Effects of lactic acid-producing bacteria as direct-fed microbials on the ruminal microbiome

The Effect of a Direct Fed Microbial on Liveweight and Milk Production in Dairy Cattle

This longitudinal study aimed to quantify the effects of dietary supplementation of a direct-fed microbial (DFM) consisting of three lactobacilli isolates on milk yield, milk fat and protein yields, somatic cell count (SCC), and liveweight in a single dairy herd in Australia. A total of 150 dairy cows were randomly selected based on parity and days in milk and divided into two groups: control (n = 75) and DFM treatment (n = 75). Throughout the study, the two groups of cows were housed separately in a dry lot yard, and each group had their own feeding area. For the DFM treatment group, selected cows in mid-lactation were supplemented with 10 mL/cow/day of the DFM via top dressing of the feed for the remainder of the lactation and through the dry period, extending into subsequent lactation. The control group had no supplementation. The milk yield and liveweight were recorded daily. Milk samples were collected every two months for milk component analysis (fat, protein, and somatic cell count [SCC]). The DFM-treated cows gained more liveweight across the study (19.40 kg, 95% CI 0.44 kg; 38.30 kg, p = 0.05) compared to the control cows. In the second production year, the DFM-treated cows mobilized more liveweight (-6.06 kg, 95% CI -10.49 kg; -1.61 kg, p = 0.01) and produced more milk (0.39 L/d 95% CI 0.10; 0.89, p = 0.05). Over a full lactation, DFM cows yielded at least 258 L (95% CI 252 L; 265 L) more milk than controls. No significant differences were found in fat and protein yield or SCC. This study suggests that consistent and ongoing supplementation with a Lacticaseibacillus- and Lentilactobacillus-based DFM could have a positive effect on milk production, but further research is needed to understand the underlying mechanism.

Effects of monensin and cashew nut-shell extract on bacterial community composition in a dual-flow continuous culture system

The objective of this study was to evaluate the effects of including monensin and two doses of CNSE in a high producing dairy cow diet on ruminal bacterial communities. A dual-flow continuous culture system was used in a replicated 4 × 4 Latin Square design. A basal diet was formulated to meet the requirements of a cow producing 45 kg of milk per d (17% crude protein and 27% starch). There were four experimental treatments: the basal diet without any feed additive (CON), 2.5 μM monensin (MON), 100 ppm CNSE granule (CNSE100), and 200 ppm CNSE granule (CNSE200). Samples were collected from the fluid and solid effluents at 3, 6, and 9 h after feeding; a composite of all time points was made for each fermenter within their respective fractions. Bacterial community composition was analyzed by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Treatment responses for bacterial community structure were analyzed with the PERMANOVA test run with the R Vegan package. Treatment responses for correlations were analyzed with the CORR procedure of SAS. Orthogonal contrasts were used to test the effects of (1) ADD (CON vs. MON, CNSE100, and CNSE200); (2) MCN (MON vs. CNSE100 and CNSE200); and (3) DOSE (CNSE100 vs. CNSE200). Significance was declared at P ≤ 0.05. We observed that the relative abundance of Sharpea (P < 0.01), Mailhella (P = 0.05), Ruminococcus (P = 0.03), Eubacterium (P = 0.01), and Coprococcus (P < 0.01) from the liquid fraction and the relative abundance of Ruminococcus (P = 0.03) and Catonella (P = 0.02) from the solid fraction decreased, while the relative abundance of Syntrophococcus (P = 0.02) increased in response to MON when compared to CNSE treatments. Our results demonstrate that CNSE and monensin have similar effects on the major ruminal bacterial genera, while some differences were observed in some minor genera. Overall, the tested additives would affect the ruminal fermentation in a similar pattern.

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.

Effect of a High-Starch or a High-Fat Diet on the Milk Performance, Apparent Nutrient Digestibility, Hindgut Fermentation Parameters and Microbiota of Lactating Cows

In this study, changes in milk performance, nutrient digestibility, hindgut fermentation parameters and microflora were observed by inducing milk fat depression (MFD) in dairy cows fed with a high-starch or a high-fat diet. Eight Holstein cows were paired in a completely randomized cross-over design within two 35 d periods (18 d control period and 17d induction period). During the control period, all cows were fed the low-starch and low-fat diet (CON), and at the induction period, four of the cows were fed a high-starch diet with crushed wheat (IS), and the other cows were fed a high-fat diet with sunflower fat (IO). The results showed that, compared to when the cows were fed the CON diet, when cows were fed the IS or IO diet, they had lower milk fat concentrations, energy corrected milk, 3.5% fat-corrected milk yield, feed efficiency and apparent digestibility of NDF and ADF. However, cows fed the IO diet had a lower apparent digestibility of ether extracts. In addition, we observed that when cows were fed the high-starch (IS) or high-fat (IO) diet, they had a higher fecal concentration of propionate and acetate, and a lower NH3-N. Compared to when the cows were fed the CON diet, cows fed the IS diet had a lower pH, and cows fed the IO diet had a lower concentration of valerate in feces. In the hindgut microbiota, the relative abundance of Oscillospiraceae_UCG-005 was increased, while the Verrucomicrobiota and Lachnospiraceae_AC2044_group were decreased when cows were fed the IO diet. The relative abundance of Prevotellaceae_UCG-003 was increased, while the Alistipes and Verrucomicrobiota decreased, and the Treponema, Spirochaetota and Lachnospiraceae_AC2044_group showed a decreasing trend when cows were fed the IS diet. In summary, this study suggested that high-starch or high-fat feeding could induce MFD in dairy cows, and the high-fat diet had the greatest effect on milk fat; the high-starch or high-fat diet affected hindgut fermentation and apparent fiber digestibility. The changes in hindgut flora suggested that hindgut microbiota may be associated with MFD in cows.

Can dietary magnesium sources and buffer change the ruminal microbiota composition and fermentation of lactating dairy cows?

Magnesium oxide (MgO) is one of the most used Mg supplements in livestock. However, to avoid relying upon only one Mg source, it is important to have alternative Mg sources. Therefore, the objective of this study was to evaluate the effects of the interaction of two Mg sources with buffer use on the ruminal microbiota composition, ruminal fermentation, and nutrient digestibility in lactating dairy cows. Twenty lactating Holstein cows were blocked by parity and days in milk into five blocks with four cows each, in a 2 × 2 factorial design. Within blocks, cows were assigned to one of four treatments: 1) MgO; 2) MgO + Na sesquicarbonate (MgO+); 3) calcium-magnesium hydroxide (CaMgOH); 4) CaMgOH + Na sesquicarbonate (CaMgOH+). For 60 d, cows were individually fed a corn silage-based diet, and treatments were top-dressed. Ruminal fluid was collected via an orogastric tube, for analyses of the microbiota composition, volatile fatty acids (VFA), lactate, and ammonia nitrogen (NH3-N). The microbiota composition was analyzed using V4/16S rRNA gene sequencing, and taxonomy was assigned using the Silva database. Statistical analysis was carried out following the procedures of block design analysis, where block and cow were considered random variables. Effects of Mg source, buffer, and the interaction between Mg Source × Buffer were analyzed through orthogonal contrasts. There was no interaction effect of the two factors evaluated. There was a greater concentration of NH3-N, lactate, and butyrate in the ruminal fluid of cows fed with CaMg(OH)2, regardless of the buffer use. The increase in these fermentation intermediates/ end-products can be explained by an increase in abundance of micro-organisms of the genus Prevotella, Lactobacillus, and Butyrivibrio, which are micro-organisms mainly responsible for proteolysis, lactate-production, and butyrate-production in the rumen, respectively. Also, dietary buffer use did not affect the ruminal fermentation metabolites and pH; however, an improvement of the apparent total tract digestibility of dry matter (DM), organic matter (OM), neutral fiber detergent (NDF), and acid fiber detergent (ADF) were found for animals fed with dietary buffer. In summary, there was no interaction effect of buffer use and Mg source, whereas buffer improved total tract apparent digestibility of DM and OM through an increase in NDF and ADF digestibility and CaMg(OH)2 increased ruminal concentration of butyrate and abundance of butyrate-producing bacteria.

Effects of Dietary Capsaicin and Yucca schidigera Extracts as Feed Additives on Rumen Fermentation and Microflora of Beef Cattle Fed with a Moderate-Energy Diet

Capsaicin (CAP) and Yucca schidigera extract (YSE) are two types of plant extracts that can change rumen fermentation. This study was conducted to investigate whether supplementation of beef cattle diets with CAP and YSE for 90 days would affect rumen fermentation and microflora. Forty-five healthy Angus steers (initial body weight = 510.54 ± 41.27 kg) were divided into three groups: control (CON), CAP, and YSE. Ammonia nitrogen (NH3-N) and total volatile fatty acid (TVFA) concentrations were significantly higher in the YSE group than in the CON group and significantly lower in the CAP group than in the CON group. At the phylum level, YSE increased the relative abundances of Bacteroidota and Patescibacteria and reduced that of Bacillota. At the genus level, CAP and YSE both increased the relative abundances of genera subordinate to Bacteroidota and decreased the relative abundances of genera subordinate to Bacillota. Our study shows that YSE and CAP have different effects on rumen fermentation and microflora after long-term supplementation.

Corn Straw Total Mix Dietary Supplementation of Bacillus Subtilis-Enhanced Growth Performance of Lambs by Favorably Modulating Rumen Bacterial Microbiome

In this experiment, B. subtilis was added to pelletized straw-based total mixed ration, and the rumen microbial diversity of house-fed Duhan hybrid sheep was compared. Ten 3-month-old weaned Duhan hybrid lambs were separated into two groups and fattened for 80 days using a single-factor trial design. During the fattening period, the control and the experiment groups were fed with the same ration, except that the experiment group was supplemented with B. subtilis. The results showed that the addition of B. subtilis could significantly increase the daily weight gain, total weight gain, rumen microbial abundance, and rumen microbial diversity of the Duhan lamb. Among them, the proportion of microbial flora such as Bacteroidetes was significantly increased, producing more acetate, iso-butyrate, and butyrate, obtaining higher energy efficiency.

Effects of Replacing Alfalfa Hay with Oat Hay in Fermented Total Mixed Ration on Growth Performance and Rumen Microbiota in Lambs

The use of the fermented total mixed ration (FTMR) is a promising approach for the preservation of feedstuff, but the effect of FTMR on the between growth performance and ruminal microflora of lambs are still limited. This study aimed to assess the effects of different roughage types in the FTMR on growth performance and rumen microbiota of lambs. Forty-five six-month-old Small tail Han sheep × Ujumqin male lambs were randomly allocated into three groups (three pens per treatment and five lambs per pen) with the initial body weight (BW) of 28.50 ± 1.50 kg. The three treatments were as follows: the low oat percentages group (LO) contained 200 g/kg oat hay + 400 g/kg alfalfa hay, the medium oat percentages group (MO) contained 300 g/kg oat hay + 300 g/kg alfalfa hay, and the high oat percentages group (HO) contained 400 g/kg oat hay + 200 g/kg alfalfa hay. The result revealed that the dry matter intake and average daily gain were markedly (p < 0.05) higher in the MO treatment than in the LO and HO treatments, whereas no significant difference (p > 0.05) was found in the final body weight. There were no significant (p > 0.05) differences on the Shannon and Simpson index among the three treatments. The PCoA score plot illustrated the individual separation in the LO, MO, and HO treatments. At the phylum level, the presence of Bacteroidetes and Firmicutes belonging to the dominant phyla is widely described in rumen communities among the three treatments. The relative abundances of Prevotella, Fibrobacter, and Succinivibrio in the level of the genes were remarkably higher (p < 0.05) in MO treatment than that in LO and HO treatments, while the relative abundance of Sediminispirochaeta was remarkably higher (p < 0.05) in LO treatment than that in MO and HO treatments. These results indicated that the MO treatments could more effectively improve growth performance than the LO and HO treatments, and also revealed that the different forage types in diets reshaped the compositions and function of the rumen microbiota. Consequently, the findings presented in this study provide a reference for the application of FTMR in animal production and the understanding of the interaction between diet, animal performance, and ruminal microbiota.

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.

Possibility of Using By-Products with High NDF Content to Alter the Fecal Short Chain Fatty Acid Profiles, Bacterial Community, and Digestibility of Lactating Dairy Cows

This study aimed to investigate whether agricultural by-products with a high NDF content and small-particle-size substitute for forage could cause hindgut acidosis and dysbacteriosis in lactating dairy cows. We investigated the impact of soybean hull and beet pulp on the fecal fermentation, bacterial community, and digestibility of cows. Sixteen lactating Holstein cows were treated as follows (% of dry matter (DM)): amount of by-product added was 0 (control, CON), 1.67% (low by-products, LB), 3.33% (medium by-products, MB), and 5% (high by-products, HB). The results showed the fecal pH of cows to be 7.23–7.29, implying no hindgut acidosis. With increased inclusion of by-products in the diets, the proportion of fecal propionate; relative abundance of the phylum Bacteroidetes, the family Lachnospiraceae, and genera unclassified_f_Lachnospiraceae, Acetitomaculum, and Prevotella; and the DM and NDF digestibility of cows all increased linearly. Meanwhile, the fecal genera Turicibacter and Clostridium_sensu_stricto_1 decreased linearly. By-products promoted the abundance of fecal bacteria genes related to energy metabolism, glycolysis/gluconeogenesis, and propanoate metabolism; and correlations between fecal short chain fatty acids, digestibility, and the bacteria genera were seen. Overall, our study suggested that adding 5% by-products could be a viable dietary formulation strategy that promotes digestibility and makes positive changes in hindgut fermentation and bacteria.

Effects of Lactic Acid Bacteria-Inoculated Corn Silage on Bacterial Communities and Metabolites of Digestive Tract of Sheep

Silage is widely used as ruminant feed all over the world. Lactic acid bacteria inoculants are commonly applied in silage production to improve preservation efficiency. To investigate the effects of lactic acid bacteria-inoculated silage on the bacterial communities and metabolites of the digestive tract, twenty-four local hybrid rams (a hybrid of Small Tail Han sheep and Mongolian sheep with an average initial BW 27.8 ± 3.05 kg) were randomly divided into four groups fed with corn stalk (S), corn stalk silage, corn stalk silage treated with Lentilactobacillusplantarum (P), or corn stalk silage treated with L. buchneri (B). The results showed that compared with the control and B groups, the inoculant with P significantly increased silage dry matter (DM) content, while the pH value was significantly higher than that in group B, and the aerobic stability was significantly lower than that in group B. Firmicutes and Bacteroidetes were the two dominant phyla of digestive tract microbiota in sheep. Compared with corn stalk, sheep fed with corn stalk silage showed a higher relative abundance of Prevotella. P-treated silage decreased the relative abundance of Firmicutes at the phylum level in rumen fluid. Silage treated with P or B increased the relative abundance of Prevotella, Ruminococcus, and Fibrobacter at the genus level in the rumen. A total of 498 differential metabolites in the rumen were detected when comparing the corn stalk and corn stalk silage groups. A total of 257 and 141 differential metabolites were detected when comparing the untreated silage and silages treated with P and B, respectively. These metabolites in the sheep rumen were correlated with bacterial communities, especially Butyrivibrio, Fibrobacter, and Prevotella. In conclusion, the addition of P and B during ensiling could change the fermentation and metabolites in the rumen by influencing the bacterial community. The change induced by these inoculants might be beneficial for animals’ performance and the health of ruminants.

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.

Feeding Date-Palm Leaves Ensiled with Fibrolytic Enzymes or Multi-Species Probiotics to Farafra Ewes: Intake, Digestibility, Ruminal Fermentation, Blood Chemistry, Milk Production and Milk Fatty Acid Profile

The present experiment evaluated the feeding of date palm leaves (DPL) ensiled with fibrolytic enzymes (ENZ) or multi-species probiotics (MSP) on nutrient utilization and lactational performance of ewes. Fifty multiparous lactating Farafra ewes were used in a completely randomized design for 90 d. The treatments consisted of the control diet with a concentrate feed mixture and date palm leaves (at 60:40, DM basis) ensiled without additive (control) or DPL ensiled with ENZ or MSP replacing control DPL at 50 or 100%. Both ENZ and MSP increased (p < 0.01) DPL and total intakes, digestibility of all nutrients, concentrations of ammonia, total volatile fatty acids, acetate and propionate in the rumen. Increased milk production, concentrations of fat, lactose and energy in milk, and feed efficiency were observed with MSP and ENZ compared to the control treatment. Moreover, ENZ and MSP increased (p < 0.05) the concentrations of total n3, n6 fatty acids, polyunsaturated fatty acids and conjugated linoleic acids and decreased (p < 0.001) the atherogenicity. The differences between ENZ and MSP and between the low and high replacement levels were minor for all measured parameters. Ensiling of DPL with MSP or fibrolytic enzymes is recommended to improve feed efficiency and improve lactational performance of ewes.