Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer
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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
Xiaofeng N, Jian C, Jingjing W, Zhanbo Q, Yifei S, Jing Z, Shuwen H
Journal
BMC microbiology
Year
2023
Keywords:
Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression
BACKGROUND: The most common toxic side effect after chemotherapy, one of the main treatments for colorectal cancer (CRC), is myelosuppression. OBJECTIVE: To analyze the correlation between gut microbiota and leukopenia after chemotherapy in CRC patients. METHODS: Stool samples were collected from 56 healthy individuals and 55 CRC patients. According to the leukocytes levels in peripheral blood, the CRC patients were divided into hypoleukocytes group (n = 13) and normal leukocytes group (n = 42). Shannon index, Simpson index, Ace index, Chao index and Coverage index were used to analyze the diversity of gut microbiota. LDA and Student's t-test(St test) were used for analysis of differences. Six machine learning algorithms, including logistic regression (LR) algorithm, random forest (RF) algorithm, neural network (NN) algorithm, support vector machine (SVM) algorithm, catboost algorithm and gradient boosting tree algorithm, were used to construct the prediction model of gut microbiota with leukopenia after chemotherapy for CRC. RESULTS: Compared with healthy group, the microbiota alpha diversity of CRC patients was significantly decreased (p < 0.05). After analyzing the gut microbiota differences of the two groups, 15 differential bacteria, such as Bacteroides, Faecalibacterium and Streptococcus, were screened. RF prediction model had the highest accuracy, and the gut microbiota with the highest predictive value were Peptostreptococcus, Faecalibacterium, and norank_f__Ruminococcaceae, respectively. Compared with normal leukocytes group, the microbiota alpha diversity of hypoleukocytes group was significantly decreased (p < 0.05). The proportion of Escherichia-Shigella was significantly decreased in the hypoleukocytes group. After analyzing the gut microbiota differences of the two groups, 9 differential bacteria, such as Escherichia-Shigella, Fusicatenibacter and Cetobacterium, were screened. RF prediction model had the highest accuracy, and the gut microbiota with the highest predictive value were Fusicatenibacte, Cetobacterium, and Paraeggerthella. CONCLUSION: Gut microbiota is related to leukopenia after chemotherapy. The gut microbiota may provide a novel method for predicting myelosuppression after chemotherapy in CRC patients.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-20
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
- Colorectal carcinoma cancer of large bowel,cancer of large intestine,cancer of the large bowel,cancer of the large intestine,carcinoma of colorectum,carcinoma of large bowel,carcinoma of large intestine,carcinoma of the large bowel,carcinoma of the large intestine,colorectal (colon or rectal) cancer,colorectal cancer,colorectal carcinoma,colorectum carcinoma,CRC,large bowel cancer,large bowel carcinoma,large intestine cancer,large intestine carcinoma,Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colorectal cancer (CRC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who has colorectal cancer (CRC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 56
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- 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
- 2.00
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 2024-6-20
Source: Fig. 2B
Description: Gut microbiota with significant differences in colorectal cancer (CRC) patients compared to healthy individuals.
Abundance in Group 1: increased abundance in Colorectal cancer (CRC)
Revision editor(s): Ayibatari, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-20
Source: Fig. 2B
Description: Gut microbiota with significant differences in colorectal cancer (CRC) patients compared to healthy individuals.
Abundance in Group 1: decreased abundance in Colorectal cancer (CRC)
Revision editor(s): Scholastica
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-20
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Leukopenia leukocytopenia,Leukopenia,leukopenia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal leukocytes
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hypoleukocytes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal cancer patients with lower-than-normal levels of leukocytes (below 3.5 × 10^9/L) after chemotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-20
Source: Fig. 6B
Description: Gut microbiota with significant differences in colorectal cancer (CRC) patients with hypoleukocytes compared to normal leukocytes.
Abundance in Group 1: increased abundance in Hypoleukocytes
| NCBI | Quality Control | Links |
|---|---|---|
| Cetobacterium | ||
| Eggerthia | ||
| Granulicatella | ||
| unclassified Candidatus Saccharibacteria | ||
| Coriobacteriaceae_UCG-002Coriobacteriaceae_UCG-002 |
Revision editor(s): Ayibatari, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-20
Source: Fig. 6B
Description: Gut microbiota with significant differences in colorectal cancer (CRC) patients with hypoleukocytes compared to normal leukocytes.
Abundance in Group 1: decreased abundance in Hypoleukocytes
Revision editor(s): Ayibatari, Scholastica
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