To understand your Organisms page, it is important to understand microbial taxonomy. Taxonomy is the science of naming, describing and classifying organisms into groups based on shared characteristics such as their shape, genetic makeup and how they interact with their environment. Taxonomy is like organizing the entire living world into a giant, structured family tree. This tree acts as a roadmap that helps us navigate the complex world of microorganisms living inside us, allowing us to better understand how they interact with each other and our health.

Domain: The highest and broadest level of classification. Domains group all life into three main categories: Bacteria, Archaea and Eukaryota. Organisms are grouped here based on the fundamental differences in their cell structure and genetics. The gut microbiome often contains organisms from all three domains.

Kingdom: The second level of classification under Domain. Each Domain is divided into multiple Kingdoms based on broad characteristics. Organisms are grouped based on major differences in their cellular organization and nutritional methods. Within the domain Bacteria, there is only one Kingdom: Eubacteria.

Phylum: A rank below Kingdom that groups organisms based on major structural similarities and genetic relationships. Organisms within a Phylum often share similar body plans or significant features. The Phylum Bacillota (formerly Firmicutes) is common in the gut microbiome.

Class: A division within a Phylum, grouping organisms that share even more specific similarities. Organisms within a Class often share more detailed features and often similar metabolic functions. For example, within Bacillota, one of the classes is Clostridia, which includes bacteria that are important for fermenting dietary fiber in the gut.

Order: A rank under Class that groups organisms with further specific similarities. Organisms in an Order typically share particular structural features or functional roles. Order Clostridiales is within the Class Clostridia, containing many bacteria that produce beneficial short-chain fatty acids.

Family: A rank below Order, grouping even more closely related organisms. Organisms in a Family often share more detailed genetic and functional traits. Family Ruminococcaceae is a family within the Order Clostridiales, known for its members’ role in breaking down complex carbohydrates.

Genus: A rank under Family, grouping species that are very closely related. Organisms in a Genus are very similar and are often functionally and structurally alike. Genus Ruminococcus is within the Family Ruminococcaceae, including bacteria that help digest dietary fiber.

Species: The most specific formal level of classification, identifying individual organisms that can interbreed. Organisms within a Species are nearly identical and share the same ecological niche. Species Ruminococcus bromii is a specific bacterium within the Genus Ruminococcus, known for its ability to break down resistant starch in the gut.

Strain: A strain is a genetic variant or subtype of a species. Often these genetic variants have no functional difference within a species, but there are known circumstances in which different strains of the same species have been shown to exhibit different biological effects.

The Jona organisms page, pictured below, is where you can find detailed information about each of the organisms we found in your microbiome.

For each organism in your gut, we provide you with two numbers: Your relative abundance and the normal range. Relative abundance (RA) is the proportion of that organism in your gut compared to all of the other types of organisms. The RA reflects the percentage of your microbiome is made up of that organism relative to all other organisms in the same taxonomic rank. A such, the RA of all organisms of a particular rank will sum to 100%. The Normal Range reflects the relative abundance found in the general population of healthy (disease-free) individuals. This number is there to give you an idea of where your relative abundance falls compared to the general population. It is not universally good or bad to be high or low in any particular organism, apart from a select few. Some organisms can be associated with unhealthy conditions at both high or low levels and some organisms may not be associated to any known health conditions at all. Linking each organism levels with health concerns is done in the rest of your report.

On the organisms page, you can filter which organisms are shown using three categories: Organism type, abundance and taxonomy.

These options allow you to narrow your view to see only organisms that you are interested in, whether it be by their characteristics, abundance or taxonomic level. For example, the filters pictured above will show only microbes classified as bacteria that were found below the normal range in your microbiome.