Paradigms for microbiome analysis in infectious and non-communicable diseases

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Next-generation sequencing and bioinformatics have enabled detailed analysis of the human gut microbiome.
• The gut microbiome's role in health, infectious diseases, and noncommunicable diseases is increasingly recognized.
• Current understanding challenges previous assumptions about the microbiota's direct causal impact.

Purpose of the Study:

• To highlight the clinical significance of microbiome diagnostics and therapeutics.
• To advocate for standardized, validated deep metagenomic sequencing methods.
• To enable strain-level microbiome analysis and classification of individual microbiomes.

Main Methods:

• Implementing deep metagenomic sequencing.
• Utilizing standardized and validated laboratory procedures.
• Developing index-scores for classifying microbiomes as dysbiotic or eubiotic.

Main Results:

• Deciphering the human gut microbiome at a strain level.
• Establishing criteria for classifying microbiomes as associated with disease (dysbiotic) or health (eubiotic).

Conclusions:

• Metagenomic insights are key to advancing microbiome diagnostics.
• Standardized sequencing and classification are essential for clinical applications.
• Metagenomically informed therapies, including live biotherapeutic products and fecal microbiota transfer, hold promise for personalized medicine.