Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI, Valdes AM
Journal
Gut microbes
Year
2020
Keywords:
Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis
There is increasing evidence for the role of gut microbial composition in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Nonalcoholic steatohepatitis (NASH) is the most serious form of NAFLD where inflammation causes liver damage that can progress to cirrhosis. We have characterized the gut microbiome composition in UK patients with biopsy-proven NASH (n = 65) and compared it to that in healthy controls (n = 76). We report a 7% lower Shannon alpha diversity in NASH patients without cirrhosis (n = 40) compared to controls (p = 2.7x 10-4) and a 14% drop in NASH patients with cirrhosis (n = 25, p = 5.0x 10-4). Beta diversity (Unweighted UniFrac distance) was also significantly reduced in both NASH (p = 5.6x 10-25) and NASH-cirrhosis (p = 8.1x 10-7) groups. The genus most strongly associated with NASH in this study was Collinsella (0.29% abundance in controls, 3.45% in NASH without cirrhosis (False Discovery Rate (FDR) p = .008), and 4.38% in NASH with cirrhosis (FDR p = .02)). This genus, which has been linked previously to obesity and atherosclerosis, was also positively correlated with fasting levels of triglycerides (p = .01) and total cholesterol (p = 1.2x 10-4) and negatively correlated with high-density lipoprotein cholesterol (p = 2.8x 10-6) suggesting that some of the pathways present in this microbial genus may influence lipid metabolism in the host. In patients, we also found decreased abundance of some of the Ruminococcaceae which are known to produce high levels of short-chain fatty acids which can lower inflammation. This may thus contribute to pathology associated with NASH.
Statistical test
Kruskall-Wallis
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Curated date: 2021/08/11
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Atrayees
Subjects
- Location of subjects
- United Kingdom
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- non-alcoholic steatohepatitis NASH,nash - nonalcoholic Steatohepatitis,non alcoholic steatohepatitis,non-alcoholic steatohepatitis,nonalcoholic Steatohepatitis,nonalcoholic steatohepatitis
- 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
- Individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Source: Figure 4
Description: Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis)
Abundance in Group 1: increased abundance in Individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Collinsella | ||
| Eggerthella | ||
| Fusicatenibacter | ||
| Hungatella | ||
| Lachnoclostridium | ||
| Lachnospiraceae bacterium | ||
| Rhodospirillaceae |
Revision editor(s): Madhubani Dey
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Source: Figure 4
Description: Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis)
Abundance in Group 1: decreased abundance in Individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis)
Revision editor(s): Madhubani Dey, Merit
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Curated date: 2021/08/11
Curator: Madhubani Dey
Revision editor(s): WikiWorks, Madhubani Dey, Atrayees
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Source: Figure 4
Description: Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis
Abundance in Group 1: increased abundance in Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Collinsella | ||
| Eggerthella | ||
| Hungatella | ||
| Lachnoclostridium |
Revision editor(s): Madhubani Dey
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Source: Figure 4
Description: Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis
Abundance in Group 1: decreased abundance in Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Barnesiella | ||
| Odoribacter | ||
| Parabacteroides | ||
| Peptoclostridium | ||
| Ruminiclostridium sp. | ||
| Terrisporobacter | ||
| unclassified Porphyromonadaceae | ||
| Odoribacteraceae |
Revision editor(s): Madhubani Dey, Merit
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