Microscopic partners

In the late 17th century, the Dutch naturalist Anton van Leeuwenhoek looked at his own dental plaque through a microscope and saw a world of tiny cells “very prettily a-moving”.

He could not have predicted that a few centuries later, the trillions of microbes that share our lives - collectively known as the microbiome - would rank among the hottest areas of
biology.

These microscopic partners help us by digesting our food, training our immune systems and crowding out other harmful microbes that could cause disease.

In return, everything from the food we eat to the medicines we take can shape our microbial communities - with important implications for our health. Studies have found that changes in our microbiome accompany medical problems from obesity to diabetes to colon cancer.

As these correlations have unfurled, so has the hope that we might fix these
ailments by shunting our bugs toward healthier states.

The gigantic probiotics industry certainly wants you to think that, although there is little evidence that swallowing a few billion yoghurt-borne bacteria has more than a small impact on the trillions in our guts.

The booming genre of microbiome diet books - self-help manuals for the bacterial self - peddles a similar line, even though our knowledge of microbe-manipulating menus is still in its infancy.

The archaeology writer, Jeff Leach views the Western microbiome as “a hot
microbial mess,” he wrote on his blog. Poor diets, antibiotics and overly sanitised
environments have gentrified the Western gut, he wrote, “potentially dragging us closer to ill health”.

This reasoning is faulty. It romanticises our relationships with our microbes, painting them as happy partnerships that were better off in the good old days. It also invokes an
increasingly common trope: that there is a “normal” or “healthy” microbiome that one should aim for.

There is not. The microbiome is complex, varied, ever changing and context-dependent -
qualities that are the enemies of easy categorisation.

“Healthy” microbes can easily turn rogue. Those in our guts are undoubtedly helpful, but if they cross the lining of the intestine and enter our bloodstream, they can trigger a debilitating immune response.

The same microbes can be beneficial allies or dangerous threats, all for the difference of a few millimeters.

Conversely, “unhealthy” configurations of microbes can be normal, even necessary. Ruth E Ley at Cornell University and colleagues demonstrated this in dramatic fashion when they found that micro-biomes go through a huge upheaval by the third trimester of pregnancy.

They end up looking like the microbiomes of people with metabolic syndrome - a disorder that involves obesity, high blood sugar and a higher risk of diabetes and heart disease.

These communities might indicate someone on the verge of chronic disease - or merely motherhood. Packing fat and building up blood sugar makes sense when you are nourishing a growing foetus.

Here is another example. Common medical wisdom says that healthy vaginal microbiomes are dominated by the acid-making Lactobacillus group that creates an inhospitable environment for disease-causing microbes.

But Larry J Forney at the University of Idaho and colleagues found that a quarter of women didn’t fit this pattern, despite being perfectly healthy.

They also showed that their vaginal communities can change dramatically and rapidly, even over a single day, flitting in and out of states that are supposedly conducive to disease, but with neither clear causes nor ill effects.

The microbiome is a teeming collection of thousands of species, all constantly
competing with one another, negotiating with their host, evolving, changing.

While your genome is the same as it was last year, your microbiome has shifted since your last meal or sunrise.

We need to start thinking about it as an ecosystem, like a rain forest or grassland, with all the complexities that entails.

And just as the gorillas and leopards of African forests differ from the wolves and moose of American ones, so, too, do microbiomes vary around the world.

So, can one microbiome be worse than the other? Better? I suspect the answer is neither. It is simply theirs. It is adapted to the food they eat, the dirt they
walk upon, the parasites that plague them.

Our lifestyles are very different, and our microbes have probably adapted accordingly.

Generations of bacteria can be measured in minutes; our genomes have had little time to adapt to modern life, but our microbiomes have had plenty.

The microbiome is the sum of our experiences throughout our lives: the genes we inherited, the drugs we took, the food we ate, the hands we shook.

It is unlikely to yield one-size-fits-all solutions to modern maladies. We cling to the desire for simple panaceas that will bestow good health with minimal effort. But biology is rarely that charitable.

So, we need to learn how tweaking our diets, lifestyles and environments can nudge and shape the ecosystems in our bodies.

And we need ways of regularly monitoring a person’s microbiome to understand how its
members flicker over time, and whether certain communities are more steadfast than others.

Our microbes are truly part of us, and just as we are vast in our variety, so, too, are they. We must embrace this complexity if we hope to benefit from it.