Microbiome analyses of poultry feeds: Part II: Comparison of different poultry feeds.

Authors: OLSON, ELENA - University Of Wisconsin; DITTOE, DANA - University Of Wisconsin; MICCICHE, ANDREW - University Of Arkansas; STOCK, DAVID - Stetson University; RUBINELLI, PETER - University Of Arkansas; Rothrock, Michael; RICKE, STEVEN - University Of Wisconsin

Submitted to: Journal of Environmental Science and Health
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2024
Publication Date: 6/5/2024
Citation: Olson, E.G., Dittoe, D.K., Micciche, A.C., Stock, D.A., Rubinelli, P.M., Rothrock Jr, M.J., Ricke, S.C. 2024. Microbiome analyses of poultry feeds: Part II: Comparison of different poultry feeds. Journal of Environmental Science and Health. https://doi.org/10.1080/03601234.2024.2361596.
DOI: https://doi.org/10.1080/03601234.2024.2361596

Interpretive Summary: Microbial feed quality is an ongoing concern for poultry feed mill operations. As such, a microbial quality baseline must be established for improving and maintaining commercial feeds. Therefore, in this two-part study ( Part II ), the objective was to elucidate this baseline using 16S rDNA sequencing. Nine commercial poultry feeds formulated as a starter, grower, starter/grower, or supplement diet were selected: Purina ® flock raiser crumbles (PC); Purina ® starter/grower medicated crumbles (PM); Manna Pro ® meatbird starter/grower crumbles with probiotics (MPP); Manna Pro ® scratch mixed grains (MPG); Manna Pro ® organic grower crumbles (MPO); Hiland Natural ® starter crumbles (HN); Durvet Strike III ® poultry pellets (DS); leastcost formulated crumbled starter diet (LCC); least-cost formulated pelleted grower diet (LCP). Genomic DNA was extracted using methodologies described in Part I , amplified using custom dual-indexed primers, and sequenced (Illumina MiSeq). Sequencing data were analyzed in QIIME2-2021.4 and R Studio with alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, compositional taxonomic differences (ANCOM), and core microbiomes ( core_members ) being determined. Main and pairwise effects were considered significant at P £ 0.05 and Q £ 0.05. MPP and PM feeds and starter/grower diet type had the lowest evenness and diversity compared to other feeds and diet types (P < 0.05; Q < 0.05). As well, MPP and starter/grower diet consisted of significantly different microbiome compositions and feed supplemented with probiotics or medicated feed produced different, yet phylogenetically similar, microbial abundances across treatments (P < 0.05; Q < 0.05). Using ANCOM, 46 different phyla were different between the nine feed types with Proteobacteria, Firmicutes, Bacteroidota, Campylobacterota, Actinobacteriota, and Cyanobacteria being the most abundant. Among the four diet types, the phyla Alpha-proteobacteria and Chloroflexi were different as well as the core microbiomes were not the same between diet types. The results of the study indicate that there is a diverse microbial population among commercial feeds, and the relationship of poultry feeds to the early poultry gastrointestinal tract (GIT) should be explored.

Technical Abstract: Microbial feed quality is an ongoing concern for poultry feed mill operations. As such, a microbial quality baseline must be established for improving and maintaining commercial feeds. Therefore, in this two-part study ( Part II ), the objective was to elucidate this baseline using 16S rDNA sequencing. Nine commercial poultry feeds formulated as a starter, grower, starter/grower, or supplement diet were selected: Purina ® flock raiser crumbles (PC); Purina ® starter/grower medicated crumbles (PM); Manna Pro ® meatbird starter/grower crumbles with probiotics (MPP); Manna Pro ® scratch mixed grains (MPG); Manna Pro ® organic grower crumbles (MPO); Hiland Natural ® starter crumbles (HN); Durvet Strike III ® poultry pellets (DS); leastcost formulated crumbled starter diet (LCC); least-cost formulated pelleted grower diet (LCP). Genomic DNA was extracted using methodologies described in Part I , amplified using custom dual-indexed primers, and sequenced (Illumina MiSeq). Sequencing data were analyzed in QIIME2-2021.4 and R Studio with alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, compositional taxonomic differences (ANCOM), and core microbiomes ( core_members ) being determined. Main and pairwise effects were considered significant at P £ 0.05 and Q £ 0.05. MPP and PM feeds and starter/grower diet type had the lowest evenness and diversity compared to other feeds and diet types (P < 0.05; Q < 0.05). As well, MPP and starter/grower diet consisted of significantly different microbiome compositions and feed supplemented with probiotics or medicated feed produced different, yet phylogenetically similar, microbial abundances across treatments (P < 0.05; Q < 0.05). Using ANCOM, 46 different phyla were different between the nine feed types with Proteobacteria, Firmicutes, Bacteroidota, Campylobacterota, Actinobacteriota, and Cyanobacteria being the most abundant. Among the four diet types, the phyla Alpha-proteobacteria and Chloroflexi were different as well as the core microbiomes were not the same between diet types. The results of the study indicate that there is a diverse microbial population among commercial feeds, and the relationship of poultry feeds to the early poultry gastrointestinal tract (GIT) should be explored.