The Problem with ‘Microbiome’

Abstract

The term “microbiome” is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, “microbiome” is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communities. Widespread convenient and affordable 16S rRNA sequencing pipelines have accelerated continued use of such a “microbiome”, but at what intellectual and practical costs? Here we show that the use of “microbiome” in ribosomal gene-based studies has been egregiously misapplied, and discuss potential impacts. We argue that the current focus of “microbiome” research, predominantly on only ‘bacteria’, presents a dangerous narrowing of scope which encourages dismissal and even ignorance of other organisms’ contributions to microbial diversity, sensu stricto, and as etiologic agents; we put this in context by discussing cases in both marine microbial diversity and the role of pathogens in global amphibian decline. Fortunately, the solution is simple. We must use descriptive nouns that strictly reflect the outcomes attainable by the methods used. “Microbiome”, as a descriptive noun, should only be used when diversity in the three recognized domains is explored.

The Interaction between the Gut Microbiome and Bile Acids in Cardiometabolic Diseases

“…However, in the context of the GM, it becomes clear that a complex relationship between the microorganisms exists, which can help produce beneficial and harmful metabolites [3]. Therefore, much more research is needed to better understand these kingdoms in the context of the holobiont and the eventual implications and possible strategies to improve human (metabolic) health [110]. It is beyond the scope of this review to address other gut microbiome members.…”

Signatures of functional bacteriome structure in a tropical direct-developing amphibian species

“…The amphibian skin tissue that Bd infects is highly biologically active. In addition to the skin’s role in breathing and homeostasis, it also produces mucus secretions and chemical compounds that create distinct microhabitats for diverse host-associated bacterial communities (bacteriome) [ 14 ] known to influence host-Bd interactions [ 15 – 19 ]. Extreme variation in Bd pathogenicity has been reported across hundreds of tested host species, with many examples of host bacteriome composition correlating with Bd pathogenicity [ 20 , 21 ].…”