Culture-based methods involve growing live microorganisms in laboratory conditions using specific nutrient media. These methods are useful for isolating and characterising individual organisms, confirming the presence of certain pathogens, and performing antimicrobial susceptibility testing. However, many gut microorganisms have complex growth requirements or are difficult to cultivate outside their natural environment. Research suggests that culture conditions have been established for approximately 63% of known gut microbial species, and cultivating these organisms would require numerous specialised conditions. Consequently, routine culture-based testing captures only a portion of the gut microbial community.
Shotgun metagenomic sequencing, the technology used by Microbiome Explorer, analyses DNA extracted directly from a stool sample without requiring microorganisms to be cultured. This approach enables the identification of bacteria, archaea, fungi, protists and DNA viruses, often at species level and, in some cases, strain level. It can also identify previously uncharacterised microorganisms and provide insights into microbial genes and metabolic pathways, helping us understand both which organisms are present and their potential biological functions.
While culture-based methods remain valuable for targeted investigations, particularly when viable organisms need to be isolated or antimicrobial susceptibility assessed, shotgun metagenomic sequencing provides a more comprehensive, community-wide view of the gut microbiome.
By assessing microbial composition, diversity and functional potential in a single analysis, Microba testing offers a detailed understanding of the gut microbial ecosystem beyond what routine culture-based testing can provide.