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. 2020 Jun 3;15(6):e0225921.
doi: 10.1371/journal.pone.0225921. eCollection 2020.

Cecal microbiome composition and metabolic function in probiotic treated broilers

Denise R Rodrigues  1 , Whitney Briggs  1 , Audrey Duff  1 , Kaylin Chasser  1 , Raj Murugesan  2 , Chasity Pender  2 , Shelby Ramirez  2 , Luis Valenzuela  3 , Lisa Bielke  1
Affiliations

Cecal microbiome composition and metabolic function in probiotic treated broilers

Denise R Rodrigues et al. PLoS One. .

Abstract

Probiotics have become increasingly popular in the poultry industry as a promising nutritional intervention to promote the modulation of intestinal microbial communities and their metabolic activities as a means of improving health and performance. This study aimed to determine the influence of different probiotic formulations on the taxonomic and metabolic profiling of cecal microbial communities, as well as to define associations between cecal microbiota and growth parameters in 21 and 42-day-old broilers. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-forming Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Dietary inclusion of SYNBIO, YEAST, SINGLE2, and SINGLE3 into the diets supported a significant stimulation of BW and BWG by 7 days of age. Besides, SYNBIO reduced the overall mortality rate by 42d (p<0.05). No significant variation was observed among different probiotic-based formulations for cecal microbiota composition. However, there was a treatment-specific effect on the metabolic profiles, with a particular beneficial metabolic adaptation by the microbiota when supplemented by SYNBIO and SINGLE2. Furthermore, the population of Lactobacillales was identified to be strongly associated with lower Enterobacteriales colonization, higher BW means, and lower mortality rate of growing broilers. Overall, the results emphasize that probiotic supplementation may enhance the microbial energy metabolism in the ceca of young broilers.

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Conflict of interest statement

The authors have read the journal's policy and have the following conflicts: Authors RM, CP, and SR are employed by BIOMIN America Inc.. Author LV is employed by BIOMIN Holding GmbH. There are no patents, products in development or marketed products to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Cecal bacterial abundance at phylum-level of broilers fed different probiotics by 21 and 42 days of age.
(A) Heatmap plot represents the composition of cecal microbiota from broilers fed basal diet without probiotics (CON), synbiotic (SYNBIO), yeast-based probiotic (YEAST), or single-strain formulations composed of Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2), and B. licheniformis (SINGLE3) by 21 and (B) 42 days of age. Hierarchical clustering in the rows is based on the composition similarity between treatments, while that in the columns is based on the microbial relative abundance's closeness. Statistical differences (p<0.05) between groups were reported for each bacterial population (*).
Fig 2
Fig 2. Microbial composition in the ceca digesta of 21-day-old broilers.
Box plots show the relative abundance of the top four order-level bacterial population found in the ceca in broilers, including (A) Bifidobacteriales, (B) Enterobacteriales, (C) Clostridiales, and (D) Lactobacillales.
Fig 3
Fig 3. Order-level taxonomic distribution among samples from cecal contents of 42-day-old broilers.
Box plots represent the mean relative percentage of each bacterial population within samples from broilers treated with a basal diet without probiotics (CON), synbiotic (SYNBIO), yeast-based probiotic (YEAST), or single-strain formulations composed of Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2), and B. licheniformis (SINGLE3). (A) Bifidobacteriales, (B) Enterobacteriales, (C) Clostridiales, and (D) Lactobacillales.
Fig 4
Fig 4. Predicted metabolic functions in probiotic treated broilers.
(A) Principal component analyses (PCA) plots represent the potential metabolic functions of microbiota from broilers treated with a basal diet without probiotics (CON; blue sphere), synbiotic (SYNBIO; green triangle), yeast-based probiotic (YEAST; turquoise sphere), or single-strain formulations composed of Bacillus amyloliquefaciens (SINGLE1; dark orange down-pointing triangle), B. subtilis (SINGLE2; purple diamond), and B. licheniformis (SINGLE3; orange square). (B) Column bar graph showing the predicted metabolic pathways in SYNBIO in comparison with CON group.
Fig 5
Fig 5. The abundance of metabolic pathways.
(A) Predicted MetaCyc pathways in microbial communities from broilers supplemented with a yeast-based probiotic (YEAST) and (B) Bacillus amyloliquefaciens (SINGLE1) related to a basal diet without probiotics (CON).
Fig 6
Fig 6. Functional annotation based on MetaCyc pathways.
(A) Predicted metabolic pathways in cecal microbiota from broilers supplemented with a Bacillus subtilis (SINGLE2) and (B) B. licheniformis (SINGLE3) compared to a basal diet without probiotics (CON).
Fig 7
Fig 7. Spearman’s rank correlation matrix of the dominant microbial populations and growth performance parameters.
(A) Large circles indicate strong correlations. The colors of the scale bar denote the nature of the correlation with 1 indicating a perfect positive correlation (dark blue) and -1 indicating perfect negative correlation (dark red).
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Publication types

Grants and funding

This work was supported by BIOMIN (http://www.biomin.net). The funder provided support in the form of salaries for authors RM, CP, SR, LV and research materials, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’. There was no additional external funding received for this study.