Effects of a blend of Saccharomyces cerevisiae-based direct-fed microbial and fermentation products on plasma carbonyl-metabolome and fecal bacterial community of beef steers

Feeding a Saccharomyces cerevisiae fermentation product during a gut barrier challenge in lactating Holstein cows impacts the ruminal microbiota and metabolome

Through its influence on the gut microbiota, the feeding of Saccharomyces cerevisiae fermentation products (SCFP) has been a successful strategy to enhance the health of dairy cows during periods of physiological stresses. Although production and metabolic outcomes from feeding SCFP are well-known, its combined impacts on the ruminal microbiota and metabolome during gut barrier challenges remain unclear. To address this gap in knowledge, multiparous Holstein cows (97.1 ± 7.6 DIM [SD]; n = 8/group) fed a control diet (CON) or CON plus 19 g/d SCFP for 9 wk were subjected to a feed restriction (FR) challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before FR. The DNA extracted from ruminal fluid was subjected to PacBio full-length 16S rRNA gene sequencing, real-time PCR of 12 major ruminal bacteria, and metabolomics analysis of up to 189 metabolites via GC/MS. High-quality amplicon sequence analyses were performed with the TADA (Targeted Amplicon Diversity Analysis), MicrobiomeAnalyst, PICRUSt2, and STAMP software packages, and metabolomics data were analyzed via MetaboAnalyst 5.0. Ruminal fluid metabolites from the SCFP group exhibited a greater α-diversity Chao 1 (P = 0.03) and Shannon indices (P = 0.05), and the partial least squares discriminant analysis clearly discriminated metabolite profiles between dietary groups. The abundance of CPla_4_termite_group, Candidatus Saccharimonas, Oribacterium, and Pirellula genus in cows fed SCFP was greater. In the SCFP group, concentrations of ethanolamine, 2-amino-4,6-dihydroxypyrimidine, glyoxylic acid, serine, threonine, cytosine, stearic acid, and pyrrole-2-carboxylic acid were greater in ruminal fluid. Both Fretibacterium and Succinivibrio abundances were positively correlated with metabolites across various biological processes: gamma-aminobutyric acid, galactose, butane-2,3-diol, fructose, 5-amino pentanoic acid, β-aminoisobutyric acid, ornithine, malonic acid, 3-hydroxy-3-methylbutyric acid, hexanoic acid, heptanoic acid, cadaverine, glycolic acid, β-alanine, 2-hydroxybutyric acid, methyl alanine, and alanine. In the SCFP group, compared with CON, the mean proportion of 14 predicted pathways based on metabolomics data was greater, whereas 10 predicted pathways were lower. Integrating metabolites and upregulated predicted enzymes (NADP+-dependent glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, serine: glyoxylate aminotransferase, and d-glycerate 3-kinase) indicated that the pentose phosphate pathway and photorespiration pathway were most upregulated by SCFP. Overall, SCFP during FR led to alterations in ruminal microbiota composition and key metabolic pathways. Among those, we identified a shift from the tricarboxylic acid cycle to the glyoxylate cycle, and nitrogenous base production was enhanced.

Effects of direct-fed microbial supplement on ruminal and plasma metabolome of early-lactation dairy cows: Untargeted metabolomics approach

We examined the effects of 2 multispecies direct-fed microbial (DFM) supplements on ruminal and plasma metabolome of early-lactation dairy cows using a high-coverage untargeted metabolomics approach. A total of 45 multiparous Holstein cows (41 ± 7 DIM) were enrolled for the 14-d pre-experimental and 91-d experimental period and were a subset from a lactation performance study, which used 114 cows. Cows were blocked using pre-experimental energy-corrected milk yield and randomly assigned within each block to 1 of 3 treatments: (1) corn silage-based diet with no DFM supplement (control; CON), (2) basal diet top-dressed with a mixture of Lactobacillus animalis and Propionibacterium freudenreichii at 3 × 109 cfu/d (PRO-A), or (3) basal diet top-dressed with a mixture of L. animalis, P. freudenreichii, Bacillus subtilis, and Bacillus licheniformis at 11.8 × 109 cfu/d (PRO-B). The basal diet was fed ad libitum daily as a TMR at 0600 and 1200 h for a duration of 91 d. Rumen fluid and blood samples were taken on d -3, 28, 49, 70, and 91 and immediately stored at -80°C. Before analysis, ruminal and plasma samples from d 28, 49, 70, and 91 were composited. An in-depth, untargeted metabolome profile of the composite rumen and plasma samples and the d -3 samples was developed by using a chemical isotope labeling/liquid chromatography-mass spectrometry (LC-MS)-based technique. Differentially abundant metabolites (taking into account fold change [FC] values and false discovery rates [FDR]) were identified with a volcano plot. In the rumen, compared with the CON diet, supplemental PRO-A increased (FC ≥1.2; FDR ≤0.05) the relative concentrations of 9 metabolites, including 2-hydroxy-2,4-pentadienoic acid, glutaric acid, quinolinic acid, and shikimic acid, and PRO-B increased relative concentrations of 16 metabolites, including 2-hydroxy-2,4-pentadienoic acid, glutaric acid, 16-hydroxypalmitic acid, and 2 propionate precursors (succinic and methylsuccinic acids). Relative to PRO-A, supplemental PRO-B increased (FC ≥1.2; FDR ≤0.05) relative rumen concentrations of 3 metabolites, 16-hydroxypalmitic acid, indole-3-carboxylic acid, and 5-aminopentanoic acid, but reduced relative rumen concentrations of 13 metabolites, including carnitine, threonic acid, and shikimic acid. Compared with the CON diet, relative concentrations of 13 plasma metabolites, including myxochelin A and glyceraldehyde, were increased (FC ≥1.2; FDR ≤0.05) by PRO-A supplementation, whereas those of 9 plasma metabolites, including 4-(2-aminophenyl)-2,4-dioxobutanoic acid, N-acetylornithine, and S-norlaudanosolin, were reduced (FC ≤0.83; FDR ≤0.05). Supplemental PRO-B increased (FC ≥1.2; FDR ≤0.05) relative concentrations of 9 plasma metabolites, including trans-o-hydroxybenzylidenepyruvic acid and 3-methylsalicylaldehyde, and reduced relative concentrations of 4 plasma metabolites, including β-ethynylserine and kynurenine. Pathway analysis of the differentially abundant metabolites in both rumen and plasma revealed that these metabolites are involved in AA and fatty acid metabolism and have antimicrobial and immune-stimulating properties. The results of this study demonstrated that dietary supplementation with either PRO-A or PRO-B altered the plasma and ruminal metabolome. Notably, ruminal and plasma metabolites involved in the metabolism of AA and fatty acids and those with immunomodulatory properties were altered by either or both of the 2 microbial additives.

Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment

Introduction

Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria.

Methods

In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups.

Results

Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics.

Discussion

This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter.

Impact of precursor-derived peracetic acid on post-weaning diarrhea, intestinal microbiota, and predicted microbial functional genes in weaned pigs

Post-weaning diarrhea affects piglets in the nursery phase of production, leading to a substantial impact both at the farm and financial levels. The multifactorial etiology of this disease includes housing conditions, pig genetics, microbial composition, and metagenomic assets. Among the common therapeutic approaches, the widely used zinc oxide underwent a European Union ban in 2022 due to its negative environmental impact and correlation to increased antimicrobial resistance. During this study, we have tested two levels of inclusion of the potential antimicrobial alternative peracetic acid, delivered in water via the hydrolysis of the precursors sodium percarbonate and tetraacetylethylenediamine, in comparison to zinc oxide and an untreated control during a 2-week animal study. We assessed the microbial composition and predicted the metagenome, together with performance and physiological parameters, in order to describe the microbial functional role in etiopathology. Both zinc oxide and peracetic acid resulted in amelioration of the diarrheal status by the end of the trial period, with noticeable zinc oxide effects visible from the first week. This was accompanied by improved performance when compared to the first-week figures and a decreased stomach pH in both peracetic acid levels. A significant reduction in both stomach and caecal Proteobacteria was recorded in the zinc oxide group, and a significant reduction of Campylobacter in the stomach was reported for both zinc oxide and one of the peracetic acid concentrations. Among other functional differences, we found that the predicted ortholog for the zonula occludens toxin, a virulence factor present in pathogens like Escherichia coli and Campylobacter jejuni, was less abundant in the stomach of treated pigs compared to the control group. In water, peracetic acid delivered via precursor hydrolysis has the potential to be a valid intervention, an alternative to antimicrobial, to assist the weaning of piglets. Our findings support the view that post-weaning diarrhea is a complex multifactorial disease with an important metagenomic component characterized by the differential abundance of specific predicted orthologs and microbial genera in the stomach and caecum of pigs.

Comparison of Fecal Microbiota Communities between Primiparous and Multiparous Cows during Non-Pregnancy and Pregnancy

Imbalances in the gut microbiota composition may lead to several reproductive disorders and diseases during pregnancy. This study investigates the fecal microbiome composition between primiparous and multiparous cows during non-pregnancy and pregnancy to analyze the host-microbial balance at different stages. The fecal samples obtained from six cows before their first pregnancy (BG), six cows during their first pregnancy (FT), six open cows with more than three lactations (DCNP), and six pregnant cows with more than three lactations (DCP) were subjected to 16S rRNA sequencing, and a differential analysis of the fecal microbiota composition was performed. The three most abundant phyla in fecal microbiota were Firmicutes (48.68%), Bacteroidetes (34.45%), and Euryarchaeota (15.42%). There are 11 genera with more than 1.0% abundance at the genus level. Both alpha diversity and beta diversity showed significant differences among the four groups (p < 0.05). Further, primiparous women were associated with a profound alteration of the fecal microbiota. The most representative taxa included Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG_003, Christensenellaceae_R_7_group, Ruminococcaceae UCG-005, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Methanobrevibacter, and [Eubacterium] coprostanoligenes group, which were associated with energy metabolism and inflammation. The findings indicate that host-microbial interactions promote adaptation to pregnancy and will benefit the development of probiotics or fecal transplantation for treating dysbiosis and preventing disease development during pregnancy.

Utilizing the Gastrointestinal Microbiota to Modulate Cattle Health through the Microbiome-Gut-Organ Axes

The microorganisms inhabiting the gastrointestinal tract (GIT) of ruminants have a mutualistic relationship with the host that influences the efficiency and health of the ruminants. The GIT microbiota interacts with the host immune system to influence not only the GIT, but other organs in the body as well. The objective of this review is to highlight the importance of the role the gastrointestinal microbiota plays in modulating the health of a host through communication with different organs in the body through the microbiome-gut-organ axes. Among other things, the GIT microbiota produces metabolites for the host and prevents the colonization of pathogens. In order to prevent dysbiosis of the GIT microbiota, gut microbial therapies can be utilized to re-introduce beneficial bacteria and regain homeostasis within the rumen environment and promote gastrointestinal health. Additionally, controlling GIT dysbiosis can aid the immune system in preventing disfunction in other organ systems in the body through the microbiome-gut-brain axis, the microbiome-gut-lung axis, the microbiome-gut-mammary axis, and the microbiome-gut-reproductive axis.

Altering Methane Emission, Fatty Acid Composition, and Microbial Profile during In Vitro Ruminant Fermentation by Manipulating Dietary Fatty Acid Ratios

This study evaluated the effects of different dietary n-6/n-3 polyunsaturated fatty acid (PUFA) ratios on in vitro ruminant fermentation. Methane production, fatty acid composition, and microbial profiles were compared after the in vitro fermentation of rumen fluid collected from cows that had been fed isoenergetic and isoproteic experimental diets at three different n-6/n-3 ratios: 3.04 (HN6, high n-6 source), 2.03 (MN6, medium n-6 source), and 0.8 (LN6, low n-6 source). The fermented rumen fluid pH and total volatile fatty acid (VFA) levels were significantly decreased (p < 0.05) in the HN6 group as compared with those in the MN6 and LN6 groups. Additionally, the HN6 group produced a significantly lower (p < 0.05) proportion of methane than the MN6 group during in vitro fermentation. The MN6 and LN6 groups had significantly increased (p < 0.05) levels of C18:2n6 and C18:3n3 in the fermented rumen fluid, respectively, as compared with the HN6 group. The Chao 1 diversity index value was lower (p < 0.05) in the HN6 group than in the MN6 and LN6 groups. The observed species richness was significantly lower (p < 0.05) in the HN6 group than in the MN6 group. The reduced relative abundances of Lachnospiraceae UCG-006 and Selenomonas in the HN6 group resulted in lower pH and VFA levels (i.e., acetate, propionate, butyrate, and total VFA) during in vitro fermentation. Furthermore, n-6 and n-3 PUFAs were toxic to Butyrivibrio_2 growth, resulting in high levels of incomplete biohydrogenation. Taken together, the study findings suggest that supplementation of high-forage diets with high levels of n-6 PUFAs could reduce methane emissions, whereas both VFA concentration and pH are reduced.

Effects of Rumen-Protected Niacin on Dry Matter Intake, Milk Production, Apparent Total Tract Digestibility, and Faecal Bacterial Community in Multiparous Holstein Dairy Cow during the Postpartum Period

Extensive studies about rumen-protected niacin (RPN) supplementation on dairy cows in early-lactation have been done, but the effects of RPN on changes in dry matter intake (DMI), milk production, feed digestibility, and fecal bacterial community were conflicting. The aim of this study was to investigate them affected by RPN in postpartum cows. Multiparous Holstein dairy cows (n = 12, parity = 3.5 ± 0.5, body weights = 740 ± 28 kg) were divided into two groups supplemented with either 0 (CON) or 20 g/d RPN (RPN). Our results showed that RPN supplementation increased DMI and milk production of cows during the first three weeks after calving (p < 0.05). The concentrations of neuropeptide Y and orexin A were significantly higher in RPN group than that in the CON group during postpartum period (p < 0.05). The apparent total-tract digestibility of nutrients was similar between the CON and RPN groups at 2 weeks after calving (p > 0.05). The 16S rRNA gene sequencing analysis showed that RPN had no impact on the alpha and beta diversity, although 4 genera were changed in cow feces at 14 days after calving. Overall, 20 g/d RPN added to the diet could improve DMI and milk yield up to two weeks after calving with little influence on feed digestibility.

Comparative effects of two multispecies direct-fed microbial products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers

We examined the effects of two direct-fed microbials (DFM) containing multiple microbial species and their fermentation products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers. Nine ruminally cannulated Holstein steers (mean ± SD body weight: 243 ± 12.4 kg) were assigned to three treatments arranged in a triplicated 3 × 3 Latin square design with three 21-d periods. Dietary treatments were 1) control (CON; basal diet), 2) Commence (PROB; basal diet plus 19 g/d of Commence), and 3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both multispecies DFM products. From day 16 to 20 of each period, feed and fecal samples were collected daily to determine the apparent total tract digestibilities of nutrients using indigestible neutral detergent fiber method. On day 21 of each period, blood samples were collected for analysis of plasma glucose and nonesterified fatty acid. Ruminal contents were collected at approximately 1, 3, 6, 9, 12, and 18 h after feeding on day 21 for analysis of volatile fatty acids (VFA), lactate, ammonia-N concentrations, bacterial community, and metabolome profile. Total tract digestibilities of nutrients did not differ (P > 0.05) among treatments. Compared with CON, steers fed either supplemental PROB or SYNB had greater (P = 0.04) plasma glucose concentrations. Compared with CON, total ruminal VFA, propionate, isovalerate, and valerate concentrations increased (P ≤ 0.05) or tended to increase (P ≤ 0.10) with either supplemental PROB or SYNB, but were not different (P > 0.05) between PROB and SYNB. Compared with CON, PROB reduced (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Rikenellaceae RC9, Succinivibrionaceae UCG-001, Succiniclasticum, and Ruminococcaceae UCG-002. Supplemental SYNB decreased (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Prevotella 7, Succinivibrio, Succiniclasticum, and Ruminococcaceae UCG-014. Compared with CON, metabolome analysis revealed that some amino acids were increased (P ≤ 0.05) in steers fed PROB. This study demonstrated that, compared with CON, supplementation of either PROB or SYNB altered the ruminal bacterial community and metabolome differently; however, their effects on the ruminal VFA profile and energy status of the steers were not different from each other.

Average daily gain divergence in beef steers is associated with altered plasma metabolome and whole blood immune-related gene expression

We evaluated the plasma amine/phenol- and carbonyl-metabolome and whole-blood immune gene expression profiles in beef steers with divergent average daily gain (ADG). Forty-eight Angus crossbred beef steers (21 days postweaning; 210 ± 8.5 kg of body weight) were fed the same total mixed ration ad libitum for 42 days with free access to water. After 42 days of feeding, the steers were divided into two groups of lowest (LF: n = 8) and highest ADG (HF: n = 8). Blood samples were taken from all steers. The blood samples from LF and HF steers were used for further analysis. A subsample of the whole blood was immediately transferred into RNA-protect tubes for RNA extraction and messenger RNA expressions of 84 genes involved in innate and adaptive immune responses. Another subsample of the whole blood was immediately centrifuged to harvest the plasma for subsequent metabolome analysis. The average daily dry matter intake of the steers in LF and HF was 6.08 kg ± 0.57 and 6.04 kg ± 0.42, respectively, and was similar between the two groups (P = 0.72). The ADG (1.09 kg ± 0.13) of LF was lower (P = 0.01) than that of HF (1.63 kg ± 0.20). The expressions of 10 immune-related genes were upregulated (FC ≥ 1.2; P ≤ 0.05) in HF steers; these genes were involved in viral pathogen recognition and eradication, defense against intracellular and extracellular pathogens and parasites, and immune response homeostasis. A total number of 42 carbonyl-containing metabolites and 229 amine/phenol-containing metabolites were identified in the plasma samples of both groups. No alteration in carbonyl-metabolome was detected. Ten metabolites with immunomodulatory, anti-inflammatory, and reactive oxygen-scavenging properties were greater (FDR ≤ 0.05) in HF steers, whereas eight metabolites including arginine, phenylalanine, guanidoacetic acid, and aspartyl-threonine were greater in LF steers. This study demonstrated that beef steers with divergent ADG had altered plasma amine/phenol metabolome and immune-related gene expressions in the blood. Notably, plasma metabolites and immune-related genes of great health benefits were greater in steers with high ADG.