Excerpt from I Contain Multitudes by Ed Yong, plus links to reviews, author biography & more

Gilbert wants to understand those connections. He wants to be an all-seeing border officer for the human body, who knows exactly which microbes are coming in (and their point of origin), and which ones are leaving (and their destination). But humans make his job very difficult. We interact with so many different objects, people, and places that it becomes a nightmare to trace the paths of any particular bacterium. "I'm an ecologist; I want to treat the human being like an island," he says. "But I'm literally not allowed. I put in a proposal to take some people and lock them in a space for six weeks, and the institutional review board said no."

That's why he turned to dolphins.

"How many samples would you like?" asks veterinarian Bernie Maciol. "How many have you done?" says Gilbert.

"Three."

"Can you do replicates of those? And maybe some from another skin site? What about the armpit? No, not armpit. Whatever that is. What do you call a dolphin's armpit?"

We are in the Shedd Aquarium's dolphin exhibit – a large tank, overlooked by artificial rocks and trees. Jessica, a trainer in a black- and-blue wetsuit, sits in the water and slaps its surface with her hand. A Pacific white-sided dolphin named Sagu swims up. He's a beautiful animal, with skin like a laminated charcoal drawing. He's obedient, too: when Jessica holds her hands palms-down and waves them to the side, Sagu rolls over and exposes his milky-white stomach. Maciol reaches across, swabs Sagu's armpit with a cotton bud, seals it in a tube, and passes it back to Gilbert. She does the same for two other dolphins, Kri and Piquet, who are quietly mooching next to their respective trainers.

"We've been doing blowhole sampling, faecal sampling, and skin sampling," Jessica tells me. "For the blowhole, I'll rest their head in my hand, put an agar plate over the hole, and tap to make the dolphin do a forced exhale. For the faecal sample, I'll make them roll over, insert a small rubber catheter and pull it out. We're not short of poop around here."

This Aquarium Microbiome Project offers Gilbert what he cannot get from his Naperville house or any of the other homes that he has sampled – a kind of omniscience. Here are animals whose environment is fully known. Everything about the water – temperature, salinity, chemical content – can be measured, and regularly is. Here, Gilbert can analyse the microbiome of the dolphins' bodies, water, food, tanks, trainers, handlers, and air, and he has done so once a day for six weeks. "These are real animals with their own real microbiomes living in a real environment, and we've catalogued all of the microbial interactions they have with that environment," he says. And that should give him an unprecedented view of the connections between the microbes in an animal's body and those in the surround- ing world.

The aquarium is running several such projects to improve the lives of its charges. Bill Van Bonn, the Shedd's vice-president for animal health, tells me that the entire 3-million-gallon water supply in the main oceanarium used to pass through a life-support loop that cleaned and filtered it every three hours. "You know how much energy it takes to push that water? Why do we do it that often? Because: we're going to make this water so clean that it'll be absolutely the best thing," he says, putting on a mock gung-ho tone. "But when we back it up and do it half as much, what happens! Nothing! The water chemistry and the animals' health actually improves!"

Van Bonn suspects that in shooting for sanitation their intense cleaning regimes had gone too far. They ended up stripping the microbes from the aquarium environment, preventing mature and diverse communities from establishing themselves, and creat- ing opportunities for weedy and harmful species to exploit. Sound familiar? That's exactly what antibiotics do in the guts of hospital patients. They divest an ecosystem of its native microbes, and allow competing pathogens like C-diff to fl in their stead. In both settings, sterility is a curse not a goal, and a diverse ecosystem is bet- ter than an impoverished one. These principles are the same whether we're talking about a human intestine or an aquarium tank – or even a hospital room.

"I'm Dr Jack Gilbert, and that is a hospital," says Jack Gilbert, gesturing with his thumb at the massive hospital looming behind him.

We're now at the University of Chicago's Center for Care and Discovery, a shiny new building that looks like a giant opera gateau, with several grey, orange, and black layers. Gilbert stands in front of it, doing repeated takes for a promotional video. I'm not convinced that the cameraman's microphone is going to pick up any decent audio over the sound of Chicago's unforgiving wind. I'm more convinced that Gilbert is very cold. And I'm totally convinced that, yes, that is indeed a hospital.

Just before it opened in February 2013, Gilbert's student Simon Lax led a team of researchers through the eerily empty hallways, armed with bags of Q-tips and a plan. They swept through ten patient rooms and two nurse stations, spread over two floors: one for short- stay patients recovering from elective surgery, and another for long- term ones like cancer patients and transplant recipients. But none of the rooms were home to any humans yet. Their only residents were microbes, which Lax's team collected. They swabbed the pristine floors, the gleaming bedrails and taps, and the perfectly folded sheets.

They collected samples from light switches, door handles, air vents, phones, keyboards, and more. Finally, they fitted the rooms with data loggers that would measure light, temperature, humidity, and air pressure, carbon dioxide monitors that would automatically record if a room was occupied, and infrared sensors that could tell when people entered or left. After the grand opening, the team carried on their work, collecting more weekly samples from the rooms and the patients inside them.

Just as others have catalogued the developing microbiome of a newborn baby, Gilbert has, for the first time, catalogued the developing microbiome of a newborn building. His team is busy analysing the data now, to work out how the presence of humans has changed the edi- fice's microbial character, and whether those environmental microbes have flowed back into the occupants. Nowhere are those questions more important than in a hospital. There, the flow of microbes can mean life or death – a lot of deaths. In the developing world, around 5 to 10 per cent of people who check into hospitals and other healthcare institutions pick up some kind of infection during their stay, falling ill in the very places that are meant to make them healthier. In the United States alone, this means around 1.7 million infections and 90,000 deaths a year. Where do the pathogens behind these infections come from? Water? The ventilation system? Contaminated equip- ment? Hospital staff? Gilbert plans to find out. Through the mammoth set of data that his team have amassed, he should be able to trace the movements of pathogens from, say, a light switch to a doctor's hand to a patient's bedrail. And he should be able to work out ways of curtail- ing that life-threatening traffic.

This isn't a new problem. Ever since the 1860s, when Joseph Lister instigated sterile techniques in his hospital, cleaning regimes have helped to curb the spread of pathogens. Simple measures like hand-washing have undoubtedly saved countless lives. But just as we have gone overboard in taking unnecessary antibiotics or lathering ourselves in antibacterial sanitisers, we have also gone too far in cleaning our buildings – even our hospitals. As an example, one US hospital recently spent around $700,000 to install flooring that had been impregnated with antibacterial substances, despite having no evidence that such measures work. They might even make things worse. As in the dolphin enclosure and the human gut, perhaps the quest to sterilise our hospitals has created dysbiosis in the microbiomes of our buildings. By removing harmless bacteria that would otherwise impede the growth of pathogens, perhaps we have inadvertently constructed a more dangerous ecosystem.

Excerpted from I Contain Multitudes by Ed Yong. Copyright © 2016 by Ed Yong. Excerpted by permission of Ecco. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.