The vocabulary of microbiome research: a proposal

By Julian R. Marchesi, Jacques Ravel. Microbiome, 2015

988 citations recorded by the source corpus.

The advancement of DNA/RNA, proteins, and metabolite analytical platforms, combined with increased computing technologies, has transformed the field of microbial community analysis. This transformation is evident by the exponential increase in the number of publications describing the composition and structure, and sometimes function, of the microbial communities inhabiting the human body. This rapid evolution of the field has been accompanied by confusion in the vocabulary used to describe different aspects of these communities and their environments. The misuse of terms such as microbiome, microbiota, metabolomic, and metagenome and metagenomics among others has contributed to misunderstanding of many study results by the scientific community and the general public alike. A few review articles have previously defined those terms, but mainly as sidebars, and no clear definitions or use cases have been published. In this editorial, we aim to propose clear definitions of each of these terms, which we would implore scientists in the field to adopt and perfect.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b68f941e508f336da25566a4c7fca5893be9e9a3

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Citations in the corpus

The gut microbiota and inflammatory bowel disease (2014, background): “…of IBD management such as different drug use and surgery, 3) birth cohorts such as Lifelines NEXT 80 to capture microbial perturbations early on in life, and 4) large-scale general population cohorts to capture pre-IBD and post-IBD disease states and to gain insight into the fluctuations…”
The Vaginal Microenvironment: The Physiologic Role of Lactobacilli (2018, background): “The vagina also harbors numerous microorganisms (the “microbiota”), that exist (in conjunction with their genes and products) in a regulated mutualistic relationship with the host (the “microbiome”) (4).”
Advances and Trends in Omics Technology Development (2022, background): “…of a microbial community by integrating multiple omics information such as genomics, transcriptomics, proteomics and metabolomics, where all microorganisms of a given environment, called microbiome, are analyzed to study the potential role that such microorganisms have in diseases (253, 254).”
Microbiome definition re-visited: old concepts and new challenges (2020, background): “Microbiota is usually defined as the assemblage of living microorganisms present in a defined environment [25].”
A practical guide to amplicon and metagenomic analysis of microbiome data (2020, background): “Microbiome refers to an entire microhabitat, including its microorganisms, their genomes, and the surrounding environment (Marchesi and Ravel, 2015).”
Antibiotics as Major Disruptors of Gut Microbiota (2020, background): “Microbiota is defined as the assemblage of microorganisms present in a particular environment, while the term “microbiome” refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes , and viruses) , the ir genomes and the environmental conditions that”
A review of methods and databases for metagenomic classification and assembly (2019, methodology): “In this review, we follow the proposal of Marchesi and Ravel [1] on terminology, and use the term ‘metataxonomics’ for marker gene”