Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP)
From BugSigDB
Jump to:navigation, search
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
Xue H, Wang Y, Mei C, Han L, Lu M, Li X, Chen T, Wang F, Tang X
Journal
mSystems
Year
2024
Keywords:
16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome
UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption. Recent evidence suggests that the gut microbiome may influence lactose levels in the gut. However, there is limited understanding regarding the alterations in microbiota and metabolism between individuals with LI and non-LI. This study conducted a paired-sample investigation utilizing data from the American Gut Project (AGP) and performed metagenomic and untargeted metabolomic analyses in a Chinese cohort to explore the interaction between the gut microbiome and serum metabolites. In addition, fecal microbiota transplantation (FMT) experiments were conducted to further examine the impact of the LI-associated gut microbiome on inflammatory outcomes. We identified 14 microbial genera that significantly differed between LI and controls from AGP data. Using a machine learning approach, group separation was predicted based on seven species and nine metabolites in the Chinese cohort. Notably, increased levels of Escherichia coli in the LI group were negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively correlated with indole and furazolidone. FMT-LI rats displayed visceral hypersensitivity and an altered gut microbiota composition compared to FMT-HC rats. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI, which was confirmed by FMT-LI rats showing higher expression of ERK and RAS, along with increased concentrations of proinflammatory cytokines. This study provides valuable insights into the disrupted microbial and metabolic traits associated with LI, emphasizing potential microbiome-based approaches for its prevention and treatment. IMPORTANCE: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms after lactose consumption due to a deficiency of lactase. There is limited understanding regarding the microbiota and metabolic alterations between individuals with LI and non-LI. This study represents the first exploration to investigate metagenomic and metabolomic signatures among subjects with lactose intolerance as far as our knowledge. We identified 14 microbial genera in the Western cohort and 7 microbial species, along with 9 circulating metabolites in the Chinese cohort, which significantly differed in LI patients. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI patients. This finding was confirmed by FMT-LI rats, exhibiting increased expression of ERK and RAS, along with higher concentrations of pro-inflammatory cytokines. Our study provides insights into the disrupted functional and metabolic traits of the gut microbiome in LI, highlighting potential microbiome-based approaches for preventing and treating LI.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Subjects
- Location of subjects
- Canada
- United Kingdom
- United States of America
- 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
- Lactose intolerance lactase persistence,lactose intolerance,lactose intolerance (disease),LM - lactose malabsorption,Lactose intolerance
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants without Lactose Intolerance(Non-LI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Lactose Intolerance(LI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 562
- Group 1 sample size Number of subjects in the case (exposed) group
- 562
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months.
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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol consumption measurement, body mass index, diet, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Fig 1c
Description: Gut microbiota alterations between LI cohort and non-LI cohort assessed using the linear discriminative analysis (LDA) effect size (LEfSe).
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Fig 1c
Description: Gut microbiota alterations between LI cohort and non-LI cohort assessed using the linear discriminative analysis (LDA) effect size (LEfSe)'.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Differences from previous experiment shown
Subjects
- Location of subjects
- China
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Fig 3b
Description: LeFSe analysis reveals significant taxonomic differences between LI Patients and HCs.
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Fig 3b
Description: LeFSe analysis reveals significant taxonomic differences between LI Patients and HCs.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance(LI)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. AF36-18BH | ||
| Eubacterium sp. | ||
| Faecalibacterium sp. CAG:82 | ||
| Lachnospira eligens | ||
| unclassified Faecalibacterium | ||
| uncultured Ruminococcus sp. |
Revision editor(s): Nathcynthia, Rahila, Tosin
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Differences from previous experiment shown
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT-Healthy Controls group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-Lactose Intolerance group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats receiving gut microbiota from LI patients .
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Statistical test
- Spearman Correlation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 7D
Description: Heatmap based on the relative abundance of the genera between FMT-HC (FMT-Healthy control group) and FMT-LI (FMT-Lactose intolerance group).
Abundance in Group 1: increased abundance in FMT-Lactose Intolerance group
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillus | ||
| Dielma | ||
| Escherichia/Shigella sp. | ||
| Sutterella |
Revision editor(s): Nathcynthia, Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 7D
Description: Heatmap based on the relative abundance of the genera between FMT-HC (Healthy control group) and FMT-LI (Lactose intolerance group).
Abundance in Group 1: decreased abundance in FMT-Lactose Intolerance group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum hallii | ||
| Faecalibacterium | ||
| Fusicatenibacter |
Revision editor(s): Nathcynthia, Tosin
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Differences from previous experiment shown
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- 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
- Participants with Lactose intolerance (LI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Statistical test
- T-Test
- 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
- unchanged
- 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 Svetlana up on 2024-11-27
Source: Figure 3d-I.
Description: Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups.
Abundance in Group 1: increased abundance in Participants with Lactose intolerance (LI)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Dialister massiliensis | ||
| Escherichia coli | ||
| Shigella flexneri | ||
| Streptococcus salivarius |
Revision editor(s): Tosin, Nathcynthia
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 3d-I
Description: Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups.
Abundance in Group 1: decreased abundance in Participants with Lactose intolerance (LI)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium sp. |
Revision editor(s): Tosin, Nathcynthia
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Lactose Intolerance
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 3c
Description: Heatmap based on the relative abundance of the genera between Healthy control group and Lactose Intolerance group.
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia |
Revision editor(s): Tosin, Nathcynthia
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 3c
Description: Heatmap based on the relative abundance of the genera between Healthy control group and Lactose Intolerance group.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Thomasclavelia | ||
| Veillonella |
Revision editor(s): Tosin, Nathcynthia
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_1151&oldid=136647"
