16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation

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Reviewed Marked as Reviewed by Atrayees on 2023-6-26
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Montassier E, Batard E, Massart S, Gastinne T, Carton T, Caillon J, Le Fresne S, Caroff N, Hardouin JB, Moreau P, Potel G, Le Vacon F, de La Cochetière MF
Journal
Microbial ecology
Year
2014
Gastrointestinal disturbances are a side-effect frequently associated with haematological malignancies due to the intensive cytotoxic treatment given in connection with bone marrow transplantation (BMT). However, intestinal microbiota changes during chemotherapy remain poorly described, probably due to the use of culture-based and low-resolution molecular methods in previous studies. The objective of our study was to apply a next generation DNA sequencing technology to analyse chemotherapy-induced changes in faecal microbiota. We included eight patients with non-Hodgkin's lymphoma undergoing one course of BMT conditioning chemotherapy. We collected a prechemotherapy faecal sample, the day before chemotherapy was initiated, and a postchemotherapy sample, collected 1 week after the initiation of chemotherapy. Total DNA was extracted from faecal samples, denaturing high-performance liquid chromatography based on amplification of the V6 to V8 region of the 16S ribosomal RNA (rRNA) gene, and 454-pyrosequencing of the 16 S rRNA gene, using PCR primers targeting the V5 and V6 hypervariable 16S rRNA gene regions were performed. Raw sequence data were screened, trimmed, and filtered using the QIIME pipeline. We observed a steep reduction in alpha diversity and significant differences in the composition of the intestinal microbiota in response to chemotherapy. Chemotherapy was associated with a drastic drop in Faecalibacterium and accompanied by an increase of Escherichia. The chemotherapy-induced shift in the intestinal microbiota could induce severe side effects in immunocompromised cancer patients. Our study is a first step in identifying patients at risk for gastrointestinal disturbances and to promote strategies to prevent this drastic shift in intestinal microbiota.

Experiment 1


Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Atrayees

Subjects

Location of subjects
France
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
non-Hodgkins lymphoma NHL,non-Hodgkin lymphoma,non-Hodgkin's lymphoma,non-Hodgkin's lymphoma (NHL),non-Hodgkins lymphoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
pre-chemotherapy
Group 1 name Corresponds to the case (exposed) group for case-control studies
post-chemotherapy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
8
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
all antibiotics after starting chemotherapy

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V5-V6
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Aiyshaaaa, Atrayees

Source: Figure 4, 5, text

Description: Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data

Abundance in Group 1: increased abundance in post-chemotherapy

NCBI Quality ControlLinks
Bacteroides
Bacteroidota
Escherichia
Pseudomonadota

Revision editor(s): WikiWorks, Aiyshaaaa, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: Figure 4, 5, text

Description: Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data

Abundance in Group 1: decreased abundance in post-chemotherapy

NCBI Quality ControlLinks
Bacillota
Actinomycetota
Blautia
Faecalibacterium
Roseburia
Bifidobacterium

Revision editor(s): WikiWorks, Atrayees