title: Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients.
abstract: OBJECTIVE
  Celiac disease (CD)-associated duodenal dysbiosis has not yet been clearly defined, and the mechanisms by which CD-associated dysbiosis could concur to CD development or exacerbation are unknown. In this study, we analyzed the duodenal microbiome of CD patients.
  
  
  METHODS
  The microbiome was evaluated in duodenal biopsy samples of 20 adult patients with active CD, 6 CD patients on a gluten-free diet, and 15 controls by DNA sequencing of 16S ribosomal RNA libraries. Bacterial species were cultured, isolated and identified by mass spectrometry. Isolated bacterial species were used to infect CaCo-2 cells, and to stimulate normal duodenal explants and cultured human and murine dendritic cells (DCs). Inflammatory markers and cytokines were evaluated by immunofluorescence and ELISA, respectively.
  
  
  RESULTS
  Proteobacteria was the most abundant and Firmicutes and Actinobacteria the least abundant phyla in the microbiome profiles of active CD patients. Members of the Neisseria genus (Betaproteobacteria class) were significantly more abundant in active CD patients than in the other two groups (P=0.03). Neisseria flavescens (CD-Nf) was the most abundant Neisseria species in active CD duodenum. Whole-genome sequencing of CD-Nf and control-Nf showed genetic diversity of the iron acquisition systems and of some hemoglobin-related genes. CD-Nf was able to escape the lysosomal compartment in CaCo-2 cells and to induce an inflammatory response in DCs and in ex-vivo mucosal explants.
  
  
  CONCLUSIONS
  Marked dysbiosis and an abundance of a peculiar CD-Nf strain characterize the duodenal microbiome in active CD patients thus suggesting that the CD-associated microbiota could contribute to the many inflammatory signals in this disorder.
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
authors.forename: Valeria
authors.initials: V
authors.lastname: D'Argenio
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Casaburi
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
authors.forename: Vincenza
authors.initials: V
authors.lastname: Precone
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Pagliuca
authors.affiliation: Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Colicchio
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Sarnataro
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University of Naples Federico II, Naples, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Discepolo
authors.affiliation: Department of Medicine and the University of Chicago Celiac Disease Center, University of Chicago, Chicago, Illinois, USA.
authors.forename: Sangman M
authors.initials: SM
authors.lastname: Kim
authors.affiliation: Department of Medicine and Surgery, University of Salerno, Salerno, Italy.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Russo
authors.affiliation: Department of System Medicine, University of Rome Tor Vergata, Rome, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Del Vecchio Blanco
authors.affiliation: Department of Biosciences, University of Milan, Milan, Italy.
authors.forename: David S
authors.initials: DS
authors.lastname: Horner
authors.affiliation: Department of Biosciences, University of Milan, Milan, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Chiara
authors.affiliation: Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy.|Department of Biochemistry and Molecular Biology, University of Bari A. Moro, Bari, Italy.
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Salvatore
authors.affiliation: Department of System Medicine, University of Rome Tor Vergata, Rome, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Monteleone
authors.affiliation: Department of Medicine and Surgery, University of Salerno, Salerno, Italy.
authors.forename: Carolina
authors.initials: C
authors.lastname: Ciacci
authors.affiliation: Northern Arizona University, Flagstaff, Arizona, USA.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Caporaso
authors.affiliation: Department of Medicine and the University of Chicago Celiac Disease Center, University of Chicago, Chicago, Illinois, USA.
authors.forename: Bana
authors.initials: B
authors.lastname: Jabrì
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.|Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.|IRCCS-Fondazione SDN, Naples, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Salvatore
authors.affiliation: CEINGE-Biotecnologie Avanzate, Naples, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Sacchetti
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000302:isolation & purification; D000328:Adult; D001706:Biopsy; D018938:Caco-2 Cells; D002446:Celiac Disease / Q000382:microbiology*; D055050:Diet, Gluten-Free; D004386:Duodenum / Q000382:microbiology*; D064806:Dysbiosis / Q000382:microbiology*; D004797:Enzyme-Linked Immunosorbent Assay; D005260:Female; D005455:Fluorescent Antibody Technique; D006801:Humans; D007558:Italy; D008297:Male; D056186:Metagenomics; D064307:Microbiota; D009343:Neisseria / Q000145:classification / Q000302:isolation & purification*; D020560:Proteobacteria / Q000145:classification / Q000302:isolation & purification