A termite queen and king, about 5 cm and 1 cm long, respectivelyChina Photos / Stringer / Getty

The 19th-century American scientist Joseph Leidy has been described as the “last man who knew everything.” An extraordinary polymath, Leidy was a scholar of parasites, a discoverer of dinosaurs, a collector of gemstones, a curator of museums, an exceptional illustrator, and the first person to use a microscope to solve a murder mystery. But learned though he was, he was still shocked by what we saw when he cut open some termites in an attempt to find out what they ate.

Gazing at the dissected insects through his microscope, Leidy saw hordes of small specks evacuating their corpses, like “a multitude of persons from the door of a crowded meetinghouse,” he wrote. He billed them as parasites, and for good reason. It was 1889, 30 years after the publication of Charles Darwin’s provocative opus, On the Origin of Species by Means of Natural Selection, and biologists had begun to see nature as a red-blooded gladiatorial arena, where only the fittest survive. And in previous decades, scientists had shown that many infamous diseases, like gonorrhea and tuberculosis, were the work of microscopic bacteria. With nature framed in terms of conflict, and bacteria framed as germs, any microbes living in the bodies of animals were instantly vilified as parasites.

We now know that this view is deeply incorrect. Every individual animal is a thriving community of microbes, most of which are harmless, and many of which are beneficial. These microbiomes bestow their owners with amazing abilities.

Those of termites, for example, help them to digest their food. The ones that Leidy saw are protists—microbes that have more in common with us than with bacteria, but that still consist of a single, tiny cell. They produce enzymes that help termites to digest the otherwise indigestible chemicals in the wood that they eat, to survive on a rich and abundant food source that would otherwise be inaccessible to them.

You can learn more about that microbiome in the video below—the first in a series of online films produced by HHMI Tangled Bank Studios, which adapt the stories in my book, I Contain Multitudes.

There are different kinds of termites, too. The misleadingly named lower termites rely on protists as partners in digestion. The higher termites, which evolved later, rely more on bacteria, which they house in a series of cowlike stomachs. And the macrotermites—the most recent of these groups—rely on both architecture and agriculture. They feed bits of wood to a fungus, which breaks them down and creates a compost that the termites can swallow. In their guts, bacteria digest the wood pulp even further.

This is true for every member of a macrotermite colony except the huge and grossly swollen queen. Her distended body lacks gut microbes, but she can eat because her daughters regurgitate predigested fluids into her mouth. She has effectively turned her entire nest—towering, fungus-laced walls; thousands of diligent laboring daughters, and their billions of attendant microbes—into her gut.

Even the microbes of termites can have their own microbiomes. One species of Australian termite carries a protist in its gut called Mixotricha paradoxa—a pear-shaped microbe whose name means “paradoxical being with mixed-up hairs.” Those “hairs,” which propel the microbe through the gut, are actually bacteria—and close relatives of those that cause syphilis. Lynn Margulis, one of the most vocal proponents of the interconnectedness of life, showed that Mixotricha carries around no fewer than four types of bacteria—one inside itself, and three on its surface. As she and her son once wrote:

“Scrutinizing any organism at the microscopic level is like moving ever closer to a pointillist painting by Georges Seurat: The seemingly solid figures of humans, dogs, and trees, on close inspection, turn out to be made up of innumerable tiny dots and dashes, each with its own attributes of color, density, and form.”

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