Altered gut microbiota and microbial biomarkers associated with chronic kidney disease

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/6

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30088332

DOI Digital object identifier for electronic documents.

10.1002/mbo3.678

URI

Authors

Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F, Wang Y

Journal

MicrobiologyOpen

Year

2019

Keywords:

chronic kidney disease, gut microbiota, hemodialysis, intestinal dysbiosis, microbial biomarker

The present study aimed to determine the differences in gut microbiota between patients with chronic kidney disease (CKD) and healthy controls (HC) and search for better microbial biomarkers associated with CKD. The 16S rRNA gene sequencing approach was used to investigate the differences in gut microbiota between the CKD and HC groups. The study found that 12 phylotypes were overrepresented in the CKD group and 19 in the HC group at the genus level. Furthermore, genera Lachnospira and Ruminococcus_gnavus performed the best in differentiating between HC and CKD populations. In addition, this novel study found that the genera Holdemanella, Megamonas, Prevotella 2, Dielma, and Scardovia were associated with the progression of CKD and hemodialysis. In conclusion, the composition of gut microbiota was different in CKD populations compared with healthy populations, and Lachnospira and R._gnavus were better microbial biomarkers. In addition, five phylotypes, including Holdemanella, Megamonas, Prevotella2, Dielma, and Scardovia, served as an indicator of the progression of CKD and hemodialysis. However, large-scale prospective studies should be performed to identify the reliability of the set of these phylotypes as biomarkers.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/5

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Chronic kidney disease chronic kidney disease,chronic kidney failure,Chronic Kidney Insufficiencies,Chronic Kidney Insufficiency,chronic renal disease,Chronic Renal Failure,chronic renal failure syndrome,Chronic Renal Insufficiencies,chronic renal insufficiency,CKD,CKD - chronic kidney disease,Disease, End-Stage Kidney,Disease, End-Stage Renal,END STAGE KIDNEY DIS,End Stage Kidney Disease,END STAGE RENAL DIS,End Stage Renal Disease,End-Stage Kidney Disease,End-Stage Renal Disease,End-Stage Renal Failure,ESRD,kidney disease, chronic,Kidney Disease, End-Stage,Kidney Failure, Chronic,Kidney Insufficiencies, Chronic,Kidney Insufficiency, Chronic,RENAL DIS END STAGE,Renal Disease, End Stage,Renal Disease, End-Stage,renal failure - chronic,Renal Failure, Chronic,Renal Failure, End Stage,Renal Failure, End-Stage,Renal Insufficiencies, Chronic,Renal Insufficiency, Chronic,Chronic kidney disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: chronic kidney disease

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients with chronic kidney disease

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Group 1 sample size Number of subjects in the case (exposed) group: 49

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Signature 1

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Curated date: 2021/01/10

Curator: Fatima Zohra

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Source: Figure 3b

Description: Comparison of gut bacteria between the HC and chronic kidney disease groups

Abundance in Group 1: increased abundance in chronic kidney disease

NCBI	Quality Control	Links
Bacteroidaceae
Bacteroidales
Bacteroides
Bacteroidota
Bacteroidia
Eggerthella
Enterobacterales
Enterobacteriaceae
Thomasclavelia
Escherichia
Flavonifractor
Gammaproteobacteria
Lactobacillaceae
Parabacteroides
Porphyromonadaceae
Ruminiclostridium
Sellimonas
Shigella
Weissella
Mediterraneibacter gnavus CAG:126
[Ruminococcus] torques CAG:61
[Clostridium] innocuum

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Figure 3b

Description: Comparison of gut bacteria between the HC and chronic kidney disease groups

Abundance in Group 1: decreased abundance in chronic kidney disease

NCBI	Quality Control	Links
Lachnospiraceae
Tyzzerella
Anaerobutyricum hallii
Oscillospiraceae
Collinsella
Butyricicoccus
Romboutsia
Ruminococcus
Peptostreptococcaceae
Roseburia
Coprococcus
Eubacterium coprostanoligenes
Subdoligranulum
Lachnospira
Carnobacterium
Agathobacter rectalis CAG:36
Prevotellaceae
Dialister
Selenomonadales
Negativicutes
Veillonellaceae
Clostridia
Eubacteriales
Bacillota

Revision editor(s): WikiWorks