Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis
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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.
URI
Authors
Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi
Journal
Scientific Reports 14
Year
2024
Pages:
First page:
Keywords:
Acute pancreatitis, gut microbiota, metabolomics, metagenomics
Acute pancreatitis (AP) is an inflammatory disease of the pancreas. Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy. Gut microbial dysbiosis and its derived-metabolites disorder have been shown to play an important role in the development of AP, however, little is known regarding the crosstalk between gut microbiota and metabolites. In this study, we assessed the alterations in gut microbiota and metabolites by constructing three AP mouse models by means of metagenomic and metabolomic sequencing, and further clarified their relationship by correlation analysis. The results revealed that each model exhibited unique flora and metabolite profiles. KEGG analysis showed that the differential flora and metabolite-enriched pathway functions were correlated with lipid metabolism and amino acid metabolism. Moreover, two core differential bacterial species on Burkholderiales bacterium YL45 and Bifidobacterium pseudolongum along with eleven differential metabolites appeared to exert certain effects during the course of AP. In conclusion, further exploration of the crosstalk between microbiota and derived metabolites may provide novel insights and strategies into the diagnosis and treatment of AP.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Acute pancreatitis acute necrotizing pancreatitis,acute pancreatic necrosis,acute pancreatitis,acute pancreatitis (disorder) [ambiguous],pancreatitis necrotizing,pancreatitis, acute,Acute pancreatitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Caeurulein group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Caerulein group was induced by hourly intraperitoneal (i.p.) injection of caerulein (200 μg/kg, once an hour for a total of 10 times).
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Source: Table S1
Description: Differential abundance in the gut microbiota between control group and caerulein group
Abundance in Group 1: increased abundance in Caeurulein group
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Source: Table S1
Description: Differential abundance in the gut microbiota between control group and caerulein group
Abundance in Group 1: decreased abundance in Caeurulein group
Revision editor(s): KateRasheed
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Source: Fig. 4C
Description: Differential abundance in the gut microbiota between control group and caerulein group
Abundance in Group 1: increased abundance in Caeurulein group
Revision editor(s): KateRasheed, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Source: Fig. 4C
Description: Differential abundance in the gut microbiota between control group and caerulein group
Abundance in Group 1: decreased abundance in Caeurulein group
Revision editor(s): KateRasheed
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Caeurulein+LPS group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Caerulein + LPS group was administered by hourly i.p. injection of caerulein (200 μg/kg, once an hour for a total of 10 times) combined with a dose of 5 mg/kg lipopolysaccharide (LPS).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Source: Fig. 4D
Description: Differential abundance in the gut microbiota between control group and caerulein+LPS group
Abundance in Group 1: increased abundance in Caeurulein+LPS group
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderiales bacterium YL45 | ||
| Butyricimonas faecalis | ||
| Escherichia coli | ||
| Muribaculum intestinale | ||
| Parabacteroides distasonis | ||
| Phocaeicola vulgatus | ||
| Muribaculum gordoncarteri |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Source: Fig. 4D
Description: Differential abundance in the gut microbiota between control group and caerulein+LPS group
Abundance in Group 1: decreased abundance in Caeurulein+LPS group
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes communis | ||
| Alistipes dispar | ||
| Alistipes finegoldii | ||
| Alistipes megaguti | ||
| Alistipes onderdonkii | ||
| Duncaniella dubosii |
Revision editor(s): KateRasheed
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- L-arginine group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice in the L-arginine group received 2 times i.p. injection of L-arginine (4 g/kg, once an hour, twice in total).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Source: Fig. 4E
Description: Differential abundance in the gut microbiota between control group and L-arginine group
Abundance in Group 1: increased abundance in L-arginine group
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderiales bacterium YL45 | ||
| Lactobacillus gasseri | ||
| Lactobacillus johnsonii | ||
| Ligilactobacillus murinus |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-10-29
Source: Fig. 4E
Description: Differential abundance in the gut microbiota between control group and L-arginine group
Abundance in Group 1: decreased abundance in L-arginine group
Revision editor(s): KateRasheed, Folakunmi
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Caeurulein+LPS group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Caerulein + LPS group was administered by hourly i.p. injection of caerulein (200 μg/kg, once an hour for a total of 10 times) combined with a dose of 5 mg/kg lipopolysaccharide (LPS).
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Source: Table S1
Description: Differential abundance in the gut microbiota between control group and caerulein+LPS group
Abundance in Group 1: increased abundance in Caeurulein+LPS group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Candidatus Zixiibacteriota | ||
| Fibrobacterota | ||
| Deferribacterota | ||
| Coprothermobacterota | ||
| Verrucomicrobiota |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Source: Table S1
Description: Differential abundance in the gut microbiota between control group and caerulein+LPS group
Abundance in Group 1: decreased abundance in Caeurulein+LPS group
| NCBI | Quality Control | Links |
|---|---|---|
| Caldisericota | ||
| Candidatus Saccharibacteria | ||
| Candidatus Gracilibacteria | ||
| Thermoproteota |
Revision editor(s): KateRasheed
Experiment 6
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- L-arginine group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice in the L-arginine group received 2 times i.p. injection of L-arginine (4 g/kg, once an hour, twice in total).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Source: Table S1
Description: Differential abundance in the gut microbiota between control group and L-arginine group
Abundance in Group 1: decreased abundance in L-arginine group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Bipolaricaulota | ||
| Caldisericota | ||
| Promethearchaeota | ||
| Nitrososphaerota | ||
| Methanobacteriota |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-11-4
Source: Table S1
Description: Differential abundance in the gut microbiota between control group and L-arginine group
Abundance in Group 1: increased abundance in L-arginine group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Chlorobiota | ||
| Bacillota | ||
| Candidatus Zixiibacteriota | ||
| Candidatus Micrarchaeota | ||
| Pseudomonadota | ||
| Fibrobacterota |
Revision editor(s): KateRasheed
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