Assessing the statistical training in animal science graduate programs in the United States: survey on statistical training.

Statistical analysis of data and understanding of experimental design are critical skills needed by animal science graduate students (ASGS). These skills are even more valuable with the increased development of high-throughput technologies. The objective of this study was to evaluate the perceived statistical training of U.S. ASGS. A survey with 38 questions was shared across U.S. universities, and 416 eligible ASGS from 43 universities participated in this study. The survey included questions on the demographics and overall training, graduate education on statistics, and self-assessment on statistics and career path of ASGS. Several analyses were performed: relationship between perceived received education (PRE; i.e., how ASGS evaluated their graduate education in statistics) and perceived knowledge (PK; i.e., how ASGS evaluated their knowledge in statistics from their education); ranking of statistical topics based on PRE, PK, and confidence in performing statistical analyses (CPSA); cluster analysis of statistical topics for PRE, PK, and CPSA; and factors (demographic, overall training, interest in statistics, and field of study) associated with the overall scores (OS) for PRE, PK, and CPSA. Students had greater (P < 0.05) PRE than PK for most of the statistical topics included in this study. The moderate to high repeatability of answers within statistical topics indicates substantial correlations in ASGS answers between PRE and PK. The cluster analysis resulted in distinct groups of "Traditional" and "Nontraditional" statistical topics. ASGS showed lower (P < 0.05) scores of PRE, PK, and CPSA in "Nontraditional" compared with "Traditional" statistical methods. Several factors were associated (P < 0.05) with the OS of PRE, PK, and CSPA. In general, factors related to greater training and interest in statistics of ASGS were associated with greater OS, such as taking more credits in statistics courses, having additional training in statistics outside the classroom, knowing more than one statistics software, and more. This study provided comprehensive information on the perceived level of education, knowledge, and confidence in statistics in ASGS in the United States. Although objective measurements of their training in statistics are needed, the current study suggests that ASGS have limited statistical training on topics of major importance for the current and future trends of data-driven research in animal sciences.

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs.

High fat diets have been reported to negatively affect the microbiota in both mice and humans. However, there is a lack of studies in canine models. The variation among the gastrointestinal (GI) tract anatomy/physiology and typical diet compositions of these animal species may lead to vastly different results. Due to the large inclusion rate of dietary fat in pet food, it is critical to understand its effects in a canine model. Therefore, the study objective was to report the effects of high fat, low carbohydrate diets on the fecal microbiota in healthy adult dogs. Eight adult beagles were randomly assigned to one of four dietary treatments within each 15-day period of a replicated 4x4 Latin Square design. Diets contained 32% (T1), 37% (T2), 42% (T3), and 47% (T4) fat. T2, T3, and T4 were created by adding increasing levels of canola oil to T1, a commercially manufactured canned canine diet, which served as the control diet. Fresh fecal samples were collected during the last 5 days of each period for microbial analysis. DNA was extracted from fecal samples and paired-end 16S rRNA gene amplicon sequencing was performed using the Illumina MiSeq platform. When comparing whole microbial communities using PERMANOVA, no significant differences were observed among treatments (P = 0.735). Individual OTUs were analyzed using the GLIMMIX procedure of SAS with fixed effects of diet and room, and the random effects of period and animal. Out of the 100 most abundant individual OTUs, 36 showed significant differences in abundance based on treatment (q < 0.05). Overall, OTUs assigned to genera related to fat digestion increased while OTUs assigned to genera involved in carbohydrate digestion decreased. In conclusion, the microbial community adapted to dietary intervention without jeopardizing the health of the animals, evaluated by body condition score, fecal characteristics, and blood parameters.

Impact of storage conditions on protein oxidation of rendered by-product meals.

Rendered products used in animal feed and pet food undergo extreme temperatures during manufacturing and may be stored up to 2 yr. No information is available on protein oxidation in these products. The objective of this study was to determine the extent to which typical antioxidant inclusion at different storage conditions may limit protein oxidation in typical rendered protein meals. Two experiments were conducted on 14 rendered products stored at either 45 °C for 7 or 14 d, or at 20 °C for 3 or 6 mo to determine the extent to which time, temperature, and antioxidants affect protein oxidation. Results from this study show that fish meal and chicken blood meal are susceptible to protein oxidation during storage at 45 °C (P = 0.05; 0.03) as well as during storage at 20 °C (P = 0.01; 0.04). Natural antioxidants were effective at limiting carbonyl formation in fish meal during short-term storage at 45 °C, whereas ethoxyquin was effective at limiting the extent of protein oxidation in fish meal stored long term at 20 °C.

A review of feed efficiency in swine: biology and application.

Feed efficiency represents the cumulative efficiency with which the pig utilizes dietary nutrients for maintenance, lean gain and lipid accretion. It is closely linked with energy metabolism, as the oxidation of carbon-containing components in the feed drive all metabolic processes. While much is known about nutrient utilization and tissue metabolism, blending these subjects into a discussion on feed efficiency has proven to be difficult. For example, while increasing dietary energy concentration will almost certainly increase feed efficiency, the correlation between dietary energy concentration and feed efficiency is surprisingly low. This is likely due to the plethora of non-dietary factors that impact feed efficiency, such as the environment and health as well as individual variation in maintenance requirements, body composition and body weight. Nonetheless, a deeper understanding of feed efficiency is critical at many levels. To individual farms, it impacts profitability. To the pork industry, it represents its competitive position against other protein sources. To food economists, it means less demand on global feed resources. There are environmental and other societal implications as well. Interestingly, feed efficiency is not always reported simply as a ratio of body weight gain to feed consumed. This review will explain why this arithmetic calculation, as simple as it initially seems, and as universally applied as it is in science and commerce, can often be misleading due to errors inherent in recording of both weight gain and feed intake. This review discusses the importance of feed efficiency, the manner in which it can be measured and reported, its basis in biology and approaches to its improvement. It concludes with a summary of findings and recommendations for future efforts.

Fecal metabolomics of healthy breast-fed versus formula-fed infants before and during in vitro batch culture fermentation.

Nontargeted metabolomics analyses were used (1) to compare fecal metabolite profiles of healthy breast-fed (BF) and formula-fed (FF) infants before and during in vitro fermentation in batch culture and (2) to evaluate fecal metabolomics in assessing infant diet. Samples from healthy BF (n = 4) or FF (n = 4) infants were individually incubated at 37( °)C in anaerobic media containing 1% (wt/vol) galactooligosaccharides, 6'-sialyllactose, 2'-fucosyllactose, lacto-N-neotetraose, inulin, and gum arabic for up to 6 h, and supernatants were analyzed using GC/MS and LC/MS/MS to assess changes in various compounds. Comparison of over 250 metabolites prior to incubation showed that BF samples contained higher relative concentrations (P ≤ 0.05) of 14 compounds including human milk oligosaccharides and other metabolites presumably transferred through breast feeding (linoelaidate, myo-inositol) (P ≤ 0.05). Conversely, feces from FF infants contained 41 identified metabolites at higher levels (P ≤ 0.05) with many indicative of carbon limitation and protein fermentation. Our data are consistent with the notion that carbon-limited cultures catabolize protein and amino acids to obtain energy, whereas the provision of fermentable carbohydrate creates anabolic conditions relying on amino acids for bacterial growth. Results also suggest that fecal metabolomics can be a useful tool for studying interactions among diet, microbes, and host.

In vitro fermentation characteristics of select nondigestible oligosaccharides by infant fecal inocula.

This study sought to determine the fermentation potential of human milk oligosaccharides by mixed cultures of fecal microbiota from breast-fed (BF; n = 4) and formula-fed (FF; n = 4) infants. Infant fecal inocula were incubated with galactooligosaccharide (GOS), gum arabic (GA), HP inulin (HP), 2'-fucosyllactose (2'FL), 6'-sialyllactose (6'SL), and lacto-N-neotetraose (LNnt). GOS, 2'FL, and LNnT had a lower pH than other substrates after 3 h (P < 0.05). Total short chain fatty acids were greater in FF compared to BF infants at 6 h (P = 0.03) and 12 h (P = 0.01). GOS, 2'FL, and LNnT led to more lactate than 6'SL, HP, and GA (P < 0.05). Bifidobacteria populations were greater (P = 0.02) in FF at 6 and 12 h. Overall, GOS, 2'FL, and LNnT were rapidly fermented by infant fecal inocula, 6'SL and HP had intermediate fermentability, while GA had little fermentation. Inocula from FF infants fermented substrates more rapidly than inocula from BF infants, which should be accounted for when evaluating substrate fermentability. These data will aid in future infant formulas to promote optimal gut health in FF infants.