Composition of Microbiomes

All animals and plants are holobionts, containing abundant and diverse symbiotic microorganisms. Bacteria are found inside host cells (endosymbionts) and on the surfaces of different tissues (exosymbionts). The number of microbial symbionts is estimated by total (microscopic) and/or viable counts. Viable counts are generally one to three orders of magnitude lower than the total counts because of the viable-but-not culturable state. The most abundant and diverse animal and plant bacterial symbionts are present in the digestive tract, and associated with roots, respectively. Animals contain ca. 109 bacteria per gram-wet weight; in humans, this corresponds to ca. 1014 bacteria, which is similar to the total number of human cells. Primarily culture-independent DNA-based technology, 16S rRNA gene sequencing, or metagenomics determine the diversity of bacteria. Because of the large diversity of bacteria, there are several hundred times more unique genes in the human microbiome than are present in the human genome. In healthy humans, diverse bacteria are associated with most organs, including the mouth, throat, nasal cavity, small intestine, large intestine, lungs, and vagina. Although there have been great advances in culture-independent DNA analyses of microbiomes over the last decade, many problems remain, such as limits of detection, lack of positive and negative controls, and reproducibility.