Fig. 1
Adapted from Glendinning et al. (2017) and Mulholland et al. (2021)
Dynamics of microbiota colonization and succession in the avian trachea and lungs. At hatch, the avian trachea (representative of the upper respiratory tract-URT) was colonized predominantly by Pseudomonas (13%), Brevibacterium (9%), Brachybacterium (8%), Streptococcus (8%), Chryseobacterium (7%), Bacillaceae (6.5%), and Corynebacteriaceae (6%). By week 3, the tracheal microbiota shifted, with reductions in Brevibacterium (6%), Bacillaceae (4.2%), and Brachybacterium (5%). Genus Lactobacillus emerged dominantly, constituting 34.1% of the trachea. In contrast, the lung microbiota (representative of the lower respiratory tract-LRT) displayed distinct colonization. Initially, Staphylococcus (25%), Pseudomonas (16%), Achromobacter (15%), and Lactobacillus (12%) were predominant at hatch. By week 3, the composition shifted to Pseudomonas (35%), Lactobacillus (28%), and Staphylococcus (18%) as the dominant genera in the avian lungs.