arabidopsis plants with the leaf pathogen
Pseudomonas syringae.
The plants responded to the infection by recruiting
Bacillus subtilis
to bind to its roots, which caused the plants to manufacture abscisic and salicylic acids. The presence of these acids signaled the stomata to close.

The first complete human genome was sequenced in 2003, and since then scientists have been looking through our 22,000 genes for those involved in human disease. They have been successful to a degree, but some causes of genetic disease have proven elusive. The genes that cause the diseases don’t seem to be in the human genome. That’s where the Human Microbiome Project comes in—a worldwide effort by scientists to map the microbes that inhabit our bodies, starting with the 100 trillion bacteria in our gut. As we’ll see, the cause of some genetic diseases may not be found in the human genome, because the genes aren’t in the human genome. It may be that they are in the microbiome, that coating of the human body, inside and out, made up of microbes. While our human DNA has 22,000 genes, the DNA among all the kinds of microbes in our gut bacteria has 8 million.

The only human feeding study ever conducted on genetically modified foods shows that a foreign gene inserted into the DNA of soybeans spontaneously transferred out of the beans and into the DNA of gut bacteria, according to Jeffrey M. Smith in his book
Seeds of Deception
. The foreign gene produces a pesticidal toxin. The gene for production of the toxin, now residing in gut bacteria, allowed the toxin to contaminate the blood of thirty Quebec expectant mothers who ate GMO soybeans and then cross the placental barrier to contaminate the blood of their developing fetuses. The study appeared in
Reproductive Toxicology
in 2011.

If it seems incomprehensible that no long-term feeding studies in humans have been done concerning GMOs (genetically modified organisms), consider that to do so would require studying the effects of GMO foods on persons over many years, starting when they were children. There would have to be two groups of kids, one fed a diet of GMO food and another, a control group, fed exactly the same diet of non-GMO food. And there would have to be some force-feeding. If, for instance, the children eating GMO foods just picked at their vegetables while the non-GMO group readily ate them, then the GMO group would have to be force-fed the same amount of vegetables. Also, the groups would have to be isolated from the toxic chemical loads we all are exposed to, meaning they’d have to be away from home for many years. It stands to reason that it would be scientifically irresponsible and ethically immoral to conduct such a study. Better that we turn to animal studies, where we find compelling evidence from a 2012 French study that lab animals fed GMO crops for several years developed more and larger tumors, developed more kidney failure, and died earlier than a control group.

But to return to the study in
Reproductive Toxicology
showing the ability of the foreign gene for pesticide expression to contaminate the blood of mothers and their developing babies, consider that there are several serious implications. First, it means that the bacteria inside our intestines, newly equipped with this foreign gene, may create the novel protein inside of us. If it is allergenic or toxic, it may affect us for the long term, even if we give up eating genetically modified soy, because our contaminated gut bacteria will continue to express it.

According to a 2012 study published in the
Journal of Applied Toxicology,
low doses of the Bt toxin alone or in the presence of glyphosate herbicide (Roundup) kill human kidney cells. The study found that the Bt pesticide caused kidney cell death at concentrations of 100 parts per million, while Roundup at just 57.2 parts per million—two hundred times below agricultural use—killed half the test cells. “This study suggests that Bt toxins are not inert on human cells, and may indeed be toxic . . . Bt crops have previously been shown to induce liver and kidney abnormalities . . . in lab animals as well as immune responses that may be responsible for allergies,” according to the study.

In response to studies like these, the French government has announced that they will not allow Bt sweet corn to be planted in their country—for reasons of environmental safety.

Though GMO crops are still allowed to be sold unlabeled in the United States, there is a simple answer for those of us who don’t want weird Frankenfoods in our diet—eat organic. By law, organic foods must be GMO-free.

CHAPTER 4

The Conglomerate Superorganism

Scientists have begun searching the human body for the microorganisms that live on us and within us, and they’ve found them everywhere, not just as colonies of various microbes, but as whole ecologies of diverse microbes that have a profound effect on our body’s development, health, and even behavior.

And they’re everywhere on us. These ecosystems are in our mouths—some on the tongue, some on the lining of the cheeks, some on teeth, even with different ecosystems on different sides of the teeth. Some of our intestinal flora—the lactobacilli—are part of healthy mouth ecosystems that prevent tooth decay, while some are part of systems whose production of acid eats into enamel and encourages tooth decay.

There’s an ecosystem up your nose, in your vagina, on your eyeball, and different ecosystems on the back of the knee and the front of the knee, on the wrist and on the back of the hand, and these differ from the ones on each digit of your fingers. If you compare the bacteria on two people’s hands, only about 13 percent of the total will be the same. If you compare bacteria on one person’s left and right hands, only about 17 percent of the bacteria will be the same.

You get the idea: We are not just ourselves, we are a conglomerate superorganism, a veritable landscape of microorganisms. Think of the landscape of a typical long-abandoned field in the mid-Atlantic states. In the open field are many types of grasses, each one adapted to its place in the system, some with intertwining roots, others with rhizomes that run spearlike through the soil. There are annual weeds and flowering plants and perennials that return from their roots each spring. Small trees and shrubs are there, too, and fruiting brambles, and wild grapes that hoist themselves into the taller trees. One could count a thousand different plants in any square mile and a hundred different ecosystems of plants, some adapted to low, wet spots, others that thrive on the rocky hilltops, and still others that are fit for the changes in light, climate, and water that characterize any rolling hillside and valley in that part of the country.

When it comes to microorganisms, your whole body is like that landscape. There are dark and light places, moist places, dry places, and all have the unique combination of microbes that find the situation suited to their needs. As birds of a feather flock together, different microbes that share an affinity for the differing places on your body grow there and form an ecosystem.

Scientists are just now beginning to catalog the various organisms that make up the human microbiome, as the whole panoply of microbes on us and in us is called. Some are obviously friendly helpers, such as the lactobacilli, some are obviously pathogens, like certain strains of
E. coli
, but for many, it’s not entirely clear whether they are beneficial or harmful, or have both functions.

In a telling shift of focus representing the acknowledgment of large gaps in our understanding of the microbial life of our bodies, Julie Segre of the National Human Genome Research Institute in Bethesda, Maryland, says, “We’ve moved away from saying ‘What are healthy bacteria?’ to ‘What are normal bacteria?’” She’s been working on a catalog of skin bacteria for the National Institutes of Health’s Human Microbiome Project. She cites acne as an example of a bacterial skin problem. “Is it healthy? I don’t know. But it’s normal,” she told
Science News.

The microbes in a normal intestinal ecosystem can change, depending on what the host human had for dinner and the host’s wellness status, and those ecosystems can skew toward greater health or away from it. One study published in the journal
Nature
showed that the gut bacteria of people whose diets were rich in animal fats made more of a substance that leads to clogged arteries. On the other hand, a University of Maryland School of Medicine study found that healthy women had one of five kinds of bacterial ecosystems in their vaginas. Four of these were dominated by lactobacilli that made infection-preventing lactic acid, while the fifth ecosystem had few lactobacilli. You would think that this latter group of women might have an infection, but no, they were perfectly healthy. The bacteria in that ecosystem, though they weren’t lactobacilli, also made lactic acid. So with our microbiome, it’s good to look at what the microbes do, not just who they are.