Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes

The Gut Mycobiome for Precision Medicine

The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.

Association between exposure to per- and polyfluoroalkyl substances and kidney function: a population study

Background

The relationship between per- and polyfluoroalkyl substances (PFAS) and kidney function markers remains uncertain.

Methods

We used PFAS detection data from 5,947 adults in NHANES 2005-2012. We employed multivariable linear regression models to examine associations between PFAS and estimated glomerular filtration rate (eGFR), urine creatinine (UCR), urine albumin (UAL), and urine albumin/creatinine ratio (UACR). To capture non-linear trends, restricted cubic splines were applied. The WQS (weighted quantile sum) and Q-gcomp (quantile g computation) models were used for the mixture analysis. Subgroup analyses were conducted to explore potential interactions.

Results

Perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), perfluorohexane sulfonic acid (PFHxS), 2-(N-methyl-perfluorooctane sulfonamido) acetic acid (N-MEFOSAA), and perfluorononanoic acid (PFNA) were negatively related to eGFR (β = -2.04, 95% CI = -2.85, -1.23; β = -0.97, 95% CI = -1.78, -0.16; β = -1.50, 95% CI = -2.24, -0.76; β = -0.49, 95% CI = -1.25, 0.27; β = -0.68, 95% CI = -1.46, 0.10). PFOA and PFOS were positive associated with UCR (β = 10.61, 95% CI = -1.89, 23.11; β = 12.98, 95% CI = 0.56, 25.41). PFOA, PFOS, PFHxS, PFNA, and PFUA were negatively related to UAL (β = -0.53, 95% CI = -0.73, -0.32; β = -0.39, 95% CI = -0.59, -0.18; β = -0.59, 95% CI = -0.78, -0.40; β = -0.42, 95% CI = -0.65, -0.19; β = -0.04, 95% CI = -0.22, 0.14). PFDA, PFOA, PFOS, PFHxS, and PFNA are significantly inversely associated with UACR (β = -0.01, 95% CI = -0.16, 0.14; β = -0.52, 95% CI = -0.69, -0.35; β = -0.50, 95% CI = -0.67, -0.33; β = -0.49, 95% CI = -0.64, -0.33; β = -0.27, 95% CI = -0.44, -0.10). Nonlinear relationships were found between PFAS and all kidney function indicators. Mixed PFAS exposure showed a negative association with eGFR, UAL and UACR, while showed a positive relationship with UCR. Interactions between PFASs and most subgroups were observed.

Conclusion

Our study revealed significant associations between PFAS exposure and various kidney function indicators. These findings provide an epidemiological perspective on how PFAS may lead to kidney dysfunction.

A metagenome-wide study of the gut virome in chronic kidney disease

Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD+) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.

Alterations of the Gut Microbiome and TMAO Levels in Patients with Ulcerative Colitis

Background: Ulcerative colitis (UC) is an idiopathic and heterogeneous large intestine disease, characterized by chronic mucosa and submucosa inflammation. Alteration of the intestinal microbiome in UC may be responsible for modifications in metabolite production. Aim: To investigate the microbiota status and trimethylamine-N-oxide (TMAO) metabolite levels in patients with UC according to clinical and endoscopic activity. Methods: As part of a grant project AP14871959 from September 2022 to October 2023, 31 patients with UC and 15 healthy volunteers over 18 years at the Clinic of NCJSC "KMU" were assessed for blood TMAO level and metagenomic sequencing of fecal microbiome. Results: A significant depletion of the main representatives of Bacteroides, Parabacteroides, Prevotella; and an increase in the relative abundance of the genera Actinomyces, Klebsiella, Limosilactobacillus, Streptococcus, Escherichia-Shigella were detected in patients with UC. The number of p_Actinobacteria (g_Collinsella) and p_Eubacterium (g_Xylanophilum) representatives with genes encoding TMA-trimethylamine conversion is significantly reduced in UC patients. TMAO levels were significantly lower in UC patients than in healthy individuals (0.233 µmol/L, p = 0.004). TMAO decreased with disease severity and significantly differed between patients with different activities (p = 0.034). Conclusions: The composition of the intestinal microbiome changes and the level of TMAO decreases in patients with UC at different activities.

Causal relationship between gut microbiota and chronic renal failure: a two-sample Mendelian randomization study

Background

Observational studies and some experimental investigations have indicated that gut microbiota are closely associated with the incidence and progression of chronic renal failure. However, the causal relationship between gut microbiota and chronic renal failure remains unclear. The present study employs a two-sample Mendelian randomization approach to infer the causal relationship between gut microbiota and chronic renal failure at the genetic level. This research aims to determine whether there is a causal effect of gut microbiota on the risk of chronic renal failure, aiming to provide new evidence to support targeted gut therapy for the treatment of chronic renal failure.

Methods

Employing genome-wide association study (GWAS) data from the public MiBioGen and IEU OpenGWAS platform, a two-sample Mendelian randomization analysis was conducted. The causal relationship between gut microbiota and chronic renal failure was inferred using five different methods: Inverse Variance Weighted, MR-Egger, Weighted Median, Simple Mode, and Weighted Mode. The study incorporated sensitivity analyses that encompassed evaluations for pleiotropy and heterogeneity. Subsequently, the results of the Mendelian randomization analysis underwent a stringent correction for multiple testing, employing the False Discovery Rate method to enhance the validity of our findings.

Results

According to the results from the Inverse Variance Weighted method, seven bacterial genera show a significant association with the outcome variable chronic renal failure. Of these, Ruminococcus (gauvreauii group) (OR = 0.82, 95% CI = 0.71-0.94, p = 0.004) may act as a protective factor against chronic renal failure, while the genera Escherichia-Shigella (OR = 1.22, 95% CI = 1.08-1.38, p = 0.001), Lactococcus (OR = 1.1, 95% CI = 1.02-1.19, p = 0.013), Odoribacter (OR = 1.23, 95% CI = 1.03-1.49, p = 0.026), Enterorhabdus (OR = 1.14, 95% CI = 1.00-1.29, p = 0.047), Eubacterium (eligens group) (OR = 1.18, 95% CI = 1.02-1.37, p = 0.024), and Howardella (OR = 1.18, 95% CI = 1.09-1.28, p < 0.001) may be risk factors for chronic renal failure. However, after correction for multiple comparisons using False Discovery Rate, only the associations with Escherichia-Shigella and Howardella remain significant, indicating that the other genera have suggestive associations. Sensitivity analyses did not reveal any pleiotropy or heterogeneity.

Conclusion

Our two-sample Mendelian randomization study suggests that the genera Escherichia-Shigella and Howardella are risk factors for chronic renal failure, and they may serve as potential targets for future therapeutic interventions. However, the exact mechanisms of action are not yet clear, necessitating further research to elucidate their precise roles fully.