• Crohn’s disease
• microbiome
• pediatrics

• Humans
• Crohn Disease/microbiology
• Crohn Disease/diagnosis
• Crohn Disease/genetics
• Gastrointestinal Microbiome/genetics
• Child
• Metagenomics/methods
• INDEL Mutation
• Feces/microbiology
• Female
• Male
• Biomarkers/analysis
• Adolescent
• Machine Learning

• 82170542 National Natural Science Foundation of China
• 2021YFF0703700/2021YFF0703702 National Key Research and Development Program of China
• 2014008 Sun Yat-sen University Clinical Research 5010 Program
• 2019ZT08Y464 Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project

• Celiac
• Coeliac
• Gluten
• Virus

• Child
• Humans
• Celiac Disease/epidemiology
• Viruses

• Chicken
• Colistin
• Fluoroquinolone-resistant
• ST 198
• Salmonella enterica serovar Kentucky

• TANUVAS
• Biotechnology Industry Research Assistance Council

Celiac disease (CeD) is a multisystem immune-mediated multifactorial condition strongly associated with the intestinal microbiota.

To evaluate the predictive power of the gut microbiota in the diagnosis of CeD and to search for important taxa that may help to distinguish CeD patients from controls.

Microbial DNA from bacteria, viruses, and fungi, was isolated from mucosal and fecal samples of 40 children with CeD and 39 controls. All samples were sequenced using the HiSeq platform, the data were analyzed, and abundance and diversities were assessed. For this analysis, the predictive power of the microbiota was evaluated by calculating the area under the curve (AUC) using data for the entire microbiome. The Kruskal-Wallis test was used to evaluate the significance of the difference between AUCs. The Boruta logarithm, a wrapper built around the random forest classification algorithm, was used to identify important bacterial biomarkers for CeD.

In fecal samples, AUCs for bacterial, viral, and fungal microbiota were 52%, 58%, and 67.7% respectively, suggesting weak performance in predicting CeD. However, the combination of fecal bacteria and viruses showed a higher AUC of 81.8 %, indicating stronger predictive power in the diagnosis of CeD. In mucosal samples, AUCs for bacterial, viral, and fungal microbiota were 81.2%, 58.6%, and 35%, respectively, indicating that mucosal bacteria alone had the highest predictive power. Two bacteria, Bacteroides intestinalis and Burkholderiales bacterium 1-1-47, in fecal samples and one virus, Human_endogenous _retrovirus_K, in mucosal samples are predicted to be “important” biomarkers, differentiating celiac from nonceliac disease groups. Bacteroides intestinalis is known to degrade complex arabinoxylans and xylan which have a protective role in the intestinal mucosa. Similarly, several Burkholderiales species have been reported to produce peptidases that hydrolyze gluten peptides, with the potential to reduce the gluten content of food. Finally, a role for Human_endogenous _retrovirus_K in immune-mediated disease such as CeD has been reported.

The excellent predictive power of the combination of the fecal bacterial and viral microbiota with mucosal bacteria alone indicates a potential role in the diagnosis of difficult cases of CeD. Bacteroides intestinalis and Burkholderiales bacterium 1-1-47, which were found to be deficient in CeD, have a potential protective role in the development of prophylactic modalities. Further studies on the role of the microbiota in general and Human_endogenous _retrovirus_K in particular are needed.

• Celiac disease
• Microbial signature
• Children
• Saudi Arabia

• Humans
• Child
• Celiac Disease/diagnosis
• Celiac Disease/epidemiology
• Celiac Disease/metabolism
• Gastrointestinal Microbiome
• Saudi Arabia/epidemiology
• Glutens
• Biomarkers/metabolism
• Bacteria/genetics
• Bacteria/metabolism

• digestive pathology
• dysbiosis
• human
• microbiome
• probiotics

• celiac disease (CeD)
• dietary therapies
• gluten
• glutenase
• gut microbiota
• postbiotics
• prebiotics
• probiotics
• viromebiotics

• Celiac Disease
• Glutens/adverse effects
• Humans
• Probiotics/therapeutic use
• Quality of Life
• Viruses

Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans—from the oral cavity, to the gut, to fecal excretions—have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives.

• COVID-19
• metagenomics
• microbiome
• pandemic prevention
• periodontitis
• surveillance
• virome
• zoonoses

• Adult
• Bacteria
• Gastrointestinal Microbiome
• Humans
• Infant
• Virome
• Viruses/genetics

• PKDF-839636 PKDF
• HRAO-2022-076 HRAO
• 2017076 Doris Duke Charitable Foundation
• F31 AI167499 NIAID NIH HHS
• R01 DK122029 NIDDK NIH HHS
• TWCF-2021-20568 CURE, Citizens United for Research in Epilepsy
• OT2 DB000009 DB NIH HHS