Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study
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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
Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D, Balamurugan R
Journal
Nutrients
Year
2021
Keywords:
gut microbiome, knee osteoarthritis, vitamin D
BACKGROUND: Few preclinical studies have shown that Knee osteoarthritis (KOA) is linked to gut microbiome dysbiosis and chronic inflammation. This pilot study was designed to look at the gut microbiome composition in KOA patients and normal individuals with or without vitamin D deficiency (VDD, serum vitamin D <30 ng/mL). METHODS: This pilot study was conducted prospectively in 24 participants. The faecal samples of all the participants were taken for DNA extraction. The V3-V4 region of 16s rRNA was amplified, and the library was prepared and sequenced on the Illumina Miseq platform. RESULTS: The mean (±SD) age was 45.5 (±10.2) years with no defined comorbidities. Of 447 total Operational Taxonomic Units (OTUs), a differential abundance of 16 nominally significant OTUs between the groups was observed. Linear discriminate analysis (LEfSe) revealed a significant difference in bacteria among the study groups. Pseudobutyrivibrio and Odoribacter were specific for VDD, while Parabacteroides, Butyricimonas and Gordonibacter were abundant in the KOA_VDD group, and Peptococcus, Intestimonas, Delftia and Oribacterium were abundant in the KOA group. About 80% of bacterial species were common among different groups and hence labelled as core bacterial species. However, the core microbiome of KOA and VDD groups were not seen in the KOA_VDD group, suggesting that these bacterial groups were affected by the interaction of the KOA and VDD factors. CONCLUSION: Parabacteroides, Butyricimonas, Pseudobutyrivibrio, Odoribacter and Gordonibacter are the predominant bacteria in vitamin D deficient patients with or without KOA. Together these results indicate an association between the gut microbiome, vitamin D and knee osteoarthritis.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Subjects
- Location of subjects
- India
- 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
- Osteoarthritis, knee Knee Osteoarthritides\n,Knee Osteoarthritis\n,Knee, Osteoarthritis Of\n,Knees, Osteoarthritis Of\n,Osteoarthritides, Knee\n,Osteoarthritis Of Knee\n,Osteoarthritis Of Knees,osteoarthritis of the knee,osteoarthritis, knee,Osteoarthritis, knee
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Vitamin D status
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Knee osteroarthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Knee osteoarthritis
- 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
- 4
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- excluded if antibiotics for last 12 weeks
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Source: Figure 2, text
Description: A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.
Abundance in Group 1: decreased abundance in Knee osteroarthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerofilum | ||
| Porphyromonadaceae |
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Source: Figure 2, text
Description: A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.
Abundance in Group 1: increased abundance in Knee osteroarthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Intestinimonas | ||
| Parvimonas | ||
| Peptococcus | ||
| Propionibacterium | ||
| Shimwellia | ||
| unclassified Coriobacteriaceae | ||
| unclassified Erysipelotrichaceae |
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Curated date: 2022/03/09
Curator: Fatima
Revision editor(s): WikiWorks, LGeistlinger, Fatima, Victoria
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vitamin D deficiency
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Knee osteroarthritis with vit D deficiency
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Source: Figure 3
Description: differential abundance between KOA_VDD and VDD patients.
Abundance in Group 1: decreased abundance in Knee osteroarthritis with vit D deficiency
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Odoribacter | ||
| Oribacterium | ||
| Prevotella |
Revision editor(s): Fatima
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Source: Figure 3
Description: differential abundance between KOA_VDD and VDD patients.
Abundance in Group 1: increased abundance in Knee osteroarthritis with vit D deficiency
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricimonas | ||
| Candidatus Saccharimonas | ||
| Delftia | ||
| Gordonibacter | ||
| Parabacteroides | ||
| Phascolarctobacterium | ||
| Porphyromonadaceae | ||
| unclassified Coriobacteriaceae | ||
| Clostridiales bacterium |
Revision editor(s): Fatima
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