Abstract: Disclosed are microbial biomarkers and methods for accurate non-invasive diagnosis of non-alcoholic fatty liver disease (NAFLD) in subjects. The microbial biomarkers include Lactococcus lactis as well as its strains and subspecies. The microbial biomarkers include Dorea sp. 5-2. The methods include measuring abundance or copy number of the one or more microbial biomarkers in a sample from the subject. The sample may be bodily fluid, mucus, or stool. Also described are methods of treating a subject with NAFLD by administering to the subject a composition containing Lactococcus lactis and/or Dorea sp. 5-2.