title: 16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation.
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.
authors.affiliation: EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, 1 Rue G Veil, 44000, Nantes, France, emmanuelmontassier@hotmail.com.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Montassier
authors.forename: Eric
authors.initials: E
authors.lastname: Batard
authors.forename: Sébastien
authors.initials: S
authors.lastname: Massart
authors.forename: Thomas
authors.initials: T
authors.lastname: Gastinne
authors.forename: Thomas
authors.initials: T
authors.lastname: Carton
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Caillon
authors.forename: Sophie
authors.initials: S
authors.lastname: Le Fresne
authors.forename: Nathalie
authors.initials: N
authors.lastname: Caroff
authors.forename: Jean Benoit
authors.initials: JB
authors.lastname: Hardouin
authors.forename: Philippe
authors.initials: P
authors.lastname: Moreau
authors.forename: Gilles
authors.initials: G
authors.lastname: Potel
authors.forename: Françoise
authors.initials: F
authors.lastname: Le Vacon
authors.forename: Marie France
authors.initials: MF
authors.lastname: de La Cochetière
mesh_terms: D000328:Adult; D000970:Antineoplastic Agents / Q000627:therapeutic use*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D016026:Bone Marrow Transplantation; D002851:Chromatography, High Pressure Liquid; D004269:DNA, Bacterial / Q000235:genetics* / Q000302:isolation & purification; D058645:Denaturing Gradient Gel Electrophoresis; D005243:Feces / Q000382:microbiology*; D005260:Female; D005602:France; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008228:Lymphoma, Non-Hodgkin / Q000188:drug therapy / Q000628:therapy*; D008297:Male; D064307:Microbiota / Q000187:drug effects*; D008875:Middle Aged; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D000970:Antineoplastic Agents; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S