Comparisons of bacterial and archaeal communities in the rumen and a dual-flow continuous culture fermentation system using amplicon sequencing

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.

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

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

Effects of 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.

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

The objective of this study was to evaluate ruminal microbiome changes associated with feeding Lactobacillus plantarum GB-LP1 as direct-fed microbials (DFM) in high-producing dairy cow diets. 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 day (16% crude protein and 28% starch). There were 4 experimental treatments: the basal diet without any DFM (CTRL); a mixture of Lactobacillus acidophilus, 1 × 10⁹ cfu/g, and Propionibacterium freudenreichii, 2 × 10⁹ cfu/g [MLP = 0.01% of diet dry matter (DM)]; and 2 different levels of L. plantarum, 1.35 × 10⁹ cfu/g (L1 = 0.05% and L2 = 0.10% of diet DM). Bacterial samples were collected from the fluid and particulate effluents before feeding and at 2, 4, 6, and 8 h after feeding; a composite of all time points was made for each fermentor within their respective fractionations. Bacterial community composition was analyzed through sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequenced data were analyzed on DADA2, and statistical analyses were performed in R (RStudio 3.0.1, https://www.r-project.org/) and SAS 9.4 (SAS Institute Inc.); orthogonal contrasts were used to compare treatments. Different than in other fermentation scenarios (e.g., silage or beef cattle high-grain diets), treatments did not affect pH or lactic acid concentration. Effects were mainly from overall DFM inclusion, and they were mostly observed in the fluid phase. The relative abundance of the phylum Firmicutes, family Lachnospiraceae, and 6 genera decreased with DFM inclusion, with emphasis on Butyrivibrio_2, Saccharofermentans, and Ruminococcus_1 that are fibrolytic and may display peptidase activity during fermentation. Lachnospiraceae_AC2044_group and Lachnospiraceae_XPB1014_group also decreased in the fluid phase, and their relative abundances were positively correlated with NH₃-N daily outflow from the fermentors. Specific effects of MLP and L. plantarum were mostly in specific bacteria associated with proteolytic and fibrolytic functions in the rumen. These findings help to explain why, in the previous results from this study, DFM inclusion decreased NH₃-N concentration without altering pH and lactic acid concentration.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. III: Relation with solid passage rate and pH on prokaryotic fatty acid profile and community in continuous culture

Our objectives were to evaluate potential interactions in culture conditions that influence how exogenously dosed branched-chain VFA (BCVFA) would be recovered as elongated fatty acids (FA) or would affect bacterial populations. A 2 × 2 × 2 factorial arrangement of treatments evaluated 3 factors: (1) without versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate; each dose was partially substituted with ¹³C-enriched tracers before and during the collection period); (2) high versus low pH (ranging diurnally from 6.3 to 6.8 vs. 5.7 to 6.2); and (3) low versus high particulate-phase passage rate (k_p; 2.5 vs. 5.0%/h) in continuous cultures administered a 50:50 forage:concentrate diet twice daily. Samples of effluent were collected and composited before harvesting bacteria from which FA and DNA were extracted. Profiles and enrichments of FA in bacteria were evaluated by gas chromatography and isotope-ratio mass spectrometry. The ¹³C enrichment in bacterial FA was calculated as percentage recovery of dosed ¹³C-labeled BCVFA. Dosing BCVFA increased the even-chain iso-FA, preventing the reduced concentration at higher k_p and potentially as a physiological response to decreased pH. However, decreasing pH decreased recovery of ¹³C in these even-chain FA, suggesting greater reliance on isobutyrate produced from degradation of dietary valine. The iso-FA were decreased, whereas anteiso-FA and 16:0 increased with decreasing pH. Thus, 2-methylbutyrate still appeared to be important as a precursor for anteiso-FA to counter the increased rigidity of bacterial membranes that had more saturated straight-chain FA when pH decreased. Provision of BCVFA stimulated the relative sequence abundance of Fibrobacter and Treponema, both of which require isobutyrate and 2-methylbutyrate. Numerous bacterial community members were shifted by low pH, including increased Prevotella and genera within the phylum Proteobacteria, at the expense of members within phylum Firmicutes. Because of relatively few interactions with pH and k_p, supplementation of BCVFA can stimulate neutral detergent fiber degradability via key fibrolytic bacteria across a range of conditions. Decreasing pH shifted bacterial populations and their FA composition, suggesting that further research is needed to distinguish pH from dietary changes.

Effects of supplemental source of magnesium and inclusion of buffer on ruminal microbial fermentation in continuous culture

Magnesium oxide (MgO) is the most common supplemental source of Mg for dairy cows and a proven ruminal alkalizer when supplemented above NRC (2001) recommendations. However, overfeeding MgO may increase feeding costs, whereas the effects of alternative sources of Mg on ruminal fermentation are not well known. Moreover, it is still unclear if Mg supplementation influences the effects of bicarbonate-based buffers on ruminal fermentation. We aimed to evaluate the effect of Mg source on ruminal fermentation with diets formulated to a final concentration of 0.25% Mg, and to determine if the effect of sodium sesquicarbonate as a buffer varies with the source of Mg. We used 8 fermentors in a duplicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments, by combining 2 factors: (1) Mg source: using either MgO or an alternative source consisting of a blend of CaMg(OH)₄ and CaMg(CO₃)₂ (BLN) and (2) sodium sesquicarbonate buffer inclusion, at 0 or 0.6% of dry matter intake. Based on preliminary tests of reactivity, we hypothesized that BLN plus buffer would allow for greater ruminal pH, acetate molar proportion, and NDF digestibility than diets with MgO or without buffer. Four 10-d periods were completed, where the last 3 d were used for pH measurements and collection of samples for volatile fatty acids (VFA), ammonia (NH₃-N), Mg solubility, N metabolism, and nutrient digestibility. Effects of Mg source (source), sodium sesquicarbonate inclusion (buffer), and their interaction (source × buffer) were tested with the MIXED procedure of SAS (SAS Institute Inc.). We did not find an effect of Mg source on ruminal fermentation variables; however, concentration of soluble Mg in ruminal fluid was greater for MgO compared with BLN. On the other hand, buffer supplementation increased average ruminal pH, acetate molar proportion, and branched-chain VFA molar proportion; tended to increase NDF digestibility; and decreased both area under the curve and time below pH 6.0. An interaction of source × buffer was found for propionate, butyrate, and NH₃-N, the first one decreasing and the 2 others increasing only when buffer was supplemented to the BLN diet. Our results indicate that supplementing Mg with either MgO or BLN promotes similar ruminal fermentation in diets with total concentration of 0.25% Mg. Further evaluations are needed to assess Mg availability and animal performance in dairy cows fed BLN.

Effects of unprotected choline chloride on microbial fermentation in a dual-flow continuous culture depend on dietary neutral detergent fiber concentration

Choline is usually supplemented as ruminally protected choline chloride to prevent its degradation in the rumen, but the effects of unprotected choline on ruminal fermentation are unclear. Some research indicates a possible role of dietary fiber on microbial degradation of choline; therefore we aimed to evaluate the effects of unprotected choline chloride on ruminal fermentation and to investigate whether those effects depend on dietary neutral detergent fiber (NDF) concentration. Our hypothesis was that dietary NDF concentration would influence choline chloride effects on microbial ruminal fermentation. We used 8 fermentors in a duplicated 4 × 4 Latin square with a 2 × 2 factorial arrangement, combining 2 factors: (1) dietary NDF concentration and (2) unprotected choline chloride supplementation. Resulting treatments are (1) 30%NDF/Ctrl [30% NDF control diet without supplemental choline (Cho)]; (2) 30%NDF/Cho [30% NDF diet plus 1.9 g of choline ion per kg of dry matter (DM)]; (3) 40%NDF/Ctrl (40% NDF control diet without supplemental choline); and (4) 40%NDF/Cho (40% NDF diet plus 1.9 g of choline ion per kg of DM). Four 10-d periods were completed, each consisting of 7 d for adaptation and 3 d for collection of samples for estimation of nutrient disappearance and daily average concentrations of volatile fatty acids and NH₃-N. In addition, kinetics of pH, acetate, and propionate were evaluated at 0, 1, 2, 4, 6, and 8 h after morning feeding. On the last day of each period, bacteria pellets were harvested for ¹⁵N analysis and N metabolism. Fixed effects of dietary NDF concentration, unprotected choline chloride supplementation, and their interaction (NDF × Cho) were tested using the MIXED procedure of SAS version 9.4 (SAS Institute Inc., Cary, NC). Choline tended to increase total volatile fatty acid concentrations and decreased acetate molar proportion regardless of dietary NDF concentration, but it increased propionate molar proportion and decreased acetate to propionate ratio only with the 30% NDF diet. Supplementing choline decreased NDF disappearance regardless of dietary NDF; however, organic matter disappearance tended to be reduced only when choline was added to 40% NDF. Our data indicate that unprotected choline chloride effects on ruminal fermentation depend on dietary NDF concentration, allowing for a greater propionate synthesis without decreasing organic matter disappearance when fed with a 30% NDF diet.

Inhibition of methanogenesis by nitrate, with or without defaunation, in continuous culture

Within the rumen, nitrate can serve as an alternative sink for aqueous hydrogen [H₂(aq)] accumulating during fermentation, producing nitrite, which ideally is further reduced to ammonium but can accumulate under conditions not yet explained. Defaunation has also been associated with decreased methanogenesis in meta-analyses because protozoa contribute significantly to H₂ production. In the present study, we applied a 2 × 2 factorial treatment arrangement in a 4 × 4 Latin square design to dual-flow continuous culture fermentors (n = 4). Treatments were control without nitrate (-NO₃^-) versus with nitrate (+NO₃^-; 1.5% of diet dry matter), factorialized with normal protozoa (faunated, FAUN) versus defaunation (DEF) by decreasing the temperature moderately and changing filters over the first 4 d of incubation. We detected no main effects of DEF or interaction of faunation status with +NO₃^-. The main effect of +NO₃^- increased H₂(aq) by 11.0 µM (+117%) compared with -NO₃^-. The main effect of +NO₃^- also decreased daily CH₄ production by 8.17 mmol CH₄/d (31%) compared with -NO₃^-. Because there were no treatment effects on neutral detergent fiber digestibility, the main effect of +NO₃^- also decreased CH₄ production by 1.43 mmol of CH₄/g of neutral detergent fiber degraded compared with -NO₃^-. There were no effects of treatment on other nutrient digestibilities, N flow, or microbial N flow per gram of nutrient digested. The spike in H₂(aq) after feeding NO₃^- provides evidence that methanogenesis is inhibited by substrate access rather than concentration, regardless of defaunation, or by direct inhibition of NO₂^-. Methanogens were not decreased by defaunation, suggesting a compensatory increase in non-protozoa-associated methanogens or an insignificant contribution of protozoa-associated methanogens. Despite adaptive reduction of NO₃^- to NH₄⁺ and methane inhibition in continuous culture, practical considerations such as potential to depress dry matter intake and on-farm ration variability should be addressed before considering NO₃^- as an avenue for greater sustainability of greenhouse gas emissions in US dairy production.

In vitro evaluation of Lactobacillus plantarum as direct-fed microbials in high-producing dairy cows diets

The objectives of this study were: 1) to compare the effects of live yeast (LY), yeast fermentation product (YFP), a mix of Lactobacillus acidophilus and Propionibacterium freudenreichii (MLP), and Lactobacillus plantarum included as additives in dairy cows’ diets on in vitro ruminal fermentation and gas production (GP); and 2) to evaluate the effects of L. plantarum as direct-fed microbials (DFM) in dairy cows’ diets on in vitro ruminal fermentation, GP, nutrient digestibility, and N metabolism. Three experiments were carried out: Exp. 1 had the objective to compare all additives regarding ruminal fermentation parameters: an Ankom GP system was used in a completely randomized design, consisting of four 48 h incubations, and eight replications per treatment. There were eight treatments: a basal diet without additive (CTRL) or with one of the following additives: LY, YFP, MLP, or L. plantarum at four levels (% of diet Dry Matter (DM)): 0.05% (L1), 0.10% (L2), 0.15% (L3), and 0.20% (L4). In Exp. 2, a batch culture was used to evaluate ruminal fermentation, and CO₂ and CH₄ production using the same treatments and a similar experimental design, except for having 16 replications per treatment. Based on Exp. 1 and 2 results, Exp. 3 aimed at evaluating the effects of the L. plantarum on ruminal true nutrient digestibility and N utilization in order to evaluate the use of L. plantarum as DFM. The treatments CTRL, MLP, L1, and L2 were used in a replicated 4 × 4 Latin square design using a dual-flow continuous culture system. Data were analyzed using linear and nonlinear regression; treatment means were compared through contrasts, and L treatments in Exp. 1 and 2 were tested for linear, quadratic, and cubic effects. In Exp. 1, all treatments containing additives tended to reduce OM digestibility as well as reduced total volatile fatty acids (VFA) concentration and total GP. The YFP had greater OM digestibility than LY, and MLP treatment had greater total VFA concentration compared to L. plantarum treatments. In Exp. 2, additives reduced CO₂ production, and there were no major differences in CH₄. In Exp. 3, all additives reduced NH₃-N concentration. In conclusion, pH and lactate concentration were not affected in all three experiments regardless of additive tested, suggesting that these additives may not improve ruminal fermentation by pH modulation; and L. plantarum may improve ruminal N metabolism when used as DFM in high-producing dairy cows’ diets, mainly by reducing NH₃-N concentration.