Genomic, Probiotic, and Functional Properties of Bacteroides dorei RX2020 Isolated from Gut Microbiota

Abstract

Background/objectives: Gut microbiota is essential for maintaining host immune homeostasis and has been confirmed to be closely related to some intestinal and extraintestinal diseases. Bacteroides, as the dominant bacterial genus in the human gut, has attracted great attention due to its excellent metabolic activity, but there are few studies on Bacteroides dorei species. In our previous study, a gut commensal strain, Bacteroides dorei RX2020 (B. dorei), was isolated from healthy human feces and exhibited superior flavonoid metabolic activity, prompting further analysis of its uncharacterized genomic features, probiotic potential, safety, and immunomodulatory activity.

Results: The results showed that B. dorei exhibited intrinsic probiotic functionalities with preserved genomic and phenotypic stability, demonstrated safety profiles in murine models through in vivo assessments, and conferred antagonistic activity against enteric foodborne pathogens via competitive exclusion. The strain also demonstrated abundant metabolic activity and was involved in the metabolism of tryptophan and bile acids (BAs). Moreover, B. dorei can promote the production of IFNβ by dendritic cells (DCs) to inhibit the replication of influenza virus in epithelial cells, which may be achieved by regulating host metabolism.

Conclusions: This study reveals the potential of B. dorei as next-generation probiotics (NGPs), contributing to a broader understanding and application of these novel probiotics in health and disease management.

Keywords: Bacteroides; bioactive metabolites; next-generation probiotics; probiotic properties.

Figure 1

The gene function annotations of the B. dorei. (A) A phylogenetic tree constructed using a 16S rRNA sequence (neighbor-joining method). (B) KEGG database annotation results. (C) GO database annotation results. (D) Classification of the predicted CAZy from B. dorei.

Figure 2

Evaluation of probiotic characteristics of B. dorei. (A) Evaluation of tolerance to artificial gastric juices. (B) Evaluation of tolerance to artificial intestinal juice. (C) Percentage of survival at different bile salt concentrations; (D,E) Auto-aggregation and hydrophobicity activity of B. dorei; (F) DPPH radical scavenging assay (Sup: the cell-free culture supernatant of B. dorei). The statistical analyses were assessed using Student’s t-test and one-way ANOVA. Statistical significance was defined as * p < 0.05, ** p < 0.01, and *** p < 0.001.

Figure 3

Bacteriocin gene clusters of isolated B. dorei. (A–C) Bacteriocin gene clusters of isolated B. dorei strain identified using BAGEL 4; (D) Bacteriocin gene clusters of isolated B. dorei strain identified using antiSMASH.

Figure 4

The BSH activity of B. dorei. The plate assay was conducted to determine BSH activity of B. dorei on Anaerobe Basal agar supplemented with 0.3% (w/v) bile salt and 0.37 g/L CaCl₂ ((left): media containing bile salt, (right): media without bile salt).

Figure 5

Safety assessment of B. dorei. (A) The hemolytic activities of the three strains were comparatively assessed by analyzing the hemolytic rings on both Columbia blood plates (middle) and BHI blood agar plates (right) (Left: B. dorei was incubated anaerobically on BHI blood plates for 48 h). SPF C57BL/6 normal mice were given either 5 × 10⁹ CFU/d, 5 × 10¹⁰ CFU/d B. dorei, or 0.2 mL/d PBS by oral gavage for 14 days. (B,C) Changes in the BW (%)/d and immune organ indices in the treatment and control groups. (D) Histopathological examination of heart, liver, spleen, and colon of mice in the control and treatment groups. The statistical analyses were assessed using one-way ANOVA. Statistical significance was defined as ^ns p > 0.5.

Figure 6

Metabolomics analysis of B. dorei’s culture supernatant. PLS-DA score plots (A), OPLS-DA score plots (B), species and contents of metabolite (C), the volcano map (D), KEGG pathway analysis (E), and heat map (F) of culture supernatant metabolites data from blank medium group and B. dorei group at 24 h.

Figure 7

Immunomodulatory activity of B. dorei. (A) BMDCs were pretreated with B. dorei (MOI 10) for 3, 6, and 24 h. Relative IFNβ gene expression to β actin in BMDCs; IFNβ expression in culture supernatants from BMDCs. (B) Heat map of ISG and IFN gene expression. (C) Relative PR8 M1 gene expression to β actin in MLE12 cells. (D) IFNβ expression in culture supernatants from BMDMs. (E) Relative PR8 M1 gene expression to β actin in BMDMs. The statistical analyses were assessed using one-way ANOVA. Statistical significance was defined as * p < 0.05, ** p < 0.01, *** p < 0.001, and ^ns p > 0.5.