Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle.

Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet for 4 weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking point for rumen health seemed to be the second week of high grain (HG) diet, with a dysbiosis characterized by reduced alpha diversity. While we did not find changes in histological evaluations, genes related with epithelial proliferation (IGF-1, IGF-1R, EGFR, and TBP) and ZO-1 were affected by the HG feeding. Integrative analyses allowed us to define the main drivers of difference for the rumen ecosystem in response to a HG diet, identified as ZO-1, MyD88, and genus Prevotella 1. PFA supplementation reduced the concentration of potentially harmful compounds in the rumen (e.g. dopamine and 5-aminovaleric acid) and increased the tolerance of the epithelium toward the microbiota by altering the expression of TLR-2, IL-6, and IL-10. The particle-associated rumen liquid microbiota showed a quicker adaptation potential to prolonged HG feeding compared to the other microenvironments investigated, especially by the end of the experiment.

Multi-year and multi-site effects of recurrent glyphosate applications on the wheat rhizosphere microbiome.

Glyphosate (N-(phosphonomethyl)glycine) is broad-spectrum herbicide that is extensively used worldwide, but its effects on the soil microbiome are inconsistent. To provide a sound scientific basis for herbicide re-review and registration decisions, we conducted a four-year (2013-2016) study in which we consecutively applied glyphosate to a wheat (Triticum aestivum L.)-field pea (Pisum sativum L.)-canola (Brassica napus L.)-wheat crop rotation at five sites in the Canadian prairies. The glyphosate rates were 0, 1, 2, 4 and 8 kg ae ha-1, applied pre-seeding and post-harvest every year. The wheat rhizosphere was sampled in the final year of the study and analysed for microbial biomass C (MBC), the composition and diversity of the microbiome, and activities of ß-glucosidase, N-acetyl-ß-glucosiminidase, acid phosphomonoesterase and arylsulphatase. Glyphosate did not affect MBC, the composition and diversity of prokaryotes and fungi, and the activities of three of the four enzymes measured in the wheat rhizosphere. The one effect of glyphosate was a wave-like response of N-acetyl-ß-glucosaminidase activity with increasing application rates. The experimental sites had much greater effects, driven by soil pH and organic C, on the soil microbiome composition and enzyme activities than glyphosate. Soil pH was positively correlated with the relative abundance of Acidobacteriota but negatively correlated with that of Actinobacteriota and Basidiomycota. Soil organic C was positively correlated with the relative abundances of Proteobacteriota and Verrucomicrobiota, but negatively correlated with the relative abundance of Crenachaeota. The activity of acid phosphomonoesterase declined with increasing relative abundance of Acidobacteriota, but increased with that of Actinobacteriota and Basidiomycota. The activity of N-acetyl-ß-glucosaminidase also increased with increasing relative abundance of Actinobacteriota but decreased with that of Mortierellomycota. ß-glucosidase activity also decreased with increasing relative abundance of Mortierellomycota. The core fungal species observed in at least 90% of the samples were Humicola nigrescens, Gibberella tricincta and Giberella fujikuroi. Therefore, this multi-site study on the Canadian prairies revealed no significant effects of 4-year applications of glyphosate applied at different rates on most soil microbial properties despite differences in the properties among sites. However, it is important to keep evaluating glyphosate effects on the soil microbiome and its functioning because it is the most widely used herbicide worldwide.

Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation.

Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism.

MicroRNAs (miRNAs), as important post-transcriptional regulators, are ubiquitous in various tissues. The aim of this exploratory study was to determine the presence of miRNAs in rumen fluid, and to investigate the possibility of miRNA-mediated cross-talk within the ruminal ecosystem. Rumen fluid samples from four cannulated Holstein cows were collected during two feeding regimes (forage and high-grain diet) and DNA and RNA were extracted for amplicon and small RNA sequencing. Epithelial biopsies were simultaneously collected to investigate the co-expression of miRNAs in papillae and rumen fluid. We identified 377 miRNAs in rumen fluid and 638 in rumen papillae, of which 373 were shared. Analysis of microbiota revealed 20 genera to be differentially abundant between the two feeding regimes, whereas no difference in miRNAs expression was detected. Correlations with at least one genus were found for 170 miRNAs, of which, 39 were highly significant (r > |0.7| and P < 0.01). Both hierarchical clustering of the correlation matrix and WGCNA analysis identified two main miRNA groups. Putative target and functional prediction analysis for the two groups revealed shared pathways with the predicted metabolic activities of the microbiota. Hence, our study supports the hypothesis of a cross-talk within the rumen at least partly mediated by miRNAs.

Effect of Duration of High-Grain Feeding on Chewing, Feeding Behavior, and Salivary Composition in Cows with or without a Phytogenic Feed Supplement.

Switching diets from forage to a high-grain (HG) diet increases the risk of rumen fermentation disorders in cattle. However, the effects of the duration of the HG feeding, after the diet switch, on animal behavior and health have received considerably less attention. This experiment primarily aimed to assess the effects of the duration of an HG diet on the chewing, eating, and lying behavior and salivation dynamics in a control group (CON) and a group of cows receiving a phytogenic feed supplement (TRT) at 0.04% (DM basis), which included L-menthol, thymol, eugenol, mint oil, and cloves powder. The experiment was a crossover design with nine non-lactating cows, and two experimental periods with an intermediate washout of four weeks. In each period, the cows were first fed a forage diet for a week to collect baseline measurements representing week 0; then, the diet was switched over a week to HG (65% concentrate), which was fed for four continuous weeks (week 1, week 2, week 3, and week 4 on an HG diet, respectively). The cows were divided in two groups of four and five animals and were randomly allocated to CON or TRT. The data analysis revealed that at the start of the HG feeding, the dry matter intake and the cows' number of lying bouts increased, but the eating time, rumination time, and meal frequency decreased, resulting in a greater eating rate. We also found that an advanced duration on an HG diet further decreased the rumination time, total chewing time, chewing index, and sorting in favor of short feed particles, with the lowest values in week 4. The feed bolus size increased but feed the ensalivation decreased in week 4 compared to week 0. The dietary switch increased salivary lysozyme activity, and the advanced duration on the HG diet increased salivary pH, but salivary phosphate decreased in weeks 1 and 2 on the HG diet. Supplementation with TRT increased sorting in favor of physically effective NDF (peNDF) in week 2 and increased salivary pH in week 4 on an HG diet. Overall, the negative effects of the HG diet in cattle are more pronounced during the initial stage of the HG feeding. However, several detrimental effects were exacerbated with the cows' advanced duration on feed, with host adaptive changes still observed after 3 and 4 weeks following the diet switch. The TRT mitigated some of the negative effects through the temporal improvement of the salivary properties and the intake of peNDF, which are known to modulate rumen fermentation.

Supplementing a Phytogenic Feed Additive Modulates the Risk of Subacute Rumen Acidosis, Rumen Fermentation and Systemic Inflammation in Cattle Fed Acidogenic Diets.

Feeding with high-concentrate diets increases the risk of subacute ruminal acidosis (SARA). This experiment was conducted to evaluate whether supplementing a phytogenic feed additive based on L-menthol, thymol, eugenol, mint oil (Mentha arvensis) and cloves powder (Syzygium aromaticum) (PHY) can amend the ruminal fermentation profile, modulate the risk of SARA and reduce inflammation in cattle. The experiment was designed as a crossover design with nine non-lactating Holstein cows, and was conducted in two experimental runs. In each run, cows were fed a 100% forage diet one week (wk 0), and were then transitioned stepwise over one week (0 to 65% concentrate, wk adapt.) to a high concentrate diet that was fed for 4 weeks. Animals were fed diets either with PHY or without (CON). The PHY group had an increased ruminal pH compared to CON, reduced time to pH < 5.8 in wk 3, which tended to decrease further in wk 4, reduced the ruminal concentration of D-lactate, and tended to decrease total lactate (wk 3). In wk 2, PHY increased acetate, butyrate, isobutyrate, isovalerate, and the acetate to propionate ratio compared to CON. Phytogenic supplementation reduced inflammation compared to CON in wk 3. Overall, PHY had beneficial effects on ruminal fermentation, reduced inflammation, and modulated the risk of SARA starting from wk 3 of supplementation.

Supplementation With Phytogenic Compounds Modulates Salivation and Salivary Physico-Chemical Composition in Cattle Fed a High-Concentrate Diet.

Saliva facilitates feed ingestion, nutrient circulation, and represents an important pH buffer for ruminants, especially for cattle fed high-concentrate diets that promote rumen acidification. This experiment evaluated the short-term effects of nine phytogenic compounds on salivation, saliva physico-chemical composition as well as ingested feed boli characteristics in cattle. A total of nine ruminally cannulated Holstein cows were used. Each compound was tested in four of these cows as part of a high-concentrate meal (2.5 kg of total mixed ration in dry matter basis for 4 h) in low or high dose, and was compared to a control meal without compound. Saliva was sampled orally (unstimulated saliva) for physico-chemical composition analysis. Composition of the ingested saliva (stimulated saliva), salivation and feed boli characteristics were assessed from ingesta collected at the cardia during the first 30 min of the meal. Analysis of unstimulated saliva showed that supplementation with capsaicin and thyme oil increased buffer capacity, while supplementation with thymol, L-menthol and gentian root decreased saliva pH. In addition, supplementing angelica root decreased saliva osmolality. Regression analysis on unstimulated saliva showed negative associations between mucins and bicarbonate as well as with phosphate when garlic oil, thyme oil or angelica root was supplemented. Analysis of stimulated saliva demonstrated that supplementation with garlic oil increased phosphate concentration, thyme oil tended to increase osmolality, capsaicin and thymol increased buffer capacity, and ginger increased phosphate content. Furthermore, salivation rate increased with ginger and thymol, and tended to increase with garlic oil, capsaicin, L-menthol and mint oil. Feed ensalivation increased with capsaicin. A positive association was found between feed bolus size and salivation rate when any of the phytogenic compounds was supplemented. Overall, our results demonstrate positive short-term effects of several phytogenic compounds on unstimulated and stimulated saliva physico-chemical properties, salivation or feed boli characteristics. Thus, the phytogenic compounds enhancing salivary physico-chemical composition have the potential to contribute to maintain or improve ruminal health in cattle fed concentrate-rich rations.

Dynamic changes in salivation, salivary composition, and rumen fermentation associated with duration of high-grain feeding in cows.

Salivary secretions are essential for the regulation of digestive processes, as well as rumen and cow health. This research evaluated the effects of the duration of high-grain feeding, and of the time relative to a meal, on salivation, saliva properties, feed bolus characteristics, chewing activity, ruminal and reticular volatile fatty acids, as well as salivary and ruminal pH. Nine nonlactating cannulated Holstein cows were sampled at 1 and 23 d after transition to a 65% grain diet (short term and long term, respectively). Both before and after a controlled meal (2.5 kg of dry matter, offered over 4 h), unstimulated saliva was taken orally for composition analysis. Stimulated salivation and feed boli characteristics were evaluated by collection of ingesta from cardia during 30 min. Chewing and ruminal pH were measured during the controlled meal and for a total of 6 h thereafter. Results from unstimulated saliva showed no effect of the duration of high-grain feeding on bicarbonate, phosphate, total proteins, mucins, lysozyme, and buffer capacity, but increased osmolality at the long term. Lysozyme activity did not differ with high-grain feeding duration, but tended to be lower after the meal. In contrast to short-term-fed cows, the long-term-fed cows increased both meal consumption and feed bolus size, but decreased chewing and feed ensalivation (5.2 vs. 4.6 ± 0.50 g of saliva/g of dry matter), and had lower pH of the stimulated saliva (7.00 vs. 6.67 ± 0.076). These cows also had decreased chewing index (66.5 vs. 45.4 min/kg of neutral detergent fiber), and despite the increase in stimulated saliva buffer capacity (0.027 vs. 0.039 ± 0.006), mean ruminal pH decreased (6.31 vs. 6.11 ± 0.065) during ad libitum feeding. Both in the rumen and reticulum, the concentration of total volatile fatty acids was lower and propionate proportion was higher at the long term. Linear regression analyses revealed a positive influence of the flow rates of salivary bicarbonate and phosphate on ruminal pH during the short term. For every 1-mol increment in the flow of bicarbonate or phosphate, ruminal pH increased by 0.062 or 0.439 units, respectively. Overall, salivary buffers are key determinants of ruminal pH regulation, especially during short-term grain feeding. However, in the long term, ruminal pH drop during ad libitum feeding was stronger, and this effect seems to be exacerbated by increased feed bolus size, accompanied by reductions in feed ensalivation, stimulated saliva pH, and chewing index.

Short-term screening of multiple phytogenic compounds for their potential to modulate chewing behavior, ruminal fermentation profile, and pH in cattle fed grain-rich diets.

In cattle, proper rumen functioning and digestion are intimately linked to chewing behavior. Yet, high grain feeding impairs chewing activity, increasing the risk of subacute ruminal acidosis and dysfermentation. This study aimed to screen 9 different phytogenic compounds for their potential to modulate chewing activity, meal size, rumino-reticular short-chain fatty acids (SCFA), and pH during consumption in a first daily meal and shortly thereafter in cattle fed a grain-rich diet. Treatments were control (total mixed ration without phytogenic) or addition of a phytogenic compound at a low or high dose. Phytogenic compounds and doses (all in mg/kg) were angelica root (6.6 and 66), capsaicin (10 and 100), gentian root (6.6 and 66), garlic oil (0.3 and 3), ginger extract (40 and 400), L-menthol (6.7 and 67), mint oil (15.3 and 153), thyme oil (9.4 and 94), and thymol (5 and 50), for the low and high groups, respectively. Before the start of the screening experiment, cows were fed to reach subacute ruminal acidosis conditions, confirmed with the time of ruminal pH <5.8 being 655 ± 148.2 min/d. During the screening experiment, the treatments were offered in a controlled meal (2.5 kg of DM for 4 h) as part of the daily diet with 65% concentrate. Each treatment was tested in 4 of the 9 cannulated Holstein cows using an incomplete Latin square design. Ruminal and reticular fluids were sampled before and after each treatment, and data collected before the meal were used as covariates. Chewing and ruminal pH were monitored during the treatment, followed by 2 h of complete feed restriction, and then 4 h of ad libitum feed intake without phytogenic. Data showed that supplementation of angelica root tended to linearly increase rumination time immediately after the first meal when feed was restricted (27.3, 41.9, and 42.6 ± 5.99 min for control, low and high groups, respectively). Capsaicin increased eating time (43.6, 49.4, and 66.4 ± 4.93 min) during consumption but did not affect ruminal total SCFA or mean ruminal pH. Garlic oil reduced the concentration of reticular total SCFA (75.7, 71.3, and 60.1 mM) and tended to decrease ruminal acetate-to-propionate ratio (2.50, 1.78, and 1.87 ± 0.177) with no effect on ruminal pH. The L-menthol affected reticular total SCFA quadratically (76.1, 64.9, and 81.0 ± 4.22%), and ruminal pH responded quadratically when feed was reintroduced ad libitum (6.0, 6.3, and 6.1 ± 0.07). Mint oil did not affect chewing or total SCFA during consumption, but the low dose increased ruminal pH (6.5, 6.7, and 6.5 ± 0.08). Thyme oil tended to lower the severity of ruminal acidosis. Overall, phytogenic compounds demonstrated distinct dose-dependent effects to beneficially influence chewing behavior, modulate fermentation, and mitigate ruminal acidosis in dairy cows under a high-grain challenge diet.

Betaine Modulates Rumen Archaeal Community and Functioning during Heat and Osmotic Stress Conditions In Vitro.

Rumen archaea play an important role in scavenging ruminal hydrogen (H2) and thus facilitate rumen fermentation. They require optimum temperature and osmolality for their growth and metabolism; however, a number of external factors may put archaea under heat and osmotic stress. Betaine is an osmolyte, molecular chaperone, and antioxidant; therefore, it bears potential to combat against these stressors. In this in vitro study, three betaine levels, namely, 0 (control), 51 (low), and 286 (high) ppm, were used. Each of these was subjected to two temperatures (39.5 and 42°C) and two osmolality conditions (295 and 420 mOsmol kg-1) with n = 6 per treatment. Sequencing analyses of the solid phase (which use solid materials containing primarily fibrous materials of low-density feed particles) and the liquid phase (rumen fermenter liquid) using 16S rRNA revealed that more than 99.8% of the ruminal archaea in fermenters belong to the phylum Euryarchaeota. At the genus level, Methanobrevibacter was the most prevalent in both phases, and Methanosaeta was only detected in the liquid phase. The genera Methanobrevibacter and Methanobacterium both showed a positive correlation with methane (CH4) formation in the liquid and solid phases, respectively (P < 0.05). Heat stress increased the relative abundance of genus Methanimicrococcus at the expense of candidate archaeal genus Vadin CA11 (P < 0.05). In the solid phase, osmotic stress significantly reduced the Shannon and Simpson indices of diversity, and relative abundance was higher for Methanobrevibacter at the expense of Methanimicrococcus. In the liquid phase, osmotic stress increased not only the abundance-based coverage estimator (ACE) and singles parameters of diversity but also the relative abundances of Methanosphaera and Methanobacterium. The overall decrease in all gas parameters and estimated metabolic hydrogen ([2H]) utilization was observed during osmotic stress conditions (P < 0.05). Betaine enhanced the diversity of solid phase archaea as indicated by the increase in ACE and singles during heat stress, and only a high dose improved all diversity parameters in the liquid phase during osmotic stress (P < 0.05). Thus, betaine alleviates the effects of heat stress and osmotic stress on the archaea community.

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations.

Starch-rich diets can cause subacute ruminal acidosis (SARA) in dairy cows with potentially different susceptibility according to lactation number. We wanted to evaluate the bacterial community and the fermentation end products in feces to study susceptibility to hindgut acidosis and dysbiosis. Sixteen dairy cows received a medium-concentrate diet (MC, 40% concentrate, 18.8% starch) for one week and a high-concentrate diet (HC, 60% concentrate, 27.7% starch, DM) for four weeks. Milk yield, dry-matter intake, chewing activity, ruminal pH, milk constituents, and fecal samples for short-chain fatty acids (SCFA), pH, and 16S rRNA-gene sequencing were investigated. The HC feeding caused a reduction in fecal pH, bacterial diversity and richness, an increase in total SCFA, and a separate phylogenetic clustering of MC and HC samples. Ruminal and fecal pH had fair correlation (r = 0.5). Cows in the second lactation (2ndL) had lower dry matter intake (DMI) than cows of third or fourth or more lactations (3rdL; ≥4 L), whereas DMI/kg body weight was lower for ≥4 L than for 2ndL and 3rdL cows. The mean ruminal pH was highest in ≥4 L, whereas the time spent below the SARA threshold was highest for 3rdL cows. The latter also had higher total SCFA in the feces. Our results suggest that hindgut dysbiosis is caused by increased substrate flow to the hindgut, but further investigations are needed to define hindgut acidosis. The 3rdL cows were most susceptible to rumen acidosis and hindgut dysbiosis due to high DMI level, but missing counter regulations, as suggested happening in 2ndL and ≥4 L cows.

Evaluation of fecal fermentation profile and bacterial community in organically fed dairy cows consuming forage-rich diets with different particle sizes.

Organic cattle farming encourages the use of forage-rich diets, and the reduction of particle size has been suggested as an approach to improve forage utilization and enhance nutrient intake of cows. However, reducing forage particle size increases passage rate, as well as the flow of potentially fermentable nutrients out of the rumen, and the consequences for hindgut fermentation have not been evaluated yet. This study evaluated the effects of decreasing dietary forage particle size on the fecal short-chain fatty acid (SCFA) profile and the bacterial community structure of dairy cows fed forage-based rations. Twenty-one organically fed lactating Holstein cows (4 primiparous and 17 multiparous; mean and standard deviation 703 ± 65 kg body weight, 135 ± 104 days in milk) were divided into 2 groups and fed 1 of 2 diets for 34 d. Diets contained 20% concentrate and 80% forage (dry matter basis), and were fed either as a control with a forage geometric mean particle size of 52 mm (CON; 11 cows) or as a diet with the forage particle size reduced to a geometric mean size of 7 mm (RED; 10 cows). Fecal samples were collected at the end of the experiment, and samples were immediately frozen at -20°C. Samples were analyzed for SCFA, and the fecal bacterial community was evaluated using 16S rRNA sequencing. Data showed that the concentration of total SCFA was not affected by treatment, but the proportion of propionate, a key glucogenic precursor in cattle, tended to be greater for RED (13.3 and 13.8 ± 0.1%, respectively). The predominant bacterial phyla, including Firmicutes (58.0 ± 0.7%), Bacteroidetes (26.9 ± 0.4%), and Verrucomicrobia (4.0 ± 0.4%), were not affected by forage particle size. Family Lachnospiraceae increased in relative abundance when the RED diet was fed (12.1 and 13.9 ± 0.5% for CON and RED, respectively), and genera Acetitomaculum (1.1 and 1.8 ± 0.2%), Turicibacter (0.7 and 0.9 ± 0.1%), and Ruminobacter (0.1 and 0.4 ± 0.1%) increased in relative abundance when RED was fed. In addition, relative abundance of some fecal bacterial taxa was correlated with major fecal SCFA and pH. Reducing the particle size of forages, from 52 to 7 mm geometric mean particle size, maintained fecal concentration of total SCFA and tended to enhance propionate concentration, without risk of dysbiosis. Thus, results suggest that reduction of forage particle size represents an effective approach to optimizing forage utilization while maintaining hindgut fermentation and fecal bacterial diversity in dairy cows fed forage-rich diets.

Effects of clay mineral supplementation on particle-associated and epimural microbiota, and gene expression in the rumen of cows fed high-concentrate diet.

The increased concentrate amounts in cow diets may initiate changes in both particle-associated (PaM) and epimural microbiota (EpM) with the potential for promoting the establishment of pathogens. Clay minerals have shown promising potentials in binding harmful microorganisms and metabolites due to their high adsorption capacity. This study evaluated the effects of a clay-mineral based product (CM) on PaM, EpM, fermentation parameters, and epithelial gene expression in cows fed a high-concentrate diet. Eight rumen-cannulated non-lactating Holstein cows received a concentrate mix supplemented with CM or not (CON) in a change-over design with an initial 100% roughage diet phase (RD, 1 week), followed by intermittent 65%-high-concentrate-diet phases (HC1, HC2; 1 and 2 week duration, respectively), interrupted by 1 week roughage only. Rumen samples for short-chain fatty acids, ammonia, and lactate quantification, as well as PaM, and epithelial biopsies for EpM examination and epithelial gene expression were collected via the cannula once during each feeding phase. Phylogenetic distance analysis of Illumina MiSeq sequencing of the 16S rRNA gene region V345 showed a clear clustering of RD microbiota compared to HC in PaM, showing the impact of the high-concentrate diet on the bacterial community. In the EpM this effect was less pronounced, due to higher variability in RD. In the PaM, a decrease (P < 0.01) of community diversity occurred with the onset of HC feeding, while in the EpM there was an increase in diversity (P < 0.05). In the PaM, CM increased the relative abundance of genus Butyrivibrio (P < 0.01), a commensal bacterium of the rumen, which was, with 6.4%, the second most abundant genus. There, the CM supplementation decreased the genera Lactobacillus, Fusobacterium, and Treponema (P = 0.05), which are potentially either lactate producing or opportunistic pathogens. In the EpM, CM decreased the relative abundance of Succiniclasticum genus (P < 0.01), a possible endotoxin producer, and increased bacteria that are associated with a normobiotic rumen, such as Campylobacter (P = 0.06). Barrier function genes were upregulated in HC2 and nutrient transport genes downregulated in HC1 (P < 0.05); however, there was little effect on pro-inflammatory genes at the epithelium. The CM showed a significant decreasing effect on the cellular metabolism genes HMGCS1 (P = 0.04). Our results suggest that CM supplementation can increase the relative abundance of commensal microbiota and decrease bacteria that could negatively impact the rumen milieu and health during high-concentrate feeding.

A nutritional and rumen ecological evaluation of the biorefinery by-product alfalfa silage cake supplemented with Scrophularia striata extract using the rumen simulation technique.

BACKGROUND: By-products of the food production chain are gaining importance as feedstuffs for ruminants. Alfalfa silage cake (AC) is an unexploited biorefinery by-product rich in fiber. The aim of this study was to test AC, using an in vitro rumen simulation technique (Rusitec), for its suitability as a fiber source for cattle. Three diets with similar crude protein (CP) content were formulated; they contained the biorefinery by-product AC, the original alfalfa silage (OA), or a fiber-rich hay. As fibrous feedstuffs are known to promote ruminal methanogenesis, we additionally tested a plant extract of Scrophularia striata (60 mg g-1 dry matter) for its methane mitigation and antimicrobial properties. RESULTS: Diets containing AC displayed lower nutrient degradability, with the largest difference in CP degradation (P < 0.001). Sequencing of microbial DNA revealed several effects of the diet and of the addition of S. striata extract, but no inhibitory effect on methanogens. Likewise, methane production, which, in general, is lower with AC and OA diets, was not inhibited by S. striata extract, while the short chain fatty acid (SCFA) profiles were unaffected. CONCLUSION: Although CP degradation of the AC diet was lower, degradation of the fiber fractions was similar among diets. According to the present results, AC can be used as fibrous feedstuff for ruminants. Supplementation with S. striata extract did not inhibit methane formation. © 2019 Society of Chemical Industry.

Feed Restriction Modifies Intestinal Microbiota-Host Mucosal Networking in Chickens Divergent in Residual Feed Intake.

Differences in chickens' feed intake may be the underlying factor influencing feed-efficiency (FE)-associated variation in intestinal microbiota and physiology. In chickens eating the same amount of feed, quantitative feed restriction may create similar intestinal conditions and help clarify this cause-and-effect relationship. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on ileal and cecal microbiota, concentrations of short-chain fatty acids, visceral organ size, intestinal morphology, permeability, and expression of genes related to nutrient uptake, barrier function, and innate immune response in broiler chickens with divergent residual feed intake (RFI; metric for FE). On day 30 posthatch, 28 low-RFI (good FE) and 29 high-RFI (poor FE) chickens across both feeding-level groups (n = 112) were selected. Supervised multigroup data integration and relevance network analyses showed that especially Lactobacillus (negative) in ileal digesta, Turicibacter (positive) in cecal digesta, and Enterobacteriaceae (positive) in both intestinal segments depended on chicken's feed intake, whereas the level of Anaerotruncus in cecal digesta was most discriminative for high RFI. Moreover, shallower crypts and fewer goblet cells in ceca indicated host-related energy-saving mechanisms with low RFI, whereas greater tissue resistance suggested a stronger jejunal barrier function in low-RFI chickens. Values corresponding to feed intake level × RFI interactions indicated larger pancreas and lower levels of ileal and cecal short-chain fatty acids in restrictively fed high-RFI chickens than in the other 3 groups, suggesting host physiological adaptations to support greater energy and nutrient needs of high-RFI chickens compensating for the restricted feeding. IMPORTANCE The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.

Feed Restriction Modulates the Fecal Microbiota Composition, Nutrient Retention, and Feed Efficiency in Chickens Divergent in Residual Feed Intake.

There is a great interest to understand the impact of the gut microbiota on host's nutrient use and FE in chicken production. Both chicken's feed intake and gut bacterial microbiota differ between high and low-feed efficient chickens. To evaluate the impact of the feed intake level on the feed efficiency (FE)-associated variation in the chicken intestinal microbiota, differently feed efficient chickens need to eat the same amount of feed, which can be achieved by feeding chickens restrictively. Therefore, we investigated the effect of restrictive vs. ad libitum feeding on the fecal microbiome at 16 and 29 days posthatch (dph), FE and nutrient retention in chickens of low and high residual feed intake (RFI; metric for FE). Restrictively fed chickens were provided the same amount of feed which corresponded to 85% of the ad libitum fed group from 9 dph. FE was determined for the period between 9 and 30 dph and feces for nutrient retention were collected on 31 to 32 dph. From the 112 chickens (n = 56 fed ad libitum, and n = 56 fed restrictively), 14 low RFI and 15 high RFI ad libitum fed chickens, and 14 low RFI (n = 7 per sex) and 14 high RFI restrictively fed chickens were selected as the extremes in RFI and were retrospectively chosen for data analysis. Bray-Curtis dissimilarity matrices showed significant separation between time points, and feeding level groups at 29 dph for the fecal bacterial communities. Relevance networking indicated positive associations between Acinetobacter and feed intake at 16 dph, whereas at 29 dph Escherichia/Shigella and Turicibacter positively and Lactobacillus negatively correlated to chicken's feed intake. Enterobacteriaceae was indicative for low RFI at 16 dph, whereas Acinetobacter was linked to high RFI across time points. However, restrictive feeding-associated changes in the fecal microbiota were not similar in low and high RFI chickens, which may have been related to the higher nutrient retention and thus lower fecal nutrient availability in restrictively fed high RFI chickens. This may also explain the decreased RFI value in restrictively fed high RFI chickens indicating improved FE, with a stronger effect in females.

Correction: Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling.

[This corrects the article DOI: 10.1371/journal.pone.0182271.].

Changes in Rumen Microbial Profiles and Subcutaneous Fat Composition When Feeding Extruded Flaxseed Mixed With or Before Hay.

Extruded flaxseed (25%) and ground hay (75%) were each fed (DM basis) either together in a total mixed ration (TMR) or as flaxseed first followed by hay (non-TMR) to three pens of eight crossbred steers (n = 24 per diet) for 240 days. Compared to TMR, feeding non-TMR enriched subcutaneous fat with α-linolenic acid (ALA, 18:3n-3) and its biohydrogenation intermediates including vaccenic acid [trans(t)11-18:1], rumenic acid [cis(c)9,t11-conjugated linoleic acid] and conjugated linolenic acid (CLnA). Rumen microbial analysis using QIIME indicated that 14 genera differed (P ≤ 0.05) between TMR and the non-TMR. Azoarcus and Streptococcus were the only genera which increased in relative abundance in the TMR fed steers, whereas Methanimicrococcus, Moryella, Prevotella, Succiniclasticum, Succinivibrio, Suttenella, and TG5 decreased as compared to steers fed the non-TMR. Among these, Moryella, Succiniclasticum, and Succinivibrio, spp. were correlated with fatty acid profiles, specifically intermediates believed to be components of the major biohydrogenation pathway for ALA (i.e., t11, c15-18:2, c9, t11, c15-18:3, and total CLnA). In addition, negative correlations were found between the less abundant Ruminoccocus-like OTU60 and major ALA biohydrogenation intermediates, as well as positive correlations with several intermediates from alternative pathways that did not involve the formation of trans 11 double bonds. The present results suggest a number of pathways for ALA biohydrogenation are operating concurrently in the rumen, with their balance being influenced by diet and driven by less abundant species rather than members of the core bacterial population.

Transglycosylated Starch Modulates the Gut Microbiome and Expression of Genes Related to Lipid Synthesis in Liver and Adipose Tissue of Pigs.

Dietary inclusion of resistant starches can promote host health through modulation of the gastrointestinal microbiota, short-chain fatty acid (SCFA) profiles, and lipid metabolism. This study investigated the impact of a transglycosylated cornstarch (TGS) on gastric, ileal, cecal, proximal-colonic, and mid-colonic bacterial community profiles and fermentation metabolites using a growing pig model. It additionally evaluated the effect of TGS on the expression of host genes related to glucose and SCFA absorption, incretins, and satiety in the gut as well as host genes related to lipid metabolism in hepatic and adipose tissue. Sixteen growing pigs (4 months of age) were fed either a TGS or control (CON) diet for 11 days. Bacterial profiles were determined via Illumina MiSeq sequencing of the V3-5 region of the 16S rRNA gene, whereas SCFA and gene expression were measured using gas chromatography and reverse transcription-quantitative PCR. Megasphaera, which was increased at all gut sites, began to benefit from TGS feeding in gastric digesta, likely through cross-feeding with other microbes, such as Lactobacillus. Shifts in the bacterial profiles from dietary TGS consumption in the cecum, proximal colon, and mid colon were similar. Relative abundances of Ruminococcus and unclassified Ruminococcaceae genus were lower, whereas that of unclassified Veillonellaceae genus was higher in TGS- compared to CON-fed pigs (p < 0.05). TGS consumption also increased (p < 0.05) concentrations of SCFA, especially propionate, and lactate in the distal hindgut compared to the CON diet which might have up-regulated GLP1 expression in the cecum (p < 0.05) and mid colon compared to the control diet (p < 0.10). TGS-fed pigs showed increased hepatic and decreased adipocyte expression of genes for lipid synthesis (FASN, SREBP1, and ACACA) compared to CON-fed pigs, which may be related to postprandial portal nutrient flow and reduced systemic insulin signaling. Overall, our data show that TGS consumption may affect gastrointestinal bacterial signaling, caused by changes in gut bacterial profiles and the action of propionate, and host lipid metabolism.

Fecal Microbiota Transplant from Highly Feed-Efficient Donors Shows Little Effect on Age-Related Changes in Feed-Efficiency-Associated Fecal Microbiota from Chickens.

Chickens with good or poor feed efficiency (FE) have been shown to differ in their intestinal microbiota composition. This study investigated differences in the fecal bacterial community of highly and poorly feed-efficient chickens at 16 and 29 days posthatch (dph) and evaluated whether a fecal microbiota transplant (FMT) from feed-efficient donors early in life can affect the fecal microbiota in chickens at 16 and 29 dph and chicken FE and nutrient retention at 4 weeks of age. A total of 110 chickens were inoculated with a FMT or a control transplant (CT) on dph 1, 6, and 9 and ranked according to residual feed intake (RFI; the metric for FE) on 30 dph. Fifty-six chickens across both inoculation groups were selected as the extremes in RFI (29 low, 27 high). RFI-related fecal bacterial profiles were discernible at 16 and 29 dph. In particular, Lactobacillus salivarius, Lactobacillus crispatus, and Anaerobacterium operational taxonomic units were associated with low RFI (good FE). Multiple administrations of the FMT only slightly changed the fecal bacterial composition, which was supported by weighted UniFrac analysis, showing similar bacterial communities in the feces of both inoculation groups at 16 and 29 dph. Moreover, the FMT did not change the RFI and nutrient retention of highly and poorly feed-efficient recipients, whereas it tended to increase feed intake and body weight gain in female chickens. This finding suggests that host- and environment-related factors may more strongly affect chicken fecal microbiota and FE than the FMT.IMPORTANCE Modulating the chicken's early microbial colonization using a FMT from highly feed-efficient donor chickens may be a promising tool to establish a more desirable bacterial profile in recipient chickens, thereby improving host FE. Although FE-associated fecal bacterial profiles at 16 and 29 dph could be established, the microbiota composition of a FMT, when administered early in life, may not be a strong factor modulating the fecal microbiota at 2 to 4 weeks of life and reducing the variation in chicken's FE. Nevertheless, the present FMT may have potential benefits for growth performance in female chickens.