Rheumatic diseases are a kind of chronic inflammatory and autoimmune disease affecting the connection
or supporting structures of the human body, such as the most common diseases Ankylosing spondylitis
(AS), gout and Systemic lupus erythematosus (SLE). Although the precise etiology and pathogenesis of the different
types of rheumatic diseases remain mostly unknown, it is now commonly believed that these diseases are
attributed to some complex interactions between genetics and environmental factors, especially the gut microbiome.
Altered microbiome showed clinical improvement in disease symptoms and partially restored to normality
after prescribing disease-modifying antirheumatic drugs (DMARDs) or other treatment strategies. Recent
advances in next-generation sequencing-based microbial profiling technology, especially metagenomics, have
identified alteration of the composition and function of the gut microbiota in patients. Clinical and experimental
data suggest that dysbiosis may play a pivotal role in the pathogenesis of these diseases. In this paper, we provide
a brief review of the advances in the microbial profiling technology and up-to-date resources for accurate
taxonomic assignment of metagenomic reads, which is a key step for metagenomics studies. In addition, we review
the altered gut microbiota signatures that have been reported so far across various studies, upon which diagnostics
classification models can be constructed, and the drug-induced regulation of the host microbiota can
be used to control disease progression and symptoms.