Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

Animal Science

First Advisor

Crystal Levesque

Second Advisor

Benoit St-Pierre


Weaning is a critical time in a young pig’s life that will greatly impact its adult growth and development. The objective of this research was to evaluate the effects of various protein sources on the bacterial composition within luminal and mucosal populations in simple and complex diets to gain a better understanding of factors influencing gut health. Weaned pigs were fed 1 of 3 simple experimental diets: 1) basic diet containing corn and soybean meal (Negative Control - NEG), 2) basic diet + fishmeal (FM; Positive Control - POS), and 3) basic diet + microbially-enhanced soybean meal (MSBM). Phase I POS and MSBM diets (d0 – d7 post-wean) included FM or MSBM at 7.5%, while Phase II POS and MSBM diets (d8 – d21) included FM or MSBM at 5.0%, respectively. Host tissue and ileal digesta were collected from euthanized pigs at d21 (8 pigs/diet) to assess gut histology and intestinal bacterial profiles, respectively. Lactobacillus-affiliated sequences were found to be the most highly represented across treatments. Accordingly, the 3 most abundant Operational Taxonomic Units (OTUs) were affiliated with Lactobacillus, with each showing a distinct abundance pattern with regards to dietary treatment. L. amylovorus, was found to be more abundant in NEG and POS samples, compared to MSBM samples, L. johnsonii, was more highly represented in POS and MSBM samples compared to NEG, L. delbrueckii, was found in highest abundance in ileal samples from MSBM-fed pigs. In trial 2, pens of weaned pigs (21d of age, 6.56 ± 0.87 kg; n=5 pens/diet; 7 pigs/pen) in 2 equal blocks of pigs were fed one of 4 complex experimental diets: 1) positive control, containing corn, soybean meal, spray dried plasma (SDP), and FM identified as CON, 2) SDP and MSBM (MSBM+SDP), 3) FM and MSBM (MSBM+FM), and 4) MSBM in both Phase I (d1-7 post-wean; 0, 12.75, 20.40, 34% MSBM inclusion, respectively) and II (d8-21; 0, 5, 8, 15% MSBM inclusion, respectively). Ileal digesta was collected from 5 pigs/diet at d21 (1 pig/pen). Ileal mucosa tissue was collected from 10 pigs/diet at d21 (1pig/pen). Lactobacillaceae appeared to be the dominant family in both luminal and mucosal block 1 populations, whereas Clostridiaceae was most prevalent in block 2 mucosal samples. A dominant Lactobacillus presence was demonstrated in 8 and 2 mucosal samples within block 1 and block 2, respectively. The dominant presence of Clostridia was comprised of only 2 OTU within the mucosal population; these were closely related to C. ventriculi and C. saudiense. Luminal populations were primarily comprised of 2 dominant OTU, which were closely related to L. amylovorus and L. delbrueckii. The mucosal population contained twice the level of species biodiversity and was dominated by only one OTU, which was closely related to L. amylovorus. Luminal populations remained more homogenous in their population with higher proportions of select species, primarily Lactobacillus. Neither trial demonstrated an effect of treatment (P > 0.05) on relative abundance of phyla, family, or genera within luminal or mucosal samples, with the exception of one OTU identified as L. reuter in MSBM+FM (0.05±0.03%). Bacterial profiles, in both simple and complex luminal populations, demonstrated a dominance of select Lactobacillus OTU in both trials. Furthermore, Lactobacillus remained a prominent presence in mucosal samples, but to a lesser degree as Clostridia increased its population in block 2 samples. The identification of bacterial populations may provide evidence that unique location-based profiles exist and that certain non-dietary factors have the potential to alter mucosal populations, while having minimal influence on luminal populations.

Library of Congress Subject Headings

Swine -- Feeding and feeds.
Piglets -- Feeding and feeds.
Proteins in animal nutrition.
Gastrointestinal system -- Microbiology.



Number of Pages



South Dakota State University



Rights Statement

In Copyright