What have we learned?
The various comments confirm that the term microbiome means different things to different people.
Lita points out that in the early days when HMP was formed, the NIH officially defined the human microbiome as “all of the microorganisms and their genes and genomes which make up the microbial communities that inhabit the human body.” It seems that they did not distinguish between option A and B but fused them together.
Several commenters propose that the term refers to the whole ecosystem, not just the organisms. (Vicky, Pedro, Jacques). Biome alone means ecosystem but Rob points out that it depends on whether you parse microbiome “micro-biome” or “microbi-ome.” The latter may suggest that it’s another “-ome, sensu genome, transcriptome, etc.
Some prefer metagenome for option B (Mike, Pedro). Jonathan points out that it refers to non-microbial cases as well.
Some suggest that there is no need to differentiate between options A and B (Christoph, Sponch) because most microbes have not been cultivated and are known from their genome. Ergo, their genome IS the organism.
In keeping with the confusion, there is disagreement about whether microbiome and microbiota are synonymous.
The numbers indicate that there is no consensus about the usage of the term microbiome. Option A gets more votes, but not by a huge factor. Thus, vox populi did not resolve the question. It remains open.