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Page 6 of 23 Poznyak et al. Microbiome Res Rep. 2026;5:3

other taxa, including Collinsella or Prevotella. Without direct assessment of total bacterial load, it is not
possible to distinguish genuine microbial loss from compositional artifacts [71,72] . Relative shifts in genera such
as Roseburia and Faecalibacterium may therefore not necessarily reflect true increases or decreases in their
absolute abundance, but rather proportional changes resulting from alterations in other community
members.

Several methodological approaches have been proposed to overcome these limitations, including quantitative
PCR-based normalization, flow cytometry-assisted microbial counting, and the use of spike-in standards to
estimate absolute microbial abundances. While these methods improve biological interpretability and
cross-study comparability, they remain underutilized in RA research due to increased technical complexity
and cost [73,74] . Without direct quantification of total bacterial load, it is not possible to distinguish genuine
biological expansions or contractions from compositional artifacts. Integration of absolute quantification
approaches, such as quantitative PCR-based normalization or spike-in standards, would be required to
clarify the direct relationship between these taxa and RA [75,76] .

In collagen-induced arthritis (CIA) mouse models, butyrate has been demonstrated to alleviate arthritis
symptoms. However, its ability to activate IL-23 and promote Th17 cell differentiation also raises the
possibility that butyrate may contribute to RA development. Further investigation is needed to establish the
significance of intestinal integrity as a therapeutic target for RA and to understand the effects of
butyrate-producing bacteria on the disease [77-79] .

Lactobacillaceae
The growth of Lactobacillaceae has been observed in patients with early and established RA; however, a
decrease in Lactobacillaceae levels occurs in individuals with long-standing RA. Notably, Ligilactobacillus
salivarius (L. salivarius), present in both the oral cavity and intestines, has been associated with disease
severity [80,81] . This connection between Lactobacillaceae and RA is supported by findings from animal studies.
For example, the introduction of L. bifidus into IL-1ra-/- mice was sufficient to induce arthritis, and an
increased abundance of Lactobacillaceae was detected in CIA mice before the onset of arthritis. Similar to
Prevotella, Lactobacillaceae are believed to contribute to RA development by promoting Th17 cell activity
and associated cytokines, as well as activating Th1-cell responses [82-85] .

Despite this association, various studies in both animals and humans have shown that Lactobacillaceae
consumption can alleviate arthritis symptoms and reduce inflammation. For instance, treatment with
Lacticaseibacillus casei in rats has been reported to restore gut dysbiosis, diminish arthritis severity, and
lower pro-inflammatory cytokine levels. Moreover, both L. salivarius and Lactobacillus plantarum have been
found to decrease Th17 cells while increasing Tregs in CIA mice, resulting in milder arthritis. A
comprehensive review concluded that while Lactobacillaceae supplementation reduces IL-6 levels, it does not
significantly impact arthritis in humans. Therefore, the implications of findings related to Lactobacillaceae
warrant caution, and further research is necessary, particularly given the widespread use of Lactobacillaceae
species as probiotics [86-88] .

The apparently contradictory effects of Lactobacillaceae taxa in RA are best explained by strain-specific
functional differences and strong dependence on the host microenvironment. Experimental studies indicate
that certain taxa enriched in untreated RA - often reported at the species level (e.g., L. salivarius) rather than
as fully characterized strains - can promote Th17-associated immune responses and exacerbate inflammatory
pathology. In contrast, well-characterized probiotic strains, including Lacticaseibacillus rhamnosus (L.
rhamnosus) GG, Lacticaseibacillus paracasei Shirota strain (LcS), Lactobacillus helveticus R0052, and