Hi,

The easiest of these to define is 'microbes'. These are any organisms which are microscopic; they can be both multi and unicellular. 

The difference between microbiome and microbiota can be a little confusing (see link). Some researchers use the term 'microbiota' to mean the microbes found within a specific environment and the term 'microbiome' to mean the collection of microbial genomes in an environment. I quite like this as it can indicate whether a paper has fully sequenced the genomes of the microbes it is examining or whether it has just identified them by 16S rRNA or culturing. 

However, over time many researchers have started to use these words interchangeably so it is not uncommon to see the word microbiome used in a paper where the author has identified the bacteria present in an environment but hasn't sequenced their genomes. 

'Microbes' is a colloquial term for microorganisms, but usually referring to bacteria only, 'microbiota' is a collective term for microorganisms, generally assumed to include all taxa (bacteria, yeasts, filamentous fungi, archaea and maybe even viruses);  'microbiome' refers to the microbial community  (composition unspecified) associated with a particular 'habitat' (e.g., a plant leaf microbiome would be the microorganisms on the surface (and inside) plant leaves of a particular plant species;  insect gut microbiome, human skin microbiome, etc.).

Hi,

The easiest of these to define is 'microbes'. These are any organisms which are microscopic; they can be both multi and unicellular. 

The difference between microbiome and microbiota can be a little confusing (see link). Some researchers use the term 'microbiota' to mean the microbes found within a specific environment and the term 'microbiome' to mean the collection of microbial genomes in an environment. I quite like this as it can indicate whether a paper has fully sequenced the genomes of the microbes it is examining or whether it has just identified them by 16S rRNA or culturing. 

However, over time many researchers have started to use these words interchangeably so it is not uncommon to see the word microbiome used in a paper where the author has identified the bacteria present in an environment but hasn't sequenced their genomes. 

Appreciate the responses. These two answers give different definitions. I think Donald's explain is more reasonable. 

I have found this definition from Whiteside et al. (2015) to be most useful:  Different approaches to define the population provide different information. a | Microbiota: 16S rRNA surveys are used to taxonomically identify the microorganisms in the environment. b | Metagenome: the genes and genomes of the microbiota, including plasmids, highlighting the genetic potential of the population. c | Microbiome: the genes and genomes of the microbiota, as well as the products of the microbiota and the host environment. 

An illustrative figure of this is available at: http://www.nature.com/nrurol/journal/v12/n2/fig_tab/nrurol.2014.361_F1.html

See following ref: Inoue Y, Shimojo N. Microbiome/microbiota and allergies. Semin Immunopathol. 2015 Jan;37(1):57-64. doi: 10.1007/s00281-014-0453-5.

see this paper: Article The Plant Microbiome at Work