| Literature DB >> 35909674 |
Lorena Varriale1, Lorena Coretti2,3, Ludovico Dipineto1,3, Brian D Green4, Antonino Pace1, Francesca Lembo2,3, Lucia Francesca Menna1, Alessandro Fioretti1, Luca Borrelli1,3.
Abstract
Characterizing the gut microbiota of free-range and alternative poultry production systems provides information, which can be used to improve poultry welfare, performance, and environmental sustainability. Gut microbiota influence not only the health and metabolism of the host but also the presence of zoonotic agents contaminating food of animal origin. In this study, the composition and diversity of the cecal microbiota community of free-range grown chickens were characterized by 16S rDNA high-throughput Illumina sequencing. Significant differences were observed in the composition of chicken cecal microbiota at the time points of 28 days of age (Indoor group) and 56 days of age (Outdoor group), i.e., before and after the outdoor access period of chicken groups. The Outdoor group showed a richer and more complex microbial community, characterized by the onset of new phyla such as Deferribacterota and Synergistota, while the Indoor group showed an increase in Campylobacterota. At the species level, it is noteworthy that the occurrence of Mucispirillum schaedleri in Outdoor group is known to potentially stimulate mucus layer formation in the distal intestinal tract, thus being associated with a healthy gut. We also report a significant decrease in the Outdoor group of Helicobacter pullorum, highlighting that the lower abundance at the age of slaughter reduced the possibility to contaminate chickens' carcasses and, consequently, its zoonotic potential. As revealed by a mutual exclusion study in network analysis, H. pullorum was present only if Bacteroides barnesiae, an uncultured organism of the genus Synergistes, and Bacteroides gallinaceum were absent. Finally, microbiome predictive analysis revealed an increase of vitamins and micronutrient biosyntheses such as queuosine (Q) and its precursor pre Q0, in the Outdoor group, suggesting that the outdoor evolved microbiota of chickens do contribute to the vitamin pool of the gut and the biosynthesis of micronutrients involved in vital cell processes.Entities:
Keywords: caecal microbiota; environmental sustainability; free-range chickens; gut microbiome prediction; mutual exclusion; zoonotic potential
Year: 2022 PMID: 35909674 PMCID: PMC9330014 DOI: 10.3389/fvets.2022.904522
Source DB: PubMed Journal: Front Vet Sci ISSN: 2297-1769
Figure 1Global changes in structure and composition of cecal bacterial communities from indoor to outdoor rearing system. (A) Bar-dot plot showing Shannon Index as a measure of intra-group bacterial diversity (mean ± SEM; *p < 0.05). (B,C) Principal coordinate analysis (PCoA) plots based on unweighted and weighted UniFrac distances (5,766 sequences/sample), with the amount of variance along each axis in brackets. On the top of each PCoA plot are reported p-values of the PERMANOVA and PERMDISP tests used to estimate the significant differences in microbial community composition between the groups.
Figure 2Phylum-level cecal microbiota assortment. (A) Bar chart showing the relative abundance of all bacterial ASVs taxonomically classified at phylum level in each sample. (B) ANCOM differential abundance volcano plot at the phylum level. Only significant bacterial phyla showing high w-stats are labeled and colored in blue or red for Indoor and Outdoor groups, respectively. (C) Bar-dot plot comparing the relative abundance of the phyla whose abundance was found to differ significantly between groups (mean ± SEM).
Figure 3Species-level cecal microbiota assortment. (A) The ANCOM differential abundance volcano plot at the species level. Only significant bacterial species showing high w-stats are labeled and colored in blue or red for Indoor and Outdoor groups, respectively. (B) Bacterial species discriminating the cecal microbiota of Indoor and Outdoor chickens based on linear discriminant analysis (LDA) combined with effect size (LEfSe) algorithm (p > 0.05 for both Kruskal–Wallis and pairwise Wilcoxon tests and a cutoff value of LDA score above 2.0; only species with relative abundances >1% in at least one group are listed). Heatmap, mean ± SEM, LDA scores, and p-values are represented for each indoor-enriched and outdoor-enriched bacterial species, as identified by LEfSe.
Figure 4Changes in predicted metagenomics from indoor to outdoor rearing system. The Sankey plot displaying the number of predicted MetaCyc pathways collapsed at the MetaCyc class level that is significantly enriched in each group as assessed by linear discriminant analysis (LDA) combined with effect size (LEfSe) algorithm (p > 0.05 for both Kruskal–Wallis and pairwise Wilcoxon tests and a cutoff value of LDA score above 2.0). Refer to Supplementary Dataset 1 for the list of all significantly predicted functions at the MetaCyc pathway level.