Biomarkers for rheumatoid arthritis and usage thereof

A method for obtaining a probability of a subject having a disease wherein the disease is rheumatoid arthritis, comprising:

• obtaining sequences of DNA extracted from a sample that is collected from the subject, wherein the sample comprises at least one of a fecal sample, a dental sample, and a salivary sample;
• calculating a relative abundance of a biomarker based on the sequences of the DNA, wherein the biomarker comprises a DNA sequence in a genome of Lactobacillus salivarius;
• and
• obtaining a probability of the subject having the disease based on the relative abundance to thereby determine that the individual has the rheumatoid arthritis,
• wherein the biomarker comprises at least one of the following metagenomic linkage groups (MLGs);
• the MLG corresponding to the fecal sample that consists of MLG ID NO:
• 2169;
• the MLG corresponding to the dental sample that consists of MLG ID NO:
• 16600;
• and
• the MLG corresponding to the salivary sample that consists of MLG ID NO:
• 4643;
• and wherein:
• the MLG ID NO:
• 2169 consists of SEQ ID NOs:
• 1-593;
• the MLG ID NO:
• 16600 consists of SEQ ID NOs:
• 594-1536;
• and
• the MLG ID NO:
• 4643 consist of SEQ ID NOs:
• 1537-259, the method further comprising administering to the individual at least one disease-modifying antirheumatic drug (DMARD) to treat said rheumatoid arthritis.