Everyone has a pet theory to explain the rise of modern scourges, things that our forbears rarely had to contend with during their short, brutish lives: obesity, diabetes, celiac disease, autism, asthma, allergies, esophageal cancer, etc. Plastics, pesticides, and genetically modified crops are perennial favorites; wheat seems to be the darling of the moment.

Martin Blaser, the director of the Human Microbiome Program at NYU, thinks that these ills are due to the overuse of antibiotics. He uses his new book, Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, to argue that the broad spectrum of antibiotics that is relied upon by modern medicine disrupt the microbiome, the diverse bacterial ecosystem that has been residing in human bodies ever since there were human bodies. The timeline corresponds; many of these disorders have exploded in prominence in the past few decades just as antibiotics began being prescribed almost indiscriminately because they always worked and "couldn't hurt."

The idea holds up scientifically too, as Blaser demonstrates. For example, the bacterial species we harbor help train our immune cells to recognize and combat pathogens, so disrupting this balance could account for the inflated rates of immune disorders we are experiencing. Further evidence for the connection is that antibiotic exposure has been positively associated with developing both asthma and celiac disease.

One of the most interesting insights that the book delivers concerns antibiotics' relationship to obesity. Farm animals get constant, subtherapeutic doses of antibiotics. These are not to treat infections, but to fatten them up. This works really well—regardless of which antibiotics they receive, the animals grow faster, larger, and fatter. American children receive, on average, three courses of antibiotics in their first two years of life, and one additional course each year for the next eight years. And American children have undeniably been getting fatter. Cold the antibiotics be doing to our kids what they're doing to our cattle?

Data from mouse studies done in Blaser's lab suggest that short, intensive doses of antibiotics—like the kind children routinely get—can in fact cause weight gain. Let’s say you are the kind of highly educated parent who knows that colds are caused by viruses and therefore won't be helped by antibiotics, someone who will refuse the amoxycillin your pediatrician tries to prescribe to make you feel like you are doing something for your kid and to get you out of his office quicker. It’s still very difficult to limit your child's exposure to antibiotics because they are still in the meat the kids eat and the milk they drink. Antibiotics are even used on organic apples and pears to combat fire blight, a bacterial disease of fruit trees.

Blaser is also incensed over the rise of Caesarian sections, a medical innovation that—like antibiotics—he thinks is overused because we have completely underestimated its cost. Like antibiotics, they should absolutely be used when medically necessary. But when a baby is removed from the womb through an incision rather than passing through the birth canal, it misses out on getting the bacteria from its mother's vagina all over its skin. This bacteria is essential in properly seeding the baby's own microbiome.

Babies born via C-section instead get seeded with bacteria from the doctors' and nurses' skin, and there are cohort studies indicating that these babies are more likely to be obese as children. His advice? If you need a C-section, do it—but then swab the baby with the mother's bacteria-rich vaginal secretions. But if you’re getting one because you just want to control your baby's birthday, or you don't want to have to do so many Kegels later in life, or your doctor wants to take a vacation for three weeks around your due date, maybe think twice.

The hidden cost of our profligate antibiotic overuse is a prominent theme in this book. Blaser started his career as an infectious disease guy and he did his time at the Centers for Disease Control; he knows full well the damage pathogens can wreak, and just how essential antibiotics are to maintaining public health. This is another reason he advocates curbing antibiotic overuse: to reduce antibiotic resistance, so these drugs will still work when we really need them.

By treating every childhood sniffle with broad spectrum antibiotics, we are killing not only dangerous pathogens but also the hundreds of trillions of bacteria that live in our bodies and have been there ever since the dawn of humanity. He thinks that those species are there for a reason, and he warns that their demise is causing big trouble—with more to come.

Ironically, antibiotic exposure has also been shown to increase susceptibility to subsequent infection, possibly because of the effects that perturbing the microbiome has on immunity.

People—especially parents—don't know that antibiotic exposure is associated with any risks. But these risks are especially notable in a child's first three years, when the composition of the microbiome is being established for life. He thinks that broad spectrum antibiotics should come with a warning: "may increase risk of asthma, obesity, diabetes, and infection." If the child needs the antibiotic to save his life or his leg, it is obviously worth the risk. But if he is receiving it so his ear infection will go away a day earlier, it might not be.

Beyond humans, plying farm animals with antibiotics just to make meat cost a few cents less at the cash register doesn't really reduce the price; instead of paying more dollars at the supermarket, we are paying later in terms of our health.

So if Blaser is so down on antibiotics, he must love probiotics right? Not so fast. They are great in theory, but he is an empiricist, and the data to support their utility is just not there yet. Probiotic pills currently on the market are unregulated, so it is impossible to know what they contain or what they will do. Experiments have not yet been done to determine which (if any) probiotics will help which person. And, since each person's microbiome is pretty much established by age three, any bacteria ingested after that may simply be flushed out without changing anything.

Our bodies have ten times more bacterial cells than human cells. There might be trillions of cells of some species—like Bacteroides—but only a few hundred cells of rarer species. As in any ecosystem, biodiversity provides robustness.

Blaser is concerned that broad spectrum antibiotics will wipe out the rare species we harbor, rendering them extinct before we ever learn what their function was supposed to be. And as in any ecosystem, once we figure out the ramifications of species extinction, it is too late to remedy them.

Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, by Martin Blaser. Henry Holt and Co., 2014.