Ruminal Microbiome Research Articles

Evaluation of stirring time through a rumen simulation technique: Influences on rumen fermentation and bacterial community.

Rumen motility is a key element that influences ruminant nutrition, whereas little is known about the effects of rumen contraction duration on rumen fermentation and ruminal microbiome. We previously reported that proper rotation speed of a rumen simulation technique (RUSITEC) system enhanced rumen fermentation and microbial protein (MCP) production. In the present study, different contraction durations and intervals were simulated by setting different stirring times and intervals of the stirrers in a RUSITEC system. The objective of this trial was to evaluate the influences of stirring time on rumen fermentation characteristics, nutrient degradation, and ruminal bacterial microbiota in vitro. This experiment was performed in a 3 × 3 Latin square design, with each experimental period comprising 4 d for adjustment and 3 d for sample collection. Three stirring time treatments were set: the constant stir (CS), the intermittent stir 1 (each stir for 5 min with an interval of 2 min, IS1), and the intermittent stir 2 (each stir for 4 min with an interval of 3 min, IS2). The total volatile fatty acid (TVFA) concentration, valerate molar proportion, ammonia nitrogen level, MCP density, protozoa count, disappearance rates of dry matter, organic matter, crude protein, neutral detergent fiber, and acid detergent fiber, emissions of total gas and methane, and the richness index Chao 1 for the bacterial community were higher (p < 0.05) in the IS1 when compared to those in the CS. The greatest TVFA, MCP, protozoa count, nutrient disappearance rates, gas productions, and bacterial richness indices of Ace and Chao 1 amongst all treatments were observed in the IS2. The relative abundance of the genus Treponema was enriched (p < 0.05) in CS, while the enrichment (p < 0.05) of Agathobacter ruminis and another two less known bacterial genera were identified in IS2. It could be concluded that the proper reduction in the stirring time might help to enhance the feed fermentation, MCP synthesis, gas production, and the relative abundances of specific bacterial taxa.

Effects of partially replacing dietary corn with sugars in a dual-flow continuous culture system on the ruminal microbiome.

The objective of this study was to evaluate the effects of feeding sugars as a replacement for starch on the ruminal microbiome using a dual-flow continuous culture system. Four periods of 10 days each were conducted with 8 fermenters in a 4 × 4 replicated Latin square design. Treatments included: 1) control with corn-CON, 2) molasses-MOL, 3) untreated condensed whey permeate-CWP, and 4) CWP treated with a caustic agent-TCWP as a partial substitute for corn. Sugars were defined as the water-soluble carbohydrates (WSC) concentration. Diets were formulated by replacing 4% of the diet DM in the form of starch from corn with the sugars in byproducts. Microbial samples for DNA analysis were collected from the solid and liquid effluent containers at 3, 6, and 9 h after feeding. Bacterial community composition was analyzed with sequencing the V4 region of the 16S rRNA gene using Illumina MiSeq platform. Data were analyzed with R 4.1.3 packages vegan, lmer, and ggplot to determine the effects of treatment on the relative abundance of taxa in the solid and liquid fractions, as well as the correlation of Acetate: Propionate ratio and pH to taxa relative abundance. Treatments did not affect alpha or beta diversity. At the phylum level the relative abundance of Proteobacteria was increased in CON compared to sugars in the solid fraction. In the liquid fraction, Firmicutes had greater relative abundance in sugar treatments while Bacteroidota and Spirochaetota were present in lower relative abundance in CWP. For solid and liquid samples, the family Lachnospiraceae had greater relative abundance in sugar treatments compared to CON. The decreased relative abundance of Christensenellaceae and Rikenellaceae paired with the greater relative abundance of Selenomonadaceae in CWP could help explain greater propionate molar proportion and decreased ruminal pH previously observed for this treatment. The genera Olsenella a lactic acid-producing bacterium, had the greatest relative abundance in MOL. Incorporating TCWP or MOL as a partial replacement for starch was more conservative of fibrolytic bacterial taxa compared to CWP. Additionally, TCWP did not increase bacterial taxa associated with synthesis of lactate as compared to MOL. Overall, replacing starch with sugars is mostly conservative of the ruminal microbiome; however, changes observed coincide with differences observed in acetate and propionate proportions and ruminal pH.

Megasphaera elsdenii and Saccharomyces cerevisiae as direct fed microbials and their impact on ruminal microbiome during an acute acidosis challenge in continuous culture.

Our objective was to evaluate the effects of combinations of Saccharomyces cerevisiae and Megasphaera elsdenii as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 108 colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 (S. cerevisiae and M. elsdenii strain 1), YM2 (S. cerevisiae and M. elsdenii strain 2), and YMM (S. cerevisiae and half of the doses of M. elsdenii strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, P = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum Proteobacteria (P = 0.05) and family Succinivibrioceae (P = 0.05) in the solid fraction and tended to increase abundance of family Succinivibrioceae (P = 0.10) and genus Succinivibrio (P = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of Proteobacteria (r = 0.36, P = 0.04) and Succinivibrioceae (r = 0.36, P = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed.

Ruminal microbiome and blood parameters in beef cattle fed with high-grain diets buffered with Lithothamnium calcareum

Context and aims DNA metabarcoding strategy was used to sequence the 16S rRNA region of ruminal fluid samples from Nellore cattle fed with concentrate-rich diets in response to modulatory effect of buffering additives calcarea seaweed (Lithothamnium calcareum) and sodium bicarbonate. Methods Besides characterising the richness and diversity indices of rumen bacterial community, the impact of potentially acidogenic diets on rumen pH, blood parameters, and short-chain fatty acid profile (SCFA) was investigated for which four male Nellore cattle were used, distributed in a 4 × 4 Latin square (treatments × periods). Treatments comprised the same highly concentrated basal diet, and were as follows: T1, without additive (CON); T2, inclusion of 90 g of sodium bicarbonate (BIC); T3, inclusion of 90 g of L. calcareum (L90); and T4, inclusion of 45 g of L. calcareum (L45). Data were analysed in R, in which diversity and abundance at gender level were analysed using Friedman’s test, with means being adjusted by False Discovery Rate (FDR) correction. The analyses of pH, biochemical parameters and SCFA were analysed using Scott–Knott test and means were evaluated with a significance level of 10% (P &lt; 0.10). Key results We identified 1474 operational taxonomic units (OTUs) belonging to 52 genera and 16 phyla of bacteria domain. The results showed that bacterial microbiota were dominated by Firmicutes (44.12%), Bacteroidetes (28.29%), and Proteobacteria (5.88%). Animals fed with L90 demonstrated greater abundance and ruminal diversity for the Prevotella genus (P &lt; 0.07% and P &lt; 0.09% respectively), whereas cattle supplemented with L45 demonstrated greater diversity of the Fibrobacter genus (P &lt; 0.05). There were differences in molar proportion for acetic (P &lt; 0.07%) and valeric (P &lt; 0.03%) acids in the period before feeding. Higher blood lactate concentrations were observed in animals supplemented with L45 (P &lt; 0.06%), while animals that received treatments L90 and BIC presented lower levels of blood lactate. This metabolite was lower in animals fed with 90 g of sodium bicarbonate and L. calcareum daily. These treatments also reduced the concentration of acetic acid and increased that of valeric acid, and improved ruminal diversity. Conclusions and implications Our results supported this choice to improve ruminal function, with a great prospective of better weight-gain performance in Nellore cattle.

Effects of plantago species herbage and silage on in vitro ruminal fermentation and microbiome

The present study aimed to compare the nutrient composition, in vitro ruminal fermentation values and microbiome in the ruminal fermentation of herbage and silage of the Plantago media, P. major and P. lanceolata species. The lactic acid (LA) content of P. lanceolata silage was higher than those of other plantago silages (p < 0.05). The α-linolenic, w-3, polyunsaturated (PUFA), medium chain (MCFA) and long-chain fatty acids (LCFA) of plantago silages were lower than those of plantago herbages (p < 0.05). The neutral detergent fibre (NDF) and acid detergent fibre (ADF) contents, total gas and methane production, metabolic energy (ME) and organic matter digestion (OMD) values and ammonia-nitrogen concentration in the in vitro fermentation fluid of P. major silage were lower than those of other plantago silages (p < 0.05). The in vitro ruminal methane production and community of archaea Methanobrevibacter in the microbiome of P. major herbage were higher than that of P. media and P. lanceolata herbages. The ensiling process significantly increased the in vitro total gas production, acetic acid concentration and Prevotellaceae bacteria of P. media and P. lanceolate compared their herbages. As a result, P. lanceolata and P. media silages provided high-quality silage fermentation; the nutrient composition was not lost to a great extent in the silage environment and the ruminal fibrolytic bacterial composition was positively affected. Plantago major silage could not provide a good silage quality and the in vitro ruminal fermentation and ruminal fibrolytic bacteria community value were negatively affected. Highlights The crude protein (CP) and very long chain fatty acids contents of P. major herbage were higher than those of P. media and P. lanceolata. However, the P. major silage had high silage CP and ammonia-nitrogen concentration, low in vitro ruminal digestion (total gas production, ME and OMD), and plant cell wall substances. The ensiling of P. lanceolata and P. media positively affected the ruminal fibrolytic bacterial composition (Rikenellaceae_RC9_gut_group, Oscillospiraceae_UCG-002 and Prevotellaceae). The in vitro ruminal methane production and community of Methanobrevibacter in the ruminal microbiome of P. major herbage were higher than those of P. media and P. lanceolata herbages.

Combinations of bacterial cultures, exogenous enzymes, and yeast-based feed additives and their impact on ruminal microbiome.

Our objective was to evaluate the effects of bacteria (Lactobacillus animalis, Propionibacterium freudenreichii, Bacillus lichenformis, Bacillus subtilis, and Enterococcus faecium), enzymes (amylase, hemicellulose, and xylanase), and yeast as additives on the ruminal microbiome. We hypothesized that inclusion of bacteria, enzymes, and yeast would impact butyric bacterial populations. Eight fermenters were arranged in a duplicated 4 × 4 Latin square with the following treatments: 1) control without additives (CTRL); 2) bacterial culture and enzyme blend (EB); 3) bacterial culture and enzyme blend with a live yeast and yeast culture blend (EBY); and 4) double dose of bacterial culture and enzyme blend and the yeast products blend (2X). We conducted four fermentation periods of 10 d each, with the last 3 d for collection of samples. Overall, 64 solid and liquid samples were analyzed by amplification of the V4 region of bacterial 16S rRNA. Data were analyzed with R and SAS. The following orthogonal contrasts were used: 1) ADD-the control compared to all treatments with additives (CTRL vs. EB, EBY, and 2X); 2) YEAST-treatment without yeast compared to those with yeast (EB vs. EBY and 2X); and 3) DOSE-the single dose of enzymes, bacteria, and yeast compared to the doubled dose (EBY vs. 2X). Family Prevotellaceae was more abundant when additives were added (ADD). Additives (ADD) also increased relative abundance of Prevotellaceae Ga6A1 and YAB2003 in solid fraction, and of Prevotellaceae Ga6A1 and two members of Lachnospiracea family in liquid fraction. Yeast (YEAST) decreased relative abundance of Succinivibrionaceae UCG-001 and increased abundance of Ruminococcus and Prevotellaceae UCG-003 in solid fraction. Doubling the dose of enzymes and microbial additives (DOSE) decreased the abundance of Succiniclasticum in solid fraction and Selenomonadaceae in the liquid. Molar proportion of butyrate was highly correlated with abundance of Prevotellaceae Ga6A1 in solid (r = 0.68) and liquid fraction (r = 0.79), and with Unclassified Lachnospiraceae in liquid (r = 0.70). Our results demonstrate that YEAST decreases abundance of succinate synthesizing bacteria, while DOSE decreases abundance of bacteria that metabolize succinate into propionate. Combined bacteria, enzymes, and yeast increase the relative abundance of specific genera primarily within the Prevotellaceae family, which may explain the increase in butyrate molar proportion observed with ADD.

Effects of ruminal lipopolysaccharides on growth and fermentation end products of pure cultured bacteria

Elevated levels of ruminal lipopolysaccharides (LPS) have been linked to ruminal acidosis; however, they result in reduced endotoxicity compared to LPS derived from species like Escherichia coli. Additionally, there is a knowledge gap on the potential effect of LPS derived from ruminal microbiome on ruminal bacteria species whose abundance is associated with ruminal acidosis. The objective of this study was to evaluate the effects of LPS-free anaerobic water (CTRL), E. coli-LPS (E. COLI), ruminal-LPS (RUM), and a 1:1 mixture of E. coli and ruminal-LPS (MIX) on the growth characteristics and fermentation end products of lactate-producing bacteria (Streptococcus bovis JB1, Selenomonas ruminantium HD4) and lactate-utilizing bacterium (Megasphaera elsdenii T81). The growth characteristics were predicted based on the logistic growth model, the ammonia concentration was determined by the phenolic acid/hypochlorite method and organic acids were analyzed with high performance liquid chromatography. Results indicate that, compared to the CTRL, the maximum specific growth rate of S. bovis JB1 decreased by approximately 19% and 23% when RUM and MIX were dosed, respectively. In addition, acetate and lactate concentrations in Se. ruminantium HD4 were reduced by approximately 30% and 18%; respectively, in response to MIX dosing. Compared to CTRL, lactate concentration from S. bovis JB1 was reduced approximately by 31% and 22% in response to RUM and MIX dosing; respectively. In summary, RUM decreased the growth and lactate production of some lactate-producing bacteria, potentially mitigating the development of subacute ruminal acidosis by restricting lactate availability to some lactate-utilizing bacteria that metabolize lactate into VFAs thus further contributing to the development of acidosis. Also, RUM did not affect Megasphaera elsdenii T81 growth.

Association between rumen microbiota and marbling grade in Hu sheep.

The marbling fat regulates the flavor of mutton and measures the fat density in the loin eye and is the most important parameter of carcass grading. The objective of this study was to explore the relationship of rumen microbiota and mutton marbling grade. One hundred and eighty-seven feedlot-finished Hu male lambs (Age: 180 day; Final BW: 46.32 ± 6.03 kg) were slaughtered, and ruminal contents and marbling grade were collected. Ruminal microbial DNA extraction and 16S rRNA gene sequencing was performed to investigate microbial composition and to predict microbial metabolic pathways. The animal cohort was then grouped based on marbling grades [low marbling (LM), marbling grade ≤ 1; Medium marbling (MM), 1 < marbling grade ≤ 3; High Marbling (HM), 3 < marbling grade ≤ 5] and intramuscular fat-associated microorganisms were pinpointed using LEfSe and random forest classification model. Intramuscular fat content had significantly differences among the three groups (P < 0.05), and was significantly correlated with VFAs profiling. HM sheep showed a higher abundance of one bacterial taxon (Kandleria), and two taxa were overrepresented in the MM sheep (Pseudobutyrivibrio and Monoglobus), respectively. In addition, the main intramuscular fat deposition pathway was found to involve peroxisome proliferator-activated receptor (PPAR) fatty acid synthesis. By studying the effect of the ruminal microbiome on the marbling of sheep, the present study provides insights into the production of high-quality mutton.

Dysbiosis and predicted function of dental and ruminal microbiome associated with bovine periodontitis.

Extensive cattle livestock is advancing in Amazonia and its low productivity, with consequent pressure to open new areas, is partly due to sanitary problems and, among them, the periodontal diseases, whose environmental triggers or modifying factors are unknown. In this study, we used high-throughput sequencing, network analysis and predicted functions to investigate the dental and ruminal microbiota of cattle raised in new livestock areas in the Amazon and identify possible keystone pathogens and proteins associated with the disease. Ninety-three genera were common in dental and ruminal fluid microbiomes and among them periodontal pathogens such as Fusobacterium, Prevotella, Porphyromonas and Actinomyces were recognized. Network analysis showed that dental microbiomes of clinically healthy animals tend to comprise a group of OTUs in homeostasis and when analyzed together, dental and ruminal fluid microbiomes of animals with periodontitis had almost twice the number of negative edges, indicating possible competition between bacteria and dysbiosis. The incisor dental and ruminal fluid microbiomes were dominated by a core community composed of members of the phyla Firmicutes and Bacteroidetes. Network results showed that members of the Prevotella genus stood out among the top five OTUs, with the largest number of hubs in the dental and ruminal microbiota of animals with periodontitis. Protein families linked to an inflammatory environment were predicted in the dental and ruminal microbiota of cattle with periodontitis. The dissimilarity between dental microbiomes, discriminating between healthy cattle and those with periodontitis and the identification of possible key pathogens, represent an important reference to elucidate the triggers involved in the etiopathogenesis of bovine periodontitis, and possibly in the development of measures to control the disease and reduce the pressures for deforestation.

Characteristics of ruminal microbiota and metabolome in Holstein cows differing in milk protein concentrations.

The rumen is a vital organ containing vast amounts of microbes that play a key role in the digestion of nutrients and affect the production performance of ruminants. However, few studies have focused on the characterization of the ruminal microbiota composition and function in cows with long-term difference milk protein concentrations, and the relationship between milk protein concentration and ruminal microbiota remains elusive. In this study, we collected the data of milk protein concentrations of 1,025 Holstein cows for 10 mo on a commercial farm. Based on the milk protein concentrations, 30 cows were selected and divided into three groups (n = 10 per group): low milk protein group (LMP, milk protein concentration < 3.1%), medium milk protein group (MMP, 3.1% ≤ milk protein concentration < 3.4%), and high milk protein group (HMP, milk protein concentration ≥ 3.4%). The ruminal microbiome, metabolome, VFA concentrations and proportions, and amino acid profiles of the three groups were analyzed. The data showed that free amino acid (FAA) levels were lower in the rumen and higher in the plasma of HMP cows (P < 0.05). In addition, lower NH3 concentrations were observed in the rumen, plasma, and milk of the HMP cows (P < 0.05). Protease activity and isobutyric acid molar proportion in the rumen were lower in the HMP group (P < 0.05). Microbiome analysis showed that HMP cows had lower microbial diversity (represented as Shannon and Simpson indices) than LMP cows. At the genus level, lower relative abundances of Prevotella_1 and Ruminococcaceae_UCG_005 were observed in the HMP group (P < 0.05). At the operational taxonomic unit (OTU) level, a lower relative abundance of OTU3 (Prevotella ruminicola) was observed in the HMP group (P < 0.05). We found that the relative abundances of ruminal Prevotella_1 and OTU3 (Prevotella ruminicola) were negatively correlated with milk protein concentration (P < 0.05). These findings suggested that the cows with long-term high milk protein concentrations had lower microbial diversity and weaker protein degradation ability in the rumen. Furthermore, our observations identified a correlation between the milk protein concentration and ruminal microbiota.

Biodegradation and hydrolysis of rice straw with corn steep liquor and urea-alkali pretreatment.

The current study evaluated the corn steep liquor (CSL) and urea-alkali pretreatment effect to enhance biodegradation and hydrolysis of rice straw (RS) by ruminal microbiome. The first used RS (1) without (Con) or with additives of (2) 4% CaO (Ca), (3) 2.5% urea plus 4% CaO (UCa) and (4) 9% corn steep liquor + 2.5% urea + 4% CaO (CUCa), and then the efficacy of CSL plus urea-alkali pretreatment was evaluated both in vitro and in vivo. The Scanning electron microscopy, X-ray diffraction analysis, cellulose degree of polymerization and Fourier-transform infrared spectroscopy, respectively, results showed that Ca, UCa, and CUCa pretreatment altered the physical and chemical structure of RS. CSL plus Urea-alkali pretreated enhanced microbial colonization by improving the enzymolysis efficiency of RS, and specially induced adhesion of Carnobacterium and Staphylococcus. The CUCa pretreatment could be developed to improve RS nutritional value as forage for ruminants, or as feedstock for biofuel production.

Effects of calcium-magnesium carbonate and calcium-magnesium hydroxide as supplemental sources of magnesium on ruminal microbiome.

Our objective was to evaluate the inclusion of calcium-magnesium carbonate [CaMg(CO3)2] and calcium-magnesium hydroxide [CaMg(OH)4] in corn silage-based diets and their impact on ruminal microbiome. Our previous work showed a lower pH and molar proportion of butyrate from diets supplemented with [CaMg(CO3)2] compared to [CaMg(OH)4]; therefore, we hypothesized that ruminal microbiome would be affected by Mg source. Four continuous culture fermenters were arranged in a 4 × 4 Latin square with the following treatments defined by the supplemental source of Mg: 1) Control (100% MgO, plus sodium sesquicarbonate as a buffer); 2) CO3 [100% CaMg(CO3)2]; 3) OH [100% CaMg(OH)4]; and 4) CO3/OH [50% Mg from CaMg(CO3)2, 50% Mg from CaMg(OH)4]. Diet nutrient concentration was held constant across treatments (16% CP, 30% NDF, 1.66 MCal NEl/kg, 0.67% Ca, and 0.25% Mg). We conducted four fermentation periods of 10 d, with the last 3 d for collection of samples of solid and liquid digesta effluents for DNA extraction. Overall, 16 solid and 16 liquid samples were analyzed by amplification of the V4 variable region of bacterial 16S rRNA. Data were analyzed with R and SAS to determine treatment effects on taxa relative abundance of liquid and solid fractions. Correlation of butyrate molar proportion with taxa relative abundance was also analyzed. Treatments did not affect alpha and beta diversities or relative abundance of phylum, class and order in either liquid or solid fractions. At the family level, relative abundance of Lachnospiraceae in solid fraction was lower for CO3 and CO3/OH compared to OH and Control (P < 0.01). For genera, abundance of Butyrivibrio (P = 0.01) and Lachnospiraceae ND3007 (P < 0.01) (both from Lachnospiraceae family) was lower and unclassified Ruminococcaceae (P = 0.03) was greater in CO3 than Control and OH in solid fraction; while abundance of Pseudobutyrivibrio (P = 0.10) and Lachnospiraceae FD2005 (P = 0.09) (both from Lachnospiraceae family) and Ruminobacter (P = 0.09) tended to decrease in CO3 compared to Control in liquid fraction. Butyrate molar proportion was negatively correlated to Ruminococcaceae (r = –0.55) in solid fraction and positively correlated to Pseudobutyrivibrio (r = 0.61) and Lachnospiraceae FD2005 (r = 0.61) in liquid. Our results indicate that source of Mg has an impact on bacterial taxa associated with ruminal butyrate synthesis, which is important for epithelial health and fatty acid synthesis.

Host genetics associated with gut microbiota and methane emission in cattle.

In livestock sector, dairy animals alone produce 18% of the total greenhouse gas emissions globally as methane (CH4). This Enteric methane is the largest component of total carbon footprints produced by livestock production system and its reduction is today's new challenge to make livestock farming sustainable for earth's environment. The production of enteric methane in ruminants is a complex phenomena involving different host factors like host genotype, rumen microbiome, host physiology along with dietary factors. Efforts have been made to reduce methane emissions largely through nutritional interventions and dietary supplements, but permanent reductions can be obtained through genetic means by selecting and breeding of low methane emitting animals. From genome-wide association studies, many important genomic QTL regions and single nucleotide polymorphisms involved in shaping the composition of the ruminal microbiome and thus their carbon footprints have been recognised, implying that methane emission traits are quantitative traits. The major bottleneck in implementation of reduced methane emission traits in the breeding programs is wide variation at phenotypic level, lack of precise methane measurements at individual level. Overall, the heritability for CH4 production traits is moderate, and it can be used in breeding programmes to target changes in microbial composition to reduce CH4 emission in the dairy industry for far-reaching environmental benefits at the cost of a minor reduction in genetic gain in production traits.

Acute interstitial pneumonia and the biology of 3-methylindole in feedlot cattle.

Acute interstitial pneumonia (AIP) of cattle has been recognized for many decades. While the pathogenesis and risk factors for this condition in pastured cattle are relatively well characterized, there remains a poor understanding of the disease as it occurs in intensively fed cattle such as in beef feedlots. Specifically, in pastured cattle, AIP results from excessive ruminal production of the pneumotoxicant 3-methylindole (3-MI). In feedlot cattle, the evidence to substantiate the role of 3-MI is comparatively deficient and further investigations into the cause, pathogenesis, and control are sorely needed. This review highlights our current understanding of AIP with a focus on the disease as it occurs in feedlot cattle. Additionally, it illustrates the need for further work in understanding the specific animal factors (e.g. the ruminal microbiome, and the role of concurrent diseases), management factors (e.g. animal stocking and vaccination protocols), and dietary factors (e.g. dietary supplements) that may impact the development of AIP and which are relatively unique to the feedlot setting. All stakeholders in the beef industry stand to benefit from a greater understanding of what remains a pressing yet poorly understood issue in beef production.

Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows.

Fermentation of pasture grasses and grains in the rumen of dairy cows and other ruminants produces methane as a by-product, wasting energy and contributing to the atmospheric load of greenhouse gasses. Many feeding trials in farmed ruminants have tested the impact of dietary components on feed efficiency, productivity and methane yield (MeY). Such diets remodel the rumen microbiome, altering bacterial, archaeal, fungal and protozoan populations, with an altered fermentation outcome. In dairy cows, some dietary grains can reduce enteric methane production. This is especially true of wheat, in comparison to corn or barley. Using a feeding trial of cows fed rolled wheat, corn or barley grain, in combination with hay and canola, we identified wheat-associated changes in the ruminal microbiome. Ruminal methane production, pH and VFA concentration data together with 16S rRNA gene amplicon sequences were used to compare ruminal bacterial and archaeal populations across diets. Differential abundance analysis of clustered sequences (OTU) identified members of the bacterial families Lachnospiraceae, Acidaminococcaceae, Eubacteriaceae, Prevotellaceae, Selenomonadaceae, Anaerovoracaceae and Fibrobacteraceae having a strong preference for growth in wheat-fed cows. Within the methanogenic archaea, (at >99% 16S rRNA sequence identity) the growth of Methanobrevibacter millerae was favoured by the non-wheat diets, while Methanobrevibacter olleyae was unaffected. From the wheat-preferring bacteria, correlation analysis found OTU strongly linked to reduced MeY, reduced pH and raised propionic acid levels. OTU from the genera Shuttleworthia and Prevotella_7 and especially Selenomonadaceae had high anti-methane correlations. An OTU likely representing (100% sequence identity) the fumarate-reducing, hydrogen-utilising, rumen bacterium Mitsuokella jalaludinii, had an especially high negative correlation coefficient (-0.83) versus MeY and moderate correlation (-0.6) with rumen pH, strongly suggesting much of the MeY suppression is due to reduced hydrogen availablity. Other OTU, representing as yet unknown species from the Selenomonadaceae family and the genera Prevotella_7, Fibrobacter and Syntrophococcus also had high to moderate negative MeY correlations, but low correlation with pH. These latter likely represent bacterial species able to reduce MeY without causing greater ruminal acidity, making them excellent candidates, provided they can be isolated, for development as anti-methane probiotics.

Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle.

Background: The impact of extreme changes in weather patterns on the economy and human welfare is one of the biggest challenges our civilization faces. From anthropogenic contributions to climate change, reducing the impact of farming activities is a priority since it is responsible for up to 18% of global greenhouse gas emissions. To this end, we tested whether ruminal and stool microbiome components could be used as biomarkers for methane emission and feed efficiency in bovine by studying 52 Brazilian Nelore bulls belonging to two feed intervention treatment groups, that is, conventional and by-product-based diets. Results: We identified a total of 5,693 amplicon sequence variants (ASVs) in the Nelore bulls’ microbiomes. A Differential abundance analysis with the ANCOM approach identified 30 bacterial and 15 archaeal ASVs as differentially abundant (DA) among treatment groups. An association analysis using Maaslin2 software and a linear mixed model indicated that bacterial ASVs are linked to the host’s residual methane emission (RCH4) and residual feed intake (RFI) phenotype variation, suggesting their potential as targets for interventions or biomarkers. Conclusion: The feed composition induced significant differences in both abundance and richness of ruminal and stool microbial populations in ruminants of the Nelore breed. The industrial by-product-based dietary treatment applied to our experimental groups influenced the microbiome diversity of bacteria and archaea but not of protozoa. ASVs were associated with RCH4 emission and RFI in ruminal and stool microbiomes. While ruminal ASVs were expected to influence CH4 emission and RFI, the relationship of stool taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits was not reported before and might be associated with host health due to their link to anti-inflammatory compounds. Overall, the ASVs associated here have the potential to be used as biomarkers for these complex phenotypes.

Association of residual feed intake with peripartal ruminal microbiome and milk fatty acid composition during early lactation in Holstein dairy cows

Residual feed intake (RFI) is a moderately heritable trait of feed efficiency in dairy cows. The main objective of the present study was to assess potential differences in the ruminal microbiome, milk fatty acid (FA) composition, and plasma concentrations of glucose, nonesterified fatty acids (NEFA), and β-hydroxybutyrate between the most (M-EFF) and the least efficient (L-EFF) dairy cows during early lactation. Forty-seven multiparous Holstein dairy cows with daily ad libitum access to a total mixed ration from 30 d before calving to 30 d in milk were used. Cows were retrospectively classified into M-EFF (i.e., low RFI, n = 29) and L-EFF (high RFI, n = 18) based on a linear regression model. Ruminal digesta and milk samples were collected from each cow at 15 and 30 d in milk for microbiome analysis using 16S rRNA gene sequencing. Microbiome sequencing data were analyzed with the QIIME 2 platform (http://qiime.org/), whereas the microbiome statistical analyses and visual explorations were performed using the web-based MicrobiomeAnalyst platform. Milk FA composition was measured via gas chromatography-mass spectrometry. The statistical model used in SAS 9.4 (SAS Institute Inc.) included RFI, time, and their interactions as fixed effects. The cor() function in R programming was used to determine Pearson correlations between relative abundance of significant bacteria and milk FA. Overall, daily milk yield did not differ due to RFI and averaged 42 ± 1.6 kg for L-EFF and 43 ± 1.3 kg for M-EFF cows. However, M-EFF cows had lower overall dry matter intake (14.9 ± 0.5 kg/d) compared with L-EFF cows (19.2 ± 0.6 kg/d). No incidence of clinical disease was recorded for cows in the study. Compared with L-EFF, overall glucose concentration was lower, whereas NEFA and β-hydroxybutyrate concentrations were greater in M-EFF cows. Ruminal digesta from both RFI groups had similar bacterial composition, but differed in the relative abundance of some bacteria. Compared with L-EFF, M-EFF cows had greater relative abundance of Lachnospiraceae, Lachnoclostridium, Papillibacter, Desulfovibrio, Sphaerochaeta, Acetobacter, and Histophilus. In contrast, relative abundance of Bifidobacterium, Ruminiclostridium, Prevotellaceae, and Erysipelotrichaceae bacterium was lower in M-EFF cows. Compared with L-EFF, M-EFF cows had greater proportions of long-chain monounsaturated FA, including 16:1 trans-9, 16:1 cis-9, 17:1 trans-10, 17:1 cis-10, 18:1 cis-9, 18:1 cis-11, whereas proportions of medium-chain saturated and 16:0 were lower in M-EFF. Acetate-producing bacteria (Sphaerochaeta and Acetobacter) were positively and significantly correlated (r ≥ 0.24) with concentrations of 16:1 cis-9 and 17:1 cis-10, whereas Prevotellaceae was significantly and negatively correlated (r = -0.25) with these FA. Butyrate-producing bacterium (Papillibacter) had a significant negative correlation (r = -0.27) with concentration of 15:0. Overall, data suggested that feed-efficient cows have unique profiles of ruminal microbiota, some of which are correlated with concentrations of milk FA during early lactation.

Effects of choline chloride on the ruminal microbiome at 2 dietary neutral detergent fiber concentrations in continuous culture

Our objective was to evaluate the effects of unprotected choline chloride (Cho) on the ruminal microbiome at 2 dietary neutral detergent fiber (NDF) concentrations. We hypothesized that the effects of Cho on ruminal bacterial populations would depend on NDF. Eight dual-flow continuous-culture fermentors were arranged in a duplicated 4 × 4 Latin square as a 2 × 2 factorial with the following treatments: (1) 30% NDF-control (30% NDF diet, no supplemental choline); (2) 30% NDF-Cho (30% NDF diet plus 1.9 g of choline ion per kg of dry matter); (3) 40% NDF-control (40% NDF diet, no supplemental choline); and (4) 40% NDF-Cho (40% NDF diet plus 1.9 g of choline ion per kg of dry matter). We did 4 fermentation periods of 10 d each and used the last 3 d for collection of samples of solid and liquid digesta effluents for DNA extraction. Overall, 32 solid and 32 liquid samples were analyzed by amplification of the V4 variable region of bacterial 16S rRNA. Data were analyzed with R (R Project for Statistical Computing) and SAS (SAS Institute Inc.) to determine effects of Cho, NDF, and NDF × Cho on taxa relative abundance. The correlation of propionate molar proportion with taxa relative abundance was also analyzed. At the phylum level, relative abundance of Firmicutes in the liquid fraction tended to be greater when Cho was supplemented with a 30% NDF diet. At the order level, Cho increased Coriobacteriales in solid fraction and decreased Fibrobacterales in liquid fraction. Moreover, Cho decreased abundance of Clostridiales and increased Selenomonadales in the solid fraction, only with the 30% NDF diet. For genera, lower abundance of Pseudobutyrivibrio resulted from Cho in solid and liquid fractions. Greater abundance of Succinivibrio in solid and Selenomonas and Selenomonas 1 in liquid resulted from Cho with the 30% NDF diet. Propionate molar proportion was positively correlated with relative abundance of order Selenomonadales in solid and liquid fractions, and with genus Succinivibrio in solid and genera Selenomonas and Selenomonas 1 in liquid. Our results indicate that Cho primarily decreases abundance of bacteria involved in fiber degradation and increases abundance of bacteria mainly involved in nonstructural carbohydrate degradation and synthesis of propionate, particularly when a diet with 30% NDF is provided.

18 Effects of Protein Concentration, Degradability, and Beta-adrenergic Agonists on Ruminal Microbial Communities in Finishing Heifers

Abstract To improve animal performance and modify growth by increasing lean tissue accretion, beef cattle production has relied on use of growth promoting technologies such as beta-adrenergic agonists. These synthetic catecholamines, combined with the variable inclusion of rumen degradable (RDP) and undegradable protein (RUP), may improve feed efficiency and rate of gain in finishing beef cattle. However, the impact of beta-adrenergic agonists and protein level and source on the ruminal microbiome is limited. The objective of this study was to determine the effect of different protein concentrations and beta-adrenergic agonist (ractopamine hydrochloride; RAC) on ruminal bacterial communities in finishing beef heifers. Heifers (n = 140) were ranked according to body weight and assigned to pens in a randomized complete design to 6 different treatments, containing 3 protein treatments (Control: 13.9% CP, 8.8% RDP, and 5.0% RUP; High RDP: 20.9% CP, 13.4% RDP, 6.1% RUP; or High RUP: 20.9% CP, 9.1% RDP, 10.4% RUP) and 2 RAC treatments (0 and 400 mg/day). Rumen samples were collected from heifers by oral lavage 7 days before harvest. The DNA from the samples were sequenced to identify bacteria based on the V1-V3 hypervariable regions of the 16S rRNA gene using the Illumina MiSeq. Sequences and data from the treatments were analyzed using the R environment and PROC MIXED in SAS 9.4 (SAS Inst.; Cary, NC). Beta diversity was analyzed using PERMANOVA based on PCoA Bray-Curtis distances and were significant among the treatments (P &amp;lt; 0.05). Alpha diversity metrics such as Chao1 and Shannon diversity indices were not significantly different (P &amp;gt; 0.05). Differences among treatments at variable taxonomic levels after analyses through DESeq2 were significantly different for the main effects of protein and RAC, as well as their interaction (P &amp;lt; 0.05). These results suggest possible effects on the microbial communities, potentially acting synergistically to improve performance.

Effect of Sainfoin (Onobrychis viciifolia) Pellets on Rumen Microbiome and Histopathology in Lambs Exposed to Gastrointestinal Nematodes

Our study analyzed the ruminal fermentation and microbiome, hematological profile, and abomasal histopathology of lambs experimentally infected with a gastrointestinal nematode (GIN) and fed sainfoin pellets (SFPs; 600 g DM/d/animal) for 14 d. Twenty-four lambs infected with Haemonchus contortus were divided into two separated groups: animals fed meadow hay (control) and animals fed SFPs. The ruminal contents, fermentation parameters, and microbiome in vitro and in vivo were determined using molecular and microscopic techniques. Ruminal contents in the SFP group indicated smaller populations of Archaea (p &lt; 0.001), Methanomicrobiales (p = 0.009), and lower methane concentrations in vitro (p = 0.046) and in vivo (p = 0.030) than the control group. The relative abundance of Butyrivibrio fibrisolvens quantified by real-time PCR was higher in the lambs with the SFP diet (p = 0.05). Haemonchosis affected the number of red blood cells of the lambs (p &lt; 0.001). The lambs in the SFP group had a higher percentage of damaged abomasa glands than did the control group (p = 0.004). The consumption of SFPs by GIN-infected lambs may affect ruminal methanogens and subsequently decrease methane emission without undesirable changes in the ruminal microbiome or the health of the animals.