Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation.

Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.

Microbiome-informed study of the mechanistic basis of methane inhibition by Asparagopsis taxiformis in dairy cattle.

Copious amounts of methane, a major constituent of greenhouse gases currently driving climate change, are emitted by livestock, and efficient methods that curb such emissions are urgently needed to reduce global warming. When fed to cows, the red seaweed Asparagopsis taxiformis (AT) can reduce enteric methane emissions by up to 80%, but the achieved results can vary widely. Livestock produce methane as a byproduct of methanogenesis, which occurs during the breakdown of feed by microbes in the rumen. The ruminant microbiome is a diverse ecosystem comprising bacteria, protozoa, fungi, and archaea, and methanogenic archaea work synergistically with bacteria to produce methane. Here, we find that an effective reduction in methane emission by high-dose AT (0.5% dry matter intake) was associated with a reduction in methanol-utilizing Methanosphaera within the rumen, suggesting that they may play a greater role in methane formation than previously thought. However, a later spike in Methanosphaera suggested an acquired resistance, possibly via the reductive dehalogenation of bromoform. While we found that AT inhibition of methanogenesis indirectly impacted ruminal bacteria and fermentation pathways due to an increase in spared H2, we also found that an increase in butyrate synthesis was due to a direct effect of AT on butyrate-producing bacteria such as Butyrivibrio, Moryella, and Eubacterium. Together, our findings provide several novel insights into the impact of AT on both methane emissions and the microbiome, thereby elucidating additional pathways that may need to be targeted to maintain its inhibitory effects while preserving microbiome health and animal productivity. IMPORTANCE: Livestock emits copious quantities of methane, a major constituent of the greenhouse gases currently driving climate change. Methanogens within the bovine rumen produce methane during the breakdown of feed. While the red seaweed Asparagopsis taxiformis (AT) can significantly reduce methane emissions when fed to cows, its effects appear short-lived. This study revealed that the effective reduction of methane emissions by AT was accompanied by the near-total elimination of methane-generating Methanosphaera. However, Methanosphaera populations subsequently rebounded due to their ability to inactivate bromoform, a major inhibitor of methane formation found in AT. This study presents novel findings on the contribution of Methanosphaera to ruminal methanogenesis, the mode of action of AT, and the possibility for complementing different strategies to effectively curb methane emissions.

Predicting subacute ruminal acidosis from milk mid-infrared estimated fatty acids and machine learning on Canadian commercial dairy herds.

Our objective was to validate the possibility of detecting SARA from milk Fourier transform mid-infrared spectroscopy estimated fatty acids (FA) and machine learning. Subacute ruminal acidosis is a common condition in modern commercial dairy herds for which the diagnostic remains challenging due to its symptoms often being subtle, nonexclusive, and not immediately apparent. This observational study aimed at evaluating the possibility of predicting SARA by developing machine learning models to be applied to farm data and to provide an estimated portrait of SARA prevalence in commercial dairy herds. A first data set composed of 488 milk samples of 67 cows (initial DIM = 8.5 ± 6.18; mean ± SD) from 7 commercial dairy farms and their corresponding SARA classification (SARA+ if rumen pH <6.0 for 300 min, else SARA-) was used for the development of machine learning models. Three sets of predictive variables: i) milk major components (MMC), ii) milk FA (MFA), and iii) MMC combined with MFA (MMCFA) were submitted to 3 different algorithms, namely Elastic net (EN), Extreme gradient boosting (XGB), and Partial least squares (PLS), and evaluated using 3 different scenarios of cross-validation. Accuracy, sensitivity, and specificity of the resulting 27 models were analyzed using a linear mixed model. Model performance was not significantly affected by the choice of algorithm. Model performance was improved by including fatty acids estimations (MFA and MMCFA as opposed to MMC alone). Based on these results, one model was selected (algorithm: EN; predictive variables: MMCFA; 60.4, 65.4, and 55.3% of accuracy, sensitivity, and specificity, respectively) and applied to a large data set comprising the first test-day record (milk major components and FA within the first 70 DIM of 211,972 Holstein cows (219,503 samples) collected from 3001 commercial dairy herds. Based on this analysis, the within-herd SARA prevalence of commercial farms was estimated at 6.6 ± 5.29% ranging from 0 to 38.3%. A subsequent linear mixed model was built to investigate the herd-level factors associated to higher within-herd SARA prevalence. Milking system, proportion of primiparous cows, herd size and seasons were all herd-level factors affecting SARA prevalence. Furthermore, milk production was positively, and milk fat yield negatively associated with SARA prevalence. Due to their moderate levels of accuracy, the SARA prediction models developed in our study, using data from continuous pH measurements on commercial farms, are not suitable for diagnostic purpose. However, these models can provide valuable information at the herd level.

Effects of amino resin-treated and heat-treated soybean meal on ruminal fermentation, nutrient digestion, and nitrogen partitioning in continuous culture.

The objective of this study was to evaluate the effects of amino resin-treated soybean meal (SBM) on ruminal fermentation, nutrient digestion, and N partitioning. Treatments were: (1) untreated solvent-extracted SBM, (2) amino resin-treated SBM (AR-SBM), and (3) heat-treated SBM (HT-SBM). The experimental design was arranged as a replicated 3 × 3 Latin square with 6 fermenters in a dual-flow continuous culture system. Treatments were randomly assigned to fermenters within a Latin square for each period. Each fermenter was fed 106 g/d of diet DM equally distributed in 2 feeding times daily at 0800 and 1800. Diets were formulated to contain 16% CP, 30% NDF, and 30% starch across treatments. The experiment consisted of 3 experimental periods, each lasting for 10 d. The first 7 d of each period were considered adaptation, and the last 3 d were used for sampling and data collection. On d 8 and 9, samples were collected for analysis of diurnal variation in concentrations of NH3-N, pH, and VFA during the first 8 h after feeding. On d 8, 9, and 10, samples were collected from the liquid and solid effluents accumulated over 24 h for analysis of daily averages of NH3-N and VFA pools, and true ruminal digestibility estimates. Data were analyzed using the MIXED procedure of SAS and significance was declared when P ≤ 0.05. The model included the fixed effect of treatment and random effects of square, period, and fermenter within square, while time and interaction treatment × time were included for analyses of diurnal variation, with time as repeated measures. Compared with SBM, the cultured ruminal contents of AR-SBM and HT-SBM had lower NH3-N concentrations, indicating lower microbial fermentation of protein. Molar proportions of isovalerate and isobutyrate were greater in SBM than AR-SBM and HT-SBM, with greater molar proportion of isobutyrate for SBM particularly during the first 2 h after feeding. Flow of NH3-N was greater for SBM compared with AR-SBM and HT-SBM, whereas NAN flow, bacterial N flow, and N efficiency were greater for AR-SBM and HT-SBM compared with SBM. Our results indicate that both the amino resin and heat treatments of SBM allow for similar decrease in microbial degradation of CP without limiting microbial protein synthesis in diets with 16% CP. Amino resin treatment may be effective in reducing microbial fermentation of protein in the rumen without adverse effects on digestibility or fermentation parameters as compared with SBM.

Dietary 5-hydroxytryptophan improves sheep growth performance by enhancing ruminal functions, antioxidant capacity, and tryptophan metabolism: in vitro and in vivo studies.

Background: Hydroxytryptophan (5-HTP) can regulate the synthesis of 5-Hydroxytryptamine (5-HT) and melatonin (MT). In a previous metabolome analysis, we found that 5-HTP is an effective ingredient in yeast culture for regulating rumen fermentation. However, research on the effect of this microbial product (5-HTP) as a functional feed additive in sheep production is still not well explained. Therefore, this study examined the effects of 5-HTP on sheep rumen function and growth performance using in vitro and in vivo models. Methods: A two-factor in vitro experiment involving different 5-HTP doses and fermentation times was conducted. Then, in the in vivo experiment, 10 sheep were divided into a control group which was fed a basal diet, and a 5-HTP group supplemented with 8 mg/kg 5-HTP for 60 days. Results: The results showed that 5-HTP supplementation had a significant effect on in vitro DMD, pH, NH3-N, acetic acid, propionic acid, and TVFA concentrations. 5-HTP altered rumen bacteria composition and diversity indices including Chao1, Shannon, and Simpson. Moreover, the in vivo study on sheep confirmed that supplementing with 8 mg/kg of 5-HTP improved rumen fermentation efficiency and microbial composition. This led to enhanced sheep growth performance and increased involvement in the tryptophan metabolic pathway, suggesting potential benefits. Conclusion: Dietary 5-HTP (8 mg/kg DM) improves sheep growth performance by enhancing ruminal functions, antioxidant capacity, and tryptophan metabolism. This study can provide a foundation for the development of 5-HTP as a functional feed additive in ruminants' production.

Effect of traditional roughage-based or limit-fed, high-energy diets on growth performance and digestion in newly received growing cattle and subsequent implications on feedlot growth performance and carcass characteristics.

The objective was to determine the effects of ad libitum-fed roughage-based diets or limit-fed high-energy diets on growth performance, behavior, health, and digestion in newly received growing cattle and subsequent implications on feedlot growth performance and carcass characteristics. In experiment 1, 409 crossbred heifers (initial body weight [BW] = 279 ±â€…24 kg) in 32 pens were used in a randomized block design. Heifers were fed one of two dietary treatments: a total mixed ration with 0.99 Mcal net energy for gain (NEg)/kg dry matter (DM) fed ad libitum (0.99AL) or 1.32 Mcal NEg/kg DM limit-fed at 85% of intake of heifers fed 0.99AL (1.32LF85%). Both diets contained 40% DM as a branded wet corn gluten feed. In experiment 2, 370 crossbred heifers (initial BW = 225 ±â€…20 kg) were used in a randomized block design and were fed a diet formulated to contain 0.99 Mcal of NEg/kg DM for ad libitum intake or a diet formulated to contain 1.32 Mcal of NEg/kg DM and fed at 2.2% of BW daily (DM basis; 1.32LF2.2). For experiments 1 and 2, treatment integrity was maintained through the finishing phase where cattle were fed a common diet. Cattle were sorted by BW into heavy and light groups prior to finishing, with light cattle fed longer than heavy cattle to reach similar harvest BW. In experiment 3, eight ruminally cannulated heifers (average BW = 305 ±â€…23 kg) were used in a 2-period cross-over design and fed treatments from experiment 1 to assess digestibility and ruminal fermentation characteristics. Gain:feed was 47% and 35% greater (P < 0.01) in experiments 1 and 2, respectively, for limit-fed heifers compared with 0.99AL heifers. Rumination time was greater (P < 0.01) for 0.99AL compared with limit-fed treatments in experiments 1 and 2. Activity was greater (P < 0.01) for 1.32LF2.2 than for 0.99AL in experiment 2. In experiment 1, more (P = 0.03) carcasses from light-sort heifers than carcasses from heavy-sort heifers had livers with large, active abscesses. In experiment 2, finishing phase morbidity was greater (P < 0.01) for 1.32LF2.2 than for 0.99AL. Light-sort groups had fewer (P < 0.01) edible livers than heavy-sort groups, suggesting that greater number of days on feed may increase the risk of liver abscess prevalence and condemnation. In experiment 3, apparent total-tract DM and organic matter digestibilities were greater (P < 0.01) for 1.32LF85% than for 0.99AL. Overall, dietary treatments during the growing phase had little carryover effect on feedlot growth performance, carcass characteristics, or liver abscesses prevalence at harvest.

Chemical Composition and Nutritive Value of Almond Hulls from Two Almond Varieties and Influence of Including Almond Hulls in the Diet on In Vitro Ruminal Fermentation and Methane Production.

Almond hulls (AH) are frequently used in dairy ruminant feeding, but information on variability of their nutritive value and their potential effects on CH4 production is still scarce. The influence of almond variety (Guara vs. Soleta) on chemical composition and energy value of AH was investigated using 10 samples per variety collected in 2 consecutive years. Guara-AH had greater (p ≤ 0.015) ash, protein, and fat content, but lower (p ≤ 0.001) fiber than Soleta-AH. The metabolizable energy content estimated from chemical composition and in vitro gas production was 8.5% greater for Guara than for Soleta samples. Harvesting year significantly affected most of the chemical fractions. The in vitro ruminal fermentation of diets for dairy ruminants including increasing amounts of dried AH (8, 16 and 24% of the total diet; fresh matter basis) indicated that AH can be included up to 16% of the diet, partially substituting corn, wheat bran and sugar beet pulp without detrimental effects on in vitro volatile fatty acid (VFA) production. In contrast, when AH replaced alfalfa hay and corn, VFA production was reduced at all levels of AH inclusion. No antimethanogenic effects of AH were detected in the in vitro incubations.

Feeding live yeast (Saccharomyces cerevisiae) improved performance of mid-lactation dairy cows by altering ruminal bacterial communities and functions of serum antioxidation and immune responses.

BACKGROUND: The utilization of live yeast (Saccharomyces cerevisiae, YE) in dairy cows is gaining traction in dairy production as a potential strategy to improve feed efficiency and milk yield. However, the effects of YE on dairy cow performance remain inconsistent across studies, leaving the underlying mechanisms unclear. Hence, the primary aim of this study was to investigate the impact of YE supplementation on lactation performance, ruminal microbiota composition and fermentation patterns, as well as serum antioxidant capacity and immune functions in dairy cows. RESULTS: Supplementation with YE (20 g/d/head) resulted in enhancements in dairy cow's dry matter intake (DMI) (P = 0.016), as well as increased yields of milk (P = 0.002) and its components, including solids (P = 0.003), fat (P = 0.014), protein (P = 0.002), and lactose (P = 0.001) yields. The addition of YE led to significant increases in the concentrations of ammonia nitrogen (NH3-N) (P = 0.023), acetate (P = 0.005), propionate (P = 0.025), valerate (P = 0.003), and total volatile fatty acids (VFAs) (P < 0.001) in rumen fermentation parameters. The analysis of 16s rRNA gene sequencing data revealed that the administration of YE resulted in a rise in the relative abundances of three primary genera including Ruminococcus_2 (P = 0.010), Rikenellaceae_RC9_gut_group (P = 0.009), and Ruminococcaceae_NK4A214_group (P = 0.054) at the genus level. Furthermore, this increase was accompanied with an enriched pathway related to amino acid metabolism. Additionally, enhanced serum antioxidative (P < 0.05) and immune functionalities (P < 0.05) were also observed in the YE group. CONCLUSIONS: In addition to improving milk performance, YE supplementation also induced changes in ruminal bacterial community composition and fermentation, while enhancing serum antioxidative and immunological responses during the mid-lactation stage. These findings suggest that YE may exert beneficial effects on both rumen and blood metabolism in mid-lactation dairy cows.

Effect of Adding Yeast Cultures to High-Grain Conditions on Production Performance, Rumen Fermentation Profile, Microbial Abundance, and Immunity in Goats.

It is a common practice among farmers to utilize high-grain diets with the intention of promoting ruminant growth. However, this approach bears the risk of inducing rumen disorders and nutrient metabolism diseases. Yeast culture (YC) showed advantages in ruminant applications. The objective of this study was to evaluate the effects of adding two different types of YC to high-grain conditions on production performance, rumen fermentation profile, microbial abundance, and immunity in goats. A total of 30 male goats with similar body condition were randomly distributed into 3 dietary treatments with 10 replicates per treatment as follows: basic diet group (CON); basic diet + 0.5% yeast culture 1 (YC1) group; basic diet + 0.5% yeast culture 2 (YC2) group. The trial lasted for 36 days. The results demonstrated that dietary YC supplementation led to an increase in the average daily gain and a reduction in feed intake and weight gain ratio in goats. It increased the apparent digestibility of crude protein, NDF, and ADF (p < 0.05). The serum concentrations of interleukin (IL)-1ß, IL-6, and Tumor Necrosis Factor-α in the control group were significantly higher than those of the YC groups (p < 0.05). The serum concentrations of Immunoglobulin (Ig)A and IgG in the control group were significantly lower than those in the YC groups (p < 0.05). The rumen concentration of microbial protein (MCP) in the control group was significantly lower than that in the YC groups (p < 0.05). There was a negative correlation between the concentration of IL-10 and Bacteroidota, Spirochaetota, and Succinivibrio, while there was a positive correlation between concentrations of IL-10 and Firmicutes. Nevertheless, discrepancies were observed in the impact of the two different types of YC on the physiological and biochemical indicators of the animals. The concentration of triglyceride in the YC1 group was significantly higher than that of the CON and YC2 groups, while the concentration of urea in the YC2 group was significantly higher than that of the CON and YC1 groups (p < 0.05). At the phylum level, the addition of YC2 to the diet significantly increased the relative abundance of Bacteroidota and Fibrobacterota and significantly decreased Firmicutes compared to the control. At the genus level, the addition of YC1 to the HGD significantly reduced the relative abundance of Rikenellaceae_RC9_gut_group, while the addition of YC2 to the HGD significantly increased the relative abundance of Prevotellace-ae_UCG-001, Fibrobacter, and Prevotellaceae_UCG-003 (p < 0.05). The addition of YC significantly improved growth performance, increased nutrient digestibility, beneficially manipulated ruminal fermentation and microbial diversity, and improved immune function. The choice of yeast cultures can be customized according to specific production conditions.

Effect of wheat middling incorporation into wet corn distillers grains with solubles on apparent diet digestibility and ruminal fermentation characteristics in growing and finishing diets.

Two separate cross-over experiments were conducted to evaluate the effects of incorporating wheat middlings into wet corn distillers grains with solubles (WDGS) on apparent diet digestibility and ruminal fermentation characteristics in growing and finishing diets. In experiment 1, four ruminally cannulated heifers (313 ±â€…42.9 kg) were limit fed a high-energy growing diet that included WDGS (CON) or WDGS + wheat middlings (CON + WM) at 40% of diet dry matter (DM). The diet also contained (DM basis) 39.5% dry-rolled corn, 7.5% supplement, and 13% warm-season grass hay. In experiment 2, four ruminally cannulated Holstein steers (321 ±â€…17.4 kg) were fed a finishing diet that included WDGS (CON) or WDGS + wheat middlings (CON + WM) at 30% of diet DM. The diet also contained (DM basis) 60.3% dry-rolled corn, 2.7% supplement, and 7.0% warm-season grass hay. Experiments consisted of two 15-d periods that were conducted concurrently. Each period included 10 d of diet adaptation, 4 d of fecal collection, and 1 d of ruminal fluid collection. Fecal samples were collected on days 11 to 14 of each period and composite samples were analyzed for chromium to estimate apparent diet digestibility. On day 15, ruminal fluid samples were collected prior to feeding and again at 2, 4, 6, 8, 12, 18, and 24-h post-feeding. In experiment 1, DM, organic matter (OM), neutral detergent fiber (NDF), and acid detergent fiber (ADF) intake did not differ (P ≥ 0.11) between diets; however, starch intake was greater (P = 0.03) for heifers fed CON + WM compared with CON. Apparent DM, OM, NDF, and starch digestibilities were similar between diets (P ≥ 0.13), but feeding CON + WM tended to lead to lesser (P = 0.06) apparent ADF digestibility. Ruminal pH and total volatile fatty acid concentrations did not differ between diets (P ≥ 0.16); however, ruminal ammonia concentrations tended to be less (P = 0.09) for CON + WM compared with CON. In experiment 2, DM intake did not differ (P = 0.65) between diets. Apparent DM digestibility was greater (P = 0.01) for CON + WM compared with CON but the difference was small. Intake and apparent digestibility of OM, NDF, ADF, and starch did not differ (P ≥ 0.25) between diets. Ruminal ammonia concentrations were lesser (P = 0.03) while ruminal pH was greater (P = 0.02) for CON + WM compared with CON. Overall, incorporation of wheat middlings into WDGS had minimal impacts on feed intake, apparent diet digestibility, and ruminal fermentation characteristics when fed to growing and finishing cattle.

Disturbances of Ruminal Microbiota and Liver Inflammation, Mediated by LPS and Histamine, in Dairy Cows Fed a High-Concentrate Diet.

The ecosystem of ruminal microbiota profoundly affects the health and milk production of dairy cows. High-concentrate diets are widely used in dairy farms and evoke a series of metabolic disorders. Several studies have reported the effects of high-concentrate diets on the ruminal microbiome, while the effect of changes in ruminal microbial flora, induced by high-concentrate diet feeding, on the liver of dairy cows has not been studied before. In this study, 12 mid-lactating Holstein Friesian cows (weight of 455 ± 28 kg; parities of 2.5 ± 0.5; starting milk yield of 31.59 ± 3.2 kg/d; DMI of 21.7 ± 1.1 kg/d; and a DIM at the start of the experiment of 135 ± 28 d) were fitted with ruminal fistulas, as well as with portal and hepatic vein catheters. All cows were randomly divided into 2 groups; then, they fed with low-concentrate diets (LC, concentrate: forage = 40:60) and high-concentrate diets (HC, concentrate: forage = 60:40) for 18 weeks. The forage sources were corn silage and alfalfa hay. After the cows of two groups were euthanized over two consecutive days, ruminal microbiota; the concentration of LPS in the rumen content; cecum content; the levels of blood and histamine in rumen fluid, blood, and the liver; the histopathological status of the rumen and cecum; and the inflammatory response of the liver were assessed in dairy cows under conditions of subacute ruminal acidosis (SARA). These conditions were caused by high-concentrate diet feeding. All data were analyzed using the independent t-test in SPSS. The results showed that high-concentrate diet feeding increased the concentration of LPS and histamine in the rumen and plasma of veins (p < 0.05). The abundance of Bacteroidetes at the phylum level, and of both Bacteroidetes and Saccharibacteria at the genus level, was decreased, while the abundance of Firmicutes at the phylum level and Oscillibacter at the genus level was increased by high-concentrate diet feeding. The decreased pH values of ruminal contents (LC = 6.02, HC = 5.90, p < 0.05) and the increased level of LPS in the rumen (LC = 4.921 × 105, HC = 7.855 × 105 EU/mL, p < 0.05) and cecum (LC = 11.960 × 105, HC = 13.115 × 105 EU/mL, p < 0.01) induced the histopathological destruction of the rumen and cecum, combined with the increased mRNA expression of IL-1ß (p < 0.05). The histamine receptor H1R and the NF-κB signaling pathway were activated in the liver samples taken from the HC group. In conclusion, the elevated concentrations of LPS and histamine in the gut may be related to changes in the ruminal microbiota. LPS and histamine induced the inflammatory response in the ruminal epithelium, cecum epithelium, and liver. However, the cause-effect mechanism needs to be proved in future research. Our study offers a novel therapeutic strategy by manipulating ruminal microbiota and metabolism to decrease LPS and histamine release and to improve the health of dairy cows.

Effects of Palm Oil Deodorizer Distillate on the Ruminal Environment of Sheep.

This study aimed to assess the impact of palm oil deodorizer distillate (POD) on the ruminal environment, including (i) microbial community, (ii) ruminal degradability, and (iii) apparent digestibility in sheep. The data used were derived from twenty rumen-cannulated sheep fed five isoproteic and isofiber diets based on elephant grass (Pennisetum purpureum Schum. cv. Roxo) silage supplemented with 0, 25, 50, 75, or 100 g kg-1 POD on a dry matter (DM) basis. Rumen fluid samples were collected three hours after feeding directly from the ventral sac of the rumen via a cannula and then subjected to DNA extraction, which was subsequently used for 16S rDNA amplification, followed by sequencing and diversity analysis. In this study, the microbial diversity was dominated by Bacteroidetes and Firmicutes, followed by Euryarchaetoa, Actinobacteria, and Tenericutes, in the ruminal environment, and was slightly modified when supplemented with the POD up to 100 g/kg (10%), leading to only a slight decrease in the diversity index. The ruminal degradability, ruminal fermentation parameters, and apparent digestibility were slightly compromised by the inclusion of up to 25 g of POD per kg of DM, and larger inclusions interfered with the ruminal degradability of fibrous fractions and the apparent digestibility of dry matter. This lipid supplement showed good results for feeding sheep and is an inexpensive and abundant alternative in the regional market.

Ruminal microbiome changes across lactation in primiparous Holstein cows with varying methane intensity: Heritability assessment.

Methane is a potent greenhouse gas produced during the ruminal fermentation and is associated with a loss of feed energy. Therefore, efforts to reduce methane emissions have been ongoing in the last decades. Methane production is highly influenced by factors such as the ruminal microbiome and host genetics. Previous studies have proposed to use the ruminal microbiome to reduce long-term methane emissions, as ruminal microbiome composition is a moderately heritable trait and genetic improvement accumulates over time. Lactation stage is another important factor that might influence methane production but potential associations with the ruminal microbiome have not been evaluated previously. This study sought to examine the changes in ruminal microbiome over the lactation period of primiparous Holstein cows differing in methane intensity and estimate the heritability of the abundance of relevant microorganisms. Ruminal content samples from 349 primiparous Holstein cows with 14 - 378 d in milk were collected from May 2018 to June 2019. Methane intensity (MI) of each cow was calculated as methane concentration/milk yield. Up to 64 taxonomic features (TF) from 20 phyla had a significant differential abundance between cows with low and high MI early in lactation, 16 TF during mid lactation, and none late in lactation. Taxonomical features within the Firmicutes, Proteobacteria, Melainabacteria, Cyanobacteria, Bacteroidetes and Actinobacteria phyla were associated to low MI, whereas eukaryotic TF and those within the Euryarchaeota, Verrucomicrobia, Kiritimatiellaeota, Lentisphaerae phyla were associated to high MI. Out of the 60 TF that were found to be differentially abundant between early and late lactation in cows with low MI, 56 TF were also significant when cows with low and high MI were compared in the first third of the lactation. In general, microbes associated with low MI were more abundant early in lactation (e.g., Acidaminococcus, Aeromonas and Weimeria genera) and showed low to moderate heritabilities (0.03 to 0.33). These results suggest some potential to modulate the rumen microbiome composition through selective breeding for lower MI. Differences in the ruminal microbiome of cows with extreme MI levels likely result from variations in the ruminal physiology of these cows and were more noticeable early in lactation probably due to important interactions between the host phenotype and environmental factors associated to that period. Our results suggest that the ruminal microbiome evaluated early in lactation may be more precise for MI difference, and hence, this should be considered to optimize sampling periods to establish a reference population in genomic selection scenarios.

Effects of the level and source of dietary physically effective fiber on feed intake, nutrient utilization, heat energy, ruminal fermentation, and milk production by Alpine goats.

Thirty-two primiparous and 31 multiparous Alpine goats were used to determine influences of diets varying in level and source of forage on performance in early to mid-lactation for 16 wk. Diets consisted of 40%, 50%, 60%, and 70% forage (designated as 40F, 50F, 60F, and 70F, respectively) with 60F and 70F containing coarsely ground grass hay (primarily orchardgrass) and 40F and 50F containing cottonseed hulls, alfalfa pellets, and coarsely ground wheat hay. Diets contained 15.9% to 16.3% crude protein and 37.8%, 42.1%, 53.5%, and 55.4% neutral detergent fiber (NDF) with 10.0%, 15.8%, 50.1%, and 55.5% particle retention on a 19-mm sieve, and 26.1%, 29.6%, 38.3%, and 40.0% physically effective NDF (peNDF) for 40F, 50F, 60F, and 70F, respectively. Dry matter intake (2.71, 2.75, 1.96, and 1.95 kg/d) and milk yield (2.82, 2.71, 2.23, and 2.10 kg/d for 40F, 50F, 60F, and 70F, respectively) were lower (P < 0.05) for the two diets highest in forage. Digestion of organic matter was similar among diets (P > 0.05), but digestibility of NDF was greater (P < 0.05) for 60F and 70F (57.5%, 58.4%, 68.9%, and 72.2% for 40F, 50F, 60F, and 70F, respectively). Diet affected (P < 0.05) milk fat (3.16%, 3.37%, 2.93%, and 2.97%) and protein concentrations (2.62%, 2.69%, 2.58%, and 2.52% for 40F, 50F, 60F, and 70F, respectively). Milk energy yield was greater (P < 0.05) for the two diets lowest in forage (7.51, 7.45, 5.68, and 5.34 MJ/d), although yield relative to dry matter intake was not affected (P > 0.05) by diet and was lower (P < 0.05) for primiparous vs. multiparous goats (2.71 and 3.09 MJ/kg). Ruminal pH and acetate proportion were greater for 60F and 70F than for the other diets and the proportion of butyrate was lower for the two diets highest in fiber. The mean lengths of time spent ruminating, eating, standing, and lying were not affected (P > 0.05) by diet or parity, but many interactions involving diet, period, hour, and parity were significant (P < 0.05). In conclusion, lactational performance of Alpine goats in early to mid-lactation will be constrained with diets high in forage of moderate quality, peNDF content, and large particle size, which appeared related to limited feed intake.

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes.

Dairy buffaloes are typically fed a high-forage, low-quality diet with high fiber. These conditions result in an inherent energy and protein inefficiency. In order to make full and rational use of feed resources and improve the production level and breeding efficiency of dairy buffaloes, the effects of various roughages on nutrient digestibility, ruminal fermentation parameters, and microorganisms in dairy buffaloes were studied in this experiment. Three ternary hybrid buffaloes, with an average body weight of 365 ± 22.1 kg, were selected and fitted with permanent rumen fistulas. They were fed six different diets, each consisting of 1 kg concentrate supplement and one of six types of roughage, including alfalfa hay (A diet), oat hay (O diet), whole corn silage (W diet), king grass (K diet), sugarcane shoot silage (S diet), and rice straw hay (R diet) according to an incomplete Latin square design of 3 × 6, respectively. The pre-feeding period of each period was 12 d. From day 13 to 15 was the official experimental period. During the prefeeding period, free feed intake for each roughage was determined, and during the experiment, the roughage was fed at 90% of the voluntary feed intake. Digestion and metabolism tests were carried out using the total manure collection method to determine the feed intake and fecal output of each buffalo, and to collect feed and fecal samples for chemical analysis. On day 15, rumen fluid samples were collected two hours after morning feeding to determine rumen fermentation parameters and bacterial 16 S rRNA high-throughput sequencing was performed. The results showed that DM and OM digestibility were greatest for the W diet and lowest for the S diet. The rumen pH of the O diet was significantly greater than that of the W diet. The concentration of rumen fluid NH3-N (mg/dL) increased with increased CP content. The concentration of total volatile fatty acids (mmol/L) in the rumen decreased with increased NDF content but increased with increased NFC content. The relative abundances of Bacteroidetes, Firmicutes, and Spirochaetes were 57.03-74.84%, 14.29-21.86%, and 0.44-1.43% in the different quality roughage groups. Bacteroidetes were mainly Prevotellaceae1 and Rikenellaceae RC_gut_group with relative abundances of 30.17-45.75% and 3.23-7.82%. The relative abundance of Patescibacteria and Spirochaetes decreased with increasing roughage quality. These results provide a theoretical and practical basis for evaluating the nutritional value of dairy buffalo feed, utilizing feed resources, matching rations, feeding scientifically, and protecting animal health.

Effects of replacing corn silage and soybean meal with an increasing percentage of fresh herbage on dairy cow nitrogen use efficiency and flows.

To improve sustainability, dairy farms can reduce protein-rich concentrate in the cows' diet providing fresh herbage produced on-farm. This study aimed to quantify effects of increasing the percentage of fresh herbage (0%, 25%, 50%, and 75%, on a dry matter [DM] basis) in a partial mixed ration-based diet on cow N use efficiency and excretion. The study was performed with five lactating cows, in a 4 × 4 Latin square design for four 3 week periods. Individual DM intake, milk yield, feces and urine excretions, and their N concentrations were measured daily. Dietary crude protein concentrations varied little among treatments (127 to 134 g/kg DM). DM intake and milk yield decreased linearly by 5.2 and 3.7 kg/day, respectively, while N use efficiency increased by 4.1 percentage points from 0% to 75% DM of fresh herbage in the diet. Urinary N was not influenced by the treatments, while fecal N decreased as the percentage of fresh herbage increased. This study highlights that replacing partial mixed ration with an increasing percentage of fresh herbage with slight changes in dietary N concentration increases N use efficiency and the percentage of urinary N in excreted N.

Influence of pH and temperature on the performance and microbial community during the production of medium-chain carboxylic acids using winery effluents as substrate.

Winery effluents containing high ethanol concentrations and diverse organic matter are ideal substrates for producing medium-chain carboxylic acids via fermentation and chain elongation. However, the process needs to be better understood. This study presents novel insights into the bioconversion mechanisms of medium-chain carboxylic acids by correlating fermentation and chain elongation kinetic profiles with the study of microbial communities at different pH (5 to 7) conditions and temperatures (30 to 40 °C). It was found that high productivities of MCCA were obtained using a native culture and winery effluents as a natural substrate. Minor pH variations significantly affected the metabolic pathway of the microorganisms for MCCA production. The maximal productivities of hexanoic (715 mg/L/d) and octanoic (350 mg/L/d) acids were found at pH 6 and 35 °C. Results evidence that the presence of Clostridium, Bacteroides, and Negativicutes promotes the high productions of MCCA. The formation of heptanoic acid was favor when Mogibacterium and Burkholderia were present.

Partially substituting alfalfa hay with hemp forage in the diet of goats improved feed efficiency, ruminal fermentation pattern and microbial profiles.

The use of hemp as a forage source in livestock diets has been less studied because bioactive residues in animal tissues may pose a risk to consumers. This study investigated the effects of partial substitution of alfalfa hay (AH) with hemp forage (HF) in growing goat diets on growth performance, carcass traits, ruminal fermentation characteristics, rumen microbial communities, blood biochemistry, and antioxidant indices. Forty Xiangdong black goats with body weight (BW) 7.82 ± 0.57 kg (mean ± SD) were grouped by BW and randomly assigned into one of the four treatment diets (n = 10/treatment) in a completely randomized design. The goats were fed ad libitum total mixed rations containing 60% forage and 40% concentrate (DM basis). The diets included control (CON; 60% AH and 40% concentrate), 55% AH and 5% HF (HF5), 50% AH and 10% HF (HF10), and 40% AH and 20% HF (HF20). Increasing the substitution of HF for AH linearly decreased (P < 0.01) DM intake and improved feed conversion efficiency. However, final BW, average daily gain, carcass traits, meat quality, and most blood biochemistry indices did not differ among treatments. The ruminal NH3-N concentration and blood urine nitrogen linearly increased (P < 0.01) with increasing substitution rate of HF, whereas the total volatile fatty acids concentration quadratically changed (P < 0.01). Substitution of AH with HF had no effect on the diversity and richness of ruminal microbes, though it linearly decreased (P = 0.040) Prevotella_1 and linearly increased (P = 0.017) Rikenellaceae_RC9_gut_group. The cannabinoids and/or their metabolites were detected in both ruminal filtrates (8) and plasma (4), however, no detectable cannabinoid-related residues were observed in meat. These results indicate that the HF could be used to partially substitute AH in goat diets, whereas the effects vary between substitution rates of HF for AH. Although no cannabinoid-related residues were detected in meat, the presence of cannabinoids residues in blood warrants further study of HF feeding to confirm the cannabinoids residues are not present in the animal products.

The Nutritional Value of Biowaste Bovine Slaughterhouse Meals for Monogastric Species Feeding: The Guinea Pig as an Animal Model.

Biowaste from slaughterhouses can be recovered to benefit food security and reduce contamination potential. More than 3 billion heads of livestock are consumed worldwide, which will increase by 17% by 2028, generating more biowaste, increasing infectious agents, and causing economic losses due to circular economy principles not being applied. This work evaluated the nutritional quality of four types of biowaste from bovine slaughter which were transformed into a meal for guinea pigs (rumen content (RCM), ears (EaM), blood (BM), and cheeks (CM)) according to their chemical composition, digestible components, energy contribution, and voluntary consumption. For the animal model, adult male guinea pigs were arranged in metabolic cages for feces collection without urinary contamination. Nine guinea pigs were used in each digestibility test. First, a direct digestibility test was conducted using a meal of barley as a reference diet (RD), the indigestibility coefficient of which allowed for the estimation of the digestibility of biowaste meals through indirect calculations; for this, diets composed of 80% of the RD and 20% of the corresponding biowaste meals were evaluated. The difference method was suitable for determining the digestibility of beef biowaste using the indigestibility coefficients of the reference diet to calculate the digestibility of ingredients which could not be offered as 100% of the meal but were incorporated as 20%. The digestible protein and metabolizable energy contents of RCM, EaM, BM, and CM were 10.2% and 2853 kcal/kg, 44.5% and 3325 kcal/kg, 70.7% and 2583 kcal/kg, and 80.8% and 3386 kcal/kg, respectively. The CM and BM feeds had the highest contributions of digestible protein due to their higher nitrogen content, and the CM and EaM feeds had the highest ME contents due to their higher fat contents. The biowaste meal consumption in descending order was CM > RCM > EaM > BM, which were consumed without problems. These results are indicative that these components can be part of guinea pigs' diets, and it is recommended to continue studies into guinea pig growth and fattening diets with different levels of these biowaste meals.

Molecular detection of ruminal micro-flora and micro-fauna in Saudi Arabian camels: Effects of season and region.

This study investigated and explored the availability of micro-flora and micro-fauna in the ruminal contents of Arabian camel (Camelus dromedarius) from three different regions in Saudi Arabia along with two seasons. Samples were prepared and tested by conventional polymerase chain reaction (PCR). This study confirmed that the bacterial flora were dominating over other microbes. Different results of the availability of each microbe in each region and season were statistically analyzed and discussed. There was no significant effect of season on the micro-flora or micro-fauna however, the location revealed a positive effect with Ruminococcus flavefaciens (p < 0 0.03) in the eastern region. This study was the first to investigate the abundance of micro-flora and micro-fauna in the ruminal contents of camels of Saudi Arabia. This study underscores the significance of camel ruminal micro-flora and micro-fauna abundance, highlighting their correlation with both seasonality and geographic location. This exploration enhances our comprehension of camel rumination and digestion processes. The initial identification of these microbial communities serves as a foundational step, laying the groundwork for future in-depth investigations into camel digestibility and nutritional requirements.