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Metagenomic method for in vitro diagnosis of gut dysbiosis

Dr Lorenza Putignani, Ospedale Pediatrico Bambino Gesù; Dr Federica Del Chierico, Ospedale Pediatrico Bambino Gesù

Ospedale Pediatrico Bambino Gesù


Gut dysbiosis is very frequent and related to very common symptoms of gastrointestinal and gastrointestinal-related diseases such as eating disorders, obesity, inflammatory bowel diseases, type I and II diabetes, cystic fibrosis, autoimmune diseases, steatosis and hepatic fibrosis, autism and malignancies. The management of the most appropriate intervention needs a personalized therapeutic approach based on an accurate quantitative diagnosis of the patient’s dysbiosis, that allows to design the most effective treatment strategy: 1. Nutritional; 2. Patient-tailored administration of prebiotics and probiotics; 3. Reversion to eubiosis by thoughtful microbiota replacement. This requires “fingerprinting” of human gut microbiota to describe and classify its bacterial components and to provide a computational interpretation of its ecological organization. The microbiota profiling requires a robust, reproducible and standardised technique/pipeline/method, to translate complicated activities of NGS (next generation sequencing) for microbial sequencing into a standardized analytical method. There is currently no effective method available for a quantitative diagnosis of dysbiosis. Current commercial solutions are in fact incomplete, scientifically incorrect and not reproducible.


The technology is based on next generation techniques applied to targeted-metagenomics sequencing. A single region of bacterial genomes is exploited to provide sequencing of the entire microbiota from different human sources. After DNA extraction from biological materials, the amplification process specifically targets the V3-V4 regions of the 16S rRNA ribosomal locus. This gene is the most widely used marker for genus and species identification and taxonomic significance in bacteria and archaea. The 16S Amplicon Sequencing provides a rapid, easy and effective access to the exploration of microbial identification, diversity and classifications in complex communities, considering the majority of natural microorganisms cannot be isolated and cultured clonally. Bioinformatic analyses are performed to select the most informative reads basing on sequences quality, length and remove possible chimeric sequencing from the dataset. Bioinformatics tools, specific for the microbiota analysis, are used to analyze the microbial profile. Finally the novel algorithm allows to compute the dysbiosis index of the gut microbiota.

Commercial Opportunity

This is the first accurate method for in vitro diagnosis of gut dysbiosis, providing a precious and low cost tool for a personalized therapeutic approach to a very common gastrointestinal and gastrointestinal-related diseases.

Development Status

Ongoing clinical validation.

Patent Situation

Patent pending applications in Italy, Europe, USA, Canada, China and Hong Kong with priority date June 16, 2016.

Further Reading

1van Dijkhuizen EHP, Del Chierico F, et al. Microbiome analytics of the gut microbiota in juvenile idiopathic arthritis patients: an observational, longitudinal cohort study. Arthritis Rheumatol. 2018 Dec 28.

2. Vernocchi P, Del Chierico F, et al. Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype. PLoS One. 2018 Dec 6;13(12):e0208171.

3. Ponziani FR, Bhoori S, Castelli C, Putignani L, et al. Hepatocellular Carcinoma Is Associated With Gut Microbiota Profile and Inflammation in Nonalcoholic Fatty Liver Disease. Hepatology. 2019 Jan;69(1):107-120. 


Metagenomic method for in vitro diagnosis of gut dysbiosis