Ecological Infectomics (Ecoinfectomics): Symbiotic Solutions to Microbial Infections

Ecoinfectomics is the ecological study of infectomes and explores symbiotic solutions to microbial infections. The most fundamental issue in ecological infectomics is how to transform situations of potential conflict (pathogenesis or Pat) into cooperation (symbiosis or Sym) by dissecting the dynamic Sym-Pat duality in microbial infections and developing symbiotic agents (symbiotics) that favor a healthy symbiosis. Symbiotics are defined as products that are beneficial to the symbiotic ecology of the super-organisms consisting of microbes and their human hosts. These include microbial (e.g., probiotic bacteria and phages) and nonmicrobial agents (e.g., prebiotics). Probiotics have been proposed as a promising way to prevent microbial infection in neonates. It has been shown that probiotics could be useful to correct ecological disorders in human intestinal microbiota associated with neonatal sepsis and meningitis, and might play a protective role in excluding pathogens from the intestine and preventing infections. Compared with commonly used antibiotics, a great advantage of phages is their narrow host range. A rational basis has been provided for the discovery and development of phage-based symbiotics that only kill pathogens but do not disturb benign microbes in normal microbiota. The systems biology study of ecoimmunity or ecoimmunome (ecoimmunomics), which is most closely related to ecoinfectomics, may provide alternative ecological strategies toward clinical challenges in infectious diseases. We propose that the balance between exosymbiosis (e.g, microbiota) and endosymbiosis (e.g., mitochondria) is essential for ecoimmunity and that the exo-endo Sym imbalance plays an important role in the pathogenesis of infectious diseases, including HIV/AIDS. Correction of disorders of the ecoimmunity in patients with AIDS may lead to a rational control of HIV infection. Holistic and integrative studies of ecoinfectomes, ecoimmunomes, and microbiome are important for our understanding of microbial pathogenesis and the development of symbiotic solutions to infectious diseases.