Scholarly Work - Animal & Range Sciences

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    Adaptive constraints at the range edge of a widespread and expanding invasive plant
    (Oxford University Press, 2023-12) Fletcher, Rebecca A.; Atwater, Daniel Z.; Haak, David C.; Bagavathiannan, Muthukumar V.; DiTommaso, Antonio; Lehnhoff, Erik; Paterson, Andrew H.; Auckland, Susan; Govindasmo, Prabhu; Lemke, Cornelia; Morris, Edward; Rainville, Lisa; Barney, Jacob N.
    Identifying the factors that facilitate and limit invasive species’ range expansion has both practical and theoretical importance, especially at the range edges. Here, we used reciprocal common garden experiments spanning the North/South and East/West range that include the North American core, intermediate and range edges of the globally invasive plant, Johnsongrass (Sorghum halepense) to investigate the interplay of climate, biotic interactions (i.e. competition) and patterns of adaptation. Our results suggest that the rapid range expansion of Johnsongrass into diverse environments across wide geographies occurred largely without local adaptation, but that further range expansion may be restricted by a fitness trade-off that limits population growth at the range edge. Interestingly, plant competition strongly dampened Johnsongrass growth but did not change the rank order performance of populations within a garden, though this varied among gardens (climates). Our findings highlight the importance of including the range edge when studying the range dynamics of invasive species, especially as we try to understand how invasive species will respond to accelerating global changes.
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    Suppression force-fields and diffuse competition: competition de-escalation is an evolutionarily stable strategy
    (The Royal Society, 2023-08) Atwater, Daniel Z.
    Competition theory is founded on the premise that individuals benefit from harming their competitors, which helps them secure resources and prevent inhibition by neighbours. When multiple individuals compete, however, competition has complex indirect effects that reverberate through competitive neighbourhoods. The consequences of such ‘diffuse’ competition are poorly understood. For example, competitive effects may dilute as they propagate through a neighbourhood, weakening benefits of neighbour suppression. Another possibility is that competitive effects may rebound on strong competitors, as their inhibitory effects on their neighbours benefit other competitors in the community. Diffuse competition is unintuitive in part because we lack a clear conceptual framework for understanding how individual interactions manifest in communities of multiple competitors. Here, I use mathematical and agent-based models to illustrate that diffuse interactions—as opposed to direct pairwise interactions—are probably the dominant mode of interaction among multiple competitors. Consequently, competitive effects may regularly rebound, incurring fitness costs under certain conditions, especially when kin–kin interactions are common. These models provide a powerful framework for investigating competitive ability and its evolution and produce clear predictions in ecologically realistic scenarios.
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    Conceptualization and implementation of the Fiber Utilization and Cell Wall Constituents Symposium
    (Oxford University Press, 2023-01) Smith, W B; Wyffels, S A; Gekara, O J
    Understanding how ruminants break down plant cell walls and digest plant fibers can help improve the efficiency of livestock production
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    Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard
    (MDPI AG, 2023-06) Haderlie, Sarah A.; Hieber, Jordan K.; Boles, Jane A.; Berardinelli, Berardinelli; Thomson, Jennifer M.
    Targets for finished livestock are often determined by expected fat, either subcutaneous or intramuscular. These targets are used frequently to improve eating quality. Lower intramuscular fat, lack of product uniformity, and insufficient tenderness can negatively impact beef acceptability. This study aimed to investigate the differences in gene expression that alter metabolism and intercellular signaling in the muscle and adipose tissue in beef carcasses at different fat endpoints. In this study, longissimus thoracis muscle samples and adipose tissue were collected at harvest, and RNA was extracted and then sequenced using RNAseq. Differential expression was determined using edgeR, and p-values were adjusted using the Benjamini–Hochberg method. A corrected p-value of 0.005 and log2 (fold change) of >1 were the threshold to identify differential expression. Comparison between intermuscular and subcutaneous fat showed no differences in the genes activated in the two adipose tissue depots, suggesting that subcutaneous fat was an adequate sample. Carcass data allowed the classification of carcasses by USDA quality grades (marbling targets). In comparing muscle from Standard and Choice carcasses, 15 genes were downregulated, and 20 were upregulated. There were 49 downregulated and 113 upregulated genes comparing adipose tissue from Standard and Choice carcasses. These genes are related to the metabolism of fat and energy. This indicates that muscle transcript expression varies less than adipose. In addition, subcutaneous fat can be used to evaluate transcript changes in fat. However, it is unclear whether these fat tissues can be used as surrogates for marbling.
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    Residual effect of narasin on feed intake and rumen fermentation characteristics in Nellore steers fed forage-based diet
    (Oxford University Press, 2023-01) Bortolanza Soares, Letícia Carolina; Marques, Rodrigo S; Vaz Pires, Alexandre; Alves Cruz, Vinicius; Ogg, Makayla Anne; Limede, Arnaldo Cintra; Gonzales Dias Junior, Paulo César; Jorge dos Santos, Isabela; Garcia de Assis, Rhaíssa; Gouvêa, Vinícius N; Maia Ferreira, Evandro; Montanher Polizel, Daniel
    This study aimed to evaluate the residual effect of narasin on intake and ruminal fermentation parameters in Nellore cattle fed a forage-based diet. Thirty rumen-cannulated Nellore steers [initial body weight (BW) = 281 ± 21 kg] were allocated to individual pens in a randomized complete block design, with 10 blocks and 3 treatments, defined according to the fasting BW at the beginning of the experiment. The animals were fed a forage-based diet containing 99% Tifton-85 haylage and 1% concentrate. Within blocks, animals were randomly assigned to one of three treatments: (1) forage-based diet without addition of narasin (CON; n = 10), (2) CON diet plus 13 mg of narasin/kg DM (N13; n = 10), or (3) CON diet plus 20 mg of narasin/kg DM (N20; n =10). The experiment lasted 156 d and was divided into two periods. The first period lasted 140 d and consisted of the daily supply of narasin. In the second period (last 16 d), the animals were not supplemented with narasin when the residual effect of the additive was evaluated. The treatments were evaluated by linear and quadratic orthogonal contrasts. The results were reported as least square means and the effect was considered significant when P ≤ 0.05. No treatment × day interaction was identified for dry matter intake (P = 0.27). There was a treatment × day (P ≤ 0.03) interaction after narasin removal for the molar proportion of acetate, propionate, ac:prop ratio, and ammonia nitrogen. The inclusion of narasin decreased linearly (P < 0.01) the molar proportion of acetate (P < 0.01), and this effect persisted until day 5 after narasin withdrawal (P < 0.01). Narasin inclusion linearly increased the molar proportion of propionate (P < 0.04), and linearly decreased (P < 0.01) ac:prop ratio up to 5 d after removing narasin from the diets. No treatment effects were observed (P > 0.45) on days 8 and 16 after the withdrawal. Narasin linearly decreased ammonia nitrogen up to 1 day after withdrawal (P < 0.01). In conclusion, the use of narasin for a prolonged period (140 d) resulted in a residual effect on rumen fermentation parameters after the removal of the additive from the diets.
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    Effects of lasalocid, narasin, or virginiamycin supplementation on rumen parameters and performance of beef cattle fed forage-based diet
    (Oxford University Press, 2023-04) Arantes Miszura, Alexandre; Marques, Rodrigo S; Montanher Polizel, Daniel; Ieda Cappellozza, Bruno; Alves Cruz, Vinicius; Ogg, Makayla Anne; Roman Barroso, José Paulo; Bagio Oliveira, Gabriela; Storti Martins, André; Cintra Limede, Arnaldo; Maia Ferreira, Evandro; Gouvêa, Vinícius N; Vaz Pires, Alexandre
    Two experiments were designed to evaluate the impacts of supplementing lasalocid (LAS), narasin (NAR), or virginiamycin (VRM) on rumen fermentation parameters, apparent nutrient digestibility, and blood parameters (Exp. 1), as well as feed intake and performance (Exp. 2) of Nellore cattle consuming a forage-based diet. In Exp. 1, 32 rumen-fistulated Nellore steers (initial shrunk body weight [BW] = 355 ± 4.4 kg) were assigned to a randomized complete block design. Within block, animals were randomly assigned to one of four treatments: 1) forage-based diet without feed additives (CON), 2) CON diet plus 13 mg/kg of dry matter (DM) of NAR, 3) CON diet plus 20 mg/kg of DM of sodium LAS, or 4) CON diet plus 20 mg/kg of DM of VRM. No treatment effects were detected (P ≥ 0.32) for intake and apparent digestibility of nutrients. Steers fed NAR had the lowest (P ≤ 0.01) molar proportion of acetate on day 28, 56, and 112 vs. CON, LAS, and VRM steers, whereas acetate did not differ (P ≥ 0.25) between LAS, VRM, and CON steers from day 28 to 84. On day 112, steers fed LAS had a lower (P < 0.02) molar proportion of acetate vs. VRM and CON, whereas it did not differ between CON and VRM (P > 0.33). Steers receiving NAR had a greater (P ≤ 0.04) ruminal propionate vs. CON, LAS, and VRM, whereas LAS steers had greater (P < 0.04) propionate vs. CON and VRM steers on day 28 and 112, and it did not differ (P > 0.22) between CON and VRM. In Exp. 2, 160 Nellore bulls were blocked by initial shrunk BW (212 ± 3.1 kg) in a 140-d feedlot trial. Diets contained the same treatments used in Exp. 1. Bulls fed NAR had greater (P < 0.02) average daily gain (ADG) vs. CON and VRM, and similar (P = 0.17) ADG between NAR and LAS, whereas ADG did not differ (P > 0.28) between LAS, VRM, and CON bulls. A treatment effect was detected (P = 0.03) for dry matter intake, being greater in NAR vs. CON, LAS, and VRM bulls, and similar (P > 0.48) between CON, LAS, and VRM bulls. A tendency was detected (P = 0.09) for feed efficiency, which was greater (P < 0.02) in NAR bulls vs. CON and VRM, and similar (P = 0.36) between NAR and LAS bulls. From day 112 to 140, bulls receiving NAR were heavier (P < 0.03) vs. CON, LAS, and VRM bulls, but no differences were observed (P > 0.51) between CON, LAS, and VRM bulls. Collectively, ruminal fermentation profile and intake were impacted by NAR supplementation, which partially contributed to the enhanced performance of Nellore bulls receiving a forage-based diet.
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    Different combinations of monensin and narasin on growth performance, carcass traits, and ruminal fermentation characteristics of finishing beef cattle
    (Frontiers Media SA, 2023-04) Baggio, Marcelo; Gouvêa, Vinícius N.; Barroso, José Paulo R.; Miszura, Alexandre A.; Limede, Arnaldo C.; Soares, Letícia C. B.; Ferraz, Marcos Vinicius C.; Vicente, Ana Carolina S.; Ferreira, Evandro M.; Marques, Rodrigo S.; Pires, Alexandre V.
    The objective of this study was to evaluate the effects of different combinations of monensin and narasin on finishing cattle. In Exp. 1, 40 rumen-cannulated Nellore steers [initial body weight (BW) = 231 ± 3.64 kg] were blocked by initial BW and assigned to one of the five treatments as follows: Control (CON): no feed additive in the basal diet during the entire feeding period; Sodium monensin (MM) at 25 mg/kg dry matter (DM) during the entire feeding period [adaptation (days 1–21) and finishing (days 22–42) periods]; Narasin (NN) at 13 mg/kg DM during the entire feeding period (adaptation and finishing periods); Sodium monensin at 25 mg/kg DM during the adaptation period and narasin at 13 mg/kg DM during the finishing period (MN); and narasin at 13 mg/kg DM during the adaptation period and sodium monensin at 25 mg/kg DM during the finishing period (NM). Steers fed MM had lower dry matter intake (DMI) during the adaptation period compared to NM (P = 0.02) but not compared to CON, MM, MN, or NN (P ≥ 0.12). No differences in DMI were observed among the treatments during the finishing (P = 0.45) or the total feeding period (P = 0.15). Treatments did not affect the nutrient intake (P ≥ 0.51) or the total apparent digestibility of nutrients (P ≥ 0.22). In Exp. 2, 120 Nellore bulls (initial BW = 425 ± 5.4 kg) were used to evaluate the effects of the same treatments of Exp. 1 on growth performance and carcass characteristics of finishing feedlot cattle. Steers fed NM had greater DMI during the adaptation period compared to CON, MM, and MN (P ≤ 0.03), but no differences were observed between NM and NN (P = 0.66) or between CON, MM, and NN (P ≥ 0.11). No other differences between treatments were observed (P ≥ 12). Feeding narasin at 13 mg/kg DM during the adaptation period increases the DMI compared to monensin at 25 mg/kg DM, but the feed additives evaluated herein did not affect the total tract apparent digestibility of nutrients, growth performance, or carcass characteristics of finishing cattle.
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    Associations among the genome, rumen metabolome, ruminal bacteria, and milk production in early-lactation Holsteins
    (Elsevier, 2023-03) Golder, H.M.; Thomson, J.; Rehberger, J.; Smith, A.H.; Block, E.; Lean, I.J.
    A multicenter observational study to evaluate genome-wide association was conducted in early-lactation Holstein cows (n = 293) from 36 herds in Canada, the USA, and Australia. Phenotypic observations included rumen metabolome, acidosis risk, ruminal bacterial taxa, and milk composition and yield measures. Diets ranged from pasture supplemented with concentrates to total mixed rations (nonfiber carbohydrates = 17 to 47, and neutral detergent fiber = 27 to 58% of dry matter). Rumen samples were collected <3 h after feeding and analyzed for pH, ammonia, d- and l-lactate, volatile fatty acid (VFA) concentrations, and abundance of bacterial phyla and families. Eigenvectors were produced using cluster and discriminant analyses from a combination of pH and ammonia, d-lactate, and VFA concentrations, and were used to estimate the probability of the risk of ruminal acidosis based on proximity to the centroid of 3 clusters, termed high (24.0% of cows), medium (24.2%), and low risk (51.8%) for acidosis. DNA of sufficient quality was successfully extracted from whole blood (218 cows) or hair (65 cows) collected simultaneously with the rumen samples and sequenced using the Geneseek Genomic Profiler Bovine 150K Illumina SNPchip. Genome-wide association used an additive model and linear regression with principal component analysis (PCA) population stratification and a Bonferroni correction for multiple comparisons. Population structure was visualized using PCA plots. Single genomic markers were associated with milk protein percent and the center logged ratio abundance of the phyla Chloroflexi, SR1, and Spirochaetes, and tended to be associated with milk fat yield, rumen acetate, butyrate, and isovalerate concentrations and with the probability of being in the low-risk acidosis group. More than one genomic marker was associated or tended to be associated with rumen isobutyrate and caproate concentrations, and the center log ratio of the phyla Bacteroidetes and Firmicutes and center log ratio of the families Prevotellaceae, BS11, S24-7, Acidaminococcaceae, Carnobacteriaceae, Lactobacillaceae, Leuconostocaceae, and Streptococcaceae. The provisional NTN4 gene, involved in several functions, had pleiotropy with 10 bacterial families, the phyla Bacteroidetes and Firmicutes, and butyrate. The ATP2CA1 gene, involved in the ATPase secretory pathway for Ca2+ transport, overlapped for the families Prevotellaceae, S24-7, and Streptococcaceae, the phylum Bacteroidetes, and isobutyrate. No genomic markers were associated with milk yield, fat percentage, protein yield, total solids, energy-corrected milk, somatic cell count, rumen pH, ammonia, propionate, valerate, total VFA, and d-, l-, or total lactate concentrations, or probability of being in the high- or medium-risk acidosis groups. Genome-wide associations with the rumen metabolome, microbial taxa, and milk composition were present across a wide geographical and management range of herds, suggesting the existence of markers for the rumen environment but not for acidosis susceptibility. The variation in pathogenesis of ruminal acidosis in the small population of cattle in the high risk for acidosis group and the dynamic nature of the rumen as cows cycle through a bout of acidosis may have precluded the identification of markers for acidosis susceptibility. Despite a limited sample size, this study provides evidence of interactions between the mammalian genome, the rumen metabolome, ruminal bacteria, and milk protein percentage.
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    Characterizing ruminal acidosis risk: A multiherd, multicountry study
    (Elsevier, 2023-03) Golder, H. M.; LeBlanc, S.J.; Duffield, T.; Rossow, H.A.; Bogdanich, R.; Hernandez, L.; Block, E.; Rehberger, J.; Smith, A.H.; Thomson, J.
    A multicenter observational study was conducted on early lactation Holstein cows (n = 261) from 32 herds from 3 regions (Australia, AU; California, CA; and Canada, CAN) to characterize their risk of acidosis into 3 groups (high, medium, or low) using a discriminant analysis model previously developed. Diets ranged from pasture supplemented with concentrates to total mixed ration (nonfiber carbohydrates = 17 to 47 and neutral detergent fiber = 27 to 58% of dry matter). Rumen fluid samples were collected <3 h after feeding and analyzed for pH, and ammonia, d- and l-lactate, and volatile fatty acid (VFA) concentrations. Eigenvectors were produced using cluster and discriminant analysis from a combination of rumen pH, and ammonia, d-lactate, and individual VFA concentrations and were used to calculate the probability of the risk of ruminal acidosis based on proximity to the centroid of 3 clusters. Bacterial 16S ribosomal DNA sequence data were analyzed to characterize bacteria. Individual cow milk volume, fat, protein, and somatic cell count values were obtained from the closest herd test to the rumen sampling date (median = 1 d before rumen sampling). Mixed model analyses were performed on the markers of rumen fermentation, production characteristics, and the probability of acidosis. A total of 26.1% of the cows were classified as high risk for acidosis, 26.8% as medium risk, and 47.1% as low risk. Acidosis risk differed among regions with AU (37.2%) and CA (39.2%) having similar prevalence of high-risk cows and CAN only 5.2%. The high-risk group had rumen phyla, fermentation, and production characteristics consistent with a model of acidosis that reflected a rapid rate of carbohydrate fermentation. Namely, an acetate to propionate (1.98 ± 0.11), concentrations of valerate (2.93 ± 0.14 mM), milk fat to protein ratio (1.11 ± 0.047), and a positive association with abundance of phylum Firmicutes. The medium-risk group contains cows that may be inappetant or that had not eaten recently or were in recovery from acidosis. The low-risk group may represent cattle that are well fed with a stable rumen and a slower rumen fermentation of carbohydrates. The high risk for acidosis group had lower diversity of bacteria than the other groups, whereas CAN had a greater diversity than AU and CA. Rumen fermentation profile, abundance of ruminal bacterial phyla, and production characteristics of early lactation dairy cattle from 3 regions were successfully categorized in 3 different acidosis risk states, with characteristics differing between acidosis risk groups. The prevalence of acidosis risk also differed between regions.
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    Influences of increasing levels of sulfate in drinking water on the intake and use of low-quality forages by beef cattle
    (American Registry of Professional Animal Scientists, 2023-02) Wyffels, Samuel A.; Van Emon, Megan L.; Nack, Makae F.; Manoukian, Marley K.; Carlisle, Tanner J.; Davis, Noah G.; Kluth, Janessa A.; DelCurto-Wyffels, Hannah M.; DelCurto, Timothy
    Objective. This study evaluated the effects of varying sulfate concentrations of water on forage and water intake, digestibility, digestive kinetics, and rumen fermentation characteristics of cattle consuming low-quality forages provided a protein supplement, with and without salt. Materials and Methods. Eight ruminally cannulated cows (2 yr of age) were used in 2 concurrent 4 × 4 Latin squares (4 cows per square) to test the effects of increasing water sulfate concentrations on forage and water intake, digestibility, digestive kinetics, and rumen fermentation characteristics of cattle consuming low-quality forages provided protein supplement with and without salt. Within each square, cows were randomly assigned to the following treatments: (1) control (<10 mg/L sulfate); (2) 473 mg/L; (3) 946 mg/L; and (4) 1,420 mg/L. All cattle were provided a crude protein supplement at 0.18% of BW daily (0800 h daily); however, protein supplement NaCl composition differed by square (no NaCl vs. addition of 25% NaCl). Each period consisted of a 14-d adaptation period, followed by a 7-d intake and digestion period with ruminal profiles conducted on d 22 and complete ruminal evacuations on d 23, 5 h after feeding. Results and Discussion. There were no observed effects of sulfate (SO4) levels on forage intake, water intake, ruminal DM and liquid fill, ruminal DM and NDF digestibility, ruminal liquid passage rate, ruminal liquid turnover, ruminal liquid flow rate, ruminal pH, ruminal ammonia, ruminal total VFA concentrations, ruminal individual VFA concentrations, or the ruminal acetate-to-propionate ratio (P ≥ 0.16). Furthermore, the addition of 25% salt to supplement had no effect on forage intake, ruminal DM and liquid fill, DM and NDF digestibility, liquid passage rate, liquid turnover, liquid flow rate, ruminal pH, or the acetate-to-propionate ratio (P ≥ 0.24). Conversely, water intake was greater for animals provided 25% salt in supplement compared with animals not provided salt (P = 0.05). Implications and Applications. Sulfate water concentrations as high as 1,420 mg/L had minimal effects on intake, digestibility, and rumen fermentation characteristics of cattle consuming low-quality forage-based diets when provided a protein supplement containing up to 25% salt.
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    Evaluating the Cumulative Effects of Livestock Grazing on Wildlife With an Integrated Population Model
    (Frontiers Media SA, 2022-05) Milligan, Megan C.; McNew, Lance B.
    Livestock grazing can shape temperate grassland ecosystems, with both positive and negative effects on wildlife documented depending on a variety of grazing and site factors. Historically, research investigating the impacts of livestock grazing on wildlife has been limited by a narrow focus on simple “grazed” vs. “ungrazed” treatments or examining how grazing affects only a single vital rate in isolation. To overcome these limitations, we used a two-stage class, female-based integrated population model (IPM) to examine whether three grazing management regimes (season-long, rest-rotation, and summer rotation) differentially impacted population growth rates of sharp-tailed grouse (Tympanachus phasianellus) in eastern Montana and western North Dakota. We estimated 14 vital rates related to survival and fecundity and examined whether subtle cumulative effects of livestock grazing were present but not detected in prior analyses focused on single vital rates. While the management regimes did not differentially impact survival or fecundity of female grouse in our study system, we found evidence for significant cumulative impacts of grazing regime on population growth rates that were only apparent when all vital rates were evaluated concurrently. Population growth rates were higher in areas managed with season-long livestock grazing. The IPM framework encourages comprehensive investigations into the influence of covariates on critical components of species life histories and can assist in guiding management decisions in a world of limited resources. This integrated approach allowed us to more efficiently use multiple data types to provide a more complete picture of the effects of management on an important indicator species.
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    Perceived Stress and Molecular-BV in the NIH Longitudinal Study of Vaginal Flora
    (Oxford University Press, 2021-05) Turpin, Rodman; Slopen, Natalie; Borgogna, Joanna C.; Yeoman, Carl J.; He, Xin; Miller, Ryan S.; Klebanoff, Mark A.; Ravel, Jacques; Brotman, Rebecca M.
    Vaginal microbiota provide the first line of defense against urogenital infections primarily through protective actions of Lactobacillus spp. Perceived stress increases susceptibility to infection through several mechanisms, including suppression of immune function. We investigated if stress was associated with deleterious changes to vaginal bacterial composition in a subsample of 572 women in the Longitudinal Study of Vaginal Flora, sampled from 1999 through 2002. Using Cox proportional-hazard models, both unadjusted and adjusted for sociodemographics and sexual behaviors, participants who exhibited a 5 unit-increase in Cohen’s perceived stress scale had greater risk (aHR=1.40, 95% CI 1.13-1.74) of developing molecular bacterial vaginosis (BV), a state with low Lactobacillus abundance and diverse anaerobic bacteria. A 5-unit stress increase was also associated with greater risks for transitioning from the L. iners-dominated community state type (26% higher) to molecular-BV (aHR=1.26, 95% CI 1.01-1.56) or maintaining molecular-BV from baseline (aHR=1.23, 95% CI 1.01-1.47). Inversely, women with baseline molecular-BV reporting a 5-unit stress increase were less likely to transition to microbiota dominated by L. crispatus, L. gasseri, or L. jensenii (aHR=0.81, 95% CI 0.68-0.99). These findings suggest psychosocial stress is associated with vaginal microbiota composition, inviting a more mechanistic exploration of the relationship between psychosocial stress and molecular-BV.
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    Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp.
    (American Society for Microbiology, 2021-04) Borgogna, Joanna-Lynn C.; Shardell, Michelle D.; Grace, Savannah G.; Santori, Elisa K.; Americus, Benjamin; Li, Zhong; Ulanov, Alexander; Forney, Larry; Nelson, Tiffanie M.; Brotman, Rebecca M.; Ravel, Jacques; Yeoman, Carl J.
    Bacterial vaginosis (BV) is the most common vaginal disorder of reproductive-aged women, yet its etiology remains enigmatic. One clinical symptom of BV, malodor, is linked to the microbial production of biogenic amines (BA). Using targeted liquid chromatography mass spectrometry, we analyzed 149 longitudinally collected vaginal samples to determine the in vivo concentrations of the most common BAs and then assessed their relationship to BV and effect upon the growth kinetics of axenically cultured vaginal Lactobacillus species. Increases in cadaverine, putrescine, and tyramine were associated with greater odds of women transitioning from L. crispatus-dominated vaginal microbiota to microbiota that have a paucity of Lactobacillus spp. and from Nugent scores of 0 to 3 to Nugent scores of 7 to 10, consistent with BV. Exposure to putrescine lengthened the lag time and/or slowed the growth of all vaginal Lactobacillus spp. except L. jensenii 62G. L. iners AB107’s lag time was lengthened by cadaverine but reduced in the presence of spermidine and spermine. The growth rate of L. crispatus VPI 3199 was slowed by cadaverine and tyramine, and strain-specific responses to spermine and spermidine were observed. BAs were associated with reduced production of d- and l-lactic acid by vaginal Lactobacillus spp., and this effect was independent of their effect upon Lactobacillus species growth. The exceptions were higher levels of d- and l-lactic acid by two strains of L. crispatus when grown in the presence of spermine. Results of this study provide evidence of a direct impact of common biogenic amines on vaginal Lactobacillus spp.
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    Bacterial communities in the rumen and feces of lactating Holstein dairy cows are not affected when fed reduced-fat dried distillers’ grains with solubles
    (Elsevier BV, 2021-07) Dankwa, A.S.; Humagain, U.; Ishaq, S.L.; Yeoman, C.J.; Clark, S.; Beitz, D.C.; Testroet, E.D.
    Reduced-fat dried distillers’ grains with solubles (RF-DDGSs) are co-products of ethanol production and contain less fat than traditional distillers’ grains. The fat in corn is ~91% unsaturated, and it is toxic to rumen microorganisms so it could influence the composition of the rumen microbiome. It has been demonstrated that RF-DDGS is a suitable ration ingredient to support the high-producing dairy cow, and this feedstuff is a promising alternative protein source for lactating dairy cows. The current study aims to better understand the effect of RF-DDGS on the rumen and fecal bacterial composition in lactating dairy cows. Thirty-six multiparous (two or three), mid-lactation Holstein cows (BW = 680 – 11 kg; 106 – 27 DIM) were randomly assigned to two groups which were fed a control diet made up of corn, corn silage, and alfalfa hay supplemented with expeller soybean meal or with added RF-DDGS (20% of the DM) containing approximately 6.0% fat. Whole rumen contents (rumen fluid and digesta; esophageal tubing method) and feces (free-catch method) were collected on day 35 of the experimental period, after the 14-d acclimation period. Rumen contents and feces from each cow were used for DNA extraction. The bacterial community composition in rumen and fecal samples was assessed via the 16S rRNA gene by using the Illumina MiSeq sequencing platform. Bacteroidetes, Actinobacteria, and Firmicutes were the most abundant phyla in rumen contents. The fecal microbiota was dominated by the phyla Firmicutes and Bacteroidetes, as well as Actinobacteria and Chloroflexi. RF-DGGS increased bacterial richness, evenness, and Shannon diversity in both rumen and fecal samples and was associated with several taxa that had different abundance in treatment versus control comparisons. The RF-DGGS, however, did not significantly alter the bacterial community in the rumen or feces. In general, these findings demonstrated that dietary inclusion of RF-DDGS did not impose any serious short-term (within 30 days) health or production consequences, as would be expected. With this study, we present further evidence that inclusion of 20% (DM basis) RF-DDGS in the diet of lactating dairy cows can be done without consequence on the microbiome of the rumen.
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    Relationships among intramammary health, udder and teat characteristics, and productivity of extensively managed ewes
    (Oxford University Press, 2021-02) Knuth, Ryan M.; Stewart, Whit C.; Taylor, Joshua B.; Bisha, Bledar; Yeoman, Carl J.; Van Emon, Megan L.; Murphy, Thomas W.
    Mastitis is an economically important disease and its subclinical state is difficult to diagnose, which makes mitigation more challenging. The objectives of this study were to screen clinically healthy ewes in order to 1) identify cultivable microbial species in milk, 2) evaluate somatic cell count (SCC) thresholds associated with intramammary infection, and 3) estimate relationships between udder and teat morphometric traits, SCC, and ewe productivity. Milk was collected from two flocks in early (<5 d) and peak (30 to 45 d) lactation to quantify SCC (n = 530) and numerate cultivable microbial species by culture-based isolation followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; n = 243) identification. Within flock and lactation stage, 11% to 74% (mean = 36%) of samples were culture positive. More than 50 unique identifications were classified by MALDI-TOF MS analysis, and Bacillus licheniformis (18% to 27%), Micrococcus flavus (25%), Bacillus amyloliquefaciens (7% to 18%), and Staphylococcus epidermidis (26%) were among the most common within flock and across lactation stage. Optimum SCC thresholds to identify culture-positive samples ranged from 175 × 103 to 1,675 × 103 cells/mL. Ewe productivity was assessed as total 120-d adjusted litter weight (LW120) and analyzed within flock with breed, parity, year, and the linear covariate of log10 SCC (LSCC) at early or peak lactation. Although dependent on lactation stage and year, each 1-unit increase in LSCC (e.g., an increase in SCC from 100 × 103 to 1,000 × 103 cells/mL) was predicted to decrease LW120 between 9.5 and 16.1 kg when significant. Udder and teat traits included udder circumference, teat length, teat placement, and degree of separation of the udder halves. Correlations between traits were generally low to moderate within and across lactation stage and most were not consistently predictive of ewe LSCC. Overall, the frequencies of bacteria-positive milk samples indicated that subclinical mastitis (SCM) is common in these flocks and can impact ewe productivity. Therefore, future research is warranted to investigate pathways and timing of microbial invasion, genomic regions associated with susceptibility, and husbandry to mitigate the impact of SCM in extensively managed ewes.
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    In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
    (American Society for Microbiology, 2021-04) Yeoman, Carl J.; Fields, Christopher J.; Lepercq, Pascale; Ruiz, Philippe; Forano, Evelyne; White, Bryan A.; Mosoni, Pascale
    Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes , Ruminococcus albus , and Ruminococcus flavefaciens , has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production.
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    Evaluating the effects of finishing diet and feeding location on sheep performance, carcass characteristics, and internal parasites
    (Korean Society of Animal Science and Technology, 2021-05) Ragen, Devon L.; Butler, Molly R.; Boles, Jane A.; Layton, William A.; Craig, Thomas M.; Hatfield, Patrick G.
    A 3 yr experiment was conducted to evaluate the influence of diet and feeding location on animal performance, carcass characteristics, whole blood counts, and internal parasite burden of lambs assigned to 1 of 4 treatments: 1) confinement fed 71% alfalfa, 18% barley pellet, 5% molasses, 0.013% Bovatec, 6.1% vitamin/mineral package diet (CALF), 2) confinement fed 60% barley, 26% alfalfa pellet, 4% molasses, 2.5% soybean-hi pro, 0.016% Bovatec, 7.4% vitamin/mineral package diet (CBAR), 3) field fed 71% alfalfa, 18% barley pellet, 5% molasses, 0.013% Bovatec, 6.1% vitamin/mineral package diet (FALF), and 4) field fed 60% barley, 26% alfalfa pellet, 4% molasses, 2.5% soybean-hi pro, 0.016% Bovatec, 7.4% vitamin/mineral package diet (FBAR). A year × location interaction was detected for ending body weight (BW), average daily gain (ADG), and dry matter intake (DMI); therefore results are presented by year. In all years, cost of gain and DMI were greater for CALF and FALF than for CBAR and FBAR feed treatments (p ≤ 0.03). In yr 2 and 3 field treatments had greater ending BW and ADG than confinement treatments. For all years, diet did not affect ending BW or ADG. In yr 1 dressing percent and rib eye area were greater for field finished lambs than confinement finished (p ≤ 0.02) and Warner-Bratzler shear force was greater for CALF and FALF (p = 0.03). In yr 2 lambs in FALF and FBAR treatments had greater leg scores and conformation than CALF and CBAR (p = 0.09). In yr 1, FALF had a greater small intestine total worm count than all other treatments. In yr 1, ending Trichostrongyle type egg counts were greater for FALF (p = 0.05). In yr 2, ending Nematodirus spp. egg counts were greater for FALF and lowest for CBAR (p < 0.01). Abomasum Teladorsagia circumcinta worm burden was greater in CALF than all other treatments (p = 0.07) in yr 2. While field finishing lambs with a grain- or forage-based diet we conclude that it is possible to produce a quality lamb product without adverse effects to animal performance, carcass quality or increasing parasite burdens.
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    Direct Phenotyping and Principal Component Analysis of Type Traits Implicate Novel QTL in Bovine Mastitis through Genome-Wide Association
    (MDPI AG, 2021-04) Miles, Asha M.; Posbergh, Christian J.; Huson, Heather J.
    Our objectives were to robustly characterize a cohort of Holstein cows for udder and teat type traits and perform high-density genome-wide association studies for those traits within the same group of animals, thereby improving the accuracy of the phenotypic measurements and genomic association study. Additionally, we sought to identify a novel udder and teat trait composite risk index to determine loci with potential pleiotropic effects related to mastitis. This approach was aimed at improving the biological understanding of the genetic factors influencing mastitis. Cows (N = 471) were genotyped on the Illumina BovineHD777k beadchip and scored for front and rear teat length, width, end shape, and placement; fore udder attachment; udder cleft; udder depth; rear udder height; and rear udder width. We used principal component analysis to create a single composite measure describing type traits previously linked to high odds of developing mastitis within our cohort of cows. Genome-wide associations were performed, and 28 genomic regions were significantly associated (Bonferroni-corrected p < 0.05). Interrogation of these genomic regions revealed a number of biologically plausible genes whicht may contribute to the development of mastitis and whose functions range from regulating cell proliferation to immune system signaling, including ZNF683, DHX9, CUX1, TNNT1, and SPRY1. Genetic investigation of the risk composite trait implicated a novel locus and candidate genes that have potentially pleiotropic effects related to mastitis.
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    Identification of Genomic Regions for Carcass Quality Traits within the American Simmental Association Carcass Merit Program
    (MDPI, 2021-02) Hieber, Jordan K.; Endecott, Rachel L.; Boles, Jane A.; Thomson, Jennifer M.
    USDA quality and yield grade are primary driving forces for carcass value in the United States. Carcass improvements can be achieved by making selection decisions based on the results of genetic evaluations in the form of expected progeny differences (EPD), real-time ultrasound imaging, and physical evaluation of candidate breeding animals. In an effort to advance their ability to accurately predict the breeding value of potential sires for carcass traits, the American Simmental Association launched the Carcass Merit Program as a means to collect progeny sire group carcass information. All records were extracted from the American Simmental Association database. Progeny data were organized by sire family and progeny performance phenotypes were constructed. Sire genotypes were filtered, and a multi-locus mixed linear model was used to perform an association analysis on the genotype data, while correcting for cryptic relatedness and pedigree structure. Three chromosomes were found to have genome-wide significance and this conservative approach identified putative QTL in those regions. Three hundred ninety-three novel regions were identified across all traits, as well as 290 novel positional candidate genes. Correlations between carcass characteristics and maternal traits were less unfavorable than those previously reported.
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    Differential haptoglobin responsiveness to a Mannheimia haemolytica challenge altered immunologic, physiologic, and behavior responses in beef steers
    (Oxford University Press, 2021-01) Wottlin, Lauren R.; Carstens, Gordon E.; Kayser, William C.; Pinchak, William E.; Thomson, Jennifer M.; Copie, Valerie; O'Shea-Stone, Galen P.
    Indicator traits associated with disease resiliency would be useful to improve the health and welfare of feedlot cattle. A post hoc analysis of data collected previously (Kayser et al., 2019a) was conducted to investigate differences in immunologic, physiologic, and behavioral responses of steers (N = 36, initial BW = 386 ± 24 kg) that had differential haptoglobin (HPT) responses to an experimentally induced challenge with Mannheimia haemolytica (MH). Rumen temperature, DMI, and feeding behavior data were collected continuously, and serial blood samples were collected following the MH challenge. Retrospectively, it was determined that 9 of the 18 MH-challenged steers mounted a minimal HPT response, despite having similar leukocyte and temperature responses to other MH-challenged steers with a greater HPT response. Our objective was to examine differences in behavioral and physiological responses between MH-challenged HPT responsive (RES; n = 9), MH-challenged HPT nonresponsive (NON; n = 9), and phosphate-buffered saline-inoculated controls (CON; n = 18). Additionally, 1H NMR analysis was conducted to determine whether the HPT-responsive phenotype affected serum metabolite profiles. The RES steers had lesser (P < 0.05) cortisol concentrations than NON and CON steers. The magnitude of the increases in neutrophil concentrations and rumen temperature, and the reduction in DMI following the MH challenge were greatest (P < 0.05) in RES steers. Univariate analysis of serum metabolites indicated differences between RES, NON, and CON steers following the MH challenge; however, multivariate analysis revealed no difference between HPT-responsive phenotypes. Prior to the MH challenge, RES steers had longer (P < 0.05) head down and bunk visit durations, slower eating rates (P < 0.01) and greater (P < 0.05) daily variances in bunk visit frequency and head down duration compared with NON steers, suggesting that feeding behavior patterns were associated with the HPT-responsive phenotype. During the 28-d postchallenge period, RES steers had decreased (P < 0.05) final BW, tended (P = 0.06) to have lesser DMI, and had greater (P < 0.05) daily variances in head down and bunk visit durations compared with NON steers, which may have been attributed to their greater acute-phase protein response to the MH challenge. These results indicate that the HPT-responsive phenotype affected feeding behavior patterns and may be associated with disease resiliency in beef cattle.
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