Gut microbiome investigation in celiac disease: from methods to its pathogenetic role

Our body is inhabited by a variety of microbes (microbiota), mainly bacteria, that outnumber our own cells. Until recently, most of what we knew about the human microbiota was based on culture methods, whereas a large part of the microbiota is uncultivable, and consequently previous information was limited. The advent of culture-independent methods and, particularly, of next-generation sequencing (NGS) methodology, marked a turning point in studies of the microbiota in terms of its composition and of the genes encoded by these microbes (microbiome). The microbiome is influenced predominantly by environmental factors that cause a large inter-individual variability (~20%) being its heritability only 1.9%. The gut microbiome plays a relevant role in human physiology, and its alteration ("dysbiosis") has been linked to a variety of inflammatory gut diseases, including celiac disease (CD). CD is a chronic, immune-mediated disorder that is triggered by both genetic (mainly HLA-DQ2/DQ8 haplotypes) and environmental factors (gluten), but, in recent years, a large body of experimental evidence suggested that the gut microbiome is an additional contributing factor to the pathogenesis of CD. In this review, we summarize the literature that has investigated the gut microbiome associated with CD, the methods and biological samples usually employed in CD microbiome investigations and the putative pathogenetic role of specific microbial alterations in CD. In conclusion, both gluten-microbe and host-microbe interactions drive the gluten-mediated immune response. However, it remains to be established whether the CD-associated dysbiosis is the consequence of the disease, a simple concomitant association or a concurring causative factor.

Setup of Quantitative PCR for Oral Neisseria spp. Evaluation in Celiac Disease Diagnosis

Coeliac disease (CD) is a multifactorial autoimmune disorder and gut dysbiosis contributes to its pathogenesis. We previously profiled by 16S rRNA sequencing duodenal and oropharyngeal microbiomes in active CD (a-CD), gluten-free diet (GFD) patients, and controls (CO) and found significantly higher levels of Neisseria spp., with pro-inflammatory activities, in a-CD patients than in the other two groups. In this study, we developed a fast and simple qPCR-based method to evaluate the abundance of the oral Neisseria spp. and the diagnostic performances of the test in CD diagnosis. The Neisseria spp. abundances detected by quantitative PCR (qPCR) were: CO = 0.14, GFD = 0.15, a-CD = 2.08, showing a similar trend to those previously measured by next generation sequencing (NGS). In particular, Neisseria spp. values obtained by both methods were significantly higher (p < 0.001) in a-CD than in the other two groups GFD and CO—the latter almost overlapping. We calculated by ROC curve analysis the threshold of 1.12 ng/μL of Neisseria spp. to discriminate between CO+GFD and a-CD patients with 100% and 96.7% of diagnostic sensitivity and specificity, respectively. In conclusion, our data, if confirmed in other cohorts, suggest the q-PCR evaluation of oral Neisseria spp. could be a fast and simple method to assess CD-associated dysbiosis for diagnostic purposes.

Neisseria flavescens Infection in Atypical Multiple Vallecular Cysts

A 53 year-old female patient presented with symptoms of intermittent odynophagia and halitosis persisting for 2 months. Physical examination revealed bilateral lingual tonsillar cysts and multiple vallecular cysts with clear fluid. Laboratory studies were unremarkable. The patient underwent surgery, during which uncapping of the multiple vallecular cysts was performed, and multiple microbiological samples and biopsies were taken. After surgery, the patient had complete resolution of all her symptoms. Pathological results demonstrated lymphoepithelial cysts. Microbiological tests demonstrated an infection by Neisseria flavescens, which is a non-pathogenic commensal of the oropharynx, and has never been described as causing agent of infected vallecular cysts.

Celiac disease-associated Neisseria flavescens decreases mitochondrial respiration in CaCo-2 epithelial cells: Impact of Lactobacillus paracasei CBA L74 on bacterial-induced cellular imbalance

We previously identified a Neisseria flavescens strain in the duodenum of celiac disease (CD) patients that induced immune inflammation in ex vivo duodenal mucosal explants and in CaCo‐2 cells. We also found that vesicular trafficking was delayed after the CD‐immunogenic P31‐43 gliadin peptide‐entered CaCo‐2 cells and that Lactobacillus paracasei CBA L74 (L. paracasei‐CBA) supernatant reduced peptide entry. In this study, we evaluated if metabolism and trafficking was altered in CD‐N. flavescens‐infected CaCo‐2 cells and if any alteration could be mitigated by pretreating cells with L. paracasei‐CBA supernatant, despite the presence of P31‐43. We measured CaCo‐2 bioenergetics by an extracellular flux analyser, N. flavescens and P31‐43 intracellular trafficking by immunofluorescence, cellular stress by TBARS assay, and ATP by bioluminescence. We found that CD‐N. flavescens colocalised more than control N. flavescens with early endocytic vesicles and more escaped autophagy thereby surviving longer in infected cells. P31‐43 increased colocalisation of N. flavescens with early vesicles. Mitochondrial respiration was lower (P < .05) in CD‐N. flavescens‐infected cells versus not‐treated CaCo‐2 cells, whereas pretreatment with L. paracasei‐CBA reduced CD‐N. flavescens viability and improved cell bioenergetics and trafficking. In conclusion, CD‐N. flavescens induces metabolic imbalance in CaCo‐2 cells, and the L. paracasei‐CBA probiotic could be used to correct CD‐associated dysbiosis.

Necrotizing pneumonia and empyema caused by Neisseria flavescens infection

Neisseria flavescens is an uncommon pathogen of human infection, pneumonia and empyema caused by N. flavescens is rarely reported. Herein, we report a 56-year-old diabetic patient presenting necrotising pneumonia and empyema due to N. flavescens infection. The main clinical manifestation of this patient was high fever, sticky pus and gradually aggravating dyspnea. The chest computed tomography (CT) scan showed there are mass of high density areas around hilus of the left lung, hollow sign with inflammation also appeared. A biopsy specimen was taken from the left principal bronchus by lung puncture biopsy and showed necrosis and inflammation. Microscopic examination of direct smear and culture of sticky pus, much more gram-negative diplococcus was present, pathogen was further identified by Vitek NH card, Vitek MS and confirmed as N. flavescens by 16S rRNA gene sequencing finally. Anti-infection therapy following the antimicrobial susceptibility test results was effectively. To our knowledge, this is the first report of pulmonary infection caused by N. flavescens.