Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients

Abstract

OBJECTIVES: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.

The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection

“…However, a recent sequencing analysis on five healthy subjects indicated Prevotella and generally Bacteroidetes to be virtually absent from duodenum mucosa 34. More recently the Proteobacteria genera Acinetobacter , Neisseria and Haemophilus , and Prevotella were reported to be the most predominant genera 35. The observation here of Streptococcus , Prevotella , Actinomyces and also of Propionibacterium , Gemella and Fusobacterium as abundant in DB is based on a cohort of 24 individuals and thus gives, for the first time, a representative overview of this environment.…”

A Commensal Bifidobacterium longum Strain Prevents Gluten-Related Immunopathology in Mice through Expression of a Serine Protease Inhibitor

“…Patients with NCG/WS also improve symptomatically on a GFD, but it is unknown whether these patients could tolerate less restrictive avoidance or could be successfully treated with other therapies. Since patients with active CeD and nonresponders to a GFD have been found to harbor dysbiotic intestinal communities (5,(17)(18)(19), probiotics have been proposed as potential candidates to restore gut microbial homeostasis. Smecuol et al found that administration of the Bifidobacterium probiotic Natren Life Start (NLS) attenuated symptoms in CeD patients on a gluten-containing diet (20), and administration of NLS was shown to modulate innate immunity in a follow-up study (3).…”

Dietary Gluten-Induced Gut Dysbiosis Is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease

“…It was suggested that increased presence of some of the bacteria involved in gluten metabolism might be associated with enteritis [39]. An unrelated report showed that Proteobacteria and not Firmicutes is the most abundant phylum in celiacs, with members of the Neisseria genus being the most represented [40]. Regardless of the exact reflection of intestinal dysbiosis that appears may vary in different categories of CD patients, it was observed that dietary gluten-induced dysbiosis is not easily restored by GFD treatment [35].…”