Fig 1.
Relative abundance and clustering of 30 samples colored by farm origin.
Samples were clustered using UPGMA with Camberra distance. Colored bars represent the relative abundance of bacterial family.
Fig 2.
Genus-level 16S rRNA gene-repertoire analysis of caeca from high and low performer farms.
The bacterial genera composition of each sample was obtained from the taxonomic annotation method RDP.
Fig 3.
Sample richness (observed OTUs).
One-hundred subsamplings of 33,654 sequences per sample were used to estimate the richness variability.
Table 1.
Caecal bacterial diversity and richness of 7-days old chicks.
Fig 4.
PCoA for ordination and Bray curtis distance.
Table 2.
Isolates obtained from each high performer farm using different culture conditions.
Fig 5.
Phylogenetic tree representing commensal species isolated from high performer chicks.
The phylogenetic tree was inferred from Muscle alignment of partial 16S rRNA-encoding gene sequences using the Maximum Likelyhood method based on the Kimura 2-parameters model with 1,000 bootstrap replicates. Identifications were classified according to the identity percentage as: 1) ‘++’ for ≥ 99–100% identity, 2) ‘+’ for 97–98% identity, 3) ‘-’ for 95–96% identity, 4) ‘—’ for 93–94% identity and 5) ‘distant’ for < 93% identity. Stars indicate families for which only one unique partial 16S rRNA gene sequence was recovered. Arrows indicate isolates likely to correspond to new species (grey arrows) or new genera (black arrows) based on limited 16S rRNA gene identity with the closest described species.
Fig 6.
Mean abundancies of families detected in cecal contents of high-performance chicks using 16S repertoire analysis.
Data are represented as Log (relative abundance +1) for better visualization, with corresponding abundancies being indicated on top of each bar. Families for which bacterial isolates affiliated to the family were recovered in culture are indicated in grey, those for which no bacterial isolates affiliated to the family were recovered in culture are indicated in black.
Table 3.
Antibiosis activities against C. jejuni ATCC 700819 and Farm #3 isolate detected in commensal strains.
Inhibition diameters were measured and scored with the following parameters: (+) for inhibition diameters ≥ 2 mm, (+/-) for 0.1 to 1.9 mm, (-) when no inhibition was observed. nd: no done due to the absence of growth in tested conditions.
Table 4.
Characteristics of the poultry farming.
Table 5.
Antibiotics and concentrations used to selectively grow a variety of gut commensal species.