The article "The vocabulary of microbiome research: a proposal" by Julian R. Marchesi and Jacques Ravel aims to clarify and standardize the terminology used in microbiome research. The authors highlight the rapid evolution of the field, driven by advancements in DNA/RNA, protein, and metabolite analytical platforms, as well as increased computing technologies. This evolution has led to an exponential increase in publications on microbial communities, but it has also resulted in confusion over the use of terms such as "microbiome," "microbiota," "metagenome," and "metagenomics." The authors propose clear definitions for these terms: - **Microbiota**: The assemblage of microorganisms present in a defined environment, typically characterized using molecular methods like 16S rRNA gene analysis. - **Metataxonomics**: The high-throughput process used to characterize the entire microbiota and create a metataxonomic tree. - **Metagenome**: The collection of genomes and genes from the members of a microbiota, obtained through shotgun sequencing and assembly. - **Microbiome**: The entire habitat, including microorganisms, their genomes, and surrounding environmental conditions. - **Metabolomics**: Analytical approaches to determine the metabolite profile in a given strain or tissue. - **Metabonomics**: A variant of metabolomics, used to generate metabolite profiles from complex systems. - **Metatranscriptomics**: Analysis of expressed RNAs by high-throughput sequencing of meta-cDNAs. - **Metaproteomics**: Large-scale characterization of the entire protein complement of environmental or clinical samples. The authors also address common misnomers, such as the use of "16S survey" or "16S sequencing," and the outdated term "microflora," which should be replaced with "microbiota" to accurately describe microbial communities. They emphasize the need for a standardized language in the scientific community to improve communication and understanding of microbiome research.The article "The vocabulary of microbiome research: a proposal" by Julian R. Marchesi and Jacques Ravel aims to clarify and standardize the terminology used in microbiome research. The authors highlight the rapid evolution of the field, driven by advancements in DNA/RNA, protein, and metabolite analytical platforms, as well as increased computing technologies. This evolution has led to an exponential increase in publications on microbial communities, but it has also resulted in confusion over the use of terms such as "microbiome," "microbiota," "metagenome," and "metagenomics." The authors propose clear definitions for these terms: - **Microbiota**: The assemblage of microorganisms present in a defined environment, typically characterized using molecular methods like 16S rRNA gene analysis. - **Metataxonomics**: The high-throughput process used to characterize the entire microbiota and create a metataxonomic tree. - **Metagenome**: The collection of genomes and genes from the members of a microbiota, obtained through shotgun sequencing and assembly. - **Microbiome**: The entire habitat, including microorganisms, their genomes, and surrounding environmental conditions. - **Metabolomics**: Analytical approaches to determine the metabolite profile in a given strain or tissue. - **Metabonomics**: A variant of metabolomics, used to generate metabolite profiles from complex systems. - **Metatranscriptomics**: Analysis of expressed RNAs by high-throughput sequencing of meta-cDNAs. - **Metaproteomics**: Large-scale characterization of the entire protein complement of environmental or clinical samples. The authors also address common misnomers, such as the use of "16S survey" or "16S sequencing," and the outdated term "microflora," which should be replaced with "microbiota" to accurately describe microbial communities. They emphasize the need for a standardized language in the scientific community to improve communication and understanding of microbiome research.