Microbes in our guts have been with us for millions of years

By Ann Gibbons

Humans did not evolve alone. Tens of trillions of microbes have followed us on our journey from prehistoric ape, evolving with us along the way, according to a new study. But the work also finds that we’ve lost some of the ancient microbes that still inhabit our great ape cousins, which could explain some human diseases and even obesity and mental disorders.

Researchers have known for some time that humans and the other great apes harbor many types of bacteria, especially in their guts, a collection known as the microbiome. But where did these microbes come from: our ancient ancestors, or our environment? A study of fecal bacteria across all mammals suggested that the microbes are more likely to be inherited than acquired from the environment. But other studies have found that diet plays a major role in shaping the bacteria in our guts.

To solve the mystery, Andrew Moeller turned to wild apes. As part of his doctoral dissertation, the evolutionary biologist, now a postdoc at the University of California, Berkeley, studied gut bacteria isolated from fecal samples from 47 chimpanzees from Tanzania, 24 bonobos from the Democratic Republic of the Congo, 24 gorillas from Cameroon, and 16 humans from Connecticut. In these samples, he and colleagues at the University of Texas (UT), Austin, compared the DNA sequences of a single rapidly evolving gene that is common in the gut bacteria in apes, including humans. They then sorted the different DNA gene sequences into family trees.

It turns out that most of our gut microbes have been evolving with us for a long time. Moeller found that two of three major families of gut bacteria in apes and humans trace their origins to a common ancestor more than 15 million years ago, not primarily to bugs picked up from their environment. But as the different species of apes diverged from this ancestor, their gut bacteria also split into new strains, and coevolved in parallel (a process known as cospeciation) to adapt to differences in the diets, habitats, and diseases in the gastrointestinal tracts of their hosts, the team reports today in Science. Today, these microbes are finely adapted to help train our immune systems, guide the development of our intestines, and even modulate our moods and behaviors.

“It’s surprising that our gut microbes, which we could get from many sources in the environment, have actually been coevolving inside us for such a long time,” says project leader Howard Ochman, an evolutionary biologist at UT Austin.

After the ape species diverged, some also lost distinct strains of bacteria that persisted in other primates, likely another sign of adaptation in the host, the team found.

In a final experiment, the researchers probed deeper into the human microbiome. They compared the same DNA sequence they had analyzed in all of the apes, but this time between the people from Connecticut and people from Malawi. They found that the bacterial strains from these Africans diverged from those of the Americans about 1.7 million years ago, which corresponds with the earliest exodus of human ancestors out of Africa. This suggests that gut bacteria can be used to trace early human and animal migrations, Moeller says. Interestingly, the Americans lacked some of the strains of bacteria found in Malawians—and in gorillas and chimps—which fits with the general reduction in gut microbiome diversity that has been observed in people in industrialized societies, perhaps because of changes in diet and the use of antibiotics.

The work “represents a significant step in understanding human microbiota coevolutionary history,” says Justin Sonnenburg of Stanford University in Palo Alto, California, who was not involved with the research. “It elegantly shows that gut microbes are passed vertically, between generations over millions of years.” Microbiologist Martin Blaser of New York University in New York City agrees: “The path of transmission was from mom apes to baby apes for hundreds of thousands of generations at least.”

But the extinction of some strains of bacteria that persist in other apes but not humans raises a red flag for our health. “What happens if a human mom takes antibiotic when she’s pregnant? What happens if she takes it at the moment of delivery?” Blaser asks.

“We are coming to understand how fundamental our gut microbes are for health,” Sonnenburg says. “These findings have huge implications for how we should pursue understanding what a truly healthy microbiome looks like.”


Thanks to Kebmodee for bringing this to the It’s Interesting community.

Depression and some antidepressant medications may raise risk of gut infection


Two studies have found that depression and the use of certain antidepressants are both associated with increased risk for Clostridium difficile infection, an increasingly common cause of diarrhea that in the worst cases can be fatal.

Researchers studied 16,781 men and women, average age 68, using hospital records and interviews to record cases of the infection, often called C. diff, and diagnoses of depression. The interviews were conducted biennially from 1991 to 2007 to gather self-reports of feelings of sadness and other emotional problems. There were 404 cases of C. difficile infection. After adjusting for other variables, the researchers found that the risk of C. diff infection among people with a history of depression or depressive symptoms was 36 to 47 percent greater than among people without depression.

A second study, involving 4,047 hospitalized patients, average age 58, found a similar association of infection with depression. In addition, it found an association of some antidepressants — Remeron, Prozac and trazodone — with C. diff infection. There was no association with other antidepressants. “We have known for a long time that depression is associated with changes in the gastrointestinal system,” said the lead author, Mary A.M. Rogers, a research assistant professor at the University of Michigan, “and this interaction between the brain and the gut deserves more study.”

Both reports appeared in the journal BMC Medicine.

Microbes discovered to be thriving high in the atmosphere


Each year, hundreds of millions of metric tons of dust, water, and humanmade pollutants make their way into the atmosphere, often traveling between continents on jet streams. Now a new study confirms that some microbes make the trip with them, seeding the skies with billions of bacteria and other organisms—and potentially affecting the weather. What’s more, some of these high-flying organisms may actually be able to feed while traveling through the clouds, forming an active ecosystem high above the surface of the Earth.

The discovery came about when a team of scientists based at the Georgia Institute of Technology in Atlanta hitched a ride on nine NASA airplane flights aimed at studying hurricanes. Previous studies carried out at the tops of mountains hinted that researchers were likely to find microorganisms at high altitudes, but no one had ever attempted to catalog the microscopic life floating above the oceans—let alone during raging tropical storms. After all, it isn’t easy to take air samples while your plane is flying through a hurricane.

Despite the technical challenges, the researchers managed to collect thousands upon thousands of airborne microorganisms floating in the troposphere about 10 kilometers over the Caribbean, as well as the continental United States and the coast of California. Studying their genes back on Earth, the scientists counted an average of 5100 bacterial cells per cubic meter of air, they report in the Proceedings of the National Academy of Sciences. Although the researchers also captured various types of fungal cells, the bacteria were over two orders of magnitude more abundant in their samples. Well over 60% of all the microbes collected were still alive.

The researchers cataloged a total of 314 different families of bacteria in their samples. Because the type of genetic analysis they used didn’t allow them to identify precise species, it’s not clear if any of the bugs they found are pathogens. Still, the scientists offer the somewhat reassuring news that bacteria associated with human and animal feces only showed up in the air samples taken after Hurricanes Karl and Earl. In fact, these storms seemed to kick up a wide variety of microbes, especially from populated areas, that don’t normally make it to the troposphere.

This uptick in aerial microbial diversity after hurricanes supports the idea that the storms “serve as an atmospheric escalator,” plucking dirt, dust, seawater, and, now, microbes off Earth’s surface and carrying them high into the sky, says Dale Griffin, an environmental and public health microbiologist with the U.S. Geological Survey in St. Petersburg, Florida, who was not involved in the study.

Although many of the organisms borne aloft are likely occasional visitors to the upper troposphere, 17 types of bacteria turned up in every sample. Researchers like environmental microbiologist and co-author Kostas Konstantinidis suspect that these microbes may have evolved to survive for weeks in the sky, perhaps as a way to travel from place to place and spread their genes across the globe. “Not everybody makes it up there,” he says. “It’s only a few that have something unique about their cells” that allows them survive the trip.

The scientists point out that two of the 17 most common families of bacteria in the upper troposphere feed on oxalic acid, one of the most abundant chemical compounds in the sky. This observation raises the question of whether the traveling bacteria might be eating, growing, and perhaps even reproducing 10 kilometers above the surface of Earth. “That’s a big question in the field right now,” Griffin says. “Can you view [the atmosphere] as an ecosystem?”

David Smith, a microbiologist at NASA’s Kennedy Space Center in Florida, warns against jumping to such dramatic conclusions. He also observed a wide variety of microbes in the air above Oregon’s Mount Bachelor in a separate study, but he believes they must hibernate for the duration of their long, cold trips between far-flung terrestrial ecosystems. “While it’s really exciting to think about microorganisms in the atmosphere that are potentially making a living, there’s no evidence of that so far.”

Even if microbes spend their atmospheric travels in dormancy, that doesn’t mean they don’t have a job to do up there. Many microbial cells are the perfect size and texture to cause water vapor to condense or even form ice around them, meaning that they may be able to seed clouds. If these microorganisms are causing clouds to form, they could be having a substantial impact on the weather. By continuing to study the sky’s microbiome, Konstantinidis and his team hope to soon be able to incorporate its effects into atmospheric models.


New type of bacteria discovered in Indiana man’s gruesome wound


An Indiana man’s nasty injury led scientists to discover a new type of bacteria that sheds light on symbiotic microbes in insects.

Two years ago, Thomas Fritz cut down a dead crab apple tree in his yard. He fell while hauling away the woody debris and a branch from the tree impaled his right hand between the thumb and index finger.

Fritz, a 71-year-old retired inventor, engineer and volunteer firefighter, bandaged the gash himself. He waited a few days to see a doctor and by the time of his appointment, the puncture wound became infected. The doctor took a sample of the cyst that formed at the site of the cut and sent it to a lab.

After an abscess, swelling and more pain, Fritz’s wound eventually healed. But the sample from his infection puzzled scientists at the lab who couldn’t identify what type of bacteria they were looking at. The sample was eventually sent to ARUP Laboratories, a national pathology reference library operated by the University of Utah, where scientists named the new strain human Sodalis or HS.

Colin Dale, a biologist at the University of Utah, said that genetic analyses of HS showed it is related to Sodalis, a genus of bacteria that he discovered in 1999 and has been found to live symbiotically in 17 insect species, including tsetse flies, weevils, stinkbugs and bird lice. In such symbiotic relationships, both the host and the bacteria gain — for example, while Sodalis bacteria get shelter and nutrition from their insect hosts, they also provide the insects vital B vitamins and amino acids.

Though symbiotic relationships between microorganisms and insects are common, their origins are often a mystery. The new evidence provides “a missing link in our understanding of how beneficial insect-bacteria relationships originate,” Dale said, adding that the findings show that these relationships arise independently in each insect.

As the strain of Sodalis in this case likely came from a tree, the discovery suggests that insects can get infected by pathogenic bacteria from plants or animals in their environment, and the bacteria can evolve to become less virulent and to provide symbiotic benefits to the insect. Then, instead of spreading the bacteria to other insects by infection, mother insects pass down the microbes to their offspring, the researchers said.

“The insect picks up a pathogen that is widespread in the environment and then domesticates it,” Dale explained in a statement from the National Science Foundation, which funded the research. “This happens independently in each insect.”

The research was detailed earlier this month online in the journal PLoS Genetics.