PSI-10 Effects of a Moderate and Aggressive Implant Strategy on the Rumen Microbial Community in Steers

Abstract The effects of growth-promoting implant strategies have been well-defined in research for their ability to impact growth performance in beef cattle. Production-relevant microbiomes in the rumen have also been associated with growth traits. However, the role of implant strategies on the rumen microbiome is not understood. The objective was to determine if varying doses of implant hormones cause gain-associated ruminal microbial community shifts. To assess this, a completely randomized design was used and 336 fall-born steers from the germplasm evaluation population between 450–470 days of age at the U.S. Meat Animal Research Center (Clay Center, NE) were divided into two treatment groups: 1) a moderate implant strategy of Revalor-IS (80 mg trenbolone acetate, 16 mg estradiol) followed by Revalor-S (120 mg trenbolone acetate, 24 mg estradiol) and 2) an aggressive implant strategy of Revalor-IS followed by Revalor-200 (200 mg trenbolone acetate, 20 mg estradiol). Steers were fed the same diet (57.0% dry-rolled corn, 30% wet distiller’s grains with solubles, 8.0% alfalfa hay, 4.25% supplement, and 0.75% urea, DM basis). Body weights were collected once per month with initial weights of 439.8 ± 43.1 kg. After implants were administered for 84 days, rumen content was collected via orogastric tubing. Samples were sequenced targeting bacterial V1-V3 16S rRNA gene regions, V3-V4 for archaea, and partial 18S rRNA gene of protozoa. Sequences were processed in R utilizing Phyloseq and analyzed with DESeq2 to test differential abundances. Production data between implant strategies were analyzed using a mixed model ANOVA (SASv9.4, Cary, NC). Alpha- and beta-diversity between strategies did not differ for bacteria, archaea, or protozoa (P > 0.05). Average daily gain was different (P = 0.01; 1.72 vs 1.66 ± 0.02 kg, aggressive vs moderate, respectively); however, large microbial community shifts were not associated implant strategy. USDA is an equal opportunity provider and employer.

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The nasopharyngeal, ruminal, and vaginal microbiota and the core taxa shared across these microbiomes in virgin yearling heifers exposed to divergent in utero nutrition during their first trimester of gestation and in pregnant beef heifers in response to mineral supplementation

10.1101/2021.06.03.446997 ◽

2021 ◽

Author(s):

Samat Amat ◽

Devin B Holman ◽

Kaycie Schmidt ◽

Ana Clara B Menezes ◽

Friederike Baumgaertner ◽

...

Keyword(s):

Mixed Model ◽

Linear Mixed Model ◽

First Trimester ◽

Nervous System Development ◽

Vaginal Microbiota ◽

Rrna Gene ◽

Beef Heifers ◽

Mineral Supplement ◽

Alpha And Beta Diversity ◽

Significant Difference

Emerging evidence has indicated that microbial transmission from the bovine dam to her fetus may take place before birth, and that the maternal microbiota during pregnancy modulates programming of fetal metabolic and nervous system development, highlighting the potential and extended role of the maternal microbiome in calf health and development. In the present study, we characterized the nasopharyngeal, ruminal and vaginal microbiota from two cohorts of beef heifers managed at the same location: 1) virgin yearling heifers (9 months old) born from dams received gestational diets which resulted in low (LG, n = 22) or medium (MG, n = 23) weight gain during the first 84 days of gestation; and 2) pregnant replacement heifers that received a vitamin and mineral supplement (VTM, n = 17) or not (Control, n = 15) during the first 6 months of gestation. Nasopharyngeal and vaginal swabs as well as ruminal fluid were collected from both cohorts and the microbiota of each sample was assessed using 16S rRNA gene sequencing. In addition to the comparison between treatment groups within each cohort, the similarity of the microbiota of the three sample types were evaluated, and shared taxa amongst these communities were identified. The bacterial genera present in the rumen and vagina that can influence methanogenic archaeal genera were predicted using a stepwise-selected generalized linear mixed model. No significant difference was observed in the alpha and beta diversity in any of the nasopharyngeal, ruminal and vaginal microbiota between LG and MG offspring virgin heifers, or between the control and VTM pregnant heifers (p > 0.05). Subtle compositional changes in the vaginal microbiota in yearling heifers, and in the nasopharyngeal and ruminal microbiota of pregnant heifers were detected in response to treatments. Forty-one archaeal and bacterial OTUs were shared by over 60% of all samples from both virgin and pregnant heifers. Two taxa within the Methanobrevibacter genus were identified as core taxa and this genus was more relatively abundant in pregnant heifers compared to virgin heifers. Among the 25 top genera, Prevotella and Prevotella UCG-003 (negative) and Christensenellaceae R-7 group (positive) were predicted to have a significant effect on ruminal Methanobrevibacter spp. The results of this study indicate that there is little impact of divergent gestational nutrition during the first trimester on the calf microbiome at 9 months postnatal, and that VTM supplementation during pregnancy may not alter the maternal microbiome. This study provides evidence that there are several microbial taxa, including methanogenic archaea, that are shared across the respiratory, gastrointestinal, and reproductive tracts, suggesting the need for a holistic evaluation of the bovine microbiota when considering potential maternal sources for seeding calves with pioneer microbiota.

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Characterization of growth traits of Greenland and Silver coypus under captivity conditions

The Journal of Agricultural Science ◽

10.1017/s0021859605005265 ◽

2005 ◽

Vol 143 (2-3) ◽

pp. 199-207 ◽

Cited By ~ 3

Author(s):

C. FAVERIN ◽

C. A. MEZZADRA ◽

H. M. FERNÁNDEZ ◽

L. M. MELUCCI

Keyword(s):

Mixed Model ◽

Growth Traits ◽

Average Daily Gain ◽

Von Bertalanffy ◽

Birth Season ◽

Myocastor Coypus ◽

Mean Values ◽

Estimated Parameters ◽

Maturation Rate ◽

Almost All

Brody, Gompertz, Logistic, Richards and von Bertalanffy functions were compared as descriptors of growth in 319 coypus (Myocastor coypus) of Greenland and Silver varieties, from birth to 10–19 months of age. Several criteria were considered for the selection of the model: (a) bias in the asymptotic weight; (b) bias in birth weight; (c) error sum of squares; (d) error mean squares weighted by the number of animals converging in all functions; (e) determination coefficient. To adjust the curves NLIN procedure from SAS and iterative method of Marquardt were applied. A mixed model was used to analyse the parameters of the selected growth curve (asymptotic weight, A; constant of integration, B; and maturation rate, k) which included effects of farm, variety, sex, sire within farm and variety, reproductive status within sex, birth season and first order interactions. The effect of sire was considered as random. The von Bertalanffy function was selected and mean values for the parameters of this function were 8016 g and 0·008 g/g per day, for A and k respectively. There were differences in the estimated parameters between sexes; males had larger values of A and k than females.Weights at fixed ages (birth, weaning, 6–7 months) were analysed, as well as the final recorded weight and average postweaning gain. The model of analysis was similar to the previous one. There were no differences between varieties. Significant differences between sexes for almost all studied traits were detected. With age, weight difference between males and females increased. At 6 months of age, males were 37% heavier than females. Male average daily gain was higher than that of females, sexual dimorphism being evident in all analysed traits.

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Succession of bacterial communities on carrion is independent of vertebrate scavengers

10.1101/744748 ◽

2019 ◽

Author(s):

Cody R. Dangerfield ◽

Ethan Frehner ◽

Evan Buechley ◽

Çağan H. Şekercioğlu ◽

William J. Brazelton

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Rrna Gene ◽

Scavenging Activity ◽

Ecological Interactions ◽

Tissue Samples ◽

Ultimate Result ◽

Community Shifts ◽

Micro Organisms ◽

Carrion Decomposition

AbstractThe decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by scavenging.

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Ethnic variation of oral microbiota in children

Scientific Reports ◽

10.1038/s41598-020-71422-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Thyagaseely S. Premaraj ◽

Raven Vella ◽

Jennifer Chung ◽

Qingqi Lin ◽

Panier Hunter ◽

...

Keyword(s):

Microbial Community ◽

Ethnic Group ◽

Ethnic Groups ◽

Bacterial Species ◽

Plaque Index ◽

Rrna Gene ◽

Oral Microbiota ◽

Ethnic Variation ◽

Alpha And Beta Diversity ◽

Supragingival Plaque

Abstract Despite widely used preventive measures such as sealant programs to control caries prevalence, disparities are seen among ethnic groups. Supragingival plaque harbors hundreds of bacterial species, playing a significant role in oral health and disease. It is unknown whether the ethnic variation influences the supragingival microbiota in children. In our study, variations in microbiota of the supragingival plaque was investigated from 96 children between 6 and 11 years old in four ethnic groups (African American, Burmese, Caucasian, and Hispanic) from the same geographic location by 16S rRNA gene sequencing. We found that the microbial alpha and beta diversity of supragingival microbiota significantly differed between ethnic groups. The supragingival plaque microbiota had the most complex microbial community in Burmese children. Within-group microbiota similarity in Burmese or Caucasian children was significantly higher than between-groups similarity. We identified seven ethnic group-specific bacterial taxa after adjusting for dental plaque index, decayed missing filled teeth (DMFT) and the frequency of brushing. Children with high plaque index and high DMFT values were more similar to each other in the overall microbial community, compared to low plaque index or low DMFT groups in which inter-subject variation is high. Several bacterial taxa associated with high plaque index or high DMFT were ethnic group-specific. These results demonstrated that supragingival microbiota differed among ethnicity groups in children.

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Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa211 ◽

2020 ◽

Vol 96 (12) ◽

Author(s):

Alicia Balbín-Suárez ◽

Maik Lucas ◽

Doris Vetterlein ◽

Søren J Sørensen ◽

Traud Winkelmann ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Rrna Gene ◽

Apple Rootstocks ◽

Apple Replant Disease ◽

Alpha And Beta Diversity ◽

Replant Disease ◽

Split Root ◽

And Control

ABSTRACT Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible ‘M26’ apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil–root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil–root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.

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69 The ability of an artificial sweetener (Sucram®) to influence microbial community structure in the rumen papillae and content through the production of microbial-based neurochemicals

Journal of Animal Science ◽

10.1093/jas/skz258.208 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 100-101

Author(s):

Mark Lyte ◽

Lucas Koester ◽

Stephan Schmitz-Esser

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Ex Vivo ◽

16S Rrna Gene Sequencing ◽

Rumen Content ◽

Rrna Gene ◽

Artificial Sweetener ◽

Rumen Microbes ◽

Host Physiology ◽

Methane Reduction

Abstract The study of microorganisms to produce and utilize neurochemical signaling molecules that interact with the host is the emerging field known as microbial endocrinology. Production of these molecules can be regulated by several different environmental factors, including diet. The effect of artificial sweeteners on ruminant gastrointestinal tract microbiota and the ability of individual members to produce neurochemicals that may determine community composition and affect host physiology are unknown. To analyze whether an artificial sweetener (Sucram®, Pancosma, Switzerland) affects rumen content (RC) and rumen papillae (RP) microbiota, six fistulated, lactating Holstein cows were sampled before (baseline) and after exposure to Sucram®. 16S rRNA gene sequencing was conducted to identify Sucram®-induced microbial community changes. Additionally, ex vivo microbial cultures were used to identify neurochemical production in RP bacteria. Exposure to Sucram significantly increased the abundance of Operational Taxonomic Units (OTUs) belonging to Ruminobacter, Prevotella, Sharpea, Ruminococcus and Rikenella on the RP. These organisms have been reported to aid in digestion of feedstuffs and methane reduction, suggesting that Sucram® may induce beneficial shifts in rumen microbial communities. To gain preliminary insight into neurochemical production of RP microorganisms, we tested four different Lactobacillus isolates from RP for neurochemical production. We observed that the neurochemicals DOPAC (3,4-Dihydroxyphenylacetic acid) and L-DOPA (L-3,4-dihydroxyphenylalanine) were produced by three and four isolates, respectively. Ongoing experiments are evaluating the effects of Sucram® on neurochemical production in a larger number of rumen microbes. Overall, we observed significant differences in OTU abundance in response to the addition of Sucram®. Additionally, we confirmed that RP bacteria can produce neurochemicals. Both of these results are key to understanding how Sucram® modifies microbial communities within the rumen and possibly influences host physiology. Research into microbial endocrinology-based neurochemical signaling between rumen microbiota and their animal hosts may lead to advancement of livestock feed efficiency and welfare.

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Evaluating the Impact of Wastewater Effluent on Microbial Communities in the Panke, an Urban River

Water ◽

10.3390/w11050888 ◽

2019 ◽

Vol 11 (5) ◽

pp. 888 ◽

Cited By ~ 2

Author(s):

Marcella Nega ◽

Burga Braun ◽

Sven Künzel ◽

Ulrich Szewzyk

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Sampling Site ◽

River Sediments ◽

Microbial Community Composition ◽

Rrna Gene ◽

Sequencing Data ◽

Alpha And Beta Diversity ◽

The Impact

Pharmaceuticals are consumed in high amounts and can enter as emerging organic compounds in surface waters as they are only partially retained in wastewater treatment plants (WWTPs). Receiving pharmaceuticals may burden the aquatic environment, as they are designed to be bioactive even at low concentrations. Sediment biofilm populations were analyzed in river sediments due to the exposure of an inflow of WWTP effluents. Illumina MiSeq 16S rRNA gene amplicon sequencing was performed of 108 sediment samples, which were taken from multiple cores within three sampling locations in the Panke River, with one sampling site located downstream of the inflow. Sequencing data were processed to infer microbial community structure in samples concerning the environmental variables, such as micropollutants and physicochemical parameters measured for each core. More than 25 different micropollutants were measured in pore water samples, in which bezafibrate, clofibric acid, carbamazepine, and diclofenac were detected at high concentrations. Bacterial 16S rRNA gene amplicons revealed Nitrospirae, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Bacteroidetes, and Ignavibacteriae as the most abundant groups in the samples. Differences in microbial community composition were observed with respect to micropollutants. However, our findings revealed that the composition of the microbial community was not only governed by the effluent. The significant changes in the alpha- and beta-diversity were explained by phenobarbital and SO42−, which did not originate from the WWTP indicating that more unobserved factors are also likely to play a role in affecting the biofilm community’s composition.

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Conventional and Mixed Model Approach to Estimate Heterosis of the Growth Traits in Boer Goat’s Crossbred Offspring Populations

Caraka Tani Journal of Sustainable Agriculture ◽

10.20961/carakatani.v34i1.27620 ◽

2019 ◽

Vol 34 (1) ◽

pp. 55

Author(s):

Nuzul Widyas ◽

Sigit Prastowo ◽

Tristianto Nugroho ◽

Adi Ratriyanto

Keyword(s):

Conventional Method ◽

Mixed Model ◽

Growth Traits ◽

Average Daily Gain ◽

Random Effect ◽

Model Analysis ◽

Parameters Estimation ◽

Mixed Model Analysis ◽

Mixed Model Approach ◽

Model Approach

Heterosis is often utilized as a success indicator in a crossbreeding program. It is defined as the deviation of the crossbred means relative to their parental breeds. Heterosis mechanism is highly dependent on the genetic factors and thus, we incorporated genetic information in its estimation. The objective of this article was to compare heterosis estimated with conventional and mixed model approaches. In total, phenotypes of 3804 individuals were recorded. Data were obtained from a crossbreeding experiment involving Boer bucks and Jawarandu does. Observed traits were birth weight, weaning weight and average daily gain. Conventional and mixed model methods were used to estimate the heterosis. The heterosis values (%) between B×B vs B×J, estimated with conventional method were -11.38, -10.51 and -10.39; with mixed model were -6.23, -9.27 and -9.68 for BW, WW and ADG respectively. Heterosis values in B×(B×J) relative to B×B, estimated with conventional method were -6.16, -10.35 and -11.69; whereas with mixed model were -8.01, -10.82 and -9.14 for BW, WW and ADG respectively. Conventional method tends to underestimate the means phenotype with lower standard errors compared to mixed model analysis results in all traits. Conventional method also introduces biased heterosis estimates compared to the mixed model. Conventional method ignores any potential effects in the estimation procedures; whereas mixed model approach incorporates all the systematic and random effect including family relationship information. Thus, mixed model produced more reliable results in genetic parameters estimation. We recommend employing mixed model analysis in estimating heterosis.

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Cerumen microbial community shifts between healthy and otitis affected dogs

PLoS ONE ◽

10.1371/journal.pone.0241447 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241447

Author(s):

Giorgia Borriello ◽

Rubina Paradiso ◽

Carlotta Catozzi ◽

Roberta Brunetti ◽

Paola Roccabianca ◽

...

Keyword(s):

Bacterial Community ◽

Otitis Externa ◽

Pcr Amplification ◽

Personal Genome ◽

Rrna Gene ◽

Alpha And Beta Diversity ◽

Paired Samples ◽

Community Shifts ◽

Healthy Dogs ◽

The Right

Otitis externa is a common multifactorial disease in dogs, characterized by broad and complex modifications of the ear microbiota. The goal of our study was to describe the ear cerumen microbiota of healthy dogs, within the same animal and between different animals, and to compare the cerumen microbiota of otitis affected dogs with that of healthy animals. The present study included 26 healthy dogs, 16 animals affected by bilateral otitis externa and 4 animals affected by monolateral otitis externa. For each animal cerumen samples from the right and left ear were separately collected with sterile swabs, and processed for DNA extraction and PCR amplification of the 16S rRNA gene. Amplicon libraries were sequenced using an Ion Torrent Personal Genome Machine (PGM), and taxonomical assignment and clustering were performed using QIIME 2 software. Our results indicate that the bacterial community of the cerumen in healthy dogs was characterized by extensive variability, with the most abundant phyla represented by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Fusobacteria. The analysis of both alpha and beta diversity between pairs of left and right ear samples from the same dog within the group of affected animals displayed higher differences than between paired samples across healthy dogs. Moreover we observed reduced bacterial richness in the affected group as compared with controls and increased variability in population structure within otitis affected animals, often associated with the proliferation of a single bacterial taxon over the others. Moreover, Staphylococcus and Pseudomonas resulted to be the bacterial genera responsible for most distances between the two groups, in association with differences in the bacterial community structure. The cerumen microbiota in healthy dogs exhibits a complex bacterial population which undergoes significant modifications in otitis affected animals.

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PSIV-17 Impacts of high forage crude protein concentrations on the equine fecal microbiome

Journal of Animal Science ◽

10.1093/jas/skab235.546 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 297-297

Author(s):

Jennifer R Weinert ◽

Amy S Biddle ◽

Carey A Williams

Keyword(s):

Amino Acid ◽

Beta Diversity ◽

Crude Protein ◽

Mixed Model ◽

Short Chain Fatty Acids ◽

Acid Synthesis ◽

Rrna Gene ◽

Amino Acid Synthesis ◽

Fecal Microbiome ◽

Alpha And Beta Diversity

Abstract The objective of this study was to evaluate effects of forage crude protein (CP) concentrations on the equine fecal microbiome. Six mares were assigned to either a high-protein (HP; 24% CP) or normal-protein (NP; 15% CP) hay cube diet in a randomized cross-over design. Fecal samples were collected on the last day of each 35-d period. Branched-chain and short-chain fatty acids (SCFA) were measured by GC-MS; data were analyzed by mixed model ANOVA in R. 16S rRNA gene sequence analysis was conducted in Qiime2. Alpha and beta diversity were assessed by Kruskall-Wallis Tests and PERMANOVA. Taxonomy was assigned using SILVA. Metacyc pathways were predicted with PICRUSt2. Differential genus-level and pathway abundances were analyzed by LefSe (LDA >2.0). Significance was set at p≤0.05. Species richness did not differ by diet, but evenness was greater in NP vs. HP. Beta diversity metrics including Weighted UniFrac also differed by diet. Genera including Methanocorpusculum, Rikenellaceae RC9 gut group, and Eubacterium coprostanoligenes group were more abundant in HP. Treponema and Fibrobacters were more abundant in NP. Twenty pathways related to amino acid synthesis were identified as markers of NP, while 10 pathways related to amino acid degradation and SCFA synthesis were markers of HP. Pathway predictions were supported by metabolite analyses, with acetate (HP: 751; LP: 632 ± 49 ug/g), propionate (HP: 565; NP: 421 ± 43 ug/g), butyrate (HP: 341; LP: 210 ± 34 ug/g), and valerate (HP: 80; NP: 42 ± 11 ug/g) greater in HP than NP. Isobutyrate (HP: 108; NP: 94 ± 7 ug/g; P = 0.09), and isovalerate (HP: 91; NP: 48 ± 10 ug/g) were also greater in HP. These results demonstrate that consuming higher-CP forages impacts equine hindgut microbiota structure and function, leading to increased rates of protein fermentation. Further research is needed to determine physiological significance in forage-fed horses.

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