100 NEW HEALTH DISCOVERIES

Microbiome CRIME-SOLVING BACTERIA • RESISTANT BACTERIA ARE EVERYWHERE • GERMS FROM KISSING • HOW YOUR GUT AFFECTS CHOLESTEROL • HOW CLEAN ARE YOUR CONTACTS? • THE CELIAC DISEASE CONNECTION • EARLY ANTIBIOTICS • PREMATURE BIRTH AND BACTERIA .OUR OWN GERM CLOUDS • TRUTH ABOUT ANTIBACTERIAL SOAP

A Strange New Way to Solve Crimes The bacteria growing in and on the human body are so unique—and so revealing—that scientists believe germs will soon help catch bad guys BY MANDY OAKLANDER

Few thieves are silly enough to burgle a house in broad Florida daylight—let alone a house where three crime-scene-investigation police vans are already parked out front. This is obviously Bill Stewart's first time as a criminal. "Can I crawl through your window?" he asks one of the homeowners. "If it doesn't break anything?" Stewart is a detective sergeant in the Fort Lauderdale Police Department, and though he may be a failure as a burglar, he knows exactly how real ones operate—and that's why he's here. In his more than two decades on the force, he's searched hundreds of windowsills, garden tools and hastily discarded gloves for clues about whodunit. Now, by playacting the role of a typical burglar, he's participating in an unusual scientific study that could ultimately change how crimes get solved. But first he and his partner need to muck up the place, which belongs to a scientist involved in the study. They squeeze through a small square window—a popular point of entry for burglars—and once inside, split up and go looking for valuables. They switch on the lights and rummage through drawers. One raids the fridge and drinks half a Diet Coke. They grab a pillowcase to stuff their loot in—something robbers often do, says Stewart. Then they sit on the couch next to the family cat, Sammie, and slip an iPad and a laptop into the pillowcase before yanking the TV's cords from the wall to cart it away. After they leave, scientists in sterile gear file in. Led by Jarrad Hampton-Marcell, a research coordinator at Argonne National Laboratory, which is funded by the U.S. Department of Energy, a team goes room by room collecting cotton-tipped swabs of what the "thieves" left behind. 44

MICROBOOME

1.

South Florida detectives drive CSI vans to a mock crime scene where a novel tool in forensics will be tested. 2. Staging a burglary in the name of science,detectives break into a house through (front window. 3. Scientists later swab the window to collect and analyze invisible bacteria left behind by the "burglars." 4. Switches and other surfaces that were touched in the mock crime also get swabbed. 5. Uniformed members of the crime-scene unit wear sterile gear to prevent contaminating the scene. 6. The scientists bag &bacterial samples and later sequence them to discover leads.

ANATOMY OF A CRIME

So far, this crime-scene activity looks as routine as the pacing of a television police procedural. But there's a twist: The scientists won't be gathering and analyzing DNA or fingerprints. They'll be analyzing bacterial cells left behind by the robbers. Think of it as CSI: E. coll. New science is finding that 46

each one of us brings with us (and can't help but leave behind) a unique bacterial signature everywhere we go—a germy John Hancock. As you move through a scene and shed your microbes, the space starts to reflect your bacterial signature, potentially tying you to it and giving away a lot about you in the process. To test how much bacteria gets left behind and what it can reveal about identity, scientists will compare the bacterial cells collected from the burglars and see if they can differentiate them from those of the homeowners and their cat, whose paw the scientists also swabbed. They will also try to see if they can tease out the signatures from the samples from the scene. If they can, it will provide early proof that an outsider's bacteria is distinct enough from the homeowners' to confirm that a stranger was in the house. If this holds true—and evidence suggests it might—it

will mean that crime scenes are riddled with valuable clues that are currently left untested. Crime experts agree that the field of forensics needs cheaper, faster ways to gather investigative leads like these. Trace evidence— the kind found through hairs, fibers or paint—typically requires chemical analysis, which can be expensive and inaccurate if there's not enough of it to analyze. Thanks to advances in science, however, bacterial evidence can be sequenced affordably, quickly and with startling accuracy. That's why forensics experts are saying it's the leading contender for next-generation investigations. The criminal-justice system is always looking for one thing: they're looking for probable cause, any kind of thing that can give them information about a possible suspect," says George Duncan, the DNA unit manager at the Broward County sheriff's office crime lab. "The crime-scene people, they think bacterial forensics is just as exciting as hell." Your bacterial makeup, called the microbiome, can give away a lot about you. So far, most research has focused on the densest site for bacteria, the gut, which houses roughly four pounds of bugs. But bacteria aren't just in us; we're covered in the stuff too. By age 3, everyone, even identical twins, has a unique coat of it that changes somewhat but remains largely consistent at its core and over time. In scientific studies, researchers have successfully matched smartphones and keyboards to the people who used them by analyzing their microbial signatures. And in a study published last year in the journal Science, researchers followed seven families for six weeks and were able to match them to their homes through bacteria alone. The more intimate you are with someone, the study found, the more microbes you share—though your makeup is still distinct from that person's. "There's a continuum between you and your world, not a brick wall that ends at your skin," says Jack Gilbert, a microbial ecologist at Argonne and the principal investigator in that study. He and his team discovered that even when a family moved, it took only hours for the new house to look nearly bacterially identical to the old one. Scientists' ability to track bacteria left behind by people is where the forensic potential lies. Gilbert, who has studied microbes for i6 years, thinks bacterial forensics will be the next great contribution to crime fighting. "We're ramping up to be able to leverage signature profiles in a really robust way," he says. "It's what people did for fingerprints years ago." Court challenges will follow the scientific ones—it took a decade for DNA to become a courtroom staple— but here's how it could play out: In a murder case, the prime suspects are usually people closest to the victim. So if a wife is killed, says Stewart Mosher, a sergeant with the Broward County sheriff's office crime-scene unit, "the first person you've got to look at is the husband." Consider, however, if the husband says he was

out of town when it happened. Bacterial signatures last 4 8 to 72 hours once a person has left. "So if his bacterial profile is absent from the house, and that matches his sworn statement, which we would have to substantiate, it's going to be extremely difficult to be able to say he had anything to do with it. That clue alone could be huge." It's a brand-new area of physical evidence, says David Carter, a forensic specialist who assists the Honolulu police. "We've lacked science and technology to analyze microbial communities," he says. But with fast new ways to sequence microbes without having to grow them in a lab, "now we can get a level of resolution that we never had before." Of course, there's a chasm between the potential of bacterial forensics and its widespread adoption. Some legal experts cast doubt on how reliable the technique is—and how useful, given that DNA would likely be wherever bacteria are present. And what does it mean if the signatures are close but not identical? These are some of the questions that need answering before it's admissible in court. "I don't see this, so far, as revolutionizing forensic science," says David H. Kaye, a law professor at Pennsylvania State University and forensic-science expert. On top of all that, there are also some hairy ethical questions to be grappled with first. Depending on how they're sequenced, microbial samples can reveal private information about their hosts, from what diseases they might have to what kind of work they do to their ethnicity. That information, some caution, is far too sensitive to put into a database. But Gilbert doesn't see how it's ethically different from collecting genetic information left at a crime scene. "It may come to a point where, if you perform a criminal act, you have your microbiome collected and database d," he says. "We're a long way off that, but it's something I would like to work toward." In the meantime, thousands of volunteers are willingly sharing their bacterial signatures with researchers. Microbiomes are being sequenced on a large scale, and scientists are finding valuable correlations by comparing the bacteria of one person with a database of others'. For instance, after analyzing the bacteria collected from the faux burglary, Hampton-Marcell found that the intruders' bacteria were indicative of two quirky factors: alcohol consumption and migraines. The owners of the house, another comparison revealed, were omnivores and popped vitamin B and calcium. (Turns out Stewart does get migraines and drinks an occasional beer, and the homeowners do eat everything—including vitamins.) So, in addition to proving a stranger has been in a home, scientists theorize that bacteria could also tell investigators more about what kind of person the suspect is. Cops won't be swabbing for bacteria tomorrow. But, says Kaye, "I can imagine some cases where this starts to be used for investigative purposes in five to to years." 47

IF

MICROBDOME

Antibiotic-Resistant Bacteria Are Now in Every Part of the World

OVERUSE OF AN'THEJOT CS IS SLOWLY WIPING OUT THE GOOD BACTERIA WITH THE BAD, AND THAT IS BRINGING WITH IT SERIOUS CONSEQUENCES FOR HUMAN HEALTH

Bacteria Spread Through One Kiss First base is a great place to get your mouth microbes some new friends, finds a study in the journal Microbiome. A to-second French kiss can spread 8o million bacteria between mouths. Study author Remco Kort, a professor and scientist at the Netherlands Organisation for Applied Scientific Research, asked couples visiting a zoo in the Netherlands if they wanted to participate in a study on French kissing. Twenty-one couples agreed and had their tongues swabbed and saliva collected, both before and after a kiss. Researchers discovered that the-bacteria on the tongues of couples was much more similar than the oral bacteria of two strangers. Kissing might also act as a form of immunization, adds Kort, allowing you to build up resistance from exposing yourself to more microorganisms. "If you look at it from this point of view, kissing is very healthy." 48

In a 2015 report, the World Health Organization found that bacterial infections that can't be treated with the antibiotics of last resort have emerged in every part of the world. That means patients who pick up E. coli or staph infections may not have an effective way to fight the bacteria. Even more concerning, scientists are learning, is how these antibiotics are affecting the makeup of both good and bad bacteria that live within us—our microbiome. Martin Blaser, director of the Human Microbiome Program at New York University Langone Medical Center and author of Missing Microbes, says, "Antibiotics are extinguishing our microbiome and changing human development." Bacteria aren't de facto enemies of a healthy body—quite the opposite, in fact. Most of our bacteria act like an ally, helping us digest food, fight off disease-causing bugs, resist pathogens and more. But overuse of antibiotics is slowly wiping out the good bacteria with the bad, and that may have serious consequences for public health. "What we urgently need is a solid global plan which provides for the rational use of antibiotics so that [the drugs] reach those who need them but are not overused or priced beyond reach," says. Jennifer Cohn, the medical director of Doctors Without Borders' Access Campaign.

How Bacteria Control Your Cholesterol Evidence is mounting that the bacteria that live on and in our bodies are harbingers of our health. They're also responsible for—or at least implicated in—bodily functions that appear, on the surface, to have nothing to do with microbes, and certainly nothing to do with the gut. But in a study published in the journal Circulation Research, scientists led by Jingyuan Fu of the University Medical Center Groningen in the Netherlands quantified for the first time exactly how much the microbes in the gut contribute to blood cholesterol levels. Studying 893 people who provided fecal and blood samples, Fu and her team genetically sequenced the microbial material to get a better sense for which bacterial populations occupied the gut. They found 34 unique bacterial

BEYOND DIGESTION

New Intel into How Clean Your Contact Lenses Are The magical clear disks that bring your world into focus may be doing some bad things to your eye bacteria, according to a 2015 study. "The eye has a normal community of bacteria, expected to confer resistance to invaders," says senior study investigator Maria Gloria DominguezBello, an associate professor in the Human Microbiome Program at New York University School of Medicine. But inserting contact lenses seems to mess with that delicate balance, the researchers found. They wanted to compare the colonies of bacteria living on the eyeballs of contact-lens wearers with those on non-wearers' eyes, so they recruited zo people for the new research, presented at the annual meeting of the American Society for Microbiology. They swabbed different parts of the eye, sequenced the bacteria and found major differences between lens wearers and people who didn't wear lenses. Bacteria in the eyes of contacts wearers looked more like the colonies of bacteria found on their skin than those normally found in eyes, compared with the normal bacteria of the lens-free group.

Gut bacteria affects cholesterol levels.

sequences that were linked to body mass index (BMI, a measure of height and weight) and blood lipid levels. Then they calculated how much variation in these groups of bacteria affected BMI and lipid levels. After factoring in age, gender and genetics, they concluded that the gut microbes accounted for 4.5% to 6% of the differences among participants in triglyceride and HDL (good) cholesterol levels. Triglycerides are linked to a higher risk of diabetes and heart disease; HDL is connected with a lower risk of these problems. When they included the microbiome along with age, gender and genetics in looking at BMI and lipids, the combined contribution explained 26% of the differences in HDL. (Without the microbial information, the other factors explained 19% to zo% of the variation among people.) Having hard numbers to understand how much gut microbes might be contributing to metabolism, and therefore to the risk of chronic conditions such as heart disease, diabetes and obesity, may create new ways of treating them. "We can intervene with bacterial populations in the future," says Fu, "because the microbiome can be targeted for treatment with probiotics or medicine." 49

MBEROBDOREE

A New Lead on the Cause of Celiac Disease Celiac disease affects about IS4 of the world's population, but scientists still don't fully understand it. It's still unclear why some people get the autoimmune disease and other people don't. It seems to affect people of all ages, and you can't blame an increased consumption of food that contains gluten; USDA data shows we're not eating more of it. It's possible something in the environment or the overuse of antibiotics is culpable, or something could be different about gluten itself. Alessio Fasano, director of the Center for Celiac Research at Massachusetts General Hospital for Children, suspects it may come down to how the modern, hyper-processed diet has influenced the makeup of our gut bacteria. Fasano hopes to explore the microbiome in his ongoing research, in which he says he'll follow kids from birth and search for a signature in their microbiome that predicts the activation of their gluten-averse genes, which leads to a child developing celiac disease. The hope, then, is that a probiotic or prebiotic intervention will bring the troubled guts back from "belligerent to friendly:" he says.

The Lasting Effects of Antibiotics In a new study, scientists document the possible long-term effects of antibiotics when they're used early in life. Martin Blaser of NYU tested mice on antibiotic regimens and compared them with mice that received a placebo. The antibiotic-treated animals had less diverse bacteria, the proportions of their microbes were different, and the changes persisted even to the animals' death. Blaser notes that while antibiotics are a lifesaving treatment, their risks might be greater than their benefits for some infections. "If what we found in mice is true for human children, then this is yet another reason to be cautious in using antibiotics," he says. He suggests that doctors be especially judicious when prescribing antibiotics for children under 3.

SUPERDRUGS

so

Antibiotics can have lifelong impact.

Premature Births Linked to Some Bacteria In the most complete look yet at how the microbes that live within us change during pregnancy, scientists reported in the Proceedings of the National Academy of Sciences this year that there may be a particular profile of bacteria residing in the vagina that is associated with a higher risk of preterm birth. Women who had preterm birth housed a more diverse array of bacteria, including gardnerella and ureaplasma. While these don't normally cause disease, they have been associated with conditions such as bacterial vaginosis, an infection of the vagina, and inflammation of the urethra in men. Exactly why or how the presence of these species are linked to the higher rate of preterm birth isn't clear yet. But the ultimate goal is to use that information to better predict which women might be at a higher risk of having a preterm birth. And if the role of microbes is strong enough, it may be possible to even intervene with antibiotics or probiotics.

Humans Produce Their Own Germ Clouds We all continually emit our own microbial residue into the air and onto nearby—and not so nearby—surfaces. According to a 2015 study in the open-access journal Peed, scientists Can distinguish the makeup of the cloud that is uniquely yours—a personal marker as particular to you as your fingerprints or your genome. The new study was conducted by investigators from the University of Oregon. To determine how distinct microbial clouds are, the scientists ran two experiments. In the first, they had three subjects spend two hours one day and four hours the next sealed alone inside a sanitized chamber. Microbial samples were then collected from several dishes placed near the subject. In the second experiment, eight different subjects spent 90 minutes at a time confined in the chamber. After that, the air, not the surfaces, was sampled for microbes. Comparing the samples they collected from the chamber with samples they collected directly from each individual, the researchers found that while all of the subjects emitted more or less the same collection of microbes, the ratios of each were indeed unique to the individuals. The differences among the samples ranged from as little as 4% of the bacterial population to as much as 61%. If the study proves anything, it's that all of us, as Walt Whitman would have it, contain multitudes. And more than we ever knew, we are forever letting a whole lot of our interior critters out to play.

WITHIN JUST A FEW DAYS OF MOVING INTO A NEW HOME, THE OCCUPANTS HAVE ALREADY

FELLED THE Al AND SEEDED THE SURFACES WITH DETECTABLE MICROSCOPIC ORGANISMS

D'aSK ED,:

Is Antibacterial Soap Worth It? If you're bothering to wash your hands regularly—and you should be—you're probably using antibacterials. But researchers have found, as they detail in a 2015 report published in the Journal of Antimicrobial Chemotherapy, that antibacterial formulas do not kill any more bacteria than traditional soap and water. Both fared the same after 20 seconds, which is the length of time that the World Health Organization recommends for handwashing. Scientists at Korea University compared antibacterial soaps and standard soaps on 20 strains of bacteria. The antibacterials performed no better. The only difference that they made was in an experiment in which the scientists left bacteria on an antibacterial soap solution for nine hours. Only then did the antibacterial soaps eliminate more bacteria than plain soap. Since nobody is expected wash her hands for nine hours, the lesson is that when it comes to washing your hands, you don't need antibacterial formulas.

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