In March, 2020, campus restrictions associated with COVID-19 necessitated significant changes to ... more In March, 2020, campus restrictions associated with COVID-19 necessitated significant changes to undergraduate instruction at institutions of higher education. Rapid, unplanned transitions to remote learning caused disruptions for all educators, especially those who traditionally facilitate student learning via wet labs or live animal interactions, as is common within equine science and management courses. This study sought to identify teaching challenges and strategies associated with pandemic-era instruction among educators in equine science and management. Educators who taught undergraduate equine science or management courses in the United States before and after the spring of 2020 (n=43 respondents) completed an online survey
microbiota during the first 7 d post-weaning. The introduction of solid feed, and gradual transit... more microbiota during the first 7 d post-weaning. The introduction of solid feed, and gradual transition off a milk-based diet before weaning, may have allowed the microbiota to remain largely unchanged.
negative attitudes, long days, weather, and time away from family. The top positive themes or ben... more negative attitudes, long days, weather, and time away from family. The top positive themes or benefits included continued learning, meeting people, and personal fulfillment. Respondents were also asked why they became judges. Top responses included giving back to the program, helping others, and working with horses and youth, all of which may enhance the quality of life of judges and exhibitors. This information is important as it informs both the literature for future research on the horse judging experience, as well as administrators who may question the staff investment and impacts of 4-H horse judging activities.
possible that these materials may perform better than common products, but testing with horses is... more possible that these materials may perform better than common products, but testing with horses is limited. A pilot study was conducted to compare bedding characteristics of sawdust, hemp shavings, and chopped miscanthus as bedding materials for stalled horses. Sawdust and hemp were commercially produced and purchased. Miscanthus was grown, dried, and processed at the Murray State University West Farm. Treatments were evenly distributed between 12 stalls with horses randomly assigned to treatment. The order in which stalls were selected for evaluation of bedding characteristics was random. Bedding characteristics were evaluated daily by both stall cleaners and assigned reviewers, and included: urine containment (well, some, poor), ease of cleaning (easy, moderate, difficult), presence of odors (none, some, lots), and appearance (attractive, moderate, unattractive) of the bedding. Evaluations were performed using a standardized rubric based on a Likert-type scale for scoring, and comments were collected. After 10 d, the bedding was stripped from the stall and a different bedding evaluated. Routine daily exercise and turnout schedules were maintained, but horses spent the majority of their time in stalls. Chi-squared tests were performed using the PROC FREQ procedure of SAS to determine the relationship between bedding types and characteristics with significance declared at P < 0.05. Differences were found between bedding types for urine containment, ease of cleaning, appearance, and odor (P < 0.0001). Sawdust was reported to contain urine well 79.9% of the time as compared with only 49.1% and 39.9% for hemp and miscanthus, respectively. Stall cleaners indicated that sawdust was easy to clean 65.6% of the time, while hemp and miscanthus were more difficult to clean (29.7% and 71.6%, respectively). Sawdust was reported to have no odor 100% of the time, while miscanthus (8.2%) and hemp (10.7%) were reported to have either some or lots of odor. Finally, sawdust, hemp, and miscanthus were found to be attractive 94.9%, 61.3%, and 37.6% of the time, respectively. Miscanthus was reported as unattractive 35.3% of the time as compared with sawdust or hemp (0.8% and 18.2%, respectively). In conclusion, sawdust performed better than hemp and miscanthus as bedding material for stalled horses.
Integrating warm-season grasses into cool-season equine grazing systems can increase pasture avai... more Integrating warm-season grasses into cool-season equine grazing systems can increase pasture availability during summer months. The objective of this study was to evaluate effects of this management strategy on the fecal microbiome and relationships between fecal microbiota, forage nutrients, and metabolic responses of grazing horses. Fecal samples were collected from 8 mares after grazing cool-season pasture in spring, warm-season pasture in summer, and cool-season pasture in fall as well as after adaptation to standardized hay diets prior to spring grazing and at the end of the grazing season. Random forest classification was able to predict forage type based on microbial composition (accuracy: 0.90 ± 0.09); regression predicted forage crude protein (CP) and non-structural carbohydrate (NSC) concentrations (p < 0.0001). Akkermansia and Clostridium butyricum were enriched in horses grazing warm-season pasture and were positively correlated with CP and negatively with NSC; Clostr...
This study reports differential responses of the equine gut microbiome to protein- and/or carbohy... more This study reports differential responses of the equine gut microbiome to protein- and/or carbohydrate-based on keeper status [easy keeper (EK), medium keeper (MK), hard keeper (HK)]. Anaerobic microcosms were inoculated with equine feces from healthy animals on the same diets (n=12 total, n = 3 / EK, MK, HK of four breeds) with three dietary treatments [C = Carb (cornmeal), P = Protein (soybean meal), M = mix (50% C, 50% P), and F = fecal (no additive)]. Over 48 hours, fermentation products were measured using colorimetric assays and high performance liquid chromatography. Microbial populations were surveyed using 16S rRNA gene sequencing analyzed by QIIME2. Total SCFA production was not different between keeper status but the acetate: propionate ratio and isobutyrate production was greatest for HK and least for EK. Residual protein and carbohydrate at hour 48 was greatest in HK pointing to less efficient nutrient utilization. Diversity measures were not different between keeper st...
<p>Comparison of the distribution of the closest relatives of all <i>C</i>. <... more <p>Comparison of the distribution of the closest relatives of all <i>C</i>. <i>phytofermentans</i> open reading frames among sequenced bacterial genomes (left) to that of closest relatives of its glycoside hydrolases (right).</p
Background Diet is a key driver of equine hindgut microbial community structure and composition. ... more Background Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C–W) and WSG to CSG (W–C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing. Results Regardless of IRS or transition (C–W vs. W–C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting...
<p><b>(A)</b> A conceptual illustration of how GH (blue), ABC transporters (pur... more <p><b>(A)</b> A conceptual illustration of how GH (blue), ABC transporters (purple) and AraC regulators (red) may work together. <b>(B)</b> Number of AraC transcriptional regulators per genome. <b>(C)</b> Number of GH domains per genome. Organisms having both GH48 and GH9 are marked with two asterisks, and organisms having GH9 alone are marked with one asterisk. <b>(D)</b> Number of putative ABC transporters per genome.</p
<p>Taxa with sequenced genomes are marked with an asterisk. Cluster numbers correspond to t... more <p>Taxa with sequenced genomes are marked with an asterisk. Cluster numbers correspond to the cluster system of Collins et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118285#pone.0118285.ref068" target="_blank">68</a>]. Bootstrap values were determined for 1,000 replicates.</p
Antibiotic (AB) therapies commonly used by veterinarians to treat bacterial infections can have s... more Antibiotic (AB) therapies commonly used by veterinarians to treat bacterial infections can have side effects that stem from a disruption of the hindgut microbiota with a reduction of celluloytic bacteria and a proliferation of pathogenic strains. In practice, many veterinarians recommend a direct fed microbial (DFM) along with AB as DFM have been shown to mitigate some of the effects of AB on fecal microbiota. However, many commercially available DFM supplements also contain prebiotics, and there is little research on these microbial support supplements during AB administration. The purpose of this study was to determine the impact of Biome Fix (NutraWorks Equine) during AB treatment on fecal microbiome. Biome Fix is a blend of prebiotics (MOS, FOS, and Asperigullus niger extract), DigestaWell® Buffer (Probiotech International, Inc.), and DigestaWell® Fiber (Probiotech International, Inc.). Both DigestaWell® Buffer and Fiber have been previously shown to buffer fecal pH through reduced lactate production, and improve fiber digestibility in horses, respectively. Horses (n = 16) were assigned (blocked by age, sex, and BCS) to either Control (C:no supplement) or Biome Fix (BF:480g/d) for the 27d trial period. At d 0, all horses received AB (trimethoprim plus sulfadizine tablets (Uniprim) at 30mg/kg/d) for 7d. Fecal samples were collected at d 0, 7, 21, and 27. After DNA extraction from samples, the V3–V4 region of the bacterial 16S rRNA gene was amplified by PCR and amplicons were sequenced using Illumina MiSeq. Sequence analysis was conducted in QIIME 2, taxonomy was assigned against the SILVA database, and pair-wise t-tests were used to determine differences. Between d 0 and 27 in BF, there was an increase in Clostridium butyricum, a butyrate producer (P = 0.037), Anaerovibrio sp., a lipid degrader (P = 0.02), and 3 groups of Ruminococcaceae involved in fiber digestion (P
Dietary nutrients have been identified as drivers of gut microbial composition across animal spec... more Dietary nutrients have been identified as drivers of gut microbial composition across animal species. The aim of this study was to apply a biologically relevant computational approach to explore relationships between forage nutrients and the equine fecal microbiome. Fecal samples were collected from 8 mares grazing cool-season (CSG) and warm-season grass (WSG) rotational pastures at 5 time points: following initial 3-wk adaptation to CSG hay; after 2–3 weeks grazing CSG (spring), WSG (summer), and CSG (fall); and after transition back to hay in the fall. Forage samples were collected on 3 random days per period (0800–1000), and nutrient content was analyzed by NIRS. Sequence analysis of the 16S rRNA gene was conducted in QIIME 2, and taxonomy was assigned using SILVA. From 3482 amplicon sequence variants (ASV) generated in QIIME 2, 354 bacterial co-abundance groups (BCG) were then identified using Sparse Cooccurrence Network Investigation for Compositional data. Random forest regression showed that mean Crude Protein (CP), Acid Detergent Fiber (ADF), and Water-Soluble Carbohydrate (WSC) concentration could be predicted based on microbial composition (R > 0.5; P 0.5 and P
Additional file 1. Sequence counts of blank sequencing control. Absolute abundance counts for bla... more Additional file 1. Sequence counts of blank sequencing control. Absolute abundance counts for blank sequencing control. Highlighted in blue are OTUs found in 100% of the experimental samples.
Additional file 6. PCoA plots of Unifrac distances. PCoA plots of unweighted Unifrac distances by... more Additional file 6. PCoA plots of Unifrac distances. PCoA plots of unweighted Unifrac distances by Management (A) and Age (B). PCoA plots of weighted Unifrac distances colored by Management (C) and Age (D).
Additional file 3. Group significance based on breed and study. Group significance test for breed... more Additional file 3. Group significance based on breed and study. Group significance test for breed by Kruskal-Wallis (GS_KW_SBP) and nonparametric t-test (GS_NPT_SBP). Group significance test for study by Kruskal-Wallis (GS_KW_Study)
In March, 2020, campus restrictions associated with COVID-19 necessitated significant changes to ... more In March, 2020, campus restrictions associated with COVID-19 necessitated significant changes to undergraduate instruction at institutions of higher education. Rapid, unplanned transitions to remote learning caused disruptions for all educators, especially those who traditionally facilitate student learning via wet labs or live animal interactions, as is common within equine science and management courses. This study sought to identify teaching challenges and strategies associated with pandemic-era instruction among educators in equine science and management. Educators who taught undergraduate equine science or management courses in the United States before and after the spring of 2020 (n=43 respondents) completed an online survey
microbiota during the first 7 d post-weaning. The introduction of solid feed, and gradual transit... more microbiota during the first 7 d post-weaning. The introduction of solid feed, and gradual transition off a milk-based diet before weaning, may have allowed the microbiota to remain largely unchanged.
negative attitudes, long days, weather, and time away from family. The top positive themes or ben... more negative attitudes, long days, weather, and time away from family. The top positive themes or benefits included continued learning, meeting people, and personal fulfillment. Respondents were also asked why they became judges. Top responses included giving back to the program, helping others, and working with horses and youth, all of which may enhance the quality of life of judges and exhibitors. This information is important as it informs both the literature for future research on the horse judging experience, as well as administrators who may question the staff investment and impacts of 4-H horse judging activities.
possible that these materials may perform better than common products, but testing with horses is... more possible that these materials may perform better than common products, but testing with horses is limited. A pilot study was conducted to compare bedding characteristics of sawdust, hemp shavings, and chopped miscanthus as bedding materials for stalled horses. Sawdust and hemp were commercially produced and purchased. Miscanthus was grown, dried, and processed at the Murray State University West Farm. Treatments were evenly distributed between 12 stalls with horses randomly assigned to treatment. The order in which stalls were selected for evaluation of bedding characteristics was random. Bedding characteristics were evaluated daily by both stall cleaners and assigned reviewers, and included: urine containment (well, some, poor), ease of cleaning (easy, moderate, difficult), presence of odors (none, some, lots), and appearance (attractive, moderate, unattractive) of the bedding. Evaluations were performed using a standardized rubric based on a Likert-type scale for scoring, and comments were collected. After 10 d, the bedding was stripped from the stall and a different bedding evaluated. Routine daily exercise and turnout schedules were maintained, but horses spent the majority of their time in stalls. Chi-squared tests were performed using the PROC FREQ procedure of SAS to determine the relationship between bedding types and characteristics with significance declared at P < 0.05. Differences were found between bedding types for urine containment, ease of cleaning, appearance, and odor (P < 0.0001). Sawdust was reported to contain urine well 79.9% of the time as compared with only 49.1% and 39.9% for hemp and miscanthus, respectively. Stall cleaners indicated that sawdust was easy to clean 65.6% of the time, while hemp and miscanthus were more difficult to clean (29.7% and 71.6%, respectively). Sawdust was reported to have no odor 100% of the time, while miscanthus (8.2%) and hemp (10.7%) were reported to have either some or lots of odor. Finally, sawdust, hemp, and miscanthus were found to be attractive 94.9%, 61.3%, and 37.6% of the time, respectively. Miscanthus was reported as unattractive 35.3% of the time as compared with sawdust or hemp (0.8% and 18.2%, respectively). In conclusion, sawdust performed better than hemp and miscanthus as bedding material for stalled horses.
Integrating warm-season grasses into cool-season equine grazing systems can increase pasture avai... more Integrating warm-season grasses into cool-season equine grazing systems can increase pasture availability during summer months. The objective of this study was to evaluate effects of this management strategy on the fecal microbiome and relationships between fecal microbiota, forage nutrients, and metabolic responses of grazing horses. Fecal samples were collected from 8 mares after grazing cool-season pasture in spring, warm-season pasture in summer, and cool-season pasture in fall as well as after adaptation to standardized hay diets prior to spring grazing and at the end of the grazing season. Random forest classification was able to predict forage type based on microbial composition (accuracy: 0.90 ± 0.09); regression predicted forage crude protein (CP) and non-structural carbohydrate (NSC) concentrations (p < 0.0001). Akkermansia and Clostridium butyricum were enriched in horses grazing warm-season pasture and were positively correlated with CP and negatively with NSC; Clostr...
This study reports differential responses of the equine gut microbiome to protein- and/or carbohy... more This study reports differential responses of the equine gut microbiome to protein- and/or carbohydrate-based on keeper status [easy keeper (EK), medium keeper (MK), hard keeper (HK)]. Anaerobic microcosms were inoculated with equine feces from healthy animals on the same diets (n=12 total, n = 3 / EK, MK, HK of four breeds) with three dietary treatments [C = Carb (cornmeal), P = Protein (soybean meal), M = mix (50% C, 50% P), and F = fecal (no additive)]. Over 48 hours, fermentation products were measured using colorimetric assays and high performance liquid chromatography. Microbial populations were surveyed using 16S rRNA gene sequencing analyzed by QIIME2. Total SCFA production was not different between keeper status but the acetate: propionate ratio and isobutyrate production was greatest for HK and least for EK. Residual protein and carbohydrate at hour 48 was greatest in HK pointing to less efficient nutrient utilization. Diversity measures were not different between keeper st...
<p>Comparison of the distribution of the closest relatives of all <i>C</i>. <... more <p>Comparison of the distribution of the closest relatives of all <i>C</i>. <i>phytofermentans</i> open reading frames among sequenced bacterial genomes (left) to that of closest relatives of its glycoside hydrolases (right).</p
Background Diet is a key driver of equine hindgut microbial community structure and composition. ... more Background Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C–W) and WSG to CSG (W–C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing. Results Regardless of IRS or transition (C–W vs. W–C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting...
<p><b>(A)</b> A conceptual illustration of how GH (blue), ABC transporters (pur... more <p><b>(A)</b> A conceptual illustration of how GH (blue), ABC transporters (purple) and AraC regulators (red) may work together. <b>(B)</b> Number of AraC transcriptional regulators per genome. <b>(C)</b> Number of GH domains per genome. Organisms having both GH48 and GH9 are marked with two asterisks, and organisms having GH9 alone are marked with one asterisk. <b>(D)</b> Number of putative ABC transporters per genome.</p
<p>Taxa with sequenced genomes are marked with an asterisk. Cluster numbers correspond to t... more <p>Taxa with sequenced genomes are marked with an asterisk. Cluster numbers correspond to the cluster system of Collins et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118285#pone.0118285.ref068" target="_blank">68</a>]. Bootstrap values were determined for 1,000 replicates.</p
Antibiotic (AB) therapies commonly used by veterinarians to treat bacterial infections can have s... more Antibiotic (AB) therapies commonly used by veterinarians to treat bacterial infections can have side effects that stem from a disruption of the hindgut microbiota with a reduction of celluloytic bacteria and a proliferation of pathogenic strains. In practice, many veterinarians recommend a direct fed microbial (DFM) along with AB as DFM have been shown to mitigate some of the effects of AB on fecal microbiota. However, many commercially available DFM supplements also contain prebiotics, and there is little research on these microbial support supplements during AB administration. The purpose of this study was to determine the impact of Biome Fix (NutraWorks Equine) during AB treatment on fecal microbiome. Biome Fix is a blend of prebiotics (MOS, FOS, and Asperigullus niger extract), DigestaWell® Buffer (Probiotech International, Inc.), and DigestaWell® Fiber (Probiotech International, Inc.). Both DigestaWell® Buffer and Fiber have been previously shown to buffer fecal pH through reduced lactate production, and improve fiber digestibility in horses, respectively. Horses (n = 16) were assigned (blocked by age, sex, and BCS) to either Control (C:no supplement) or Biome Fix (BF:480g/d) for the 27d trial period. At d 0, all horses received AB (trimethoprim plus sulfadizine tablets (Uniprim) at 30mg/kg/d) for 7d. Fecal samples were collected at d 0, 7, 21, and 27. After DNA extraction from samples, the V3–V4 region of the bacterial 16S rRNA gene was amplified by PCR and amplicons were sequenced using Illumina MiSeq. Sequence analysis was conducted in QIIME 2, taxonomy was assigned against the SILVA database, and pair-wise t-tests were used to determine differences. Between d 0 and 27 in BF, there was an increase in Clostridium butyricum, a butyrate producer (P = 0.037), Anaerovibrio sp., a lipid degrader (P = 0.02), and 3 groups of Ruminococcaceae involved in fiber digestion (P
Dietary nutrients have been identified as drivers of gut microbial composition across animal spec... more Dietary nutrients have been identified as drivers of gut microbial composition across animal species. The aim of this study was to apply a biologically relevant computational approach to explore relationships between forage nutrients and the equine fecal microbiome. Fecal samples were collected from 8 mares grazing cool-season (CSG) and warm-season grass (WSG) rotational pastures at 5 time points: following initial 3-wk adaptation to CSG hay; after 2–3 weeks grazing CSG (spring), WSG (summer), and CSG (fall); and after transition back to hay in the fall. Forage samples were collected on 3 random days per period (0800–1000), and nutrient content was analyzed by NIRS. Sequence analysis of the 16S rRNA gene was conducted in QIIME 2, and taxonomy was assigned using SILVA. From 3482 amplicon sequence variants (ASV) generated in QIIME 2, 354 bacterial co-abundance groups (BCG) were then identified using Sparse Cooccurrence Network Investigation for Compositional data. Random forest regression showed that mean Crude Protein (CP), Acid Detergent Fiber (ADF), and Water-Soluble Carbohydrate (WSC) concentration could be predicted based on microbial composition (R > 0.5; P 0.5 and P
Additional file 1. Sequence counts of blank sequencing control. Absolute abundance counts for bla... more Additional file 1. Sequence counts of blank sequencing control. Absolute abundance counts for blank sequencing control. Highlighted in blue are OTUs found in 100% of the experimental samples.
Additional file 6. PCoA plots of Unifrac distances. PCoA plots of unweighted Unifrac distances by... more Additional file 6. PCoA plots of Unifrac distances. PCoA plots of unweighted Unifrac distances by Management (A) and Age (B). PCoA plots of weighted Unifrac distances colored by Management (C) and Age (D).
Additional file 3. Group significance based on breed and study. Group significance test for breed... more Additional file 3. Group significance based on breed and study. Group significance test for breed by Kruskal-Wallis (GS_KW_SBP) and nonparametric t-test (GS_NPT_SBP). Group significance test for study by Kruskal-Wallis (GS_KW_Study)
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