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The fecal and liver abscess microbiota of feedlot steers managed in natural and conventional programs




Fuerniss, Luke Konrad, author
Martin, Jennifer N., advisor
Engle, Terry E., committee member
Metcalf, Jessica L., committee member
Scanga, John A., committee member
Garry, Franklyn B., committee member

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The fecal and liver abscess microbiota of steers managed in a single commercial feedlot in natural and conventional programs were evaluated. Steers managed in the conventional program (n = 7 pens) were administered hormonal implants, tylosin, monensin, and ractopamine; steers managed in the natural program (n = 7 pens) were raised without growth-promoting technologies or antimicrobials. The objective of the first study was to characterize the longitudinal changes in the fecal microbiota and to evaluate differences between management programs after placement (T1), after transition to the finishing diet (T2), immediately before the beta-adrenergic agoinst feeding period (T3), and immediately before shipment for harvest (T4). The phyla Firmicutes and Bacteroidetes composed greater than 85% of the fecal microbiota over the entire feeding period. Across both programs, 23 families were differentially abundant from T1 to T2; 13 families were differentially abundant from T2 to T3; one family was differentially abundant from T3 to T4. From T1 to T2, an increase in the relative abundance of Prevotellaceae (W = 117) and a decrease in the relative abundance of Bifidobacteriaceae (W = 126) were observed. At T1, the fecal microbiota of naturally managed steers had greater alpha diversity (measured as Shannon Diversity Index) than that of conventionally managed steers (P = <0.001), but no difference was detected between programs for Shannon Diversity Index (P = 0.774) at T4. Across both management programs, greater Shannon Diversity (based on pen-level composited samples) at T4 was associated with reduced liver abscess prevalence (rs = -0.438). The objective of the second study was to characterize the microbiota of liver abscess purulent material and to evaluate differences between microbial communities from steers in natural and conventional management programs. The dominant phyla included Fusobacteria (64.42% of reads) and Bacteroidetes (34.87% of reads). The genera identified in greater than 1% relative abundance of all reads included Fusobacterium (64.18% of reads; 100% of samples), Bacteroides (33.59% of reads; 93.33% of samples), and Porphyromonas (1.25% of reads; 7.62% of samples). Rare genera (identified in less than 1% abundance of all reads) included bacteria of the Ruminococcaceae, Provotellaceae, Clostridiaceae 1, Spirochaetaceae, Erysipelotrichaceae, and Peptostreptococcaceae families. The rare taxa discovered had been previously identified in rumen contents and on the rumen epithelium. The rare families present in liver abscess purulent material were also identified in the fecal samples from the same population of steers. While a greater taxonomic resolution is needed to identify potential homology between families present within both feces and liver abscess purulent material, the results suggest that escape of bacteria from the hind gut could be a factor in the formation of polymicrobial liver abscesses.


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