Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases
Authors: Jose U. Scher, Dan R. Littman, Steven B. Abramson
Journal: Arthritis & Rheumatology (2015)

Ever since its modern conception as a medical discipline, the study of microorganisms has paralleled the many technological advances in microbiology. In the 17th century, the inventor of the microscope, Antony van Leeuwenhoek, was also the first to describe – in the plaque of his own gums- the millions of microorganisms (or “animalcules”) that reside within us. It is that multitude of microbes populating most human body cavities and surfaces, including its genetic and enzymatic composition, what defines our microbiome1.

For centuries, the role of the microbiome as potential determinant of health and disease has been rather ignored. This has been true in most fields of human research, but particularly so in autoimmune and rheumatic conditions. The reasons are multifactorial. Chief among those was the advent of the Koch’s postulates in the late 1800’s, which exerted a profound influence on how investigators thought about causality in Medicine2. Unbeknownst at the time, however, was the fact that asymptomatic carriers are a common feature of many infectious diseases and that several microorganisms are fastidious in nature with complex nutritional requirements in order to grow. The latter fundamentally prevented the study of bacteria within the context of a dynamic biological community, the role of commensal taxa, the downstream molecular events and the resulting immune interactions between microorgansims and their host.

Consequently, only the prevalent microbiologic techniques were utilized in the past to characterize unique agents capable of triggering clinical rheumatic syndromes. Over time, the search led to correlative studies of specific bacteria and viruses in the etiopathogenesis of these disorders, most notably of rheumatoid arthritis (RA), psoriasis (PsO), inflammatory bowel disease (IBD), and the related spondyloarthritis (SpA), including ankylosing spondylitis (AS) and reactive arthritis (ReA).

The revolution of culture-independent, high-throughput microbial DNA sequencing, in parallel with the resurgence and further understanding of mucosal immunity, has exponentially advanced our knowledge of the interplay between our microbes and ourselves. That profound, bidirectional interaction and its consequences in physiology and disease have led to a whole new field of research. Despite the relative novelty of the Human Microbiome as a discipline, a substantial body of evidence has accumulated addressing its potential involvement in the pathogenesis of rheumatic disease3. Here, we will critically review the available data in animal and human studies, focusing on the role of intestinal microbiome in RA, PsA, and SpA. The role of the microbiome in autoimmunity and other rheumatic diseases has been reviewed elsewhere and is beyond the scope of this manuscript4,5. We include a description of the prospects of microbiome manipulation for therapeutic purposes and conclude by delineating challenges and opportunities in the field.

Human Microbiome and Mucosal Immunity in Physiology and Disease
With the advent of massively parallel sequencing technologies and ever more sophisticated multi’omics methodologies, the human microbiome is now better understood in both its composition and functionality. It is now recognized that over 100 trillion cells inhabiting our human bodies are rather prokaryotic in nature. At any given time, we carry 3–6 pounds of bacteria that contain roughly 3 million protein coding genes6. We have also come to realize that different biological niches are populated by unique microbial consortia that can only survive under certain nutritional conditions. For example, the intestinal microbiome is entirely differentiated from that of the skin or the genitourinary tract7. And this is in part related to the various metabolic functions that derive from our own physiological needs. In fact, our intestinal microbes (represented by more than 1000 different species) have co-evolved in a mutually beneficial manner and provide the enzymatic machinery to help us degrade complex polysaccharides from the diet and extract essential vitamins and amino acids required for our evolutionary success. As a result, this new knowledge all but challenged our understanding of the self, leading to the notion that we should consider human beings as supraorganisms8.

This evolutionary process of co-adaptation between intestinal microbiome and host immune responses is now increasingly appreciated. In fact, it is now well established that the intestinal microbiota shapes the immune system and modulates homeostasis in healthy states or promotes inflammation when dysbiosis occurs9.

In order to keep this massive antigenic load compartmentalized in the intestinal lumen, mammals have developed multiple protective mechanisms. These include a physico-chemical barrier composed by a mucus layer, antimicrobial proteins and secretory IgA (sIgA) that keep the microbiota away from epithelial cells. Evading bacteria encounter tightly adherent intestinal epithelial cells, a mechanical barrier containing sensors of pathogen-associated molecular patterns (PAMPs) [i.e, toll-like receptors (TLRs)] and a variety of antibacterial molecules. The innate immune cells, most notably macrophages and dendritic cells (DCs), continuously sense the lumen and survey for detrimental antigens10. Ultimately, antigens are presented by MHC II molecules and interact with B- or T-cell receptors to induce adaptive immune responses. Depending on the microbial antigen, a specific cytokine milieu is then generated to influence a specific type of CD4+ T cell differentiation. While T helper 1 (Th1) cells develop in response to intracellular pathogens and produce IFNγ, both Th2 and Th17 cells are stimulated by extracellular microorganisms (producing IL-4 and IL-17, respectively). Regulatory T cells (Tregs), by contrast, actively prevent these pro-inflammatory properties via generation of anti-inflammatory cytokines such as IL-10. This fine homeostatic equilibrium is required to maintain a state of basal ”physiological inflammation” in the lamina propria11.

With this in mind, the NIH Human Microbiome Project was launched12 to address two central questions: 1) Is there a core human microbiome?, and 2) Do perturbations in the microbiome composition and/or its metabolites correlate with human disease states? Concomitantly, the DNA sequencing and multi’omics technological revolution has provided the necessary scientific tools13,14. Most analytical approaches in human studies have utilized novel bioinformatics tools coupled with parallel DNA sequencing platforms to: 1) describe the taxonomic relative abundance of bacterial species in a given sample (taking advantage of 16s rRNA gene amplification) and/or 2) better understand the overall functional enzymatic potential of a microbiome of interest (using whole-genome shotgun sequencing for metagenomics analysis). This has been complemented at times by the use of metabolomics [measuring the actual content of bacterial metabolites, such as short- and medium-chain fatty acids (SCFAs, MCFAs)], proteomics and metatranscriptomics15. These methods evaluate the possibility that associations with disease states may rather be dependent on the presence of certain bacterial components or by-products, and not necessarily the microorganism per se. Multiple examples of microbiome correlations with metabolic, neoplastic and autoimmune diseases have now been reported, including those in obesity and diabetes16,17, gastrointestinal cancer18, atherosclerosis19 and psoriasis20. As expected, many of the original contributions to the field in autoimmunity were originated in the IBD literature. Noticeably, IBD patients reveal a dysbiotic process characterized by decreased intestinal (beneficial) microbiota diversity21,22 and increase in enterobacteria23.