title: Chemotherapy-driven dysbiosis in the intestinal microbiome.
abstract: BACKGROUND
  Chemotherapy is commonly used as myeloablative conditioning treatment to prepare patients for haematopoietic stem cell transplantation (HSCT). Chemotherapy leads to several side effects, with gastrointestinal (GI) mucositis being one of the most frequent. Current models of GI mucositis pathophysiology are generally silent on the role of the intestinal microbiome.
  
  
  OBJECTIVE
  To identify functional mechanisms by which the intestinal microbiome may play a key role in the pathophysiology of GI mucositis, we applied high-throughput DNA-sequencing analysis to identify microbes and microbial functions that are modulated following chemotherapy.
  
  
  METHODS
  We amplified and sequenced 16S rRNA genes from faecal samples before and after chemotherapy in 28 patients with non-Hodgkin's lymphoma who received the same myeloablative conditioning regimen and no other concomitant therapy such as antibiotics.
  
  
  RESULTS
  We found that faecal samples collected after chemotherapy exhibited significant decreases in abundances of Firmicutes (P = 0.0002) and Actinobacteria (P = 0.002) and significant increases in abundances of Proteobacteria (P = 0.0002) compared to samples collected before chemotherapy. Following chemotherapy, patients had reduced capacity for nucleotide metabolism (P = 0.0001), energy metabolism (P = 0.001), metabolism of cofactors and vitamins (P = 0.006), and increased capacity for glycan metabolism (P = 0.0002), signal transduction (P = 0.0002) and xenobiotics biodegradation (P = 0.002).
  
  
  CONCLUSIONS
  Our study identifies a severe compositional and functional imbalance in the gut microbial community associated with chemotherapy-induced GI mucositis. The functional pathways implicated in our analysis suggest potential directions for the development of intestinal microbiome-targeted interventions in cancer patients.
authors.affiliation: EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France.|Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
authors.forename: E
authors.initials: E
authors.lastname: Montassier
authors.affiliation: Department of Hematology, Nantes University Hospital, Nantes, France.
authors.forename: T
authors.initials: T
authors.lastname: Gastinne
authors.affiliation: Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA.
authors.forename: P
authors.initials: P
authors.lastname: Vangay
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.|Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA.
authors.forename: G A
authors.initials: GA
authors.lastname: Al-Ghalith
authors.affiliation: Institut des Maladies de l'Appareil Digestif, Nantes University Hospital, Nantes, France.
authors.forename: S
authors.initials: S
authors.lastname: Bruley des Varannes
authors.affiliation: Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
authors.forename: S
authors.initials: S
authors.lastname: Massart
authors.affiliation: Department of Hematology, Nantes University Hospital, Nantes, France.
authors.forename: P
authors.initials: P
authors.lastname: Moreau
authors.affiliation: EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France.
authors.forename: G
authors.initials: G
authors.lastname: Potel
authors.affiliation: EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, INSERM, Université de Nantes, Nantes, France.
authors.forename: M F
authors.initials: MF
authors.lastname: de La Cochetière
authors.affiliation: EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France.
authors.forename: E
authors.initials: E
authors.lastname: Batard
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.|BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
authors.forename: D
authors.initials: D
authors.lastname: Knights
mesh_terms: D039903:Actinobacteria / Q000187:drug effects; D000328:Adult; D000970:Antineoplastic Agents / Q000009:adverse effects* / Q000627:therapeutic use; D064806:Dysbiosis / Q000139:chemically induced / Q000378:metabolism / Q000382:microbiology; D005243:Feces / Q000382:microbiology; D005260:Female; D000068536:Bacillota / Q000187:drug effects; D000069196:Gastrointestinal Microbiome / Q000187:drug effects; D018380:Hematopoietic Stem Cell Transplantation / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008228:Lymphoma, Non-Hodgkin / Q000188:drug therapy* / Q000628:therapy; D008297:Male; D008875:Middle Aged; D052016:Mucositis / Q000139:chemically induced* / Q000378:metabolism* / Q000382:microbiology; D020560:Proteobacteria / Q000187:drug effects; D012336:RNA, Ribosomal, 16S / Q000187:drug effects* / Q000378:metabolism
chemical_list: D000970:Antineoplastic Agents; D012336:RNA, Ribosomal, 16S