Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge

Performance of 1-year-old camel calves fed a basal ration of alfalfa hay supplemented with different levels of concentrate

BACKGROUND

The use of a high-concentrate diet in fattening camels may have significant effects on growth performance and digestion as well as economic returns. This experiment was designed to study the effects of feeding different levels of concentrate in their diet on growth performance and digestion in a desert climate.

METHODS

Eighteen 12-month-old male camel calves were used, and divided into three treatments of six each. The concentrate was administered based on their body weight (BW) at 0.7 (low), 1.0 (medium), and 1.3% (high), with free access to alfalfa and water. The experiment lasted for 6 months, in which digestibility trials took place at 14, 16, and 18 months of age, which corresponded to 2, 4, and 6 months of the experimental period.

RESULTS

No significant variations were observed in final BW, BW changes, or average daily gain among feeding treatments. Increasing the concentrate level had a negative effect on roughage intake, impacting the roughage-to-concentrate ratio (P < 0.05) and neutral detergent fiber digestibility (P < 0.05). Increasing concentrate levels significantly increased total intake (P < 0.05), leading to a worse feed conversion ratio (P < 0.05). However, animal age had no negative effect on nutrient digestibility, and there were no interactions between concentrate supplement level and animal age. Significant increases in plasma total protein (P < 0.05) and urea (P < 0.05) were observed when the leve lof concentrate was increased. A similar trend was observed in rumen ammonia concentration. Camel calves fed low vs. medium or high levels of concentrate showed a greater rumen pH (P < 0.05), which was linked to a lower concentration of volatile fatty acids (P < 0.010).

CONCLUSIONS

The present study concluded that yearling camel calves receiving different levels of concentrate with ad lib alfalfa hay could cover their nutrient requirements for maintenance and growth with a daily gain of 630 g/day when the level of concentrate was limited to 0.7% of BW and the total intake was only around 1.65% of BW, or 70.6 g/kg metabolic BW.

Prolonged feeding of high-concentrate diet remodels the hindgut microbiome and modulates nutrient degradation in the rumen and the total gastrointestinal tract of cows

The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate the effects of the high-concentrate diet on apparent total-tract nutrient digestibility in dairy cows. We also investigated the dysbiotic effects and the remodeling of the hindgut microbiome with prolonged high-concentrate feeding. Nine Holstein cows were used in 2 experimental periods; in each period, cows were first fed a 100% forage diet for 1 wk, followed by stepwise adaptation during one week to a high-concentrate (HC) diet (65% concentrate), which was then fed for 4 consecutive weeks. The kinetics of in situ ruminal degradability of grass silage (DM and NDF), corn grain and wheat grain (DM and starch), as well as the apparent total-tract nutrient digestibility were evaluated in the forage feeding and in wk 4 on the HC diet. Whereas the hindgut microbiome and fermentation profile were evaluated on a weekly basis. Regarding the in situ ruminal degradability due to grain type, the rate of degradation of the potentially degradable fraction and the effective rumen degradability of wheat grain were greater compared with corn grain. The in situ ruminal degradability of NDF decreased with the HC diet. However, the apparent total-tract digestibility of CP, fat, starch, NDF, ADF, and NFC increased with the HC diet compared with forage feeding. In addition, the HC diet increased the concentration of short-chain fatty acids in the hindgut, lowering fecal pH by 0.6 units, which correlated positively with microbial α diversity. This resulted in lower α diversity with the HC diet; however, α diversity (number of amplicon sequence variants) showed recovery in wk 3 and 4 on HC; in addition, microbial β diversity did not change from wk 2 onward on the HC diet. Two microbial enterotypes were identified: one for the forage diet with abundance of Akkermansia and Anaerosporobacter, and another enterotype for the HC diet with enrichment in Bifidobacterium and Butyrivibrio. Overall, results show that major microbial shifts and hindgut dysbiosis occurred in wk 1 on the HC diet. However, the hindgut microbial diversity of cows adapted after 3 wk of consuming the starch-rich ration. Thus, feeding the HC diet impaired fiber degradation in the rumen, but increased apparent total-tract nutrient digestibility. Likely, the forage diet contained less digestible NDF than the HC diet due to greater inclusion of forages with lower NDF digestibility and lower inclusion of more digestible nonforage NDF. Results also suggest that the adaptation of the hindgut microbial diversity of cows observed 3 weeks after the diet transition likely contributed to enhance total-tract nutrient digestibility.

Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle

With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.

Dynamic interplay of immune response, metabolome, and microbiota in cows during high-grain feeding: insights from multi-omics analysis

This study explores the dynamics of immune gene expression, ruminal metabolome, and gut microbiota in cows due to the duration of high-grain feeding, shedding light on host response and microbial dynamics in parallel. Cows consumed forage for a week, then gradually transitioned to a high-grain diet, which they consumed for 4 weeks. Immune response was evaluated in ruminal papillae by expression of genes related to the nuclear factor-kappaB (NFkB) pathway and correlated with the microbiota. Rumen metabolome was evaluated with high-performance liquid chromatography coupled with mass spectrometry and anion-exchange chromatography. Rumen and fecal microbiota were evaluated with 16S rRNA gene amplicon sequencing. In the rumen, expression of inflammation-associated genes increased with the duration on high grain, indicating activation of pro-inflammatory cascades; microbial diversity decreased with a high-grain diet but stabilized after week 3 on high grain. Changes in microbial relative abundance and metabolite enrichment were observed throughout the 4 weeks on high grain, with increments in propionogenic taxa (i.e., Succinivibrionaceae). Metabolite enrichment analysis showed that at the start of high-grain feeding, simple carbohydrates were enriched; then, these were substituted by their fermentation products. There were correlations between certain ruminal bacterial taxa (i.e., Ruminococcaceae UCG-005) and expression of genes of the NFkB pathway, suggesting the influence of these taxa on host immune response. In feces, microbial diversity and several Ruminococcaceae members initially declined but recovered by weeks 3 and 4. Overall, despite the stabilization of microbial diversity, changes in microbial relative abundance and proinflammatory genes were observed throughout high-grain feeding, suggesting that cows need more than 4 weeks to fully adjust once consuming a high-grain diet.IMPORTANCEDespite the stepwise diet transition typically assumed to serve for animal adaptation, expression of signaling receptors, mediators, and downstream targets of nuclear factor-kappaB pathway were found throughout the 4 weeks on high grain, which correlated with changes in the rumen microbial profile. In addition, although microbial diversity recovered in the feces and stabilized in the rumen in week 3 on high grain, we observed changes in microbial relative abundance throughout the 4 weeks on high grain, suggesting that cows need more than 4 weeks to adjust once consuming this diet. Findings are particularly important to consider when planning experiments involving dietary changes.

Postbiotics from Saccharomyces cerevisiae fermentation stabilize rumen solids microbiota and promote microbial network interactions and diversity of hub taxa during grain-based subacute ruminal acidosis (SARA) challenges in lactating dairy cows

Background

High-yielding dairy cows are commonly fed high-grain rations. However, this can cause subacute ruminal acidosis (SARA), a metabolic disorder in dairy cows that is usually accompanied by dysbiosis of the rumen microbiome. Postbiotics that contain functional metabolites provide a competitive niche for influential members of the rumen microbiome, may stabilize and promote their populations, and, therefore, may attenuate the adverse effects of SARA.

Methods

This study used a total of 32 rumen-cannulated lactating dairy cows, which were randomly assigned into four treatments: no SCFP (control), 14 g/d Original XPC (SCFPa), 19 g/d NutriTek (SCFPb-1X), and 38 g/d NutriTek (SCFPb-2X) (Diamond V, Cedar Rapids, IA) from 4 weeks before until 12 weeks after parturition. Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% dry matter of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. The DNA of rumen solids digesta was extracted and subjected to V3-V4 16S rRNA gene sequencing. The characteristics of rumen solids microbiota were compared between non-SARA (Pre-SARA1, week 4; Post-SARA1, week 7; and Post-SARA2, weeks 10 and 12) and SARA stages (SARA1/1, SARA1/2, SARA2/1, SARA2/2), as well as among treatments.

Results

Both SARA challenges reduced the richness and diversity of the microbiota and the relative abundances of the phylum Fibrobacteres. Supplementation with SCFP promoted the growth of several fibrolytic bacteria, including Lachnospiraceae UCG-009, Treponema, unclassified Lachnospiraceae, and unclassified Ruminococcaceae during the SARA challenges. These challenges also reduced the positive interactions and the numbers of hub taxa in the microbiota. The SCFPb treatment increased positive interactions among microbial members of the solids digesta and the number of hub taxa during the SARA and non-SARA stages. The SCFPb-2X treatment prevented changes in the network characteristics, including the number of components, clustering coefficient, modularity, positive edge percentage, and edge density of the microbiota during SARA challenges. These challenges reduced predicted carbohydrate and nitrogen metabolism in microbiota, whereas SCFP supplementation attenuated those reductions.

Conclusions

Supplementation with SCFP, especially the SCFPb-2X attenuated the adverse effects of grain-based SARA on the diversity and predicted functionality of rumen solids microbiota.

Fermented total mixed ration enhances nutrient digestibility and modulates the milk components and fecal microbial community in lactating Holstein dairy cows

Fermented total mixed ration (FTMR) is an effective method of preserving high-moisture byproducts with higher aerobic stability after fermentation. FTMR has the potential to fulfill the daily nutritional requirements of cattle and enhance their production performance. The objective of this research was to examine the influence of FTMR on lactation performance, total tract apparent digestibility, fecal microbiota communities, and fermentation profiles in lactating dairy cows. A total of 12 cows were randomly assigned into two groups: the TMR group and the FTMR group. The TMR group was fed a total mixed ration (TMR) diet, and the FTMR group was fed an FTMR diet. The FTMR did not impact milk yield in dairy cows despite a decrease in dry matter intake, which increased the efficiency of the feed. In contrast to that in the TMR group, the milk fat content in the FTMR group was greater. The FTMR group showed greater digestibility of neutral detergent fiber (NDF), organic matter (OM), dry matter (DM), crude protein (CP), and acid detergent fiber (ADF) in the total digestive tract than did the TMR group. The FTMR increased the concentration of butyrate in the fecal matter and reduced the pH of the feces. The Chao1, ACE, and Shannon indices of the archaeal community in dairy cow feces were significantly higher in cow fed the FTMR compared to those fed the TMR. LefSe analysis revealed higher levels of Oscillospira, Lactobacillus, Prevotella, and Dehalobacterium in the feces of dairy cows fed the FTMR than in those fed the TMR. However, the abundances of Roseburia, rc4-4, Bulleidia and Sharpea exhibited the opposite trend. The abundances of Halobacteria, Halobacteriales, and Halobacteriaceae, which are biomarkers for distinguishing fecal archaea in the TMR from the FTMR, were substantially greater in the feces of dairy cows that consumed the TMR than in those that consumed the FTMR. Therefore, FTMR can improve the milk fat content, total tract apparent feed digestibility efficiency, and diversity of archaea in the feces. Additionally, this work provides a theoretical basis for the feasibility of FTMR feeding for dairy cows.

Postbiotics from Saccharomyces cerevisiae fermentation stabilize microbiota in rumen liquid digesta during grain-based subacute ruminal acidosis (SARA) in lactating dairy cows

BACKGROUND

Subacute ruminal acidosis (SARA) is a common metabolic disorder of high yielding dairy cows, and it is associated with dysbiosis of the rumen and gut microbiome and host inflammation. This study evaluated the impact of two postbiotics from Saccharomyces cerevisiae fermentation products (SCFP) on rumen liquid associated microbiota of lactating dairy cows subjected to repeated grain-based SARA challenges. A total of 32 rumen cannulated cows were randomly assigned to 4 treatments from 4 weeks before until 12 weeks after parturition. Treatment groups included a Control diet or diets supplemented with postbiotics (SCFPa, 14 g/d Original XPC; SCFPb-1X, 19 g/d NutriTek; SCFPb-2X, 38 g/d NutriTek, Diamond V, Cedar Rapids, IA, USA). Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% DM of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. Total DNA from rumen liquid samples was subjected to V3-V4 16S rRNA gene amplicon sequencing. Characteristics of rumen microbiota were compared among treatments and SARA stages.

RESULTS

Both SARA challenges reduced the diversity and richness of rumen liquid microbiota, altered the overall composition (β-diversity), and its predicted functionality including carbohydrates and amino acids metabolic pathways. The SARA challenges also reduced the number of significant associations among different taxa, number of hub taxa and their composition in the microbial co-occurrence networks. Supplementation with SCFP postbiotics, in particular SCFPb-2X, enhanced the robustness of the rumen microbiota. The SCFP supplemented cows had less fluctuation in relative abundances of community members when exposed to SARA challenges. The SCFP supplementation promoted the populations of lactate utilizing and fibrolytic bacteria, including members of Ruminococcaceae and Lachnospiraceae, and also increased the numbers of hub taxa during non-SARA and SARA stages. Supplementation with SCFPb-2X prevented the fluctuations in the abundances of hub taxa that were positively correlated with the acetate concentration, and α- and β-diversity metrics in rumen liquid digesta.

CONCLUSIONS

Induction of SARA challenges reduced microbiota richness and diversity and caused fluctuations in major bacterial phyla in rumen liquid microbiota in lactating dairy cows. Supplementation of SCFP postbiotics could attenuate adverse effects of SARA on rumen liquid microbiota.

High concentrate diets altered the structure and function of rumen microbiome in goats

This study used metatranscriptomics to investigate the effects of concentrate diet level on rumen microbiome composition and function in goats. A total of 12 healthy 120-day-old Da'er goats were randomly allotted into two treatments: L group (low dietary concentrate level group, concentrate: forage ratio was 25: 75) and H group (high dietary concentrate level group, concentrate: forage ratio was 80: 20). The study included a 10-day pre-feeding period and a 60-day growth experiment. The results showed that compared with the L group, the average daily gain and the slaughter rate in the H group were increased, while the F/G was decreased; the concentration of lactate and ammonia nitrogen, and the proportion of butyrate and valerate in the rumen of the H group were increased, while the proportion of acetate, and the ratio of acetate to propionate were decreased (p < 0.05). Among rumen bacteria, compared with the L group, the H group significantly decreased the relative abundance of Firmicutes and Fibrobacteria at the phylum level, decreased the relative abundance of Bacteroidetes, Fibrobacter, and Sarcina and increased the relative abundance of Clostridium at the genus level, and decreased the relative abundance of Fibrobacter succinogenes, Sarcina sp. DSM 11001, Oscillibacter sp. KLE 1728, and Ruminococcus flavefaciens and increased the relative abundance of Clostridium sp. ND2 and Firmicutes bacteria CAG: 103 at the species level (p < 0.05). Among rumen fungi, the relative abundance of Basidiomycota, Neocallimastigomycota, Mortierella, Mortierella elongata, and Gonapodyna prolifera was lower in the H group than that in the L group (p < 0.05). Functional annotation results showed that the abundance of Glycoside hydrolases genes in rumen microbiome was significantly decreased in the H group compared to the L group (p < 0.05). The result of KEGG DEGs enrichment analysis showed that the gene expression of cellulose 1,4-β-cellobiosidase, acetyl-CoA hydrolase, lactate dehydrogenase, succinate-semialdehyde dehydrogenase, D-malate dehydrogenase and related genes in methane production pathways of rumen microbiome was decreased in the H group. In summary, feeding high concentrate diets improved the production performance of goats, altered the structure and composition of rumen microbiome and changed the function of rumen microbiome.

Changes on the rumen microbial community composition in dairy cows subjected to an acidogenic diet

In modern breeding systems, cows are subjected to many stress factors. Animals fed with a high-grain diet may have a decreased rumen pH, which would lead to subacute ruminal acidosis syndrome. The aim of this study was to investigate the evolution of microbial community composition in cows undergoing a dietary stress challenge. Twelve cows were subjected to a challenge period consisted in a rapid change of ration, from a normal (45.4:54.6 forage: concentrate) to a high-grain content diet (24.8:75.2 forage: concentrate) to induce sub-acute ruminal acidosis. Individual rumen fluid content samples were collected before (T0), and during the challenge (T3, T14, T28). DNA from rumen contents was extracted, purified, and sequenced to evaluate Bacterial populations and sequencing was performed on Illumina MiSeq. The effect of animal conditions on rumen microbial community was quantified through a linear mixed model. The acidogenic diet created 2 main clusters: ruminal hypomotility (RH) and milk fat depression (MFD). The microbial composition did not differ in T0 between the 2 groups, while during the challenge Ruminococcus spp., Treponema spp., Methanobrevibacter spp., and Methanosphaera spp. concentrations increased in RH cows; Succinivibrio spp. and Butyrivibrio spp. concentrations increased in MFD cows. Prevotella spp. and Ruminococcus spp., were negatively correlated, while Christenellaceae family were positively correlated with both Methanobrevibacter spp. and Methanosphaera spp. Moreover, the same diet affected differently cows' microbiota composition, underlying the impact of the host effect. Other studies are necessary to deepen the relationship between microbiota composition and host.

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

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

Understanding the Diversity and Roles of the Ruminal Microbiome

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

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.

Effects of High-Concentrate-Induced SARA on Antioxidant Capacity, Immune Levels and Rumen Microbiota and Function in Goats

This study aims to explore the antioxidant, immune, and enzyme metabolism aspects in goats experiencing subacute ruminal acidosis (SARA). Furthermore, we seek to elucidate the relationship between the symbiotic microbiota of goats and their metabolic function. Sixteen goats were equally divided into two groups and fed a normal-concentrate diet (NC, 55% concentrate) or a high-concentrate diet (HC, 90% concentrate) for five weeks. We found that the HC diet reduced the total antioxidant capacity (T-AOC) (p = 0.022) and increased interleukin-1β (IL-1β) (p = 0.015), interleukin-4 (IL-4) (p = 0.008) and interleukin-6 (IL-6) (p = 0.002) concentration of goats. Simultaneously, the HC diet significantly increased the concentrations of alkaline phosphatase (ALP) and amylase (AMY) in the blood and rumen fluid of goats (p < 0.05). Microbial analysis in the rumen of goats revealed that the HC diet decreased bacterial richness and diversity, as evidenced by the changed observed species, Chao 1, PD whole tree and Shannon when compared to the NC diet (p < 0.01). The proportion of Proteobacteria increased while that of Spirochaetes and Fibrobacteres significantly decreased with the HC diet (p < 0.05). The Christensenellaceae_R-7_group and Ruminococcaceae_UCG-010 in rumen was notably decreased when a diet was switched from 55% concentrate diet to 90% concentrate diet (p < 0.05). Additionally, microbial functional potentials deduced that the HC diet significantly increased the abundance of the citrate cycle (TCA cycle) (ko00020) associated with carbohydrate metabolism (p = 0.028). Furthermore, the HC diet significantly increased the glutathione metabolism (ko00480) associated with the metabolism of other amino acids (p = 0.008). Our findings suggested that SARA reduced the total antioxidant capacity and increased levels of inflammatory factors in goats, as well as decreased rumen bacterial species and abundance.

Effect of short-term abomasal corn starch infusions on postruminal fermentation and blood measures

It is possible that some of the systemic responses to subacute ruminal acidosis (SARA) may be caused by increased intestinal starch fermentation. The objective of this experiment was to evaluate the effect of abomasal infusion of up to 3 g of corn starch/kg body weight (approximately 1.6 kg of starch/d) on fecal measures of fermentation, plasma acute phase proteins, and white blood cell populations. Six ruminally cannulated cows in late lactation were randomly assigned to duplicate 3 × 3 Latin squares with 21-d periods. Cows were fed a 20.6% starch TMR twice daily and during the last 7 d of each period cows were abomasally infused with corn starch at 0 (CON), 1 (ST1), or 3 (ST3) g/kg body weight split into 2 bolus infusions, provided every 12 h. Fecal samples were collected at 0, 6, 12, and 18 h following feeding on d 21 and were analyzed for pH, VFA, lactic acid, and lipopolysaccharide (LPS). Composite fecal samples were used to estimate apparent total-tract nutrient digestibility using undigested neutral detergent fiber as an internal marker. Blood samples were collected at 0 and 6 h relative to feeding on d 14, 18, and 21 of each period. Concentrations of haptoglobin and serum amyloid A in plasma were measured in all samples, 0 h samples on d 14 and 21 were used to measure white blood cell populations, and 0 h samples from d 14, 18, and 21 were used for flow cytometric analysis of γδ T cells. Data were analyzed in SAS using models that included fixed effects of treatment and period and the random effects of cow and square. For blood measures, d 14 samples collected before the initiation of abomasal infusions were included as covariates. Time (d or h) was added as a repeated measure in variables that included multiple samples during the abomasal infusion period. A contrast was used to determine the linear effect of increasing abomasal corn starch. Abomasal corn starch linearly decreased fecal pH and linearly increased fecal total VFA and LPS, but effects were modest, with fecal pH, total VFA, and LPS changing from 6.96, 57.7 mM, and 4.14 log10 endotoxin units (EU) per gram for the CON treatment to 6.69, 64.1 mM, and 4.58 log10 EU/g for the ST3 treatment, respectively. This suggests that we did not induce hindgut acidosis. There were no effects of treatment on apparent total-tract starch digestibility or fecal starch content (mean of 96.9% and 2.2%, respectively). Treatment did not affect serum acute phase proteins or most circulating white blood cells, but the proportion of circulating γδ T cells tended to linearly decrease from 6.69% for CON to 4.61% for ST3. Contrary to our hypothesis, increased hindgut starch fermentation did not induce an inflammatory response in this study.

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.

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

Sialic acid exacerbates gut dysbiosis-associated mastitis through the microbiota-gut-mammary axis by fueling gut microbiota disruption

BACKGROUND

Mastitis is one of the most severe diseases in humans and animals, especially on dairy farms. Mounting evidence indicates that gastrointestinal dysbiosis caused by induction of subacute ruminal acidosis (SARA) by high-grain diet consumption and low in dietary fiber is associated with mastitis initiation and development, however, the underlying mechanism remains unknown.

RESULTS

In the present study, we found that cows with SARA-associated mastitis have altered metabolic profiles in the rumen, with increased sialic acids level in particular. Consumption of sialic acid (SA) in antibiotic-treated mice, but not healthy mice, induced marked mastitis. SA treatment of antibiotic-treated mice also induced mucosal and systemic inflammatory responses, as evidenced by increased colon and liver injuries and several inflammatory markers. In addition, gut dysbiosis caused by antibiotic impaired gut barrier integrity, which was aggravated by SA treatment. SA potentiated serum LPS level caused by antibiotic treatment, leading to increased activation of the TLR4-NF-κB/NLRP3 pathways in the mammary gland and colon. Moreover, SA facilitated gut dysbiosis caused by antibiotic, and especially enhanced Enterobacteriaceae and Akkermansiaceae, which correlated with mastitis parameters. Fecal microbiota transplantation from SA-antibiotic-treated mice mimicked mastitis in recipient mice. In vitro experiments showed that SA prompted Escherichia coli growth and virulence gene expression, leading to higher proinflammatory cytokine production in macrophages. Targeting the inhibition of Enterobacteriaceae by sodium tungstate or treating with the commensal Lactobacillus reuteri alleviated SA-facilitated mastitis. In addition, SARA cows had distinct ruminal microbial structure by the enrichment of SA-utilizing opportunistic pathogenic Moraxellaceae and the depletion of SA-utilizing commensal Prevotellaceae. Treating mice with the specific sialidase inhibitor zanamivir reduced SA production and Moraxellaceae abundance, and improved mastitis in mice caused by ruminal microbiota transplantation from cows with SARA-associated mastitis.

CONCLUSIONS

This study, for the first time, indicates that SA aggravates gut dysbiosis-induced mastitis by promoting gut microbiota disturbance and is regulated by commensal bacteria, indicating the important role of the microbiota-gut-mammary axis in mastitis pathogenesis and suggesting a potential strategy for mastitis intervention based on gut metabolism regulation. Video Abstract.

Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle

In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.

Population shifts in some faeces and rumen bacteria profiles and subsequent blood LPS and lactate concentrations in lambs in the early period of subacute ruminal acidosis

BACKGROUND

It is known that ruminal acidosis can induce harmal population shifts in some ruminal bacteria profiles. However, there is little information related to alterations in faecal and ruminal bacterial communities and relevant serum lipopolysaccharide (LPS) in sheep with subacute ruminal acidosis (SARA).

OBJECTIVES

This study aimed to investigate alterations in the defined faecal and ruminal bacteria profiles and serum LPS and blood lactate concentrations in lambs with empirically induced SARA.

METHODS

Fifteen lambs were served and undergone to induce SARA during a 7-day period. Faecal and ruminal samples were taken to measure the pH and to perform the bacteriological works at 0 (just before induction), 8, 9, and 10 days of the challenge. Blood samples were collected to determine the serum LPS and lactate levels. The rumen and faecal samples were cultured to specify colony-forming units (CFU) for Escherichia coli, Streptococcus Group D (SGD), and lactic acid bacteria (LAB).

RESULTS

Serum LPS value had no significant increase in the affected lambs with SARA. Significant increasing trends were observed in faecal E. coli and LAB populations (p < 0.01). Rumen bacteriology revealed a rising trend for LAB and a falling trend for SGD populations (p < 0.01).

CONCLUSION

Unlike cattle, LPS appears to be of minor importance in the pathogenesis of SARA in sheep. The increased ruminal and faecal LAB (4.00 × 10⁷ CFU/ml or g) are proposed as valuable biomarkers for improving nutritional strategy and screening SARA in lambs.

High-Grain Diet Feeding Altered Blood Metabolites, Rumen Microbiome, and Metabolomics of Yaks

Currently, information available on the comprehensive changes in the rumen bacteria and metabolites of yaks fed high-grain diets is limited. This study aimed to investigate the effects of high-grain diet feeding on the blood metabolites, rumen microbiome, and metabolomics of yaks by using 16S rDNA gene sequencing and liquid chromatography–mass spectrometry (LC/MS). Here, fourteen healthy male yaks (body weight, 249.61 ± 8.13 kg) were randomly assigned to two different diets: a hay diet (0% grain, CON, n = 7), or a high-grain diet (70% grain, HG, n = 7). At the 74th day of treatment, blood and ruminal fluid samples were collected for the blood metabolites, rumen microbiome, and metabolomics analyses. The HG diet increased lipopolysaccharides (LPS), aspartate aminotransferase (AST), gamma-glutamyltransferase (GGT), haptoglobin (HPT), serum amyloid-A (SAA), interleukin-1β (IL1-β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) serum concentrations (p < 0.05). Compared with the CON diet, the HG diet decreased rumen pH (p < 0.05), and increased total volatile fatty acids concentration, and proportion of butyrate (p < 0.05). The relative abundance of Firmicutes and Saccharibacteria were higher (p < 0.05), while Bacteroidetes was lower (p < 0.05) in the HG group than those in the CON group. At the genus level, the relative abundance of Christensenelaceae_R-7_group, Ruminococcaceae_NK4A214_group, Lachnospiraceae_NK3A20_group, and Acetitomaculum were higher than in those in the HG diet (p < 0.05). Compared with the CON group, the HG diet increased the concentrations of biogenic amines (histamine, tyramine, and putrescine), common amino acids (phenylalanine, threonine, serine, etc.), and arachidonic acid (prostaglandin H2, prostaglandin E2, 12(S)-HPETE, etc.). Collectively, these findings demonstrate that the HG diet altered the microbiota and metabolites, as well as potentially damaged their rumen health and induced inflammation in yaks.

High-energy diet modify rumen microbial composition and microbial energy metabolism pattern in fattening sheep

Higher dietary energy is often used to achieve better animal performance in mutton sheep production. Notably, changing the diet formula affects rumen fermentation and the microbiota of ruminants. In this study, we investigated the effect of dietary energy on rumen fermentation and ruminal microbiota in fattening sheep. Fifteen 2-month-old white-headed Suffolk sheep (♂) × Hu sheep (♀) crossbred lambs were randomly divided into three treatments based on the dietary energy of the feeds fed: 8.67 MJ/kg (Low energy (LE); n = 5), 10.38 MJ/kg (standard energy (CON); n = 5), and 12.31 MJ/kg (high energy (HE); n = 5) groups. After 70 days of feeding, sheep were slaughtered and the ruminal fluids were collected and analyzed to determine fermentation parameters. Microbiota was determined using metagenomics sequencing. Notably, the microbial cell protein (MCP) and butyric acid concentrations were significantly high in the HE group. Metagenomic sequencing revealed that ACE and Chao indexes of the HE group were significantly decreased. Four genera among the major classified taxa across all the kingdoms differed in relative abundance in the three dietary energy levels. The relative abundances of Prevotella_brevis, Succiniclasticum_ruminis, Prevotellace-ae_bacterium, and Lachnospiraceae_bacterium were significantly correlated with rumen fermentation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis further revealed that a high-energy diet increased lipid metabolism of microbiota. The Carbohydrate Active enzymes (CAZy) gene, which participates in energy metabolism, was upregulated, while genes regulating plant cell wall degradation were downregulated in the HE group. These results suggest that a high-energy diet had minimal influence on the rumen fermentation pattern but altered the composition of the rumen microbiota, enhancing microbial lipid metabolism and limiting crude fiber metabolism. The findings of this study provide scientific evidence of the effect of dietary energy on ruminant fermentation and fattening sheep production.

Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition

This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p < 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p < 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p < 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p < 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.

Integrating data from spontaneous and induced trans-10 shift of ruminal biohydrogenation reveals discriminant bacterial community changes at the OTU level

Introduction

Microbial digestion is of key importance for ruminants, and disturbances can affect efficiency and quality of products for human consumers. Ruminal biohydrogenation of dietary unsaturated fatty acids leads to a wide variety of specific fatty acids. Some dietary conditions can affect the pathways of this transformation, leading to trans-10 fatty acids rather than the more usual trans-11 fatty acids, this change resulting in milk fat depression in dairy cows.

Materials and methods

We combined data from an induced and spontaneous trans-10 shift of ruminal biohydrogenation, providing new insight on bacterial changes at different taxonomic levels. A trans-10 shift was induced using dietary addition of concentrate and/or unsaturated fat, and the spontaneous milk fat depression was observed in a commercial dairy herd.

Results and discussion

Most changes of microbial community related to bacteria that are not known to be involved in the biohydrogenation process, suggesting that the trans-10 shift may represent the biochemical marker of a wide change of bacterial community. At OTU level, sparse discriminant analysis revealed strong associations between this change of biohydrogenation pathway and some taxa, especially three taxa belonging to [Eubacterium] coprostanoligenes group, Muribaculaceae and Lachnospiraceae NK3A20 group, that could both be microbial markers of this disturbance and candidates for studies relative to their ability to produce trans-10 fatty acids.

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle

The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.

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.

Cow's microbiome from antepartum to postpartum: A long-term study covering two physiological challenges

Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points. Bifidobacterium increased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g., Butyrivibrio and unclassified Ruminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

BACKGROUND

The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.

RESULTS

Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.

CONCLUSIONS

Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.

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.

Parturition and postpartum dietary change altered ruminal pH and the predicted functions of rumen bacterial communities but did not alter the bacterial composition in Holstein cows

We investigated the temporal dynamics of ruminal pH and the composition and predicted functions of the rumen bacterial community in Holstein cows during the periparturient period. Eight multiparous Holstein cows (body weight; 707.4 ± 29.9 kg, parity; 3.6 ± 0.6) were used for continuous reticulo-ruminal pH measurement, among which five were also used for bacterial community analysis. Rumen fluid samples were collected at 3 weeks before and 2 and 6 weeks after parturition, and blood samples were collected 3 weeks before and 0, 2, 4, and 6 weeks after parturition. After the parturition, reduction in the 1-h mean reticulo-ruminal pH was associated with a significant (P < 0.05) increase in total volatile fatty acid concentration. However, with the exception of a significant change in an unclassified genus of Prevotellaceae (P < 0.05), we detected no significant changes in the compositions of major bacterial phyla or genera or diversity indices during the periparturient period. On the basis of predicted functional analysis, we identified a total of 53 MetaCyc pathways (45 upregulated), 200 enzyme commissions (184 upregulated), and 714 Kyoto Encyclopedia of Genes and Genomes orthologs (667 upregulated) at 6 weeks postpartum that were significantly (P < 0.05) different to those at 3 weeks prepartum. Among the 14 MetaCyc pathways (P < 0.05) in which pyruvate is an end product, PWY-3661 [log2-fold change (FC) = 5.49, false discovery rate (FDR) corrected P < 0.001] was the most highly upregulated pyruvate-producing pathway. In addition, P381-PWY [adenosylcobalamin biosynthesis II (aerobic); FC = 5.48, FDR corrected P < 0.001] was the second most upregulated adenosylcobalamin (Vitamin B12)-producing pathway. In contrast, PWY-2221 (FC = −4.54, FDR corrected P = 0.003), predominantly found in pectinolytic bacteria, was the most downregulated pathway. Our findings indicate that changes in rumen bacterial community structure are not strictly associated with transitions in parturition or diet; however, we did observe changes in reticulo-ruminal pH and the metabolic adaptation of predicted functional pathways. Consequently, predictive analysis of postpartum functional pathways may enable us to gain insights into the underlying functional adaptations of bacterial communities in Holstein cows during the periparturient period.

The Role of Rumen Microbiota and Its Metabolites in Subacute Ruminal Acidosis (SARA)-Induced Inflammatory Diseases of Ruminants

Subacute ruminal acidosis (SARA) is a common metabolic disease in ruminants. In the early stage of SARA, ruminants do not exhibit obvious clinical symptoms. However, SARA often leads to local inflammatory diseases such as laminitis, mastitis, endometritis and hepatitis. The mechanism by which SARA leads to inflammatory diseases is largely unknown. The gut microbiota is the totality of bacteria, viruses and fungi inhabiting the gastrointestinal tract. Studies have found that the gut microbiota is not only crucial to gastrointestinal health but also involved in a variety of disease processes, including metabolic diseases, autoimmune diseases, tumors and inflammatory diseases. Studies have shown that intestinal bacteria and their metabolites can migrate to extraintestinal distal organs, such as the lung, liver and brain, through endogenous pathways, leading to related diseases. Combined with the literature, we believe that the dysbiosis of the rumen microbiota, the destruction of the rumen barrier and the dysbiosis of liver function in the pathogenesis of SARA lead to the entry of rumen bacteria and/or metabolites into the body through blood or lymphatic circulation and place the body in the "chronic low-grade" inflammatory state. Meanwhile, rumen bacteria and/or their metabolites can also migrate to the mammary gland, uterus and other organs, leading to the occurrence of related inflammatory diseases. The aim of this review is to describe the mechanism by which SARA causes inflammatory diseases to obtain a more comprehensive and profound understanding of SARA and its related inflammatory diseases. Meanwhile, it is also of great significance for the joint prevention and control of diseases.

Effects of supplementation with lysophospholipids on performance, nutrient digestibility, and bacterial communities of beef cattle

An experiment was conducted to investigate the influences of supplemental lysophospholipids (LPL) on the growth performance, nutrient digestibility, and fecal bacterial profile, and short-chain fatty acids (SCFAs) of beef cattle. Thirty-six Angus beef cattle [565 ± 10.25 kg body weight (BW)] were grouped by BW and age, and randomly allocated to 1 of 3 treatment groups: (1) control (CON, basal diet); (2) LLPL [CON supplemented with 0.5 g/kg LPL, dry matter (DM) basis]; and (3) HLPL (CON supplemented with 0.75 g/kg, DM basis). The Angus cattle were fed a total mixed ration that consisted of 25% roughage and 75% concentrate (dry matter [DM] basis). The results reveal that LPL inclusion linearly increased the average daily gain (P = 0.02) and the feed efficiency (ADG/feed intake, P = 0.02), while quadratically increasing the final weight (P = 0.02) of the beef cattle. Compared with CON, the total tract digestibilities of DM (P < 0.01), ether extract (P = 0.04) and crude protein (P < 0.01) were increased with LPL supplementation. At the phylum-level, the relative abundance of Firmicutes (P = 0.05) and ratio of Firmicutes: Bacteroidetes (P = 0.04) were linearly increased, while the relative abundances of Bacteroidetes (P = 0.04) and Proteobacteria (P < 0.01) were linearly decreased with increasing LPL inclusion. At the genus-level, the relative abundances of Clostridium (P < 0.01) and Roseburia (P < 0.01) were quadratically increased, and the relative abundances of Ruminococcus was linearly increased (P < 0.01) with LPL supplementation. Additionally, increasing the dose of LPL in diets linearly increased the molar proportion of butyrate (P < 0.01) and total SCFAs (P = 0.01) concentrations. A conclusion was drawn that, as a promising feed additive, LPL promoted growth performance and nutrient digestibility, which may be associated with the change of fecal microbiome and SCFAs.

Invited review: Effect of subacute ruminal acidosis on gut health of dairy cows

Subacute ruminal acidosis (SARA) is assumed to be a common disease in high-yielding dairy cows. Despite this, the epidemiological evidence is limited by the lack of survey data. The prevalence of SARA has mainly been determined by measuring the pH of ruminal fluid collected using rumenocentesis. This may not be sufficiently accurate, because the symptoms of SARA are not solely due to ruminal pH depression, and ruminal pH varies among sites in the rumen, throughout a 24-h period, and among days. The impact of SARA has mainly been studied by conducting SARA challenges in cows, sheep, and goats based on a combination of feed restriction and high-grain feeding. The methodologies of these challenges vary considerably among studies. Variations include differences in the duration and amount of grain feeding, type of grain, amount and duration of feed restriction, number of experimental cows, and sensitivity of cows to SARA challenges. Grain-based SARA challenges affect gut health. These effects include depressing the pH in, and increasing the toxin content of, digesta. They also include altering the taxonomic composition of microbiota, reducing the functionality of the epithelia throughout the gastrointestinal tract (GIT), and a moderate inflammatory response. The effects on the epithelia include a reduction in its barrier function. Effects on microbiota include reductions in their richness and diversity, which may reduce their functionality and reflect dysbiosis. Changes in the taxonomic composition of gut microbiota throughout the GIT are evident at the phylum level, but less evident and more variable at the genus level. Effects at the phylum level include an increase in the Firmicutes to Bacteroidetes ratio. More studies on the effects of a SARA challenge on the functionality of gut microbiota are needed. The inflammatory response resulting from grain-based SARA challenges is innate and moderate and mainly consists of an acute phase response. This response is likely a combination of systemic inflammation and inflammation of the epithelia of the GIT. The systemic inflammation is assumed to be caused by translocation of immunogenic compounds, including bacterial endotoxins and bioamines, through the epithelia into the interior circulation. This translocation is increased by the increase in concentrations of toxins in digesta and a reduction of the barrier function of epithelia. Severe SARA can cause rumenitis, but moderate SARA may activate an immune response in the epithelia of the GIT. Cows grazing highly fermentable pastures with high sugar contents can also have a low ruminal pH indicative of SARA. This is not accompanied by an inflammatory response but may affect milk production and gut microbiota. Grain-based SARA affects several aspects of gut health, but SARA resulting from grazing high-digestible pastures and insufficient coarse fiber less so. We need to determine which method for inducing SARA is the most representative of on-farm conditions.

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.

Shift of dietary carbohydrate source from milk to various solid feeds reshapes the rumen and fecal microbiome in calves

The transition from milk to solid diets drastically impacts the gut microbiome of calves. We explored the microbial communities of ruminal fluid and feces of Holstein calves when fed milk on d 7 of life, and when fed solid feeds based on either medium- or high-quality hay with or without concentrate inclusion (70% in fresh matter) on d 91. Ruminal fluid and feces had distinct microbial compositions already on d 7, showing that niche specialization in early-life gut is rather diet-independent. Changes between d 7 and d 91 were accompanied by a general increase in microbial diversity. Solid diets differed largely in their carbohydrate composition, being reflected in major changes on d 91, whereby concentrate inclusion was the main driver for differences among groups and strongly decreased microbial diversity in both matrices. Fecal enterotyping revealed two clusters: concentrate-supplemented animals had an enterotype prevalent in Prevotella, Succinivibrio and Anaerovibrio, whereas the enterotype of animals without concentrate was dominated by fibrolytic Ruminococcaceae. Hay quality also affected microbial composition and, compared to medium-quality, high-quality hay reduced alpha-diversity metrics. Concluding, our study revealed that concentrate inclusion, more than hay quality, dictates the establishment of niche-specific, microbial communities in the rumen and feces of calves.

The Response of Fecal Microbiota and Host Metabolome in Dairy Cows Following Rumen Fluid Transplantation

Rumen fluid transplantation (RFT) has been used to rebuild rumen bacterial homeostasis, reshape rumen function, and restore rumen fermentation, whereas the effect of RFT on fecal microbiota and host metabolism in cows remains poorly understood. In our study, a combination of 16S rRNA sequencing and serum non-targeted metabolomics was performed to investigate the response of fecal microbiota and serum metabolome in dairy cows following RFT. Twenty-four prepartum dairy cows were randomly assigned to 3 groups (n = 8) for infusion of either saline (Con), fresh rumen fluid (FR), or sterilized rumen fluid (SR) after calving. Fourteen days after calving, fecal microbiota and serum metabolome were analyzed. The sequencing data of fecal samples revealed no changes in alpha diversity and relative abundance of dominant genera such as Ruminococcaceae UCG-005, Rikenellaceae RC9 gut and Eubacterium coprostanoligenes. However, the other genus level taxa, such as Eubacterium oxidoreducens, Anaerorhabdus furcosa, Bacillus and Selenomonas, showed distinct changes following RFT. Serum metabolome analysis showed that FR or SR infusion affected amino acids metabolism, bile acids metabolism and fatty acids metabolism (including linoleic acid, oleic acid and palmitic acid). Furthermore, correlation analysis showed that taxa from genera Clostridiales were positively correlated with metabolites involved in tryptophan and bile acid metabolisms, such as OTU1039 from genera unclassified o_Clostridiales was positively correlated to indoleacetic acid and taurolithocholic acid. These results suggest that RFT altered the composition of the fecal microbiota and modulated microbial metabolic pathways, which is vital for the development and safety assessment of rumen microbial intervention strategies.

Siqueira MC, DiLorenzo N. Polyclonal antibody preparations from avian origin as a feed additive to beef cattle: Ruminal fermentation during the step-up transition diets

This study investigated the effects of feeding an avian-derived polyclonal antibody preparation (PAP; CAMAS, Inc.) against Streptococcus bovis, Fusobacterium necrophorum, and lipopolysaccharides (40%, 35%, and 25% of the preparation, respectively) on ruminal fermentation [pH, ammonia-N (NH₃-N), lactate, and volatile fatty acids (VFA)] of beef steers during a 21-d step-up diet adaptation. Eight ruminally cannulated Angus crossbred beef steers (658 ± 79 kg of body weight) were assigned in a crossover design to be transitioned from a diet containing ad libitum bermudagrass hay [Cynodon dactylon (L.) Pers.] plus 0.45 kg/d (as fed) of molasses with 0 (CON) or 3 g of PAP (PAP) to a high-grain diet. Transition consisted of three 7-d steps of increased inclusion of cracked corn (35%, 60%, and 82% of the diet DM for STEP1, STEP2, and STEP3, respectively). On each transition day and 7 d after STEP3 (STEP3-7d), ruminal fluid samples were obtained every 3 h for 24 h. Feeding 3 g of PAP daily increased (P < 0.01) average ruminal pH during STEP3 compared with CON steers (5.6 vs. 5.4 ± 0.05, respectively). During STEP1, NH₃-N concentration was greater (P < 0.01; 9.4 vs. 6.8 ± 0.74 mM, respectively), and time (min/d) and area (time × pH) of ruminal pH below or equal to 5.2 was lesser (P ≤ 0.03) for steers consuming PAP compared with steers assigned to CON treatment (33.4 vs. 73.3 ± 21.7 min/d and 187.4 vs. 406.3 ± 119.7 min × pH/d, respectively). Steers consuming PAP had greater acetate:propionate ratio at 0, 3, and 6 h relative to diet change compared with CON (2.42, 2.35, 2.29 vs. 1.66, 1.79, and 1.72 ± 0.17, respectively), whereas butyrate molar proportions increased (P = 0.02; 17.1 vs. 11 ± 1.58 mol/100 mol for CON and PAP, respectively) when PAP was not fed at STEP2. Total ruminal lactate concentrations were not affected by PAP feeding (P > 0.11). In conclusion, feeding 3 g/d of polyclonal antibody preparation against S. bovis, F. necrophorum, and lipopolysaccharides was effective in increasing ruminal pH, A:P ratio, and NH₃-N concentrations, possibly attenuating the risks of ruminal acidosis in steers during the step-up transition from forage to high-grain diets.

Ruminal bacteria lipopolysaccharides: an immunological and microbial outlook

Lipopolysaccharides (LPS) are outer membrane components of Gram-negative bacteria made of three regions: the O-antigen; the core oligosaccharide; and a glucosamine disaccharide linked to hydroxy fatty acids, which is named lipid A. The number phosphate groups, and hydroxy fatty acid chains is associated with the immunopotency and the immunomodulatory activity of LPS, where six-acyl chain lipid A with two phosphate groups is found in virulent strains and five- or four-acyl chain lipid A with one phosphate group are found in non-virulent bacteria strains. Ruminal bacteria are predominantly Gram-negative and their LPS have not been thoroughly investigated. In the rumen, LPS is comprised of mixed ruminal LPS. Drawing upon a body of theoretical and applied work, this paper aims to critically review the scientific literature regarding single-species and mixed ruminal bacteria LPS, highlighting the importance of ruminal LPS to the host. Lastly, future research directions are suggested in order to further our understanding of the roles of LPS in the rumen. Possible suggestions for further understanding ruminal LPS include (1) in silico evaluation of major bacteria contributing to ruminal LPS, (2) structural characterization of LPS from prominent ruminal bacteria species, such as ruminal selenomonads and Megasphaera elsdenii, and, (3) ruminal epithelial tissue immune response evaluation from single-species and mixed ruminal LPS. In conclusion, this review identifies numerous areas for future research, including setting the basis for future modeling and simulation of host microbiome interactions in ruminants.

Seasonal Differences in Fecal Microbial Community Structure and Metabolism of House-Feeding Chinese Merino Fine-Wool Sheep

The digestive tract microorganisms play a very important role in the host's nutrient intake, environmental suitability, and affect the host's physiological mechanism. Previous studies showed that in different seasons, mammalian gut microbes would be different. However, most of them are concentrated in wild animals. It remains unclear how seasonal change affects the gut microbes of Chinese merino fine-wool Sheep. Therefore, in this experiment, we continuously collected blood and feces samples of 50 Chinese merino fine-wool sheep in different seasons, measured the physiological indicators of blood, and passed 16S rRNA amplicon sequencing, determined the microbial community structure of fecal microorganisms and predicted flora function by PICRUSt. The results of blood physiological indicators showed that WBC, Neu and Bas in spring were significantly higher than those of other seasons. Fecal microbial sequencing revealed seasonal changes in gut microbial diversity and richness. Among them, Chinese merino fine-wool sheep had the highest gut microbes in summer. Firmicutes and Bacteroidetes were the dominant phyla, and they were unaffected by seasonal fluctuations. LEfSE analysis was used to analyze representative microorganisms in different seasons. The Lachnospiraceae and its genera (Lachnospiraceae_NK4A136_group, Lachnospiraceae_AC2044_group, g_unclassified_f_ Lachnospiraceae) were representative microorganisms in the three seasons of spring, summer and winter with harsh environmental conditions; while in autumn with better environmental conditions, the Ruminococcaceae and its genus (Ruminococcaceae_UCG-009 and Ruminococcaceae_UCG-005) were the representative microorganism. In autumn, the ABC transporter and the pyruvate metabolic pathway were significantly higher than other seasons. Correlation analysis results showed that Lachnospiraceae participated in the ABC transporters metabolic pathway, which caused changes in the blood physiological indicators. Overall, our results showed that, in response to seasonal changes, Chinese merino fine-wool sheep under house-feeding have adjusted their own gut microbial community structure, causing changes in the metabolism, and thus changing the physiological conditions of the blood. In the cold season, producers should focus on regulating the nutritional level of feed, enhancing the level of butyric acid in young animals to increase the ABC transporter, resist the external harsh environment, and improve the survival rate.

The Remodeling Effects of High-Concentrate Diets on Microbial Composition and Function in the Hindgut of Dairy Cows

At present, research on high-concentrate (HC) diets mostly focused on the rumen, and there is a paucity of information on the hindgut microbiota of dairy cows. In the present study, a 2 × 2 crossover design with four healthy Holstein cows was used, and the metagenomics approach was adopted to reveal the remodeling effects of HC diets on hindgut microbiota and their metabolic functions. Results showed that, compared with the low-concentrate (LC) diets, HC diets have markedly decreased (p < 0.05) the abundance of cellulolytic bacteria (such as Fibrobacter, Ruminococcus, and Ruminiclostridium) and methanogens (such as Methanobrevibacter, Methanosarcina, and Methanosphaera); and correspondingly, HC diets have significantly reduced (p < 0.05) the abundance of carbohydrate-active enzymes (CAZy) related to hemicellulases (GH10, GH11, and GH54) and cellulases (GH1, GH44, and GH45) and increased the abundance of one oligosaccharide-degrading enzyme (GH32). Furthermore, 62 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of hindgut microbiota were affected (p < 0.05) by different dietary treatments, and the major pathways altered by HC diets were “Methane metabolism” (enriched in the LC group), “Lipid metabolism” (enriched in the HC group), and several sub-pathways in “Amino acid metabolism” (such as Phenylalanine metabolism, and Phenylalanine, tyrosine, and tryptophan biosynthesis). Also, the microbial genes involved in the pathways “Methane metabolism” (except 1 gene), “Tryptophan metabolism”, and “Phenylalanine metabolism” were all decreased (p < 0.05) in the present study. These findings suggested that HC diets caused the remodeling of hindgut microbiota and its potential functions, and these results may benefit in gaining a deeper understanding of the impact of HC diets on the hindgut microbiota of dairy cows.

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics-in addition to the traditional considerations when conducting an animal science study-makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type.

Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows

Subacute ruminal acidosis (SARA) is a major metabolic disease in lactating dairy cows caused by the excessive intake of high-concentrate diets. Here, we investigated the synergistic responses of rumen bacteria and epithelium to high-grain (HG)-induced SARA. Eight ruminally cannulated lactating Holstein cows were randomly assigned to 2 groups for a 3-week experiment and fed either a conventional (CON) diet or an HG diet. The results showed that the HG-feeding cows had a thickened rumen epithelial papilla with edge injury and a decreased plasma β-hydroxybutyrate concentration. The 16S rRNA gene sequencing results demonstrated that HG feeding caused changes in rumen bacterial structure and composition, which further altered rumen fermentation and metabolism. Cooccurrence network analysis revealed that the distribution of the diet-sensitive bacteria responded to the treatment (CON or HG) and that all diet-sensitive amplicon sequence variants showed low to medium degrees of cooccurrence. Metabolomics analysis indicated that the endothelial permeability-increasing factor prostaglandin E1 and the polyamine synthesis by-product 5′-methylthioadenosine were enriched under HG feeding. Transcriptome analysis suggested that cholesterol biosynthesis genes were upregulated in the rumen epithelium of HG cows. The gene expression changes, coupled with more substrate being available (total volatile fatty acids), may have caused an enrichment of intracellular cholesterol and its metabolites. All of these variations could coordinately stimulate cell proliferation, increase membrane permeability, and trigger epithelial inflammation, which eventually disrupts rumen homeostasis and negatively affects cow health.

IMPORTANCE Dairy cows are economically important livestock animals that supply milk for humans. The cow’s rumen is a complex and symbiotic ecosystem composed of diverse microorganisms, which has evolved to digest high-fiber diets. In modern dairy production, SARA is a common health problem due to overfeeding of high-concentrate diets for an ever-increasing milk yield. Although extensive studies have been conducted on SARA, it remains unclear how HG feeding affects rumen cross talk homeostasis. Here, we identified structural and taxonomic fluctuation for the rumen bacterial community, an enrichment of certain detrimental metabolites in rumen fluid, and a general upregulation of cholesterol biosynthesis genes in the rumen epithelium of HG-feeding cows by multi-omics analysis. Based on these results, we propose a speculation to explain cellular events of coordinated rumen bacterial and epithelial adaptation to HG diets. Our work provides new insights into the exploitation of molecular regulation strategies to treat and prevent SARA.

Seasonal diets supersede host species in shaping the distal gut microbiota of Yaks and Tibetan sheep

Yaks and Tibetan sheep are important and renowned livestock of the Qinghai-Tibetan Plateau (QTP). Both host genetics and environmental factors can shape the composition of gut microbiota, however, there is still no consensus on which is the more dominant factor. To investigate the influence of hosts and seasons on the gut microbiome diversity component, we collected fecal samples from yaks and Tibetan sheep across different seasons (summer and winter), during which they consumed different diets. Using 16S rRNA sequencing, principal component analysis (PCoA) data showed that PCo1 explained 57.4% of the observed variance (P = 0.001) and clearly divided winter samples from summer ones, while PCo2 explained 7.1% of observed variance (P = 0.001) and mainly highlighted differences in host species. Cluster analysis data revealed that the gut microbiota composition displayed a convergence caused by season and not by genetics. Further, we profiled the gut microbial community and found that the more dominant genera in yak and Tibetan sheep microbiota were influenced by seasonal diets factors rather than genetics. This study therefore indicated that seasonal diet can trump host genetics even at higher taxonomic levels, thus providing a cautionary note for the breeding and management of these two species.

Tannic Acid-Steeped Corn Grain Modulates in vitro Ruminal Fermentation Pattern and Microbial Metabolic Pathways

This study investigated the effects of tannic acid (TA)-treated corn on changes in ruminal fermentation characteristics and the composition of the ruminal bacterial community in vitro. Ruminal fluid was obtained from three rumen-fistulated goats fed a 60:40 (forage/concentrate) diet. The batch cultures consisted of 25 ml of strained rumen fluid in 25 ml of an anaerobic buffer containing 0.56 g of ground corn, 0.24 g of soybean meal, 0.10 g of alfalfa, and 0.10 g of oat grass. Ground corn (2 mm) was steeped in an equal quantity (i.e., in a ratio of 1:1, w/v) of water alone (Con), 15 (TA15), 25 (TA25), and 35 g/l (TA35) TA solution for 12 h. After incubation for 24 h, TA-treated corn linearly increased (P <0.05) ruminal pH and the molar proportion of acetate, but linearly reduced (P <0.05) total volatile fatty acids and the molar proportion of butyrate compared with the Con treatment. Illumina MiSeq sequencing was used to investigate the profile changes of the ruminal microbes. A principal coordinates analysis plot based on weighted UniFrac values revealed that the structure of the ruminal bacterial communities in the control group was different from that of the TA-treated corn groups. The results of changes in the rumen bacterial communities showed that TA-treated corn linearly enriched (P <0.05) Rikenellaceae_RC9_gut_group, but linearly reduced (P <0.05) Ruminococcaceae_NK4A214_group, Ruminococcus_2, and unclassified_o__Clostridiales. Functional prediction of ruminal microbiota revealed that the TA-treated corn linearly decreased ruminal microbiota function of utilizing starch through pyruvate metabolism. In conclusion, TA-treated corn can modulate the rumen fermentation characteristics, microbial composition, and metabolic pathways, which may be potentially useful for preventing the occurrence of ruminal acidosis.

Ruminal Lipid A Analysis by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Lipopolysaccharides (LPS) are cell wall components from Gram-negative bacteria and are composed of three covalently linked regions: the O-antigen, the core oligosaccharide, and the lipid A moiety, which carries most of their endotoxic activity. The objective of this study was to isolate and compare the lipid A structures from ruminal LPS derived from total mixed ration (TMR)- and pasture-fed cows, by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Ruminal bacteria were collected from two rumen-cannulated Holstein cows; one fed a TMR (60:40, forage–concentrate) and the other pasture fed. The representativeness of each sample was validated by comparing the rumen microbiome from the cows in our study to the core rumen microbiome from the previous literature. Lipopolysaccharides from each respective sample were extracted with a phenol–water extraction procedure and purified via ultracentrifugation. To isolate lipid A from the core and O-antigen, pure ruminal LPS samples were hydrolyzed with acetic acid. Lipid A derived from the TMR-fed cow potentially exhibited a tetra-acylated structure, whereas lipid A derived from the pasture-fed cow potentially exhibited a penta-acylated lipid A structure. Both samples were quantified using limulus amebocyte lysate (LAL) assay and exhibited low endotoxic activity, consistent with the MALDI-TOF MS observations. Results indicate that the lipid A acylation pattern differs between diets, and that ruminal bacteria express solely under-acylated lipid A structures contrary to hexa-acylated lipid A, typically expressed by bacteria such as E. coli.

Investigating the Reciprocal Interrelationships among the Ruminal Microbiota, Metabolome, and Mastitis in Early Lactating Holstein Dairy Cows

Simple Summary

Dairy cow mastitis is an inflammatory disease often caused by bacterial infections. In the present study, we identified the ruminal microbial biomarkers and metabolites of mastitis in dairy cows. The investigation of the reciprocal interrelationships among the ruminal microbiota, metabolome, and mastitis revealed that short-chain fatty acid (SCFA)-producing microflora and the metabolites related to anti-inflammation and antibacterial activity were significantly higher in healthy cows than in those with mastitis. The identified potential species and metabolites might provide a novel perspective to assist in targeting the ruminal microbiota with preventive/therapeutic strategies against mastitis in the future.

Abstract

Mastitis in dairy cow significantly affects animal performance, ultimately reducing profitability. The reciprocal interrelationships among ruminal microbiota, metabolome, and mastitis combining early inflammatory factors (serum proinflammatory cytokines) in lactating dairy cows has not been explored, thus, this study evaluated these reciprocal interrelationships in early lactating Holstein dairy cows to identify potential microbial biomarkers and their relationship with ruminal metabolites. The ruminal fluid was sampled from 8 healthy and 8 mastitis cows for the microbiota and metabolite analyses. The critical ruminal microbial biomarkers and metabolites related to somatic cell counts (SCC) and serum proinflammatory cytokines were identified by the linear discriminant analysis effect size (LEfSe) algorithm and Spearman’s correlation analysis, respectively. The SCC level and proinflammatory cytokines positively correlated with Sharpea and negatively correlated with Ruminococcaceae UCG-014, Ruminococcus flavefaciens, and Treponema saccharophilum. Furthermore, the metabolites xanthurenic acid, and 1-(1H-benzo[d]imidazol-2-yl) ethan-1-ol positively correlated with microbial biomarkers of healthy cows, whereas, xanthine, pantothenic acid, and anacardic acid were negatively correlated with the microbial biomarkers of mastitis cows. In conclusion, Ruminococcus flavefaciens and Treponema saccharophilum are potential strains for improving the health of dairy cows. The current study provides a novel perspective to assist in targeting the ruminal microbiota with preventive/therapeutic strategies against inflammatory diseases in the future.

Characterizing Effects of Ingredients Differing in Ruminally Degradable Protein and Fiber Supplies on the Ovine Rumen Microbiome Using Next-Generation Sequencing

The ratio of concentrate to forage within diets is known to alter rumen microbial profiles, but comparatively less information is available on the effect of differing sources of individual nutrients on the microbiome. The objective of this study was to investigate rumen microbial responses to diets composed of protein and fiber sources expected to vary in nutrient degradability. The responses of interest included relative abundances of bacterial taxa as well as estimations of community richness and diversity. Ten ruminally cannulated wethers (Suffolk, Dorset, or Suffolk × Dorset) received four diet treatments consisting of either beet pulp or timothy hay and soybean meal (SBM) or heat-treated soybean meal (HSBM) in a partially replicated 4 × 4 Latin square experiment for 21 days. Timothy hay and beet pulp were expected to provide differing rumen degradabilities of neutral detergent fiber (NDF) while the soybean meals were expected to provide differing rumen degradabilities of crude protein (CP). Solid and liquid samples of rumen contents were collected for microbial DNA isolation and Next-Generation sequencing. Numerous rumen bacterial population shifts were observed due to change in fiber source, with increased abundances (P &lt; 0.05) of fibrolytic populations associated with timothy hay diets compared with beet pulp diets. Conversely, populations of the pectin-degrading genera, Treponema and Lachnospira, increased on the beet pulp treatment (P = 0.015 and P = 0.0049, respectively). Limited impact on bacterial taxa was observed between diets differing in protein source. The Paraprevotellaceae genus YRC22 was observed to increase in abundance on HSBM diets (P = 0.023) and the phylum Spirochaetes tended to be more abundant on SBM than HSBM diets (P = 0.071). Beet pulp decreased rumen bacterial diversity (P = 0.0027) and tended to decrease bacterial species richness (P = 0.051) compared to timothy hay. Our results serve to further underscore the sensitivity of rumen microbes to changes in their preferred substrates, particularly of those associated with fiber degradation.