The Airway Pathobiome in Complex Respiratory Diseases: A Perspective in Domestic Animals

Abstract

Respiratory infections in domestic animals are a major issue for veterinary and livestock industry. Pathogens in the respiratory tract share their habitat with a myriad of commensal microorganisms. Increasing evidence points towards a respiratory pathobiome concept, integrating the dysbiotic bacterial communities, the host and the environment in a new understanding of respiratory disease etiology. During the infection, the airway microbiota likely regulates and is regulated by pathogens through diverse mechanisms, thereby acting either as a gatekeeper that provides resistance to pathogen colonization or enhancing their prevalence and bacterial co-infectivity, which often results in disease exacerbation. Insight into the complex interplay taking place in the respiratory tract between the pathogens, microbiota, the host and its environment during infection in domestic animals is a research field in its infancy in which most studies are focused on infections from enteric pathogens and gut microbiota. However, its understanding may improve pathogen control and reduce the severity of microbial-related diseases, including those with zoonotic potential.

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing

“…The common sites for animal-associated metagenomic studies are gastrointestinal tracts, reproductive tracts, respiratory tracts, skin, oral and amniotic fluids. The application of metagenomic studies in animals has focused on the contributions of the metagenomes to host health ( Oba et al, 2021 ), susceptibility to diseases ( Rodrigues Hoffmann, 2017 ; Borsanelli et al, 2018 ; Mach et al, 2021 ), physiological purposes ( Ault et al, 2019 ; Quereda et al, 2020 ), and anatomical differences ( Glendinning et al, 2017 ).…”

Assessment of the Safety and Efficacy of an Oral Probiotic-Based Vaccine Against Aspergillus Infection in Captive-Bred Humboldt Penguins (Spheniscus humboldti)

“…Decreased levels of anti-a-Gal IgA were accompanied by a reduction in the occurrence of lung granulomas, which is associated with acute aspergillosis in turkeys. These results suggest a crosstalk mechanism in birds by which the gut microbiota modulates the immune response in the lungs (73). In the infection model reported by Mateos-Hernańdez et al, 2020 (30), (i.e., the intratracheal infectious challenge with A. fumigatus), the mechanism of protection against avian aspergillosis does not seem mediated by increased anti-Gala1-3Gal IgY in sera.…”

Litter Management Strategies and Their Impact on the Environmental and Respiratory Microbiome Might Influence Health in Poultry

“…Next, we saw that despite the high E. coli load at week 3, the tracheal microbiota in BH-I evolves at the end of the fattening cycle to a profile clearly defined by Gallibacterium sp., as in BH-II at week 6. Therefore, we can interpret that this high dominance of E. coli at week 3 is transient, and mucociliary and immune clearance of the tracheal epithelium [ 6 ] restore the previous condition before litter aeration by tumbling. It is noteworthy that although a time-changing microbial structure was found in BHs, no change was observed in AF over time ( Figure 5 F).…”

“…It has come to be recognized that bacterial communities are important for maintaining respiratory health [ 5 ]. This respiratory microbiota can be conditioned by various factors that influence its composition, such as intrinsic factors of the host and extrinsic environmental factors [ 6 ] that can impact the microbiome and the subsequent progression of the disease.…”