Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing
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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
Zhang B, Gu J, Liu J, Huang B, Li J
Journal
Medical science monitor : international medical journal of experimental and clinical research
Year
2019
BACKGROUND Increasing evidence has suggested that gut flora play an important role in tumor progression and prognosis. However, the relationship between fecal microbiota and hematologic malignancy requires further investigation. This study aimed to characterize the relationship of the fecal microbial community in multiple myeloma (MM) patients. MATERIAL AND METHODS A total of 40 MM patients and healthy controls (n=17) were retrospectively collected from the First Affiliated Hospital of Sun Yat-sen University between October 2018 and May 2019. The fecal samples were collected for 16S rRNA high-throughput sequencing for the fecal microbial community, as well as diversity and correlation analysis. Furthermore, 21 MM patients and their family members were selected for the matched pair analysis to confirm the fecal microbiota taxonomic changes by qRT-PCR assay. RESULTS Diversity analysis showed that diversity measured by Shannon index was lower in MM patients compared with healthy controls. At the phylum level, higher abundances of Proteobacteria but lower abundances of Actinobacteria were identified in the MM group in comparison with the healthy control group. At the genus level, the proportion of Bacteroides, Faecalibacterium, and Roseburia was significantly higher in the MM group. The matched pair analysis showed that Pseudomonas aeruginosa and Faecalibacterium were significantly more abundant in the MM group. Further analysis on prognostic risk factors revealed that the Faecalibacterium prausnitzii level was significantly correlated with ISS stage. CONCLUSIONS Our study highlights the imbalanced composition and diversity of the gastrointestinal microbiome in MM patients, which could be further used as a potential biomarker for MM risk screening, therapeutic strategies, and prognostic prediction.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
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
- Multiple myeloma Al amyloidosis,amyloidosis, systemic,Kahler disease,Kahler's disease,medullary plasmacytoma,multiple myeloma,multiple myeloma/plasma cell myeloma,myeloid neoplasm of plasma cell,myeloma,myeloma - multiple,myeloma, multiple,myeloma, plasma cell, malignant,myelomatosis,plasma cell myeloid neoplasm,plasma cell myeloma,Multiple myeloma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Multiple Myeloma patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- 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).
- raw counts
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Table 6 & text
Description: Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level
Abundance in Group 1: increased abundance in Multiple Myeloma patient
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Table 6 & text
Description: Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level
Abundance in Group 1: decreased abundance in Multiple Myeloma patient
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
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
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 2
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Figure 3a
Description: Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls
Abundance in Group 1: increased abundance in Multiple Myeloma patient
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Pseudomonadota | ||
| Turicibacter | ||
| Cronobacter | ||
| Cronobacter sakazakii |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Figure 3a
Description: Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls
Abundance in Group 1: decreased abundance in Multiple Myeloma patient
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Metastats
- 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
- Not specified
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Table 7 and text
Description: Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients
Abundance in Group 1: increased abundance in Multiple Myeloma patient
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Faecalibacterium | ||
| Roseburia | ||
| Veillonella | ||
| Acidaminococcus | ||
| Dielma | ||
| Butyrivibrio | ||
| Nicotiana otophora | ||
| Allobaculum |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Table 7 & text
Description: Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients
Abundance in Group 1: decreased abundance in Multiple Myeloma patient
| NCBI | Quality Control | Links |
|---|---|---|
| Peptoclostridium |
Revision editor(s): Atrayees
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy relatives control
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-4
Source: Table 8 and text
Description: Intestinal Microbial detection in Multiple Myeloma patients and their family members using Quantitative Reverse Transcription Polymerase Chain Reaction
Abundance in Group 1: increased abundance in Multiple Myeloma patient
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas aeruginosa | ||
| [Clostridium] leptum |
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