Among patients with new-onset rheumatoid arthritis (RA), the pretreatment gut microbiome may predict the response to treatment with methotrexate, according to study results published in Arthritis & Rheumatology.

Methotrexate is safe, well tolerated, and associated with lower costs of treatment compared with newer treatment options for RA; it is the first-line therapy in RA. However, as many as 50% of patients treated with methotrexate monotherapy do not achieve a clinically adequate outcome.

The objective of the current study was to determine the role of the human gut microbiome as a potential predictor of response to methotrexate in patients with new-onset RA.

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The study included a training cohort of 26 patients with new-onset RA and a validation cohort of 21 patients. Biosamples and metadata were obtained before introducing methotrexate and at 1, 2, and 4 months after therapy. The 16S rRNA gene and shotgun metagenomic sequencing was performed on their baseline gut microbiomes. In addition, biosamples from 20 patients with RA who were not treated with methotrexate were analyzed as control patients.

Clinical responder status was defined as an improvement of Disease Activity Score 28 (DAS28) of 1.8 or greater and no need for the addition of a biologic agent.

The overall bacterial diversity was found to be distinct in patients who will response to methotrexate compared with patients who are not destined to respond to treatment.

There were significant associations between the abundance of gut bacterial taxa and their genes with future clinical response, including orthologs related to purine and methotrexate metabolism. The data suggest that groups of microbes or bacterial functions, and not specific dominant species, may be implicated in clinical response. Using machine-learning techniques applied to the metagenomic data, a microbiome-based model to predict the risk for lack of response to treatment with methotrexate was generated.

Notably, shotgun sequencing led to the identification of KEGG modules, pathways, and gene orthologs (KOs). Based on the abundance of 38 Boruta algorithm–confirmed KOs, it was possible to predict lack of response to methotrexate in the majority of patients in the validation cohort, indicating to the researchers that the metagenome-based classifier may serve as an important tool for to aid in the decision-making in patients with newly diagnosed RA.

In addition, fecal samples were incubated ex vivo with methotrexate, and the remaining levels of methotrexate were measured. The data showed worse clinical outcomes among patients with evidence for communities enriched for gut bacteria capable of efficiently metabolizing and/or depleting methotrexate.

The researchers noted that the model was limited to distinct RA populations and should be further explored. Additional limitations included focusing exclusively on oral methotrexate, with no data on parenteral methotrexate or other disease-modifying antirheumatic drugs.

“[T]hese results provide the first step towards predicting lack of response to oral MTX [methotrexate] in NORA [new-onset RA] patients and support the value of the gut microbiome as a possible prognostic tool and as a potential target in RA therapeutics,” concluded the researchers.


Artacho A, Isaac S, Nayak R, et al. The pre-treatment gut microbiome is associated with lack of response to methotrexate in new onset rheumatoid arthritis. Arthritis Rheumatol. 2020 Dec 13. doi: 10.1002/art.41622