Potential of multiomics technology in precision medicine

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Purpose of review

The ‘precision medicine’ refers to the generation of identification and classification criteria for advanced taxonomy of patients, exploiting advanced models to infer optimized clinical decisions for each disease phenotype.

Recent findings

The current article reviews new advances in the past 18 months on the microbiomics science intended as new discipline contributing to advanced ‘precision medicine’. Recently published data highlight the importance of multidimensional data in the description of deep disease phenotypes, including microbiome and immune profiling, and support the efficacy of the systems medicine to better stratify patients, hence optimizing diagnostics, clinical management and response to treatments.

Summary

The articles referenced in this review help inform the reader on new decision-support systems that can be based on multiomics patients’ data including microbiome and immune profiling. These harmonized and integrated data can be elaborated by artificial intelligence to generate optimized diagnostic pipelines and clinical interventions.

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Most cited references 23

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Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease

Francesca Romana Ponziani, Vincenzo Mazzaferro, Maurizio Pompili … (2018)

The gut-liver axis plays a pivotal role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD), which is the third leading cause of hepatocellular carcinoma (HCC) worldwide. However, the link between gut microbiota and hepatocarcinogenesis remains to be clarified. The aim of this study was to explore what features of the gut microbiota are associated with HCC in patients with cirrhosis and NAFLD. A consecutive series of patients with NAFLD-related cirrhosis and HCC (group 1, 21 patients), NAFLD-related cirrhosis without HCC (group 2, 20 patients), and healthy controls (group 3, 20 patients) was studied for gut microbiota profile, intestinal permeability, inflammatory status, and circulating mononuclear cells. We finally constructed a model depicting the most relevant correlations among these features, possibly involved in hepatocarcinogenesis. Patients with HCC showed increased levels of fecal calprotectin, while intestinal permeability was similar to patients with cirrhosis but without HCC. Plasma levels of interleukin 8 (IL8), IL13, chemokine (C-C motif) ligand (CCL) 3, CCL4, and CCL5 were higher in the HCC group and associated with an activated status of circulating monocytes. The fecal microbiota of the whole group of patients with cirrhosis showed higher abundance of Enterobacteriaceae and Streptococcus and a reduction in Akkermansia. Bacteroides and Ruminococcaceae were increased in the HCC group, while Bifidobacterium was reduced. Akkermansia and Bifidobacterium were inversely correlated with calprotectin concentration, which in turn was associated with humoral and cellular inflammatory markers. A similar behavior was also observed for Bacteroides. Conclusion: Our results suggest that in patients with cirrhosis and NAFLD the gut microbiota profile and systemic inflammation are significantly correlated and can concur in the process of hepatocarcinogenesis.

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Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease

Alessandra Lo Presti, Francesca Zorzi, Federica Del Chierico … (2019)

An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.

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Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture

Sofia Reddel, Federica Del Chierico, Andrea Quagliariello … (2019)

Atopic dermatitis (AD) has been hypothesised to be associated with gut microbiota (GM) composition. We performed a comparative study of the GM profile of 19 AD children and 18 healthy individuals aimed at identifying bacterial biomarkers associated with the disease. The effect of probiotic intake (Bifidobacterium breve plus Lactobacillus salivarius) on the modulation of GM and the probiotic persistence in the GM were also evaluated. Faecal samples were analysed by real-time PCR and 16S rRNA targeted metagenomics. Although the probiotics, chosen for this study, did not shape the entire GM profile, we observed the ability of these species to pass through the gastrointestinal tract and to persist (only B. breve) in the GM. Moreover, the GM of patients compared to CTRLs showed a dysbiotic status characterised by an increase of Faecalibacterium, Oscillospira, Bacteroides, Parabacteroides and Sutterella and a reduction of short-chain fatty acid (SCFA)-producing bacteria (i.e., Bifidobacterium, Blautia, Coprococcus, Eubacterium and Propionibacterium). Taken togheter these results show an alteration in AD microbiota composition with the depletion or absence of some species, opening the way to future probiotic intervention studies.

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Author and article information

Journal

Journal ID (nlm-ta): Curr Opin Gastroenterol

Journal ID (iso-abbrev): Curr. Opin. Gastroenterol

Journal ID (publisher-id): COGAS

Title: Current Opinion in Gastroenterology

Publisher: Lippincott Williams & Wilkins

ISSN (Print): 0267-1379

ISSN (Electronic): 1531-7056

Publication date (Print): November 2019

Publication date (Electronic): 10 September 2019

Volume: 35

Issue: 6

Pages: 491-498

Affiliations

[a ]Units of Parasitology and Human Microbiome, Children's Hospital and Research Institute ‘Bambino Gesù’, IRCCS

[b ]Istituto di Patologia Speciale Medica, Università Cattolica del Sacro Cuore

[c ]UOC Medicina Interna e Gastroenterologia, Area Gastroenterologia ed Oncologia Medica, Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS

[d ]Scientific Directorate, Children's Hospital and Research Institute ‘Bambino Gesù’, IRCCS, Rome, Italy

Author notes

Correspondence to Lorenza Putignani, Units of Parasitology and Human Microbiome, Children's Hospital and Research Institute ‘Bambino Gesù’, IRCCS, Piazza Sant’Onofrio 4, Rome, Italy. Tel: +00 39 06686592598 4127; e-mail: lorenza.putignani@ 123456opbg.net

Article

Publisher ID: MOG350611 Accession ID: 00004

DOI: 10.1097/MOG.0000000000000589

PMC ID: 6818999

PubMed ID: 31464810

SO-VID: 40c2e726-23ee-4002-8724-163a0980a45c

License:

This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0

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Keywords: artificial intelligence,decision-support systems,immunomics,microbiomics,personalized medicine

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Keywords: artificial intelligence, decision-support systems, immunomics, microbiomics, personalized medicine

Potential of multiomics technology in precision medicine

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Purpose of review

Recent findings

Summary

Related collections

Artificial Intelligence in Medicine

Most cited references 23

Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease

Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease

Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture

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