Search

Numerous factors impact reproductive success in beef cattle; however, the presence and activity of bacteria in the reproductive tract and its effects on fertility is relatively unknown. The objective of this study was to evaluate the relationship between reproductive tract bacterial communities and cytokine profiles prior to timed-AI (TAI) and compare between resulting pregnancy status at d30. Sixty-eight beef cows, 80 ± 2.6 d postpartum at TAI, were synchronized and subjected to TAI on d0. Pregnancy was diagnosed via transrectal ultrasonography on d30. Uterine and vaginal flushes were collected on d -21 and -2 for bacterial DNA extraction to sequence the V1-V3 hypervariable regions of the 16S rRNA gene and to measure pro-inflammatory [interlukin-6 (IL-6)] and anti-inflammatory [IL-10 and transforming growth factor-beta (TGFβ)] cytokine concentrations using validated commercial ELISAs. Concentration data were analyzed using repeated measures in PROC MIXED of SAS and correlations were performed in SAS using Pearson correlation. There were no differences in cytokine concentrations by day or status x day. There were no differences in uterine IL-6 or IL-10 concentrations (P > 0.05). Uterine TGFβ concentrations were overall elevated in pregnant cows compared to open cows (72.6 vs. 13.7 ± 12.1 pg/mL, respectively; P < 0.05). On d -2, a positive correlation exists between TGFβ and the relative abundance of Actinobacteria in the uterus of pregnant cows (r=0.93, P = 0.02). There were no differences in vaginal IL-6 or TGFβ concentrations (P > 0.05). On d -2, vaginal IL-10 concentrations were elevated in open cows compared to pregnant cows (741.6 vs. 602.1 ± 47.0 pg/mL, respectively; P < 0.05) and a positive correlation exists between IL-10 and the relative abundance of Lentisphaerae in the vagina of pregnant cows (r=0.89, P = 0.04). These data suggest a possible relationship between bacterial communities and cytokines concentrations within the reproductive tract of beef cattle which may affect fertility.

Overstocking can be a major issue in the dairy cattle industry, leading to negative changes in feeding and resting behavior. Additional stress imposed and alterations in feeding behavior may significantly impact the rumen microbiome. The rumen microbiome is responsible for the successful conversion of feed to usable energy for its host. Thus, understanding the effects of stocking density on the rumen microbiome is imperative for further elucidation of potentially negative consequences of overstocking in dairy cattle. This study implemented a Latin Square design accounting for four pens of cattle and four treatment periods so that all treatment combinations were assigned to every pen during one period of the study. Two treatment factors, including two levels of physically effective neutral detergent fiber, achieved with addition of chopped straw, and stocking density (100% vs. 142%) of freestalls and headlocks, were combined and tested within a factorial treatment design. Within each pen, three or four cannulated cows (n = 15 total) were sampled for rumen content on the final day of each treatment period. Each treatment was randomly assigned to a single pen for a 14-day period. The V1–V3 hypervariable regions of the 16S rRNA gene were targeted for bacterial analyses. Variables with approximately normally-distributed residuals and a Shapiro–Wilk statistic of ≥0.85 were analyzed using a mixed model analysis of variance with the GLIMMIX procedure with fixed effects of feed (straw vs. no straw), stocking density (100% vs. 142%), and the interaction of feed × stocking density, and random effects of pen, period, feed × stocking × pen × period. Pen was included as the experimental unit in a given period and the sampling unit as cow. Variables included Shannon’s Diversity Index, Faith’s phylogenetic diversity index, chao1, observed OTU, and Simpson’s evenness E as well as most individual taxa. Data were analyzed in SAS 9.4 utilizing the GLIMMIX procedure to perform mixed model analysis of variance. If data were not normally distributed, a ranked analysis was performed. No differences were observed in α-diversity metrics by fiber or stocking density (P > 0.05). Beta diversity was assessed using weighted and unweighted Unifrac distances in QIIME 1.9.1 and analyzed using ANOSIM. No differences were observed in weighted (P = 0.6660; R = −0.0121) nor unweighted (P = 0.9190; R = −0.0261) metrics and R values suggested similar bacterial communities among treatments. At the phylum level, Tenericutes differed among treatments with an interaction of stocking density by feed (P = 0.0066). At the genus level, several differences were observed by treatment, including Atopobium (P = 0.0129), unidentified members of order RF39 (P = 0.0139), and unidentified members of family Succinivibrionaceae (P = 0.0480). Although no diversity differences were observed, taxa differences may indicate that specific taxa are affected by the treatments, which may, in turn, affect animal production.

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community. Electronic supplementary material The online version of this article (10.1186/s13059-019-1760-x) contains supplementary material, which is available to authorized users.

Nutritional studies involving ruminants have traditionally relied on relatively short transition or wash-out periods between dietary treatments, typically two to four weeks. However, little is known about adequate adaptation periods required to reach stabilization of the rumen microbiome that could provide more accurate results from nutritional studies in ruminants. This study determined the rumen bacterial communities and rumen environment parameters over ten weeks following transition from a forage-based to concentrate-based diet. Several α-diversity metrics, including observed OTUs and Simpson’s Evenness fluctuated throughout the trial, but were typically either greatest (observed OTUs) or lowest (Simpson’s) at week 5 of the trial contrasted from weeks 1 and 10 (P P = 0.005) and predictive of the rumen microbiome signature at week 10 (R2 = 0.48; P = 0.04). Rumen microbiome stability did not occur until approximately 9 weeks following adaptation to the diet and was associated with changes in specific bacterial populations and rumen environment. The results of this study suggest that adaptation and wash-out periods must be re-evaluated in order to accommodate necessary rumen microbiome acclimation.

Studying abroad in agricultural biosciences can develop students' cultural, academic, and communication skills and enhance employability. However, in the United States, discussions of study abroad are limited to either one-way directionality (U.S. students to other countries) or to the experiences of international students who come to the United States for degree programs. We analyzed the perspectives and experiences of studying abroad by Zamorano University (Honduras) students who completed an agricultural bioscience pasantía (four-month internship) during the final year of their undergraduate program. We used mixed methods to collect data via focus group discussions and a survey with Zamorano students who had completed a pasantía in 2017, as well as key informant interviews with Zamorano pasantía coordinators. Study-abroad experiences were compared between students who completed their pasantía in the United States (37%) and those who completed their pasantía in any of 17 other countries worldwide. Significant relationships were identified (Estudiar en el extranjero puede desarrollar habilidades culturales, académicas y de comunicación en los estudiantes de biociencias agrícolas, sobre todo potencializar la empleabilidad. Sin embargo, las discusiones en los Estados Unidos sobre estudios en el extranjero son limitadas a vías unidireccionales (estudiantes de EE.UU. hacia otros países) o las experiencias de estudiantes internacionales durante sus estudios superiores en los Estados Unidos. Analizamos la perspectiva y experiencia de estudiar en el extranjero con estudiantes de la Universidad Zamorano (Honduras), quienes completaron una pasantía en biociencias agrícolas durante su último año del programa de pregrado. Utilizamos métodos mixtos para obtener datos a través de entrevistas con los coordinadores de las pasantías en Zamorano, discusión de grupos focales y encuestas a los estudiantes de Zamorano quienes habían completado su pasantía en el 2017. Se compararon estudios en el exterior entre estudiantes que completaron su pasantía en Estados Unidos (37%) contra aquellos que completaron su pasantía en cualquiera de los otros 17 países del mundo. Se identificaron relaciones significativas (P0.05) entre: realizar una pasantía en Estados (comparada a realizarla en cualquier otro lugar) y el aumento del conocimiento teórico y científico; teniendo experiencias prácticas y mejoras en la ciencia y la teoría; mejoras en la comunicación y la confianza en el uso de métodos científicos. El modelo de pasantía de Zamorano brinda información sobre el valor de estudios sobre biociencias agrícolas en el extranjero.

Next generation sequencing technologies have vastly changed the approach of sequencing of the 16S rRNA gene for studies in microbial ecology. Three distinct technologies are available for large-scale 16S sequencing. All three are subject to biases introduced by sequencing error rates, amplification primer selection, and read length, which can affect the apparent microbial community. In this study, we compared short read 16S rRNA variable regions, V1-V3, with that of near-full length 16S regions, V1-V8, using highly diverse steer rumen microbial communities, in order to examine the impact of technology selection on phylogenetic profiles. Short paired-end reads from the Illumina MiSeq platform were used to generate V1-V3 sequence, while long "circular consensus" reads from the Pacific Biosciences RSII instrument were used to generate V1-V8 data. The two platforms revealed similar microbial operational taxonomic units (OTUs), as well as similar species richness, Good's coverage, and Shannon diversity metrics. However, the V1-V8 amplified ruminal community resulted in significant increases in several orders of taxa, such as phyla Proteobacteria and Verrucomicrobia (P < 0.05). Taxonomic classification accuracy was also greater in the near full-length read. UniFrac distance matrices using jackknifed UPGMA clustering also noted differences between the communities. These data support the consensus that longer reads result in a finer phylogenetic resolution that may not be achieved by shorter 16S rRNA gene fragments. Our work on the cattle rumen bacterial community demonstrates that utilizing near full-length 16S reads may be useful in conducting a more thorough study, or for developing a niche-specific database to use in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing.

Research regarding the association between the microbial community and host feed efficiency in cattle has primarily focused on the rumen. However, the various microbial populations within the gastrointestinal tract as a whole are critical to the overall well-being of the host and need to be examined when determining the interplay between host and nonhost factors affecting feed efficiency. The objective of this study was to characterize the microbial communities of the jejunum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual ADFI and ADG were determined from animals fed the same diet. At the end of each feeding period, steers were ranked based on their standardized distance from the bivariate mean (ADG and ADFI). Four steers with the greatest deviation within each Cartesian quadrant were sampled ( = 16/group; 2 groups). Bacterial 16S rRNA gene amplicons were sequenced from the jejunum content using next-generation sequencing technology. The phylum Firmicutes accounted for up to 90% of the populations within all samples and was dominated by the families Clostridiaceae and Ruminococcaceae. UniFrac principal coordinate analyses did not indicate any separation of microbial communities within the jejunum based on feed efficiency phenotype, and no significant changes were indicated by bacterial diversity or richness metrics. The relative abundances of microbial populations and operational taxonomic units did reveal significant differences between feed efficiency groups ( < 0.05), including the phylum Proteobacteria ( = 0.030); the families Lachnospiraceae ( = 0.035), Coriobacteriaceae ( = 0.012), and Sphingomonadaceae ( = 0.035); and the genera ( = 0.019), ( = 0.018), and ( = 0.022). The study identified jejunal microbial associations with feed efficiency, ADG, and ADFI. This study suggests the association of the jejunum microbial community as a factor influencing feed efficiency at the 16S level.

Nutrition is a major component in successful heifer development, influencing age at puberty and the uterine environment, therefore, impacting reproductive efficiency. Different diets can influence systemic inflammation, however, the effect on uterine cytokines has not been determined. Our objective was to evaluate the effect of varied levels of dietary protein on inflammatory cytokines in the uterine environment of developing heifers. Commercial Angus heifers (n = 60) were blocked by body weight, then allocated to receive one of three dietary protein supplementation treatments (n = 20 per group, n = 5 per pen): 10% crude protein (CP; 100% corn), 20% CP [75% dried distillers’ grains (DDG) 25% corn], or 40% CP (75% soybean meal 25% DDG). Supplements were provided four times weekly for six months with ad libitum native grass hay, mineral supplement, and water. Body weight, BCS, and blood was taken every 14d. Uterine fluid was collected every 28d to determine presence of cytokines IL1α, IL1β, TNFα, IFNγ, IL10, IL4, and IL6. The GLIMMIX procedure (SAS 9.4) was used with fixed effects of supplementation, month, and their interaction; random effects of block, interaction of block and supplementation, and heifer within the interaction; and repeated measure of month. Concentrations of IL1β, TNFα, IFNγ, and IL10 shifted throughout development (P < 0.0002). Cytokine IFNγ was also affected by month of development (P = 0.002) and tended (P = 0.06) to decrease as CP increased. Presence of each cytokine was then recorded as binary and analyzed by the frequency procedure (SAS 9.4) to determine a uterine cytokine profile. Pro-inflammatory cytokines IL1α, IL1β, and TNFα occurred together more frequently following the beginning of supplementation. In conclusion, inflammatory cytokines shift throughout heifer development, potentially leading to differences in future reproductive success. Further research is needed to determine the dietary influence for optimal uterine environment development.

The functional capacity of the rumen is central to ruminant feed efficiency, and therefore,differences in ruminal metabolism may contribute to cattle feed efficiency variations. The objective of this study was to determine differences in rumen metabolites associated withvariations in feed efficiency. Fifty steers were utilized and maintained on a backgrounding diet (11.57% CP; 76.93% TDN DM basis; 28 mg monensin/kg DM) for 70 days following a two-week diet adaptation. Feed intake was monitored using the GrowSafe system. Following the 70-day trial, steers were ranked by residual feed intake (RFI) and divided into low- (n = 14) and high-RFI (n = 15) based on RFI ±0.5 SD around the mean. On day 70, rumen fluid was collected viaorogastric tubing and filtered through a 0.22 μM syringe filter. Untargeted metabolomics wasconducted utilizing the Dionex UltiMate 3000 UPLC system and electrospray ionization used tointroduce samples into an Exactive Plus Orbitrap MS. Eighty-eight known metabolites wereidentified using MAVEN. Metabolites were median-centered, log-transformed, and pareto-scaled using Metaboanalyst 4.0. Normality was assessed using the SAS 9.4 PROC UNIVARIATE procedure. Normal distribution was considered based on a Shapiro-Wilk score of ≥ 0.85 andvisual analysis of histogram and plots of residuals. Normally distributed metabolites wereanalyzed using one-way ANOVA in SAS with Tukey’s HSD post-hoc test, whereas non-normally distributed variables were analyzed using Wilcoxon Rank Sum and Kruskal Wallis H test. Significance was set at P ≤ 0.05. Eight metabolites differed between high- and low-RFI steers. Twelve metabolites identified as having > two-fold change between low- and high-RFI steers, including 3,4-Dihydroxyphenylacetate and sulfolactate. Orthogonal PLSDA revealed overlap ofrumen fluid metabolites from high- and low-RFI steers. Understanding rumen metabolites in high- and low-RFI steers will provide researchers with information to identify more efficient cattle.

Replacement heifer development is one of the most critical components of productive beef operations. By identifying the ideal uterine environment in pre-breeding heifers, fertility and reproductive efficiency can be maximized. Our hypothesis was that different levels of protein supplementation would affect the rate of development and uterine environment of beef heifers. To test the effects of dietary supplementation on these outcomes, a randomized complete block design with repeated measures was implemented. Commercial Angus heifers (n = 60) were blocked by BW into 4 weight classes. Within each weight class, three pens of 5 heifers each were randomly assigned to one of three treatment groups of supplemental protein [10% (control), 20% (P20), and 40% (P40)]. All heifers were allowed access to ad libitum grass hay. Bodyweight and BCS were collected every 2 weeks to monitor heifer development. Uterine fluid samples were collected monthly by flushing with sterile saline to evaluate components of the uterine environment. Relative uterine pH was calculated by subtracting saline pH from the uterine flush pH. Separate mixed model ANOVAs and mean separation via PROC GLIMMIX (SAS 9.4, Cary, NC) were used to determine if protein supplementation treatments, time and their interactions influenced BW, BCS, or uterine environment. Bodyweight of the control group was significantly lower (P < 0.05) than P20 or P40 groups from December to March. There was an interaction between treatment and time for relative uterine pH (P = 0.002). In November, the P40 group exhibited less change in pH compared to the control group (0.33±0.1 vs. 0.74±0.1; P < 0.05). Whereas in December the P40 (0.23±0.1) group showed more basic uterine environment compared to the P20 (-0.22±0.1) or control (-0.13±0.1) groups (P < 0.05). In conclusion, higher protein supplementation does improve heifer growth and development, as well as altering the pH of the uterine fluid from weaning to first breeding

Negative impacts of endophyte-infectedLolium arundinaceum (Darbyshire)(tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found inTrifolium pretense(red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in anin vitrosystem. Using a dose of 1.10 mg × L−1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type(P= 0.003) and isoflavone treatment (P= 0.005), and ADF disappearance values were significantly different in a seed x isoflavone treatment interaction (P≤ 0.05). A seed x isoflavone treatment interaction was also observed with respect to CP disappearance (P≤ 0.05). Seventeen bacterial taxa were significantly altered by seed x isoflavone treatment interaction groups (P≤ 0.05), six bacterial taxa were increased by isoflavones (P≤ 0.05), and eleven bacterial taxa were altered by seed type (P≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changesin vivo.

The interconnection of microbiology, biology, and agriculture poses unique challenges for dissemination of basic science research data in an applied format. Further, audiences including the general public, stakeholders, agricultural commodity producers, and students to which information is directed often possess various backgrounds and educational training. In response to technological advances, and the benefits of web-based learning tools to deliver complex information, an integrative approach to deliver microbial content information was developed. Through the constructed web-based interface, an interactive format to highlight the microbe of interest consisted of a main image with strategically placed hotspots to illuminate the location/environment/organ where the microbe can be found. As each hotspot is accessed, an additional image and description of the role and function of the microbe at the location is presented. To encourage regular user access with the learning tool, monthly features were created to focus on various concepts in nutritional microbiology. Monthly themes were selected by the educator to cover a specific microbe, environment, and physiological or nutritional function. Facilitation of educator operation of the interface was achieved through development of an easy-to-use dashboard, allowing for uploading of main, monthly, and hotspot images, along with information on the overview of microbe function and with details contained within the hotspot descriptions. Additionally, an archive feature was created to allow access to information that was previously covered within the learning tool. Application of this web-based interface can span across classroom settings, outreach educational events, adult and youth learning within Extension, student recruitment, and many other non-traditional learning settings to impact production agriculture with research-driven microbiological and biological concepts.

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo.

Apart from the rumen, limited knowledge exists regarding the structure and function of bacterial communities within the gastrointestinal tract and their association with beef cattle feed efficiency. The objective of this study was to characterize the microbial communities of the cecum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual feed intake and BW gain were determined from animals fed the same diet. Within both of 2 contemporary groups, BW was regressed on feed intake and 4 steers within each Cartesian quadrant were sampled ( = 16/group). Bacterial 16S rRNA gene amplicons were sequenced from the cecal content using next-generation sequencing technology. No significant changes in diversity or richness were detected among quadrants, and UniFrac principal coordinate analysis did not show any differences among quadrants for microbial communities within the cecum. The relative abundances of microbial populations and operational taxonomic units revealed significant differences among feed efficiency groups ( < 0.05). Firmicutes was the dominant cecal phylum in all groups and accounted for up to 81% of the populations among samples. Populations were also dominated by families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae, with significant shifts in the relative abundance of taxa among feed efficiency groups, including families Ruminococcaceae ( = 0.040), Lachnospiraceae ( = 0.020), Erysipelotrichaceae ( = 0.046), and Clostridiaceae ( = 0.043) and genera ( = 0.049), ( = 0.044), ( = 0.042), ( = 0.040), ( = 0.042), and ( = 0.042). The study identified cecal microbial associations with feed efficiency, ADG, and ADFI. This study suggests an association of the cecum microbial community with bovine feed efficiency at the 16S level.

Methane (CH4) gas released by cattle isa product of fermentation in the digestive tract. The 2 primary sites of CH4 production in ruminants are the reticulum-rumen complex and the cecum. Methane release from cattle represents a 2% to 12% loss of the energy intake. Reducing the proportion of feed energy lost as CH4 has the potential of improving feed efficiency as well as decreasing the contribution of cattle to greenhouse gas production. Feed intake and growth were measured on 132 fall-born steers for 70 d. Seven steers with extreme positive residual gain (RG) and 7 steers with extreme negative RG whose DMI was within 0.32 SD of the mean intake were selected for subsequent measurements. Enteric CH4 production was measured via indirect calorimetry. Rumen, cecum, and rectal contents were obtained from steers at slaughter for measurement of in vitro CH4 production and methanogen 16S rRNA levels. Enteric CH4 production did not differ (P = 0.11) between the positive RG (112 ± 13 L/d)and the negative RG (74 ± 13 L/d) steers. In vitro rumen methane production did not differ between positive RG(64.26 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (61.49 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1)DM∙min(-1); P = 0.86). In vitro cecum methane production did not differ between positive RG (4.24 ×10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (4.35 × 10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1); P = 0.97). Methanogen 16S rRNA as a percentage of the total bacteria16S rRNA did not differ between RG groups (P = 0.18). The methanogen 16S rRNA as a percentage of rumen fluid total bacteria 16S rRNA (5.3% ±3.1%) did not differ from the methanogen 16S rRNA asa percentage of cecum content total bacteria 16S rRNA(11.8% ± 3.1%; P = 0.14). The methanogen 16S rRNA as a percentage of the rectum content total bacteria 16SrRNA (0.7% ± 3.1%) was not different from the rumen content (P = 0.29) but was less than the cecum content(P = 0.01). Methanomicrobiales 16S rRNA as a percentage of total methanogen 16S rRNA did not differ across sample sites (P = 0.81); however, steers with positive RG (10.5% ± 1.6%) were more numerous than steers with negative RG (5.1% ± 1.6%; P = 0.02). Cattle that differ in RG at the same DMI do not differ in characteristics associated with CH4 production.

Improving feed utilization in cattle is required to reduce input costs, increase production, and ultimately improve sustainability of the beef cattle industry. Characterizing metabolic differences between efficient and non-efficient animals will allow stakeholders to identify more efficient cattle during backgrounding. This study used an untargeted metabolomics approach to determine differences in serum metabolites between animals of low and high residual feed intake. Residual feed intake was determined for 50 purebred Angus steers and 29 steers were selected for the study steers based on low versus high feed efficiency. Blood samples were collected from steers and analyzed using untargeted metabolomics via mass spectrometry. Metabolite data was analyzed using Metaboanalyst, visualized using orthogonal partial least squares discriminant analysis, and p-values derived from permutation testing. Non-esterified fatty acids, urea nitrogen, and glucose were measured using commercially available calorimetric assay kits. Differences in metabolites measured were grouped by residual feed intake was measured using one-way analysis of variance in SAS 9.4. Four metabolites were found to be associated with differences in feed efficiency. No differences were found in other serum metabolites, including serum urea nitrogen, non-esterified fatty acids, and glucose. Four metabolites that differed between low and high residual feed intake have important functions related to nutrient utilization, among other functions, in cattle. This information will allow identification of more efficient steers during backgrounding.

Reproductive inefficiency in cattle has major impacts on overall productivity of cattle operations, increasing cost of production, and impacting the sustainability of the cattle enterprise. Decreased reproductive success and associated disease states have been correlated with the presence of specific microbes and microbial community profiles, yet details of the relationship between microbial communities and host physiology are not well known. The present study profiles and compares the microbial communities in the bovine uterus and vagina using 16S rRNA sequencing of the V1–V3 hypervariable region at the time of artificial insemination. Significant differences (p < 0.05) between the vaginal and uterine communities were observed at the level of α-diversity metrics, including Chao1, Shannon’s Diversity Index, and observed OTU. Greater clustering of vaginal OTU was apparent in principal coordinate analysis compared to uterine OTU, despite greater diversity in the vaginal community in both weighted and unweighted UniFrac distance matrices (p < 0.05). There was a significantly greater relative abundance of unassigned taxa in the uterus (p = 0.008), otherwise there were few differences between the overall community profiles. Both vaginal and uterine communities were dominated by Firmicutes, although the relative abundance of rRNA sequences corresponding to species in this phylum was significantly (p = 0.007) lower in the uterine community. Additional differences were observed at the genus level, specifically in abundances within Clostridium (p = 0.009), Anaerofustis (p = 0.018), Atopobium (p = 0.035), Oscillospira (p = 0.035), 5-7N15 (p = 0.035), Mycoplasma (p = 0.035), Odoribacter (p = 0.042), and within the families Clostridiaceae (p = 0.006), Alcaligenaceae (p = 0.021), and Ruminococcaceae (p = 0.021). Overall, the comparison revealed differences and commonalities among bovine reproductive organs, which may be influenced by host physiology. The increased abundance of unassigned taxa found in the uterus may play a significant biological role in the reproductive status of the animal. The study represents an initial dataset for comparing bacterial communities prior to establishment of pregnancy.

Bovine respiratory disease complex (BRDC) is caused by a variety of complex factors that involves host elements, environmental elements, inadequate management and housing, as well as viral and bacterial pathogens, such as Mannheimia haemolytica and Mycoplasma bovis. The objective of the study was to develop and evaluate a deep-nasopharyngeal bacterial community database to provide greater assignment of taxa within the bovine nasopharynx and as a site-specific tool for examining microbiome dysbioses involved in BRDC. A total of 180 cattle with an overall BW ranging from 164-269 kg were obtained from Athens, Tennessee (n = 60), Maryville, Missouri (n = 60), and Richmond, Kentucky (n = 60). Cattle were transported to a feeding facility in Kansas and housed in open air, dirt floor, group housing pens. At the first diagnosis of BRD, deep nasopharyngeal samples were collected. DNA library preparation of the bacterial 16S rRNA V1–V8 hypervariable regions was performed and sequenced on the Pacific Biosciences RSII instrument. Database construction and all sequencing data were curated using mothur (v1.39.5). For validation analyses using, a subset of cattle was sampled as described above, and three samples sequenced using the V1–V3 hypervariable 16SrRNA regions and the Illumina MiSeq. In the database, Mycoplasma accounted for over 57% of the reads and Mannheimia was present at 0.7%. When validating the database using short-reads, unassigned taxa in the Greengenes analysis was 4.22% contrasted to the 0.91% of the closed reference database analysis. The two taxonomic compositions were not correlated and the correlation was statistically significant (r = -0127; P = 0.001). All alpha diversity indices between the two analysis methods differed (P < 0.05). Development of this reference database provides researchers a tool with considerable improvements in performance for the analysis of bacterial communities in the nasopharynx relating to cattle diagnosed with BRDC.

The prevalence of reproductive losses costing 1 billion dollars annually to the beef and dairy industries has led researchers to evaluate strategies to improve reproductive efficiency. The microbiome of the reproductive tract has been a recent focus in humans due to its effects on health and fertility; however, little research has evaluated the uterine and vaginal microbiomes of cattle. The present study evaluated the reproductive tract bacterial communities of postpartum beef cows undergoing estrus synchronization and the differences between cows who became pregnant and those who failed to conceive. Forty postpartum Angus cows were subjected to a 7 Day Co-Synch protocol with a pre-synchronization step 21 days prior (day -21) to artificial insemination (AI). Uterine and vaginal flushes were collected on day -21, -9, and -2 of the protocol for pH and bacterial DNA extraction to sequence the V1-V3 hypervariable regions of the 16S rRNA gene. Transrectal ultrasound was performed 30 days after AI for pregnancy diagnosis. Ten pregnant and non-pregnant animals were selected and used for analysis. Decreased numbers of bacterial species present in the uterus of cows were identified, independent of pregnancy status, leading up to AI with an average of 1180 ± 97 species on day -21 to 427 ± 99 on day -2 (P < 0.0001). Principal coordinate analyses depicted significant clustering of bacterial communities by day in the uterus (P = 0.001) and vagina (P = 0.001) as well as pregnancy status in the uterus at day -2 (P = 0.005). Additionally, at day -2, multiple significantly different uterine bacterial genera were present at >1% in non-pregnant cows while present at

Ruminal microbial fermentation plays an essential role in host nutrition, and as a result, the rumen microbiota have been a major focus of research examining bovine feed efficiency. Microbial communities within other sections of the gastrointestinal tract may also be important with regard to feed efficiency, since it is critical to the health and nutrition of the host. The objective of this study was to characterize the microbial communities of the colon among steers differing in feed efficiency. Individual feed intake (FI) and body weight (BW) gain were determined from animals fed the same ration, within two contemporary groups of steers. Four steers from each contemporary group within each Cartesian quadrant were sampled (n = 16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the colon content using next-generation sequencing technology. Within the colon content, UniFrac principal coordinate analyses did not detect any separation of microbial communities, and bacterial diversity or richness did not differ between efficiency groups. Relative abundances of microbial populations and operational taxonomic units did reveal significant differences between efficiency groups. The phylum Firmicutes accounted for up to 70% of the populations within all samples, and families Ruminococcaceae and Clostridiaceae were highly abundant. Significant population shifts in taxa were detected, including the families Ruminococcaceae, Lachnospiraceae, and Sphingomonadaceae, and the genera Butyrivibrio, Pseudobutyrivibrio, Prevotella, Faecalibacterium and Oscillospira. This study suggests the association of the colon microbial communities as a factor influencing feed efficiency at the 16S level.

The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.

The use of single-wall carbon nanotubes (SWNTs) in manufacturing and biomedical applications is increasing at a rapid rate; however data on the effects of a potential environmental release of the materials remain sparse. In this study, soils with either low or high organic matter contents as well as pure cultures of E. coli are challenged with either raw as-produced SWNTs (AP-SWNTs) or SWNTs functionalized with either polyethyleneglycol (PEG-SWNTs) or m-polyaminobenzene sulfonic acid (PABS-SWNTs). To mimic chronic exposure, the soil systems were challenged weekly for six weeks; microbial activities and community structures for both the prokaryote and eukaryote community were evaluated. Results show that repeated applications of AP-SWNTs can affect microbial community structures and induce minor changes in soil metabolic activity in the low organic matter systems. Toxicity of the three types of SWNTs was also assessed in liquid cultures using a bioluminescent E. coli-O157:H7 strain. Although decreases in light were detected in all treated samples, low light recovery following glucose addition in AP-SWNTs treatment and light absorption property of SWNTs particles suggest that AP-SWNTs suppressed metabolic activity of the E. coli, whereas the two functionalized SWNTs are less toxic. The metals released from the raw forms of SWNTs would not play a role in the effects seen in soil or the pure culture. We suggest that sorption to soil organic matter plays a controlling role in the soil microbiological responses to these nanomaterials.