Sentence:  Mostly, the microbiome is beneficial. It helps with digestion and enables people to <WSD>extract</WSD> a lot more calories from their food than would otherwise be possible. Research over the past few years, however, has implicated it in diseases from atherosclerosis to asthma to autism. 
Meaning of the word marked with <WSD> tags:  To withdraw by expression, distillation, or other mechanical or chemical process. Compare abstract (transitive verb).