Table 2 Relative abundance of the 6 dominant phyla observed in the upper and lower respiratory tract of healthy horses (n = 6) at day 0, and relative abundance of genus within each phylum

Proteobacteria (43.85%)

Sphingomonas (35.69%)

Pantoea (26.65%)

Pseudomonas (14.57%)

Massilia (5.59%)

Rhizobium (3.35%)

Mesorhizobium (2.20%)

Naxibacter (1.60%)

Serratia (1.39%)

Devosia (1.32%)

Actinobacteria (21.63%)

Agrococcus (15.67%)

Knoellia (12.98%)

Arthrobacter (12.1%)

Microbacterium (8.56%)

Corynebacterium (7.27%)

Brachybacterium (5.93%)

Ornithinimicrobium (5.06%)

Brevibacterium (4.06%)

Rhodococcus (4.03%)

Kocuria (3.88%)

Dietzia (3.71%)

Rothia (2.5%)

Clavibacter (1.87%)

Rathayibacter (1.65%)

Marmoricola (1.55%)

Streptomyces (1.29%)

Nocardioides (1.24%)

Firmicutes (16.82%)

Jeotgalicoccus (30.8%)

Planomicrobium (19.52%)

Gemella (16.63%)

Atopostipes (5.91%)

Bacillus (4.68%)

Staphylococcus (3.6%)

Sporosarcina (2.55%)

Facklamia (2.23%)

Trichococcus (1.85%)

Streptococcus (1.79%)

Carnobacterium (1.72%)

Aerococcus (1.23%)

Bacteroidetes (13.24%)

Hymenobacter (42.65%)

Pedobacter (17.93%)

Prevotella (17.42%)

Flavisolibacter (12.19%)

Gillisia (3.1%)

Chryseobacterium (2.69%)

Cloacibacterium (1.66%)

Ferruginibacter (1.51%)

Verrucomicrobia (0.79%)

Luteolibacter (20.93%)

Akkermansia (8.79%)

Chloroflexi (0.51%)

Sphaerobacter (97.84%)

Litorilinea (2.16%)