Rumen Microbiome Research Articles

Unveiling microbial biomarkers of ruminant methane emission through machine learning.

Enteric methane from cow burps, which results from microbial fermentation of high-fiber feed in the rumen, is a significant contributor to greenhouse gas emissions. A promising strategy to address this problem is microbiome-based precision feed, which involves identifying key microorganisms for methane production. While machine learning algorithms have shown success in associating human gut microbiome with various human diseases, there have been limited efforts to employ these algorithms to establish microbial biomarkers for methane emissions in ruminants. In this study, we aim to identify potential methane biomarkers for methane emission from ruminants by employing regression algorithms commonly used in human microbiome studies, coupled with different feature selection methods. To achieve this, we analyzed the microbiome compositions and identified possible confounding metadata variables in two large public datasets of Holstein cows. Using both the microbiome features and identified metadata variables, we trained different regressors to predict methane emission. With the optimized models, permutation tests were used to determine feature importance to find informative microbial features. Among the regression algorithms tested, random forest regression outperformed others and allowed the identification of several crucial microbial taxa for methane emission as members of the native rumen microbiome, including the genera Piromyces, Succinivibrionaceae UCG-002, and Acetobacter. Additionally, our results revealed that certain herd locations and feed composition markers, such as the lipid intake and neutral-detergent fiber intake, are also predictive features for methane emissions. We demonstrated that machine learning, particularly regression algorithms, can effectively predict cow methane emissions and identify relevant rumen microorganisms. Our findings offer valuable insights for the development of microbiome-based precision feed strategies aiming at reducing methane emissions.

Probiotic-Fermented Distillers Grain Alters the Rumen Microbiome, Metabolome, and Enzyme Activity, Enhancing the Immune Status of Finishing Cattle.

A total of 30 Simmental crossbred cattle (6.50 months old, 265.0 ± 22.48 kg) were randomly divided into three groups, with 10 heads per group, and fed for 45 days. The diet treatments consisted of the Control group without PFDG supplementation, the PFDG-15% group with 15% PFDG substituting for 15% concentrate, and PFDG-30% group with 30% PFDG substituting for 30% concentrate. The results showed that compared with the Control group, the average daily gain (ADG) of the cattle in the PFDG-30% group decreased significantly (0.890 vs. 0.768 kg/d, p = 0.005). The serum malondialdehyde content of cattle in the PFDG-15% and PFDG-30% groups decreased significantly (p = 0.047) compared to that of the Control group. However, the serum superoxide dismutase activity of cattle in the PFDG-30% group was significantly higher than that of the Control group (p = 0.047). Meanwhile, both the PFDG-15% and PFDG-30% groups (1758.47 vs. 2061.30 μg/mL) showed higher serum levels of immunoglobulin G, while the interleukin-10 concentration was lower in the PFDG-30% group (p = 0.027). In addition, the PFDG-15% and PFDG-30% groups shifted the rumen microbiota by improving the abundances of F082 (related to propionic acid production) and fiber-degrading bacteria (Lachnospiraceae_UGG-009 and Prevotellaceae_UCG-001) and reducing the abundance of the disease-associated bacteria Selenomonas. A Kyoto encyclopedia of genes and genomes (KEGG) analysis illustrated that three key metabolic pathways, including phenylalanine metabolism, pyrimidine metabolism, and tryptophan metabolism, were enriched in the PFDG-15% group, but eight key metabolic pathways, including arachidonic acid metabolism, were enriched in the PFDG-30% group. Importantly, both the PFDG-15% and PFDG-30% groups increased (p < 0.01) the activities of cellulase, lipase, and protease in the rumen. Finally, the different bacterial abundance in the rumen was associated with changes in the ADG, serum antioxidant capacity, immune status, rumen enzyme activity, and metabolites. These results suggest that PFDG alters rumen microbiome abundance, metabolome, and enzyme activity for enhancing serum antioxidant capacity and the immune status, but when the supplemental level reaches 30%, it has a negative effect on ADG and the anti-inflammatory factors in finishing cattle.

Molecular analysis of the bacterial microbiome in the rumen of Algerian dromedary

The bacterial community of the forestomach plays important roles in the digestive processes of ruminants and pseudo-ruminants. To investigate the rumen microbiota in the pseudo-rumen of camels (Camelus dromedarius) raised in a natural environment in Algeria, bacterial diversity was determined from 25 dromedaries using 16S rRNA gene amplicon sequencing. A total of 25 bacterial phyla were identified across all the samples, including Firmicutes (close to 85℅), Bacteroidetes (about 12%) and to a lesser extent Proteobacteria (&lt; 1%), with these three phyla together accounting for more than 97% of all sequences. Our results are consistent with previous observations of bacterial communities diversity and abundancy in the rumen or pseudo-rumen of other ruminant species (either domestic or wild), although the abundance of individual bacterial phyla showed remarkably high disparities. Links between the richness and type of diet and the composition of the rumen microbiome are discussed.

Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves

BackgroundBeef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.ResultsUsing a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.ConclusionsWithin the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.

Horizontal metaproteomics and CAZymes analysis oflignocellulolytic microbial consortia selectively enriched from cow rumen and termitegut

Selectively enriched microbial consortia are potentially useful for theconversion of lignocellulose (LC) into biofuels and commodity chemicals. Consortiaare also of interest to elucidate the roles of individual microorganisms and thedynamics of enzymes involved in LC deconstruction. Using metaproteomics, 16 S rRNAgene amplicon sequencing and multivariate discriminant analysis, we revealed thetemporal dynamics of microbial species and their proteins during anaerobicconversion of LC by microbial consortia derived from cow rumen (RWS) and termite gut(TWS) microbiomes. Bacteroidetes (Bacteroidota), Firmicutes (Bacillota) andProteobacteria (Pseudomonadota) phyla were dominant, irrespective the inoculumorigin, displaying functional complementarities. We identified a large variety ofcarbohydrate-active enzymes, distributed in 94 CAZy families, involved in biomassdeconstruction. Additionally, proteins involved in short chain fatty acidsbiosynthesis were detected. Multivariate analysis clearly differentiates RWS and TWSmetaproteomes, with differences originating in the initial inoculates. Furthersupervised discriminant analysis of the temporal succession of CAZymes revealed thatboth consortia consume easily accessible oligosaccharides during the early stage ofincubation, degrading more complex hemicellulose and cellulose fractions at laterstages, an action that pursues throughout the incubation period. Our results providenew insights regarding the functional roles and complementarities existing inlignocellulolytic consortia and highlight their potential for biorefineryapplications.

Altered rumen microbiome and correlations of the metabolome in heat-stressed dairy cows at different growth stages.

Heat stress is one of the main causes of economic losses in the dairy industry worldwide; however, the mechanisms associated with the metabolic and microbial changes in heat stress remain unclear. Here, we characterized both the changes in metabolites, rumen microbial communities, and their functional potential indices derived from rumen fluid and serum samples from cows at different growth stages and under different climates. This study highlights that the rumen microbe may be involved in the regulation of lipid metabolism by modulating the fatty acyl metabolites. Under heat stress, the changes in the metabolic status of growing heifers, heifers, and lactating cows were closely related to arachidonic acid metabolism, fatty acid biosynthesis, and energy metabolism. Moreover, this study provides new markers for further research to understand the effects of heat stress on the physiological metabolism of Holstein cows and the time-dependent changes associated with growth stages.

A Comparison of Three Artificial Rumen Systems for Rumen Microbiome Modeling

The rumen contains a complex mixture of microbes, crucial for the animal’s ability to degrade feed. Some of the feed-derived carbon is released as methane, a potent greenhouse gas, into the atmosphere. There is growing interest in reducing the loss of feed-derived carbon, making it available to the animal and improving animal productivity. Artificial rumen systems (ARSs) have been widely used to evaluate novel feed additives in terms of their ability to reduce methane production in the rumen and their effect on the rumen microbiome function prior to conducting resource-intensive animal trials. While the value of ARSs is widely acknowledged, it remains unclear which of these in vitro systems simulate the natural system most accurately. Here, we evaluated three different ARSs and compared them to in vivo rumen metrics. The results showed that all systems were capable of maintaining stable pH, redox potential, and temperature over time. The batch-style ARS simulated the rumen over 48 h. The semi-continuous ARS mimicked the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 h. Similarly, all ARSs maintained the prokaryotic and eukaryotic rumen populations over the duration of the study, with the semi-continuous ARS maintaining the natural rumen microbiome more accurately and for up to 120 h. In sum, our results suggest that three of the widely used ARSs simulate the rumen ecosystem adequately for many short-term rumen microbiome studies, with the more advanced semi-continuous ARS being more accurate when rumen simulation is extended to over 48 h.

17 The Rumen Microbiome: Realizing the Potential for Mediating Host Performance

Abstract The rumen microbiome has a critical role in multiple facets of ruminant livestock production. It is well known that the rumen microbiome is integral to animal performance through impacts on feed efficiency, greenhouse gas production, volatile fatty acid production, and numerous aspects of animal health. Therefore, understanding factors that influence the rumen microbiome at various stages of the production cycle and the interactions with other microbial niches and physiological processes is a critical area of research to aid in the goal of improving livestock performance. Our research objectives have focused on 3 primary general areas including 1) to characterize and understand the potential pathways of early gut colonization from conception throughout gestation, 2) implications of varying gestational perturbations on rumen microbiome development and calf performance post-weaning, and 3) understand the connections between the rumen microbiome and the microbiomes of the reproductive tract, blood, and respiratory tract. We hypothesize that strategies to program the rumen microbiome early in life may have lasting impacts on host performance specific to feed efficiency, reproductive fitness, and have implications on high altitude disease. These effects may not be a direct relationship between the rumen microbiome and host response, but rather through a total system level response that has the rumen microbiome as a key player in that cascade. The rumen microbiome has the potential to impact numerous aspects of host performance, as such, it is imperative that research continues to elucidate its role in host physiology and the development of intervention mechanisms to initiate specific responses in the rumen microbiome to improve downstream host response.

18 Role of the Rumen Microbiome in Beef Cattle Gut Physiology and Performance

Abstract The diverse rumen microbiome converts low-quality feedstuffs into usable energy and provides approximately 70% of the energy required by its ruminant host through fermentation byproducts. Due to microbial impacts on host health and productivity, numerous studies have associated rumen microbiome variation with important sustainability phenotypes, such as feed efficiency and methane emissions. Although diet, genetics, and environment contribute to variation in feed efficiency, selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the persistence and longevity of such phenotypes within the herd. While diet has been considered to be the primary driver for the composition and structure of the rumen microbiome, recent studies have indicated the microbial communities present in the rumen are under low-to-moderate host genetic control. The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. The ability to interrogate these systems at great depth has permitted a greater understanding of the microbiological and molecular mechanisms involved in ruminant nutrition and health. The work in our group in the field of beef cattle gut microbiology, as it relates to feed efficiency, permits the exploration of these critical microbial community networks. This knowledge will aid researchers seeking to address the grand challenge of maintaining host-efficient gut microbiomes throughout cattle production operations. This work is supported by the Agriculture and Food Research Initiative grant no. 2020-67015-30832 from the USDA National Institute of Food and Agriculture.

PSIX-19 Association of the Rumen Microbiota with Carcass Merit and Beef Quality

Abstract The microbial community in the rumen has an important role in the health and production of beef cattle providing up to 70% of the daily energy requirements from the metabolism of otherwise non-digestible dietary carbohydrates. Diet is often the largest determinant of rumen microbiome composition, but it is also affected by host age, genetics, and sex. Performance attributes such as average daily gain and feed efficiency have all been linked to the rumen microbiome and recent studies with relatively small numbers of cattle have also suggested there may be an association with certain beef quality traits such as marbling, which largely determines the carcass value. Thus, the objective of this study was to evaluate the association of the rumen microbiota with carcass merit and beef quality traits. Two hundred steers were slaughtered, and rumen samples were collected immediately post-slaughter. Subsequently, carcass merit and meat quality attributes were evaluated. The rumen microbiota of these animals was then characterized using 16S rRNA gene sequencing. Although we did not identify a significant association between marbling score and the structure of the rumen microbiota (PERMANOVA; P &amp;gt; 0.05), there were significant associations between rumen microbial community structure and commercial weight, dressed weight percentage, drip loss, and intramuscular fat content (P &amp;lt; 0.05). There were also individual bacterial taxa that were correlated with various carcass merit and beef quality traits. Members of the Acidaminococcus genus were negatively associated with both intramuscular fat content and marbling score (P &amp;lt; 0.10) while Coprococcus, Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Moryella, and Prevotella were among those genera positively correlated with intramuscular fat content (P &amp;lt; 0.10). Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Moryella, and Prevotella were also significantly associated with dressed weight percentage. Commercial weight was positively correlated with the genera Catonella, Prevotellaceae NK3B31 group, Pseudoramibacter, Selenomonas, and Sutterella and negatively associated with Oribacterium and Ruminococcaceae UCG-001 (P &amp;lt; 0.10). Therefore, bacteria within these genera may be ideal targets for future microbiome-based strategies to improve carcass merit and beef quality.

PSXII-21 Post-Weaning Impacts of Late Gestation Maternal Feed Restriction on the Calf Rumen Microbiome

Abstract Maternal gestational nutrition is known to impact gut physiology and the gut microbiome of offspring early in life; however, it remains unknown if these changes persist later in life. We hypothesized that the impacts of maternal feed restriction in late gestating beef cows on early colonization of the calf gut would impact the rumen microbiome post-weaning. Our objective was to compare the post-weaning rumen microbiome of calves born with feed restricted dams and those born to dams with adequate nutrition. Starting roughly 60 d before expected calving, dams were stratified to either receive 100% of NRC requirements (CON) or 70% intake of NRC requirements (FR) through 28 d post-parturition. Pairs were then moved on to native grass until weaning. Rumen fluid was collected from the calves at the time of weaning (PRE) and after a 70 d backgrounding feed efficiency study (POST). Microbial DNA was isolated and the V4 region of the 16S rRNA was sequenced on the MiSeq platform. Data were analyzed within each time point using QIIME2. Maternal treatment had no impact on alpha diversity (Faith’s phylogeny, Shannon’s diversity, and Evenness) in the PRE group, but CON calves had greater (q = 0.05) evenness than FR calves in the POST samples. There were differences in composition between CON and FR in the PRE samples (unweighted unifrac q = 0.04; bray-curtis q = 0.03). No differences (q ≥ 0.14) in composition were found in the POST samples. These data indicate that at the time of weaning (PRE) differences in composition existed in CON vs. FR calves, specifically in the rare taxa, but the microbial composition converged by the end of the feeding trial. Interestingly, previous findings in our lab reported differences in alpha and beta diversity 28 d after birth in these calves. Together, these data indicate the potential for long-term impacts of maternal nutrition on the gut microbiome. This coupled with the previously published work where feed efficiency tended to differ between CON and FR, suggests that early perturbations during gestation may have had lasting impacts on gut physiology and subsequent performance in the presence of rumen microbial shifts.

403 Awardee Talk: Characterization of Rumen Microbiome and Immune Genes Expression of Crossbred Beef Steers with Divergent Residual Feed Intake Phenotypes

Abstract We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake (RFI) phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were selected from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR &amp;lt; 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. Our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared with high-RFI steers.

330 Characterizing the Rumen Bacterial Community in Replacement Holstein Heifers with Divergent Genomically Enhanced Residual Feed Intake

Abstract Rumen microbes serve a vital role in feed utilization of ruminant animals, suggesting the potential of rumen microbiota to influence inter-animal variation in nutrient utilization. There is limited knowledge surrounding the influence of the rumen bacterial community in animals selected based on feed efficiency. The objective of this study was to examine the differences in the rumen bacterial community in replacement Holstein heifers with divergent genomically enhanced breeding values for residual feed intake (RFIg). Genomic breeding values for RFIg were based on RFI phenotypes of 6,563 growing Holstein heifers from STgenetics ongoing EcoFeed research program. Holstein heifers (n = 55; initial BW = 351 ± 64 kg) with low RFIg (n = 29) or high RFIg (n = 26) were selected from a contemporary group of 453 heifers (RFIg = -0.023 ± 0.211 kg/d). These heifers were assigned to 1 of 2 pens, equipped with electronic feedbunks (GrowSafe Systems) and a GreenFeed gaseous-exchange measurement system (C-Lock). Individual DMI was collected for 84-d and BW measured weekly to determine phenotypic RFI. On d-70 of the study, a rumen sample was collected from each animal via esophageal tubing and bacterial community composition determined through 16S rRNA gene sequencing of the V4 region. A total of 523 amplicon sequence variants (ASVs) were observed among the 55 samples, with the average reads per sample of 54,107 ± 42,688 across samples. To examine the rumen bacterial composition, permutational multivariate analysis of variance (PERMANOVA) utilizing the weighted and unweighted Unifrac distance matrix was used. Utilizing the weighted Unifrac no differences (P = 0.513) were observed in the bacterial composition of the rumen content between heifers with divergent RFIg; however, utilizing the unweighted Unifrac differences (P = 0.031) were identified in the bacterial composition between heifers with divergent RFIg. Based on alpha diversity metrics, observed ASVs displayed greater (P = 0.015) bacterial richness in high- compared with low-RFIg heifers; however, there was no difference (P = 0.500) in the Shannon diversity index between heifers with divergent RFIg. ASV level classification of the most differentially abundant (P &amp;lt; 0.05; log2-fold change &amp;gt; 1) ASVs demonstrated that three ASVs from the bacterial family Prevotellaceae, and one ASV from the bacterial family Ruminococcaceae was predominant in high- compared with low-RFIg heifers. Additionally, one ASV belonging to the family Prevotellaceae was predominant in low- heifers compared with their high-RFIg counterparts. Results from this study indicate greater enrichment of ruminal bacteria in high RFIg cattle, with ASVs from the Prevotellaceae and Ruminococcaceae families differing between heifers with divergent RFIg. Opportunities exist to further investigate the role of the rumen microbiome in selection of cattle based on genomic RFI, and to assess associations between specific bacterial ASVs and phenotypic feed efficiency traits in cattle.

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies

BackgroundMinimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms’ homeostasis is a guarantee of beef steers’ growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle.ResultsThe levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host.ConclusionsThis study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle.6n2QR72-A8x7PGstPh77e2Video

PSV-14 Effects of Forage or Coproduct-Based Transition Diets on the Rumen Microbiome and Ruminal Fermentation ex Vivo in Feedlot Steers

Abstract The objective was to determine the effect of replacing forage with coproducts in transition diets on rumen microbiome composition and ruminal fermentation ex vivo after steers consumed a common finishing diet. A random subset of 30 steers were selected from a larger, separate pen study. Steers were blocked by initial BW and allotted into 9 pens. Pens were then assigned to 1 of 3 dietary treatments for the 35 d adaptation period: a forage-based diet (FO; alfalfa and grass hay), a coproduct-based diet (CO; soybean hulls and modified wet distillers grains with solubles), and a coproduct-based diet pair-fed (CO-P) to isoenergetic levels of FO. Dry-rolled corn inclusion increased with either decreasing forage or coproduct inclusion. Both FO and CO were fed with slick bunk management. At d 35 and 63, rumen fluid was collected by esophageal tubing to determine differences in fermentation of the finishing diet as the substrate in an ex vivo model. Rumen fluid was also utilized for microbiome analysis using 16S rRNA sequencing on the Illumina MiSeq platform with 2 × 300 bp paired-end sequencing. Sequencing reads were analyzed within QIIME2. Statistical analyses were conducted using SAS 9.4. Fermentation data were analyzed using the MIXED procedure, while bacterial relative abundance data were analyzed in the GLIMMIX procedure. Correlations were analyzed using the CORR procedure. A treatment × sampling day interaction (P = 0.02) was observed for in vitro dry matter disappearance; on d 35, it was greater in steers fed CO compared with CO-P (58 vs. 53%, respectively), but no differences were observed on d 63. Within the rumen microbiome, there was a tendency (P = 0.06) for alpha diversity to have a treatment × day interaction. Specifically, CO steers had the greatest decrease in alpha diversity from d 35 to 63, but there was no change in alpha diversity in FO steers and CO-P steers over time. Final pH in from the ex vivo model was positively correlated (r = 0.32) with Bacteroidetes relative abundance but negatively correlated (r = -0.25) with Proteobacteria (P ≤ 0.05). In vitro dry matter disappearance was positively correlated (r = 0.38) with relative abundance of Firmicutes, but negatively correlated (r = -0.43) with Proteobacteria (P &amp;lt; 0.01). Dietary treatment did not affect (P ≥ 0.21) richness within the rumen microbiome. Rumen microbiome composition and ex vivo fermentation results suggest all treatments were adapted for the finishing diet at the conclusion of the 35-d adaptation period.

PSV-9 Characterization of the Rumen Bacterial Communities of Lambs That Transitioned from Forage to a Concentrate-Based Diet

Abstract Forage and concentrate-based diets are distinct strategies used in ruminant production. The transition from a forage-based diet to a concentrate-based diet has been shown to have a great impact on the rumen microbiome composition due to vast differences in substrates provided by each diet type. To gain further insight on the nature of the changes that occur in the rumen microbiome as a result of a switch in diet, ruminal bacterial composition was compared between lambs initially fed a forage-based diet and lambs that were switched to a concentrate-based diet for approximately 60 days. From rumen fluid that was collected after slaughter, data were generated by Illumina MiSeq 2X300 sequencing of PCR amplicons targeting the V1-V3 regions of the 16S rRNA gene. Next-Generation Sequence data were analyzed using a combination of custom Perl scripts, and publicly available software (Mothur (v.1.35.1), RDP classifier and NCBI Blast). A total of 10,693 species-level operational taxonomic units (OTUs) were identified across all samples, with 86 OTUs shared between diets. A comparative analysis using the non-parametric Kruskal-Wallis test identified 16 highly represented species-level OTUs that differed in abundance across dietary treatments (P &amp;lt; 0.05). Of these, three OTUs, RA-01223, RA1-35340, and RA1-55937, were found to be of particular interest. OTU RA-01223 was at its highest representation in samples from individuals given a concentrate-based diet, with an average abundance of 8.76% compared with 0.80% in samples from animals fed a forage-based diet. RA-01223 was predicted to be a novel species of the family Oscillospiraceae based on its low 16S rRNA gene sequence identity (94.8%) to its closest valid relative, Ruminococcoides bili. OTU RA1-35340, predicted to be a strain of Sharpea azabuensis, was also in much greater abundance in the concentrate-based diet as compared with the forage-based diet (2.83% and 0.05%, respectively). In contrast, RA1-55937, which was predicted to be a strain of Pectinatus haikarae, was at its greatest abundance in samples from individuals given a forage-based diet, with an average representation of 4.91% compared with 0.52% in samples from animals fed a concentrate-based diet. These and other specific ruminal OTUs whose abundance are affected by changes in diet can then be studied further to gain more insight on the effects of the transition from forage to concentrate on rumen physiology.

258 Investigating the Ruminal Metagenome of Neonatal Holstein Dairy Calves fed an Essential oil-Based Feed Additive

Abstract Antibiotics remain the most effective tool for treating and preventing animal diseases in livestock production. However, the widespread use of antibiotics in food animals, as well as concerns about antibiotic resistance among bacterial pathogens, have raised awareness of the need to limit their use. As neonatal dairy calves are very susceptible to gastrointestinal infections that can result in high mortality and morbidity, the need to find alternatives to antibiotics has become a priority. Although essential oils (EO) have emerged as promising anti-microbial alternatives, their potential effects on the rumen microbiome are still poorly understood due to the complexity of their chemical components and limited understanding of their mechanisms of action. To gain further insight into the effects of EO on the bacterial communities of pre-weaned calves, we investigated the rumen metagenome of neonatal Holstein dairy calves that had been supplemented with 3.75g/feeding of a blend of EO (carvacrol, caryophyllene, p-cymene, cineole, terpinene, and thymol) as part of a previous study. Genomic DNA extracted from rumen contents collected from one of the EO-supplemented animals was used for high throughput sequencing using an Illumina Miseq (2x250) platform. Raw sequence reads were assembled into genomic contigs using custom-written Perl scripts. Coding sequences (CDS) were identified and annotated using RAST, with assignment of open reading frames (ORFs) to metabolic pathways using KEGG pathways. After assembly, a total of 3,052 contigs between 279 and 259,890 nt in length were obtained. From this set, 571 contigs affiliated to Prevotella ruminicola, representing 18.7% of total contigs built, were further analyzed. Data mining for specific functions within categories such as ‘protein metabolism’, ‘carbohydrates metabolism’, and ‘amino acids and derivatives’ was performed. This analysis resulted in the identification of all the enzymes involved in glycolysis. Two outcomes were predicted for pyruvate: conversion to lactate through lactate dehydrogenases (EC 1.1.1.27, EC 1.1.1.28), and the production of formate and acetyl-CoA through the activity of pyruvate formate-lyase (EC 2.3.1.54). Acetate (acetate kinase, EC 2.7.2.1) and propionate (Propionate kinase, EC 2.7.2.15) were other predicted end products. In addition to glucose fermentation pathways, enzymes potentially involved in the utilization of plant-based secondary metabolites were also identified, such as enzymes involved in Quinate-Chorismate metabolism: 3-dehydroquinate dehydratase (EC 4.2.1.10), Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25), Shikimate kinase (EC 2.7.1.71), 5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19), and Chorismate synthase (EC 4.2.3.5). Identification of such metabolic pathways suggests that perhaps the supplemented EO additive could be used as a precursor for the synthesis of aromatic amino acids. Together, these findings indicate that EO supplementation may benefit animal health and performance by promoting the growth of bacterial species that can metabolize compounds in EO additives.

MICROBIOMES OF HUMAN, LIVESTOCK ANIMAL GASTROINTESTINAL TRACTS AND OF FOOD PRODUCTS AND COMPOUND FEEDS: CONNECTIONS AND IMPACTS. PART 1

The physiological mechanisms of food digestion in humans and feed digestion in animals are determined by the structure of the gastrointestinal tract (GIT) and diet. Accordingly, humans are omnivores, while domestic animals are divided into ruminants, monogastric herbivores, and monogastric omnivores, and birds are divided into herbivores (geese, ducks) and omnivores (chickens, turkeys, etc.). The digestion and assimilation of food and feed depends not only on own mechanisms but also on the GIT microbiome. The location of the most important part of this microbiome and its composition depend on the species: in ruminants, it is the rumen microbiome, in horses – the cecum (it is a counterpart of the rumen), in humans and pigs – the intestine, in birds – the crop, gizzard and cecum. These microbiomes are in constant close connection with the host organism, and this connection is realized through numerous molecular mechanisms of interaction between bacterial cells and host cells and tissues. GIT microorganisms not only help to assimilate food (feed) by partially digesting it, but also secrete biologically active substances that have protective, stimulating and other beneficial effects for the host. In adult hosts, this GIT microbiota is well developed and stable, while in children and young animals it can be much more mobile and vulnerable. Food and feed contain many components that are a favorable medium for the development of microorganisms. Raw materials and components of animal origin are the most contaminated, while vegetable raw materials and components, as well as premixes, contain significantly fewer microorganisms. Among the microorganisms colonizing raw materials, food and feeds, coliforms, salmonellae and molds may be present. In young animals, the feed microbiota ingested into the GIT, even without taking into account obligate or opportunistic pathogens, can cause shifts or changes in the digestive microenvironment towards deterioration, which will have a corresponding impact on the efficiency of feed absorption and, through it, on the efficiency of feeding and animal productivity.

90 Microbiome-Derived Bioactive Molecules to Reduce Enteric Methane Emissions

Abstract Microorganisms are pivotal for the development, health, and productivity of livestock. In adult ruminants, the microbiota colonizing the rumen is essential for efficient depolymerization of indigestible carbohydrates from plant biomass and their conversion into microbial protein and fermentation end-products that are used by the host for growth. In the last decades, next-generation sequencing and omics technologies provided unparalleled insights into the composition, structure, and function of the gastrointestinal (GI) tract microbiome of ruminants and helped improve our understanding of relationships between the rumen microbiota with cattle performance (efficiency) traits, as well as health and disease and greenhouse gas emissions. The ecological interactions between microbes within the rumen ecosystem are complex and involve, among others, cross-feeding, predation, parasitism, antagonism, and competition for novel (empty) niches and available resources. These diverse associations of ecological traits across distinct microbial populations that coexist in the same ecosystem represent a goldmine for the discovery of novel bioactive molecules, including compounds with potential to modulate rumen fermentation and inhibit methane emissions from enteric fermentation. These effects often result from metabolic shifts in the rumen fermentation that lead to increased production of propionate, but can also be caused by direct inhibition of methanogenic archaea or through a reduction in the production of substrates for methanogenesis. Culture-independent approaches based on genome mining and functional metagenomics demonstrated that the rumen is an underexplored resource for bioactive molecules, such as antimicrobial peptides, non-ribosomal peptides, polyketides, and secondary metabolites involved in intercellular (microbe-microbe) communication. Rumen metatranscriptomic data indicate that the expression of genes potentially encoding some of these molecules is increased during the colonization of plant biomass that enters the rumen. Nonetheless, some representatives of key taxa from the core rumen microbiome cannot be found in culture collections, which is critical to validate phenotypic predictions from genomic and metagenomic data and obtain ecological insights about the interplay between individual microbial populations in the microbiome. Culturomic technologies and high-throughput identification and characterization of microbial species that colonize the rumen could contribute to building a unique biotechnological resource that can be explored for sourcing novel bioactive compounds with anti-methanogenic activity and developing fermentation products that could reduce rumen methanogenesis while improving the health status and productivity of cattle.

92 Methane Mitigation in Dairy Animals Begins Before Birth with Opportunities to Impact Throughout Life

Abstract Research efforts are underway to identify methane mitigators in the dairy sector to reach net zero carbon emissions, and ideally, net negative global emissions. Methane mitigation is multifactorial, including strategies in genetics, management, diet composition, diet nutrient composition, and implementation of feed additives. Research efforts thus far have primarily focused on adult ruminants. Research on how calf management and its impact on phenotypic traits including milk production and methane production is currently lacking. Supplying different levels of nutrients in late lactation results in demonstrated splits in feed intake, average daily gain, metabolism, and greenhouse gas emissions from their offspring. Post-calving, nutrient-restricted heifers entering the lactating herd are hypothesized to be less productive and have greater environmental impact due to reduced productive efficiency relative to their control herd mates. Identification of feed additives that are locally sourced, alter the rumen microbiome, and have lifetime reductions on emissions are under investigation. Further research efforts include identifying metabolic and genetic profiles to identify animals in early life as either high or low methane emitters. Being able to classify animals early in life can reduce the total economic inputs used to raise animals and reduce the total environmental impact of these animals through early culling or intervention of high methane emitting animals. The goal of this presentation is to discuss current knowledge and future potential of calf management, feeding regimes, and feed additive implementation to reduce methane emissions and total environmental impact in the dairy industry.