Introduction

Nonalcoholic fatty liver disease (NAFLD) is a widespread metabolic disorder associated with intestinal dysbiosis, low-grade systemic inflammation, and small intestinal bacterial overgrowth (SIBO). Targeting the gut-liver axis through microbiome-modulating therapies may represent a promising approach to disease management.

Aims & Methods

The aim was to investigate gut microbiota alterations in NAFLD patients and assess the efficacy of microbiota-based therapy on metabolic, inflammatory, and structural liver parameters. The study included 152 NAFLD patients and 47 controls. Gut microbiota composition was evaluated using qRT-PCR, and SIBO was diagnosed via hydrogen breath testing. The therapeutic protocol included rifaximin (200 mg TID for 14 days), Saccharomyces boulardii CNCM I-745 (1 capsule BID for 30 days), and essential phospholipids (600 mg TID for 30 days). Liver function tests, inflammatory markers, and steatometry were assessed before and after treatment.

Results

Alterations in gut microbiota composition indicative of dysbiosis—including increased Firmicutes/Bacteroides ratio and Actinobacteria abundance—were identified in NAFLD. Strong correlations emerged between the F/B index and triglycerides (r = 0.78), TNF-α (r = 0.77), and between Actinobacteria and hsCRP (r = 0.66). SIBO rates declined significantly post-treatment (51% → 17%). Liver enzymes, inflammatory markers, and steatometric parameters improved substantially (p<0.05).

Conclusion

Microbiota-targeted therapy combining rifaximin, S. boulardii, and phospholipids effectively corrected dysbiosis, reduced inflammation, improved metabolic parameters, and promoted liver structural recovery in NAFLD patients. These findings support incorporating microbiome-focused interventions into routine clinical practice for NAFLD. ​

Introduction

Altered gut microbiome composition has been implicated in the pathogenesis of inflammatory bowel disease (IBD). However, detailed characterization of microbial diversity differences between IBD subtypes remains incomplete. This study aimed to evaluate gut microbiome alpha diversity in patients with Crohn's disease (CD) and ulcerative colitis (UC) compared to healthy controls using long-read 16S rRNA sequencing technology.

Aims & Methods

Fecal samples were collected from 17 patients with CD, 20 patients with UC, and 192 healthy controls without IBD. DNA was extracted using an SKYAmp stool DNA kit (SkyGen, Russia). Long-read nanopore sequencing of 16S rRNA amplicons was conducted using a MinIon™ sequencer. Taxonomic assignment was performed with EMu software by aligning FASTQ reads to the NCBI 16S database [1]. Alpha-diversity was evaluated at the species level using Chao1 and Shannon indices. Statistical comparisons between groups were conducted using Welch two-sample t-tests with Holm adjustment in R environment and the RStudio software (version 4.4.1).

Results

	Without IBD	CD	UC
Shannon index	3.452 (3.410 - 3.494)	3.165 (2.970 - 3.360)	3.270 (3.016 - 3.524)
Chao1 index	85.750 (84.046 - 87.454)	67.529 (61.087 - 73.972)	74.650 (64.729 - 84.571)

The Shannon diversity index was significantly lower in the CD group compared to the control group (p=0.01412), while no significant difference was observed between UC and control groups (p=0.15461). Chao1 richness index values were significantly reduced in both CD and UC patient groups compared to controls (p=0.00003 and p=0.03195, respectively), indicating reduced species richness in both IBD conditions.

Conclusion

This study demonstrates that both IBD subtypes exhibit reduced microbial richness as measured by the Chao1 index, while significant reduction in Shannon diversity was observed only in CD patients. These findings suggest differential impacts of CD and UC on gut microbiome composition, with CD potentially having more profound effects on overall microbial diversity. Long-read 16S rRNA sequencing provides valuable insights into the microbial signatures associated with different IBD phenotypes, which may contribute to improved diagnostics and personalized treatment approaches.

References

1. Curry KD, et al. Emu: Species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature Methods. 2022;19(7):845-853