Comparative Analysis of Bacterial Composition in the Ileum of Early Post-Weaned Piglets Fed Microbially Enhanced Soybean Meal and Fishmeal

The objective of this research was to assess bacterial populations associated with the use of microbially enhanced soybean meal (ME-PRO) and fishmeal (FM). Weaned pigs were fed one of 3 experimental diets: 1) Control (CON) containing corn and soybean meal, 2) CON + fishmeal (FM), 3) CON + ME-PRO (ME-PRO) in Phase I (d0 – 7 post-wean; FM or MEPRO at 7.5%) and Phase II (d8 – 21; FM or MEPRO at 5.0%). Ileal digesta was collected from 6 pigs/diet at d21. Digesta microbial gDNA was used for PCR amplification of the 16SrRNA gene (V1-V3 region) and amplicons sequenced via the Illumina Miseq 2x300 platform. The data produced 440,999 high quality sequences that ranged from 1,938 to 66,953 sequences/animal. Data were analyzed using Proc Mixed in SAS with pig as the experimental unit and pig(treatment) as the random effect. There was no effect of treatment (P > 0.05) on relative abundance of genera. Lactobacillus appeared to be the dominant genus. Pigs were assigned to a high (≥ 38% relative abundance) or low (≤ 10% relative abundance). In pigs fed CON and FM, 75 and 71% of the samples were assigned to the high category, respectively, compared to 50% in pigs fed ME-PRO (Chi-squared, P = 0.596). Nine OTU (Operational Taxonomic Unit) comprised the Lactobacillus genus and 3 OTU appeared to be dominant. They are closely related to L. amylovorus, L. amylovorus, and L. crispatus and represented 35.8, 0.96, and 2.1% relative abundance in pigs fed CON; 23.6, 15.8, and 2.1% relative abundance in pigs fed FM; and 9.39, 14.6, and 11.5% relative abundance in pigs fed MEPRO, respectively. Even at relatively minor dietary inclusion, alterations in protein source can lead to microbial composition shifts in the ileum of weaned pigs.

Table 1. Relative abundance of genera (% of total reads) representing >1% of total reads in the ileal digesta of pigs fed MEPRO or fishmeal
Genus	CON	FM	ME-PRO	SEM	P-value
Actinobacillus	4.61	2.39	2.39	2.22	0.687
Campylobacter	10.05	1.76	0.33	4.37	0.234
Escherichia/Shigella	0.24	2.32	9.14	4.97	0.421
Lactobacillus	49.71	49.20	36.74	14.06	0.752
Prevotella	8.92	8.16	8.43	6.42	0.996
Unclassified Pasterurellaceae	2.27	3.70	1.36	2.73	0.806