Exploring Variations in Gut Microbiome Networks among Patients with Chronic Kidney Disease (CKD)

Author Information¹
Jun, Luke²; Manik, Aryan³; Zhang, Kevin⁴
(Editor: Li, Meng-Hao⁵)

¹ All authors are listed in alphabetical order.
² Bellarmine College Preparatory, CA, ³ Portola High School, CA, ⁴ Rock Ridge High School, VA, ⁵ George Mason University, VA

Background

Currently, worldwide access to treatment for end-stage kidney disease is deficient due to the excessive cost of renal replacement therapy (RRT) combined with the necessary maintenance procedures including hemodialysis, peritoneal dialysis, and long-term dialysis. These types of chronic kidney disease (CKD) are often associated with dysbiosis within the gut microbiome, which is essential in maintaining immune balance, digestion, and metabolism within the human body [2]. The bacteria can have this effect on the kidney and the liver due to their ability to affect intestinal permeability, produce short-chain fatty acids, and affect metabolites within the system. CKD-induced dysbiosis leads to toxic metabolite accumulation and progression to ESRD due to urea conversion to ammonia, raising pH and harming beneficial bacteria. Dysbiosis impacts gut barrier function, worsened by dialysis and dietary restrictions. The gut hosts over one hundred trillion microbial cells, primarily Bacteroidetes, Actinobacteria, and Firmicutes, aiding in nutrient absorption, vitamin synthesis, and immune regulation. Dysbiosis in CKD shifts the gut microbiome, increasing harmful bacteria like Enterobacteriaceae and reducing beneficial ones like Prevotellaceae. This shift enhances uremic toxins like indoles and p-cresol, worsening CKD. There is currently limited research on the specifics of gut microbiome in patients with CKD, but there are studies conducted on chronic and end-stage liver diseases, which are known to be related to CKD and often occur at the same time. Specifically, a study has looked at the gut microbiome of patients with nonalcoholic fatty liver disease (NAFLD), which is a leading chronic liver syndrome worldwide. It is found that patients with NAFLD have a relatively higher abundance of genera, Fusobacteria, a lower abundance of Oscillospira and Ruminococcus of Ruminococcaceae and Coprococcus of Lachnospiraceae, and further bacterial species were identified in NAFLD patients, including Proteobacteria, Escherichia, and Enterobacteria 11, also Bacteroides were more in NASH patients paralleled to healthy individuals [6]. Additionally, Cirrhosis, a severe liver condition from prolonged damage, is often associated with low levels of Bacteroidetes and higher levels of Proteobacteria, Enterococcus, Veillonella, Megasphaera, Burkholderia, Prevotella, and Fusobacteria [2]. In the case of Cirrhosis patients, Dysbiosis increases intestinal permeability, allowing endotoxins to activate liver inflammation. Microbial products bind to receptors on Kupffer cells, triggering immune responses. Elevated endotoxin levels are seen in advanced cirrhosis. Bile acids, modified by gut microbiota, significantly influence this gut-liver axis and liver disease progression.

Objective

The objective of this project is to analyze the gut microbiome ecosystems of patients with isolated CKD, CKD with comorbid liver diseases, or CKD with comorbid diabetes using a network-based approach, and to compare the differences in gut microbiome networks among these three groups of patients.

Methods

Data was collected by the American Gut Project, gathering samples from real participants, primarily residing in the United States, with BMIs between 18.5 and 30, as well as no reported history of any gut related diseases such as inflammatory bowel disease and diabetes.. The populations of different species of microbiota were measured in each individual patient, as well as whether the data was collected from only the kidney or the liver as well. Diversity was tested through T- and Chi-sq. tests, which would reveal the difference in diversity between the kidney only and kidney with liver samples. Data was then analyzed through SparCC, providing correlation coefficients for each species of microbiota. The results were visualized through Gephi, creating a network connecting co-abundant species of microbiota. A filter of degree centrality was used to highlight the bacteria with strong connections to other nodes. The 10 bacterial species with the highest degree centrality is selected to be processed. 26 was selected for patients with liver comorbidities of the same highest degree centrality. All analyses were completed in R with the statistical significance being defined as p<0.05.

Results

The T-test analysis showed that (t=0.1216) there was a statistically significant difference in abundance between patients with kidney disease only and patients with kidney disease and liver comorbidities (p-value = 0.9038) (p<0.05). For patients with kidney disease only, bacteria of the species shown in Table 1 were found to have the greatest degree centrality ranging from 99-116. For patients with kidney disease and liver comorbidities, bacteria species of the species shown in table 2 were found to have the greatest degree centrality. 

Table 1. Bacterial Species with the Highest Decree Centrality in Patients with Kidney Disease Only

Bacterial species	Degree	Weighted Degree
Butyricimonas	116	232.0
Aromatoleum	99	198.0
Capnocytophaga	99	198.0
Enteractinococcus	99	198.0
Methylococcus	99	198.0
Methylotenera	99	198.0
Oligella	99	198.0
Promicromonospora	99	198.0
Rhodopirellula	99	198.0
Solibacillus	99	198.0

Table 2. Bacterial Species with the Highest Decree Centrality in Patients with Kidney and Liver Comorbidities

Bacterial species	Degree	Weighted Degree
Acetobacter	133	266.0
Achromobacter	133	266.0
Actinomycetospora	133	266.0
Alloscardovia	133	266.0
Basfia	133	266.0
Curtobacterium	133	266.0
Desulfonatronum	133	266.0
Enteractinococcus	133	266.0
Fodinicurvata	133	266.0
Helcococcus	133	266.0
Kitasatospora	133	266.0
Lentisphaera	133	266.0
Magnetospirillum	133	266.0
Nakamurella	133	266.0
Nitrosococcus	133	266.0
Oligella	133	266.0
Pelosinus	133	266.0
Peptoclostridium	133	266.0
Photorhabdus	133	266.0
Psychroflexus	133	266.0
Sphingopyxis	133	266.0
Tepidiphilus	133	266.0
Terribacillus	133	266.0
Thermaerobacter	133	266.0
Thermomonas	133	266.0
Thioalkalivibrio	133	266.0

Figure 1. Network Model of the Bacteria with highest degree centrality in patients with kidney disease only

Figure 2. Network model of the nodes with highest degree centrality in patients with kidney disease and liver comorbidities

Conclusion 

The study showed that there is no no statistically significant difference in bacterial abundance between CKD patients and CKD + Liver  patients. There are certain groups within the gut microbiome that have higher abundances by a statistically significant amount with both patients who have kidney disease only or kidney diseases with liver comorbidities. The microbes with high abundances in the experimental groups are mostly different, with only Oligella and Enteractinococcus being present in both network analysis models with a strong degree of centrality. In addition, the network analysis shows that there are strong relationships between the bacteria species shown in the tables, as a filter was used to reduce the nodes with less degree centrality. 

References

1. Gagliardi, Antonella, et al. “Rebuilding the Gut Microbiota Ecosystem.” International Journal of Environmental Research and Public Health, U.S. National Library of Medicine, 7 Aug. 2018, ncbi.nlm.nih.gov/pmc/articles/PMC6121872/. 

2. Fan, Yong, and Oluf Pedersen. “Gut microbiota in human metabolic health and disease.” Nature Reviews Microbiology 19.1 (2021): 55-71.

3. Lee, Na Young, and Ki Tae Suk. “The role of the gut microbiome in liver cirrhosis treatment.” International journal of molecular sciences 22.1 (2020): 199.

4. Liyanage, Thaminda, et al. “Worldwide access to treatment for end-stage kidney disease: a systematic review.” The Lancet 385.9981 (2015): 1975-1982.

5. Rysz, Jacek, et al. “The impact of CKD on uremic toxins and gut microbiota.” Toxins 13.4 (2021): 252.

6. Schwenger, Katherine JP, Nayima Clermont-Dejean, and Johane P. Allard. “The role of the gut microbiome in chronic liver disease: the clinical evidence revised.” JHEP Reports 1.3 (2019): 214-226.

7. Khan, Ashiq, et al. “Understanding the effects of gut microbiota dysbiosis on nonalcoholic fatty liver disease and the possible probiotics role: recent updates.” International journal of biological sciences 17.3 (2021): 818.