Respiratory microbiota as a good predictor of outcome in humoral immunodeficiency. Methodological and conceptual difficulties in comprehensive microbiome analysis.

ABSTRACT

The microbiome as a broad term defines the most dynamic ecological system in which, apart from the biocenosis, there is unique niche for its development, equally dynamic, because host-derived, contrary to physical environment in ecology. Although for years, antibodies, was recognized as a key element of the mucosal barrier, there is still no progress in comprehensive linking microbes and humoral elements. Which organism is a pathogen and which is a commensal - there are still no exact answers (and criteria). Also the discrepancy between experimental research, using more and more sophisticated techniques -showing the existence of nearly 900 bacterial species in our mouth was observed. On the contrary, bacterial infections caused by novel species have not been recognised in patients with humoral immunodeficiencies, apart from the capsular cocci and H. influenzae. Research on human virome, including CMV, is also focused on the cellular immunity, but in many situations in the clinic the humoral compartment are the exclusive, still effective, barrier against viral replication. AIM: The aim of study was to perform an integrated microbiome analysis (microbiota and host) for strict linking various microbiota constelation and end-stage clinical manifestation in humoral immunodeficiency. MATERIALS AND METHODS: This cross-study based on own clinical experience reveal crucial gap in the literature. RESULTS: It indicate the natural competition why the sentinel microorganism in humoral deficiency - S. pneumoniae dominates in some patients, and in others - Viridans Group Streptococci. Crucial role of high specific IgM level in several CVID complication was described. Furthermore, respiratory microbiota translocation with cancer regression and influence of therapeutic regimen on clinical sequel (predominantly infectious or malignant) were presented. The studies indicates numerous methodological and microecological classification difficulties, which are the source of inadequate, often contradictory conclusions from experimental research. CONCLUSIONS: Microecology describe ecosystem that consists of all the organisms and the abiotic physical environment with which they interact i.e. biocenosis and biotope but clinical immunology -microorganisms in biotic (cellular) niche in host. Unfortunately, these studies are focused on the anecdotal "healthy" biocenosis (healthy microbiome), without analyzing other elements of the niche, for example cancer. Overall, focusing on the gut microbiota clearly restrict our knowledge on the manifestation of humoral deficiencies in respiratory system. The work is a summary of the search for representative clinical models and microbiological methods (diagnostic chain) in clinical immunology practice.