Key Technologies for Progressing Discovery of Microbiome-Based Medicines

Abstract

A growing number of experimental and computational approaches are illuminating the “microbial dark matter” and uncovering the integral role of commensal microbes in human health. Through this work, it is now clear that the human microbiome presents great potential as a therapeutic target for a plethora of diseases, including inflammatory bowel disease, diabetes and obesity. The development of more efficacious and targeted treatments relies on identification of causal links between the microbiome and disease; with future progress dependent on effective links between state-of-the-art sequencing approaches, computational analyses and experimental assays. We argue determining causation is essential, which can be attained by generating hypotheses using multi-omic functional analyses and validating these hypotheses in complex, biologically relevant experimental models. In this review we discuss existing analysis and validation methods, and propose best-practice approaches required to enable the next phase of microbiome research.

The nasopharyngeal microbiome in COVID-19

“…Regarding the methodology used in these studies, different sequencing technologies, namely 16S rRNA gene sequencing and metagenomic sequencing, have been used to analyze the possible alterations in the nasopharyngeal microbiota of SARS-CoV-2 positive subjects, as well as the potential correlations between such microbiota and the severity of the COVID-19 disease (Table S1). The advantages and disadvantages of both technologies are already well-known: in summary, while 16S rRNA profiling has higher sensitivity but lower taxonomic resolution and the need to assume PCR amplification bias, metagenomic sequencing presents higher taxonomic resolution and incorporates functional information without the need of extrapolation [ 76 ]. Although the 16S rRNA gene sequencing approach to study the microbiota could introduce bias in the obtained data because this method does not allow the study of the whole microbiome, but only the genera amplified by PCR, it is the most commonly used technique to study microbiota in clinical samples.…”

Emerging microfluidic technologies for microbiome research

“…Technological advances in sequencing and multi-omics have enhanced our understanding of the microbiome. Specifically, represented by 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing, culture-independent methods are widely used for microbiome research nowadays ( Arnold et al, 2016 ; Young et al, 2021 ). These methods enable more accurate profiling of the microbiome composition and structure, because the unculturable microbial majority is also accounted during the analysis.…”

Gut Microbiome Signatures of Yorkshire Terrier Enteropathy during Disease and Remission

“…The gut microbiome shows a marked individuality, and our understanding of the factors that imbalance gut microbial communities leading to pathogenic processes, has improved thanks to technological improvement and enhanced analysis capabilities (Young et al, 2021). Microbiome studies make an essential contribution and create intervention opportunities that will allow the development of personalised medicine in veterinary and human medicine.…”