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Addition of pre- and probiotics may confer growth and health benefits when added to the diet of pigs. To determine the effects of feeding mannan oligosaccharide (MOS) and Lactobacillus mucosae (LM) as prebiotic and probiotic sources in weanling pigs under immune challenge, 96 weaned pigs were randomly allotted to 16 experimental pens within a 2 × 2 factorial arrangement of treatments. Control diets with or without 0.1% yeast-derived MOS were randomly assigned to pens and 109 cfu/pig LM broth or a control broth were top-dressed daily. Pigs were fed one of four dietary treatments (control, MOS, LM, and MOS+LM) in Phases I and II (days 0 to 7 and days 7 to 21 postweaning, respectively) and a common diet during Phase III (days 21 to 35 postweaning). On day 14, all pigs were challenged with 100 µg/kg body weight (BW) Escherichia coli lipopolysaccharide (LPS) via intraperitonial injection. Feed disappearance and pig BW were measured weekly. Blood and fecal samples were collected weekly, and additional blood samples were collected on days 1 and 3 post-LPS challenge. On days 15 and 21, one pig per pen was euthanized for collection of ileal mucosa and duodenal and ileal tissue samples. From days 0 to 14, feeding LM decreased gain-to-feed ratio (G:F; P < 0.05). An interaction between LM and MOS was observed for G:F on days 14 to 21 (P < 0.05); G:F in LM (715 g/kg) was greater compared with MOS+LM (P < 0.05; 600 g/kg) and control (P < 0.10; 615 g/kg), but was not different (P > 0.10) from MOS (674 g/kg). After pigs were fed a common diet (days 21 to 35), G:F was decreased (P < 0.05) in the LM treatment groups. Pigs fed diets that included MOS had increased serum immunoglobulin (Ig) G on days 1 and 3 post-LPS challenge and 2 wk after removal of treatments (P < 0.05) and on days 14 and 21 postweaning (P < 0.10) compared with pigs fed diets without MOS. On day 15, mucosal immunoglobulin G was increased (P < 0.05) in control vs. MOS and LM groups. Circulating IL-1β in control and MOS+LM pigs increased (P < 0.05) on day 1 post-LPS challenge but did not change (P > 0.10) in MOS and LM groups. On day 15, pigs fed LM had decreased (P < 0.05) ileal crypt depth compared with pigs fed the control diet. On day 21, fecal propionate and butyrate tended to be lower (P < 0.10) in pigs fed MOS vs. control and MOS+LM diet. These preliminary findings suggest that feeding LM alone improved feed efficiency and ileal morphological structure during the first week of LPS challenge; additionally, feeding LM and MOS may have beneficial effects relative to immune biomarkers.

Reduction in dietary crude protein and addition of fiber could mitigate the incidence and severity of post-weaning diarrhea, a common gastrointestinal condition in newly weaned pigs. Therefore, 360 weanling pigs, initially 5.0 ± 0.10 kg, were used to evaluate the effects of crude protein (CP) level and fiber source on growth performance and fecal microbial communities. At weaning, pigs were randomly assigned to pens and allotted to 1 of 8 dietary treatments in a 2 × 4 factorial with main effects of CP (21 or 18%) and fiber source (none, coarse wheat bran, oat hulls, or cellulose). There were 5 pigs per pen and 9 pens per treatment. Experimental diets were formulated in two dietary phases from d 0 to 10 and 10 to 24, with a common post-treatment diet fed from 24 to 45. The 21% CP diets contained 1.40% standardized ileal digestible (SID) Lys in phase 1 and 1.35% SID Lys in phase 2. By using a maximum SID Lys:digestible CP ratio of 6.35%, the 18% CP diets contained 1.25% SID Lys in both phases. Diets containing a fiber source were formulated to the level of insoluble fiber provided by 4% coarse wheat bran, resulting in the addition of 1.85% oat hulls and 1.55% cellulose. No fiber source × CP level interactions (P > 0.05) were observed. Decreasing CP (and subsequently SID lysine) decreased (P = 0.05) ADG and G:F during the experimental period. From d 0 to 45, ADG decreased (P = 0.05) for pigs fed 18% CP diets compared to pigs fed 21% CP. No effect of fiber source was observed for growth performance. Fecal DM on d 17 increased (P < 0.001) for pigs fed 18% CP diets compared to pigs fed 21% CP diets. Pigs fed diets with added cellulose had increased (P < 0.05) fecal dry matter during the experimental period compared to pigs fed no fiber source or wheat bran. Bacterial community structure was investigated by sequencing the V4 region of the 16S rRNA gene. Analysis indicated a significant difference between CP content at d 24 (P = 0.023) using a Weighted UniFrac distance matrix. Further investigation identified five differential Amplicon Sequence Variants associated with CP content at d 24. In conclusion, reducing crude protein (and subsequently SID Lys) decreased growth performance but increased fecal dry matter content. The source of dietary fiber in nursery diets had no impact on growth performance; but pigs fed added cellulose had increased fecal DM compared with other treatments. Microbial analysis identified differential taxa associated with CP content.

Mitigating the spread of antimicrobial resistance (AMR) has become a top priority globally over the last decade. Thus, understanding how bacterial communities acquire and transfer antibiotic resistance is of upmost importance in identifying intervention points for maintaining antibiotic efficacy. It is well documented that horizontal gene transfer (HGT) via bacteriophage transduction has the potential to shift metabolic flux in bacterial communities, yet phage mediated HGT in feedlot cattle with regard to AMR remains poorly characterized. Here we characterize the viral community of 72 beef cattle, where 36 animals received antibiotic exposure and 36 control animals received no antibiotic exposure throughout the duration of the study. Treatment groups were divided into 9 pens with 4 animals per pen. Fecal samples were collected at 3 timepoints and pooled by pen for viral enrichments. Viral particle enrichment was performed using tangential flow filtration and ultracentrifugation. Viral DNA/RNA was extracted with Zymo Quick-DNA/RNA Viral Magbead extraction kit, and shotgun metagenomic libraries were prepared using NEBNext Ultra II library prep kit for Illumina. Libraries were sequenced on the Illumina HiSeq platform (150bp paired-end reads). Sequencing reads were assembled using MEGAHIT, viral genomes were predicted using Virsorter2 and CheckV, and annotated using VIBRANT. In total, 5,875 viral genomes were predicted from the dataset. 635 of those viral genomes were > 60% complete, and 45 were complete circular genomes. 544 auxiliary metabolic genes (AMGs) were detected across all genomes, spanning 49 metabolic pathways with most genes falling under energy, amino acid, and vitamin/cofactor metabolism. Notably, 25 genes involved in secondary metabolite biosynthesis of vancomycin, validamycin, streptomycin, and monobactams were detected. Results indicate that fecal bacteriophages harbor a wide array of AMGs with diverse metabolic potential, including secondary metabolites potentially involved with AMR. The USDA is an equal opportunity provider and employer.

Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n = 24) and Holstein steers (n = 24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced, and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top 3 genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family, and genera did not differ (P > 0.05) between the 4 treatment groups. Generic richness and evenness, determined by Shannon–Weiner and Simpson’s diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.

Weaning stress and the negative health effects that occur with it cause serious concerns for pork producers. The abrupt environmental and dietary transitions that occur at weaning often take place before the gut microbiome is stabilized in the piglet. This leaves weanling piglets vulnerable to gut dysbiosis and increases susceptibility to enteric pathogens. The infections by opportunistic pathogens can be prevented with antibiotics, but due to growing concerns surrounding antimicrobial resistance in bacterial populations, direct-fed microbial (DFM) formulations have emerged as an alternative prevention method. In the current study, we isolated Lactobacillus spp. and Bifidobacterium spp. from fecal samples collected from neonatal pigs and sows that are capable of inhibiting colonization of Salmonella spp. and Escherichia coli isolated from sick pigs. Diluted fecal samples were plated on Bifidus selective medium (BSM) and deMan, Rogosa Sharpe (MRS) medium to isolate Bifidobacterium and Lactobacillus, respectively. Bacterial isolates were screened against Salmonella and E. coli isolates of porcine origin using a medium consisting of 50% MRS and 50% brain, heart, lung infusion (BHI) using disk diffusion assays. The resulting isolates that demonstrated the greaest degree of pathogen inhibition were characterized using 16s rRNA sequencing. Sequence analysis identified the top isolates as L. mucosae, L. reuteri, and B. thermacidophilum subsp. porcinum. Currently, genome sequencing of the selected isolates is underway to identify the mechanisms of inhibition.

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region. Based on a regression approach that used individual performance measures, animals were classified into divergent feed efficiency groups. Within cohort, an extreme set of 16 animals from these divergent groups was selected as a discovery population to identify differentially abundant OTUs across the rumen bacterial communities. The remaining samples from each cohort were selected to perform forward stepwise regressions using the differentially abundant OTUs as explanatory variables to distinguish predictive OTUs for the feed efficiency traits and to quantify the OTUs collective impact on feed efficiency phenotypes. OTUs belonging to the families Prevotellaceae and Victivallaceae were present across models for heifers, whereas OTUs belonging to the families Prevotellaceae and Lachnospiraceae were present across models for steers. Within the heifer cohort, models explained 19.3%, 25.3%, and 19.8% of the variation for ADFI, ADG, and G:F, respectively. Within the steer cohort, models explained 27.7%, 32.5%, and 26.9% of the variation for ADFI, ADG, and G:F, respectively. Overall, this study suggests a substantial role of the rumen microbiome on feed efficiency responses.

A study was conducted to determine the effect of nitrate and sulfate supplementation on cattle performance and methane emissions in finishing diets and to identify the effect of nitrate and sulfate addition on rumen microbiota composition and function. One hundred and thirty one day feeding trial was conducted using 24 head of cattle (initial BW = 918 lb; SD = 79 lb) where the cattle received one of four treatments no supplementation (CON), 2.0% dietary nitrate (NT), 0.54% dietary sulfate (SF) or both (COMBO), with 6 steers per treatment. Performance, volatile fatty acid (VFAs) profile and CH4:CO2 emissions data were analyzed using MIXED procedure of SAS. Rumen samples were collected and analyzed through amplicon sequencing targeting the 16S rDNA gene V4 region. Microbiome richness and composition were analyzed using Qiime2. Microbial genes involved in pathways linked to methanogenesis, nitrate, and sulfate metabolism were identified with metagenomic sequencing. Gene prediction, functional profile and pathway mapping were conducted using KEGG database. In diets with only sulfate or nitrate, diet had no impact on CH4:CO2 emissions, but nitrate and sulfate in combination decreased CH4:CO2. However, a reduction in dry matter intake (DMI) (P < 0.01), average daily gain (ADG) (P = 0.07) and gain:feed (G:F) (P = 0.09) was also recorded. Significant increase in bacterial genera with H2 utilization capability e.g. propionate, lactate forming bacteria e.g. Prevotella, Bacteroides, Megasphaera, Selenomonas, Lactobacillus; nitrate and sulfate reducing bacteria e.g. Selenomonas, Desulfovibrio was observed in COMBO diet. Differential gene abundance in metabolic pathways illustrated decrease of enzymes linked to methanogenesis in COMBO diet. This study provides evidence that methane yield is linked to diet type and differential gene abundance in the cattle rumen microbiome.

The rumen microbial community is responsible for producing a majority of the energetic needs for the animal, yet our understanding of the rumen microbiome is in its infancy. To better understand the effect of corn-ethanol coproducts on rumen microbial communities, a replicated 4 × 4 Latin square design study utilizing 12 cows in three squares was conducted to evaluate the replacement of alfalfa hay with a mixture (CoP) containing straw and dried distillers grains plus solubles (DDGS) in lactating Jersey cows. The experimental treatments were (proportions on a dry matter basis): a control diet (CON) containing 18.2% of alfalfa hay with no straw or DDGS. A low coproduct diet (LCoP) containing 12.1% alfalfa, 2.1% straw, and 6.0% DDGS. A medium coproduct diet (MCoP) containing 6.1% alfalfa, 4.2% straw, and 12.1% DDGS. A high coproduct diet (HCoP) containing 6.2% straw, 18.1% DDGS with no alfalfa. Rumen digesta samples were collected via an esophageal tube. No differences were observed for milk production and dry matter intake (P ≥ 0.307) (mean ± SEM) 19.5 kg ± 0.60, 29.6 kg ± 0.91, across treatments, while a decrease in methane was observed (P < 0.01) for the HCoP treatment. The bacterial community was assessed by sequencing the V4 region of the 16S rRNA gene. Additionally, the archaeal community was assessed by sequencing the V4-V5 region of the 16S rRNA gene on the Illumina MiSeq platform. Amplicon Sequence Variants were identified using the DADA2 pipeline. No significant differences were observed for the bacterial (P = 0.334) and archaeal (P = 0.593) communities. Although global effects in microbial community dynamics were not observed, differential taxa were observed with Lachnospiraceae being the major differentially abundant Family. The archaeal community composition demonstrated that Methanobacteriales to be the differentially abundant Order across treatments, and may contribute to methane production.

An experiment was conducted to evaluate the effect of dietary medium-chain fatty acid (MCFA) addition on nursery pig growth performance, fecal microbial composition, and mitigation of porcine epidemic diarrhea virus (PEDV) following storage. A total of 360 pigs (DNA 400 × 200, Columbus, NE; initially 6.7 ± 0.07 kg) were randomized to pens (5 pigs per pen) on the day of weaning (approximately 20 d of age), allowed a 6-d acclimation, blocked by BW, and randomized to dietary treatment (9 pens per treatment). All MCFA (Sigma–Aldrich, St. Louis, MO) were guaranteed ≥98% purity, including hexanoic (C6:0), octanoic (C8:0), and decanoic (C10:0) acids. Treatment diets were formulated in 2 phases (7 to 11 and 11 to 23 kg BW) and formulated to meet or exceed NRC requirement estimates. Treatments (n = 8) were a dose response including 0%, 0.25%, 0.5%, 1.0%, and 1.5% added MCFA blend (1:1:1 ratio C6:0, C8:0, and C10:0), as well as treatments with individual additions of 0.5% C6:0, C8:0, or C10:0. Fecal samples were collected from pigs fed control and 1.5% MCFA blend diets on days 0 and 14 and analyzed using 16s rDNA sequencing. Following feed manufacture, feed was stored in bags at barn temperature and humidity for 40 d before laboratory inoculation with PEDV. Subsamples of retained feed were inoculated with PEDV to achieve a titer of 104 TCID50/g and separate sample bottles were analyzed on 0 and 3 d post-inoculation (dpi). Overall, ADG and ADFI were increased (linear, P ≤ 0.010) and feed efficiency (G:F) improved (linear, P = 0.004) with increasing MCFA blend. Pigs fed 0.5% C8:0 had greater (P = 0.038) ADG compared with pigs fed the control diet, and G:F was improved (P ≤ 0.024) when pigs were fed 0.5% C6:0, 0.5% C8:0, or 0.5% C10:0 compared with control. An inclusion level × day interaction was observed (quadratic, P = 0.023), where PEDV Ct values increased (quadratic, P = 0.001) on 0 dpi with increasing levels of MCFA blend inclusion and also increased on 3 dpi (linear, P < 0.001). Fecal microbial diversity and composition were similar between control and 1.5% MCFA blend. In summary, the use of MCFA in nursery pig diets improves growth performance, provides residual mitigation activity against PEDV, and does not significantly alter fecal microbial composition.

A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.

A feedlot study was conducted comparing the effects of a direct-fed microbial feed additive (DFM) to no feed additive (CON) on performance and liver abscess rates in finishing beef cattle. The study utilized 60 crossbred steers (initial BW 274 kg ± 2.23) individually fed using a Calan gate system. Steers were housed in separate pens by treatment to avoid DFM cross-contamination, with pen (barn of 30 steers) assigned randomly to each treatment. Cattle were fed a diet consisting of 15% corn silage, 36.5% high moisture corn, 24.5% dry rolled corn, 20% modified distillers grains, and 4% supplement for 189 days. The DFM counts were estimated using cell cytometry and was top dressed at a concentration of approximately 81 billion bacterial cells/head/day. The DFM additive used in this study was developed to reduce the abundance of Fusobacterium necrophorum and Streptococcus bovis in the rumen. No effect of treatment on hot carcass weight (HCW), average daily gain (ADG), dry matter intake (DMI), feed efficiency (G:F), or carcass traits (Table 1) were observed. No significant difference in the occurrence of liver abscesses between treatment groups were observed with 4 steers having abscessed livers in the CON group and 3 steers in the DFM group. Additionally, there were no differences in the severity of liver abscesses; all observed liver abscesses received the score of A. The DFM utilized in this study did not significantly affect performance, liver abscess rate, or the severity of liver abscesses in finishing beef cattle.

Precision animal agriculture is poised to rise to prominence in the livestock enterprise in the domains of management, production, welfare, sustainability, health surveillance, and environmental footprint. Considerable progress has been made in the use of tools to routinely monitor and collect information from animals and farms in a less laborious manner than before. These efforts have enabled the animal sciences to embark on information technology-driven discoveries to improve animal agriculture. However, the growing amount and complexity of data generated by fully automated, high-throughput data recording or phenotyping platforms, including digital images, sensor and sound data, unmanned systems, and information obtained from real-time noninvasive computer vision, pose challenges to the successful implementation of precision animal agriculture. The emerging fields of machine learning and data mining are expected to be instrumental in helping meet the daunting challenges facing global agriculture. Yet, their impact and potential in “big data” analysis have not been adequately appreciated in the animal science community, where this recognition has remained only fragmentary. To address such knowledge gaps, this article outlines a framework for machine learning and data mining and offers a glimpse into how they can be applied to solve pressing problems in animal sciences.

The objective of this study was to compare the establishment of human fecal bacterial communities in porcine and murine animal models. Many gut microbiota studies use human microbiota-associated (HMA) rodents as translational animal models; however, it has been questioned as to how successfully a human microbiota can be established in rodents considering the many differences that exist between rodents and humans. The domestic pig (Sus scrofa domesticus) has many anatomical, physiological, and immunological similarities to humans and has been widely used as a model for humans in biomedical and nutritional studies. Thus, the porcine model may be an alternative to rodent models in gut microbiota research. The current study was designed to evaluate the establishment of the same human donor microbiota in the rodent and pig models. Both germ-free piglets and mice (C3H/HeN) were transplanted with fecal microbiota from four human donors: Infant (0–5 m), child (1–12 yrs), adult (18–64 yrs), and elderly (65+ yrs). To monitor the establishment of the transplanted microbiota, weekly fecal samples were collected for 5 wks. All fecal samples were subjected to 16S rRNA gene-based amplicon sequencing using the Illumina MiSeqTM platform to characterize bacterial community composition. Unweighted unifrac distances were compared between the bacterial communities of the human donor and the corresponding HMA porcine and murine fecal samples. Statistical significance was tested using the Mann-Whitney U test (P = 0.05). This analysis suggested that more taxa are colonized in the mice compared to the piglets receiving the same infant donor microbiota, while for the child, adult, and elderly donors, the piglet model established the human donor microbiota better than the mice receiving the same donor samples. This suggests that in the latter stages of human development, more species of the human fecal inoculum colonizes the pig gut compared to the mouse gut.

The objectives of this trial were to determine the rumen undegradable protein (RUP) of dried distillers grains with solubles (DDGS), to compare the estimates of duodenal bacterial CP (BCP) flow using diaminopumelic acid (DAPA) or DNA as bacterial markers, and to estimate duodenal protozoal CP (PCP) and yeast CP (YCP) flow when DDGS are fed. Three crossbred steers fitted with ruminal and double L-shaped duodenal cannulae (average BW 780 ± 137 kg) were used in a 3 treatment, 6 period crossover design. Animals were housed in individual free stalls and fed twice daily at 0700 and 1900 h. Diets (DM basis) were 1) CONTROL, which is 0% DDGS but with 19.5% corn bran, 20% sorghum silage, 60% brome hay, 0.5% trace minerals, and 0.25% urea, 2) LOW DDGS, which is inclusion of 9.75% DDGS replacing equal percentage of corn bran, and 3) HIGH DDGS, which is inclusion of 19.5% DDGS completely replacing corn bran. Duodenal BCP flow was estimated using DAPA and DNA as bacterial markers. In addition, duodenal PCP and YCP flow were estimated using DNA markers. The value of DDGS RUP as a percent of CP was determined to be 63.0 ± 0.64%. Estimates of duodenal BCP flow using DAPA were 473, 393, and 357 ± 78 g/d (P = 0.09) for CONTROL, LOW DDGS, and HIGH DDGS, respectively. Estimates of duodenal BCP flow using DNA were 479, 397, and 368 ± 74 g/d (P = 0.14), respectively. Average BCP flow across treatments was unaffected (P = 0.71) by marker type and were 404 and 417 ± 83 g/d for DAPA and DNA markers, respectively. Estimates of duodenal PCP flow were 82, 80, and 78 ± 12 g/d (P = 0.64) for CONTROL, LOW DDGS, and HIGH DDGS, respectively. Estimates of duodenal YCP flow were 0.15, 1.94, and 4.80 ± 0.66 g/d (P < 0.01) for CONTROL, LOW DDGS, and HIGH DDGS, respectively. Duodenal BCP flow tended to decrease with DDGS inclusion, but estimates were not affected by marker type. In addition, DDGS did not affect duodenal PCP supply and provided small amounts of duodenal YCP. Overall, the value of DDGS RUP determined in this study will contribute to a better understanding of the effect of this coproduct in ruminant nutrition.

The objectives of this study were to eval- uate the effect of dried distillers grains with solubles (DDGS) on ruminal biohydrogenation and duodenal flow of fatty acids, and to evaluate effects on the ruminal and duodenal microbial community using Roche 454 pyro- sequencing. Three crossbred steers (average BW 780 ± 137 kg) fitted with ruminal and duodenal cannulae were used in a 3-diet, 6-period crossover design. Animals were housed in individual free stalls and fed twice daily at 0700 and 1900 h. Diets (DM basis) were 1) CONTROL, 19.5% corn bran, 20% sorghum silage, 60% brome hay, 0.5% trace minerals, and 0.25% urea, but no DDGS; 2) LOW DDGS, inclusion of 9.75% DDGS replacing equal percentage of corn bran; 3) HIGH DDGS, inclusion of 19.5% DDGS completely replacing corn bran. Feed ingredients and duodenal digesta samples were analyzed for fatty acid composition. The DNA was extracted from isolated mixed ruminal bacterial samples and from intes- tinal digesta samples. The V1-V3 region of the 16S rRNA gene was sequenced, and bacterial phylogenetic analysis was conducted. Data were analyzed using the MIXED procedure of SAS. Biohydrogenation of C18:1 increased (P < 0.01) with DDGS inclusion; means were 68.3, 75.6, and 79.3 ± 4.3% for CONTROL, LOW DDGS, and HIGH DDGS, respectively. In the same order, means of biohydrogenation of C18:2 (P < 0.05) were 84.1, 91.5, and 93.3 ± 3.4%. Duodenal flow of total fatty acids increased (P < 0.01) with DDGS inclusion; means were 134, 168, and 223 ± 33 g/d for CONTROL, LOW DDGS, and HIGH DDGS, respectively. In the same order, means of C18:0 flow (P < 0.01) were 51, 86, and 121 ± 18 g/d. DDGS did not affect the predominant bacterial phyla in the gut, which were Bacteroidetes (P = 0.62) and Firmicutes (P = 0.71). However, the phylum Fibrobacteres decreased (P < 0.01) when DDGS was fed with means of 5.5, 6.0 and 3.7 ± 0.6% for CONTROL, LOW DDGS, and HIGH DDGS, respectively. Fibrobacteres were lower (P < 0.01) in isolated ruminal bacterial samples compared to duode- nal digesta samples with means of 0.1 and 10.1 ± 0.6%, respectively. Overall, the inclusion of DDGS in diets increased ruminal biohydrogenation of C18:1 and C18:2, which increased duodenal flow of C18:0. In addition, the bacterial community of the rumen clustered separately from that of the duodenum suggesting different bacterial diversity between isolated ruminal bacteria and duodenal digesta.