Yes. Many bacteria that live on and inside the human body are helpful. Together with other microbes, they make up the microbiome, which supports digestion, helps the immune system develop, and can protect against some disease-causing germs.
According to the National Institute of Environmental Health Sciences (NIEHS), microbes in the microbiome “protect us against pathogens, help our immune system develop, and enable us to digest food to produce energy.” Different body sites—such as the gut, skin, and mouth—host different microbial communities, and a person’s core microbiome forms in early life but can change with diet, medications, and environmental exposures.
Not every bacterium is beneficial, and disruptions to the microbiome (for example from certain exposures or antibiotics) can be linked to health problems. Still, in current scientific understanding, helpful bacteria are a normal and important part of human biology—not something people should try to eliminate entirely.
Source: NIEHS — Microbiome