A microbiome is the totality of microbes, their genetic elements (genomes), and environmental interactions in a particular environment. The term "microbiome" was coined by Joshua Lederberg, who argued that microorganisms inhabiting the human body should be included as part of the human genome, because of their influence on human physiology. The human body contains over 10 times more microbial cells than human cells.
Microbiomes are being characterized in many other environments as well, including soil, seawater and freshwater systems.
All plants and animals, from protists to humans, live in close association with microbial organisms. Up until relatively recently, however, the interactions of plants and animals with the microbial world have been defined mostly in the context of disease states and a relatively small number of symbiotic case studies. Organisms do not live in isolation, but have evolved in the context of complex communities. A number of advances have driven a change in this perception, which include, notably, the current ease of performing genomic and gene expression analyses of single cells and even entire microbial communities in the new disciplines of metagenomics and metatranscriptonomics, along with massive databases enabling this information to be accessible to researchers across multiple disciplines, and methods of mathematical analysis that enable sense to be made of complex data sets. It has become increasingly appreciated that microbes play an important part of an organism's phenotype far beyond the occasional symbiotic case study.
New fluorescent labeling technology that distinguishes in a single image the population size and spatial distribution of 15 different taxa has uncovered new taxon pairings that indicate unsuspected cooperation -- and standoffishness -- between members of the microbe biofilm that covers teeth, according to a presentation at the American Society for Cell Biology's Annual Meeting in Denver.
Members of the genera Prevotella and Actinomyces showed the greatest ability to interact, suggesting a central role for them in producing biofilms, reported the researchers. The study, to determine "who's who" in the human mouth was conducted by researchers at the Marine Biological Laboratory (MBL) in Woods Hole, MA,
While both genera are implicated in periodontal disease, species of Prevotella have been recovered from anaerobic lung infections. Actinomycosis is an infection of antibiotic resistant strains in the mouth and gastrointestinal tract.
Alex Valm, Ph.D., Gary Borisy, Ph.D., and collaborators refer to their new fluorescent labeling technology system as Combinatorial Labeling and Spectral Imaging (CLASI). It was designed to overcome a major limit of existing fluorescent labeling system, whose original green fluorescent protein (GFP) tag occurred in one color (green).
A whole palette of colors is now available to scientists through an ever-expanding array of fluorescent proteins or the addition of glowing molecular add-ons called fluorophores, but keeping track of more than a handful of colors becomes exponentially difficult.