yes, the use of the word microbes and beneficial bacteria are interchangeable.
From Webster:
A hint of the Greek word bios, meaning "life", can be seen in microbe. Microbes, or microorganisms, include bacteria, protozoa, fungi, algae, amoebas, and slime molds. Many people think of microbes as simply the causes of disease, but every human is actually the host to billions of microbes, and most of them are essential to our life. Much research is now going into possible microbial sources of future energy; algae looks particularly promising, as do certain newly discovered or created microbes that can produce cellulose, to be turned into ethanol and other biofuels.