Doctors are finding that cultivating beneficial bacteria can improve health. Two types of bacteria.

For a century, doctors have warred against bacteria with antibiotics. But that is changing as scientists learn more about the 100 trillion microbes that call us home — collectively known as the microbiome.

“I would like to lose the language of warfare,” said Julie Segre, a n inves-tigator at the National Human Ge-nome Research Institute in Bethesda, Maryland. “It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.”

This new approach is called medi-cal ecology. By nurturing the body’s ecosystem, doctors may be able to find alternatives to antibiotics to fight infectious diseases, and with fewer harmful side effects. Tending the mi-crobiome may also help in treating obesity and diabetes.

In June, Dr. Segre and 200 other sci-entists published the most ambitious survey of the human microbiome yet. The Human Microbiome Project tracked 242 healthy people over two years. The scientists sequenced the genetic material of bacteria from their subjects’ bodies, recovering over five million genes.

The project and other studies are revealing how our invisible residents shape our lives.

Recent reports shed light on how mothers promote babies’ health by shaping their microbiomes. In a study in June in the journal PLoS One, Dr. Kjersti Aagaard-Tillery, an obstetri-cian at Baylor College of Medicine in Houston, and her colleagues found that the diversity of vaginal bacteria changes throughout pregnancy.

During delivery, a baby will be coated by the Lactobacillus johnsonii bacteria and ingest some of it. It is usually found in the gut, where it produces enzymes that digest milk. Dr. Aagaard-Tillery suggests that this inoculation prepares the infant to digest breast milk.

A University of Idaho study found that women’s milk had up to 600 spe-cies of bacteria. The more the good bacteria thrive, the harder it is for harmful species to grow.

As the child grows, the microbiome tutors the immune system. Ecological disruptions can halt this education. Children who take high levels of anti-biotics may be at greater risk of devel-oping allergies and asthma, research suggests.

The mouth may contain 5,000 spe-cies of bacteria.

Our bodies also host viruses. Many species in the “virome” infect our resi-dent bacteria. But in DNA samples in the Human Microbiome Project’s da-tabase, Kristine Wylie of Washington University in St. Louis and her col-leagues are finding viruses that target human cells.

The microbiome also includes fungi. In the June 8 issue of Science, David Underhill, a research er at Cedars-Sinai hospital in Los Angeles, and his colleagues reported on fungal species in mammals’ guts. In mice, they cata-loged 100 new species, plus 100 already known.

The microbiome carries out many services. In the gut, microbes synthe-size vitamins and break down plant compounds.

Antibiotics kill off harmful bacteria, but some can kill off many desirable species, as well. A species of bacteria called Clostridium difficile can invade the gut after a course of antibiotics. Antibiotic-resistant C. difficile can be hard to eradicate.

Scientists think devastated micro-biomes can be restored. “At least the data is starting to argue” it may be possible, said Barbara Methé of the J. Craig Venter Institute.

One way may be to foster beneficial bacteria. But the science of so-called probiotics lags sales: $28 billion in probiotic foods and supplements were sold in 2011, according to the research firm EuroMonitor International. But few have been rigorously tested.

Some doctors are treating C. dif-ficile with fecal transplants: stool from a healthy donor is delivered like a suppository to an infected patient. The idea is that the good bacteria in the stool establish themselves in the gut and begin to compete with C. dif-ficile. Research at the University of Alberta has concluded the procedure is safe and effective.

Researchers at the Academic Medi-cal Center in Amsterdam are explor-ing whether fecal transplants can treat obesity; scientists have linked obesity to changes to the gut’s ecosystem.

“Like any ecosystem,” said Michael A. Fischbach, a microbiologist at the University of California, San Francis-co, “the microbiome is not the kind of place to find simple answers.”