A longitudinal investigation of the effects of age, dietary fiber type and level, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance of finisher pigs

Abstract

Age and diet are among the factors that influence the community composition of the fecal microbiome. Additionally, antimicrobial use can alter the composition of bacterial communities. An 86-d study with finisher pigs aimed to evaluate age-related dynamics (d 98-177 of age), effects of types and levels of dietary fiber, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance (AMR) was conducted. A total of 287 pigs, housed in 36 pens, with 7 to 8 pigs per pen, fed a corn grain and soybean meal-based basal diet, formulated to contain 8.7% neutral detergent fiber (NDF), were randomly assigned to one of three treatments: 1. basal diet with no supplement, 2. basal diet supplemented with 20% distillers dried grains with solubles (DDGS) formulated to contain 13.6% NDF, or 3. basal diet supplemented with 14.5% sugar beet pulp (SBP) formulated to contain 13.6% NDF. Five finisher pigs from each treatment group were selected randomly, and fecal samples were collected on d 98, 110, 144, and 177 of age. In addition, fecal samples were collected from pigs that were injected intramuscularly ceftiofur hydrochloride or penicillin G on d 1 and 3 along with pen-mate untreated controls on d 1. Fecal samples were subjected to 16S rRNA amplicon-based microbiome analysis and culture methods to quantify the abundance of total and AMR coliforms and enterococci populations. The alpha diversity, such as species richness, increased with age, and the overall bacterial composition changed with age (P =0.001) and diet (P = 0.001). Diet-associated shifts in the specific bacterial taxa were observed. The richness, diversity, and evenness of bacterial taxa did not differ between pigs that were injected with ceftiofur versus their untreated pen mates or by dietary treatments, but differed in pigs that received penicillin G injection. Both antimicrobial treatments contributed to changes in the overall fecal bacterial composition at the genus level. Collectively, the data demonstrate that both age and the diet (control vs. DDGS-, control vs. SBP- or DDGS- vs. SBP-based diets) were associated with overall bacterial community composition and the impact of age on variations in fecal microbiome composition was greater than the diet. Antibiotic treatment had minimal effect on bacterial diversity and relative abundance of taxa. Further, diets and antimicrobial treatment had minimal impact on the overall counts of AMR coliforms and enterococci populations in feces.

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency

“…However, the association between the Shannon diversity index and age has not been fully clarified. Gaire et al (2022) , postulated that the microbial community in growing pigs becomes more diverse and presumably more stable, with increasing age. Increased diversity is associated with improved robustness of the gut microbiota ( Larsen and Claassen, 2018 ).…”

“…The effect of Streptococcus on the host intestine is less studied than Lactobacillus ( Lan et al, 2023 ). Clostridium sensu stricto , the genus with the second-highest taxon weight in the cluster analysis, is one of the main genus detected in the feces of pigs after weaning ( Chen et al, 2017 ) and its relative abundance increases with age ( Gaire et al, 2022 ). Currently, no study has shown proteolytic capabilities in this genus.…”

Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets

“…Notably, during the early stages of piglet life, the influence of nursing mothers and breed was apparent, but it was the introduction of solid feed and subsequent weaning that predominantly drove the succession of the gut microbiome [ 45 ]. Moreover, diet, age, body weight, and antimicrobial exposure have been established as significant factors shaping the gut microbiome of productions pigs [ 30 , 46 , 47 ]. Additionally, a different investigation emphasized the substantial impact of weaning on the piglet gut microbiome, revealing significant alterations in both bacterial and fungal communities post-weaning [ 48 ].…”

Effect of Sugar Beet Pulp on the Composition and Predicted Function of Equine Fecal Microbiota

“…Sugar beet pulp is a rich source of several oligo- and monosaccharides, including mannose, rhamnose, glucuronic and galacturonic acids; glucose; galactose; arabinose; and fucose [ 50 ]. Previous work on pigs demonstrated the minimal effects of SBP supplementation on the commensal gut microbiome [ 51 ], or the selective enrichment of Eubacterium ruminantium in feces following 12 weeks of supplementation [ 52 ]. The effect of SBP on the rumen microbiome of beef calves was negligible [ 53 ]; however, the fecal microbiome of dairy cows revealed the selective enrichment of Fibrobacter sp.…”