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16S rRNA Gene Pyrosequencing Reveals Shift in Patient Faecal Microbiota During High-Dose Chemotherapy as Conditioning Regimen for Bone Marrow Transplantation

  • Host Microbe Interactions
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Abstract

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.

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Acknowledgments

This work was funded by the Nantes University Hospital Grant BRD/10/04-Q and by the Mérieux Research Grants.

Accession Number

The V5–V6 16S rDNA bacterial sequences analysed in this paper have been deposited in the GenBank Short Read Archive (Accession number: SRA116522).

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Authors and Affiliations

  1. EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, 1 Rue G Veil, 44000, Nantes, France

    Emmanuel Montassier, Eric Batard, Jocelyne Caillon, Nathalie Caroff, Gilles Potel & Marie France de La Cochetière

  2. DNA Vision S.A., 25 avenue Georges Lemaitre, Gosselies, 6041, Charleroi, Belgium

    Sébastien Massart

  3. Service d’Hématologie Clinique, Centre Hospitalier Universitaire de Nantes, 1 Place A Ricordeau, 44000, Nantes, France

    Thomas Gastinne & Philippe Moreau

  4. Biofortis, Mérieux Nutrisciences, 3 Route de la Chatterie, 44800, Saint Herblain, France

    Thomas Carton, Sophie Le Fresne & Françoise Le Vacon

  5. EA 4275 Biostatistique, Recherche Clinique et Mesures Subjectives en Santé, Faculté de Médecine, Université de Nantes, 1 Rue G Veil, 44000, Nantes, France

    Jean Benoit Hardouin

  6. INSERM, EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, 1 Rue G Veil, 44000, Nantes, France

    Marie France de La Cochetière

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  1. Emmanuel Montassier
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Correspondence to Emmanuel Montassier.

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SI Figure 1

Denaturing high-performance liquid chromatography (dHPLC) fingerprint analysis of the V6 to V8 region of the 16S rRNA gene. Example of dHPLC fingerprints obtained in one patient, S1: prechemotherapy sample, S2: postchemotherapy sample. The dominant microbiota was converted into a profile with peaks, each peak corresponds to an amplicon. (JPEG 20 kb)

High-resolution Image (TIFF 41 kb)

SI Figure 2

Most abundant phyla found in the prechemotherapy (S1) and postchemotherapy (S2) faecal samples of eight patients (p1 to p8) undergoing bone marrow transplantation conditioning chemotherapy. (JPEG 102 kb)

High-resolution Image (TIFF 88 kb)

SI Figure 3

Most abundant genera found in the prechemotherapy (S1) and postchemotherapy (S2) faecal samples of 8 patients (p1 to p8) undergoing bone marrow transplantation conditioning chemotherapy. (JPEG 165 kb)

High-resolution Image (TIFF 181 kb)

SI Table 1

OTUs that were significantly different in abundance before and after chemotherapy. (DOC 88 kb)

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Montassier, E., Batard, E., Massart, S. et al. 16S rRNA Gene Pyrosequencing Reveals Shift in Patient Faecal Microbiota During High-Dose Chemotherapy as Conditioning Regimen for Bone Marrow Transplantation. Microb Ecol 67, 690–699 (2014). https://doi.org/10.1007/s00248-013-0355-4

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