Investigating the impact of feed-induced, subacute ruminal acidosis on rumen epimural transcriptome and metatranscriptome in young calves at 8- and 17-week of age

Introduction

With the goal to maximize intake of high-fermentable diet needed to meet energy needs during weaning period, calves are at risk for ruminal acidosis. Using the calves from previously established model of feed-induced, ruminal acidosis in young calves, we aimed to investigate the changes in rumen epimural transcriptome and its microbial metatranscriptome at weaning (8-week) and post-weaning (17-week) in canulated (first occurred at 3 weeks of age) Holstein bull calves with feed-induced subacute ruminal acidosis.

Methods

Eight bull calves were randomly assigned to acidosis-inducing diet (Treated, n = 4; pelleted, 42.7% starch, 15.1% neutral detergent fiber [NDF], and 57.8% nonfiber carbohydrates), while texturized starter was fed as a control (Control, n = 4; 35.3% starch, 25.3% NDF, and 48.1% nonfiber carbohydrates) starting at 1 week through 17 weeks. Calves fed acidosis-inducing diet showed significantly less (p < 0.01) body weight over the course of the experiment, in addition to lower ruminal pH (p < 0.01) compared to the control group. Rumen epithelial (RE) tissues were collected at both 8 weeks (via biopsy) and 17 weeks (via euthanasia) and followed for whole transcriptome RNA sequencing analysis. Differentially expressed genes (DEGs) analysis was done using cufflinks2 (fold-change ≥2 and p < 0.05) between treated and control groups at 8-week of age, and between 8- and 17-week for the treated group.

Results

At 8-week of age, DEGs between treatment groups showed an enrichment of genes related to the response to lipopolysaccharide (LPS) (p < 0.005). The impact of prolonged, feed-induced acidosis was reflected by the decreased expression (p < 0.005) in genes involved in cell proliferation related pathways in the RE at 17-week of age in the treated group. Unique sets of discriminant microbial taxa were identified between 8-and 17-week calves in the treated group and the treatment groups at 8-week, indicating that active microbial community changes in the RE are an integral part of the ruminal acidosis development and progression.

Liver microbial community and associated host transcriptome in calves with feed induced acidosis

Introduction

In the dairy industry, calves are typically fed diets rich in highly fermentable carbohydrates and low in fibrous feeds to maximize ruminal papillae and tissue development. Calves on such diets are vulnerable at developing ruminal acidosis. Prevalent in cattle, liver abscess (LA) is considered a sequela to ruminal acidosis. LAs can cause significant liver function condemnation and decreased growth and production. Currently, we know little about the liver microbiome in calves with feed-induced acidosis.

Methods

Using our established model of ruminal acidosis, where young calves were fed an acidosis-inducing (AC) or -blunting (control) diet starting at birth until 17-week of age, we investigated microbial community changes in the liver resultant from ruminal acidosis. Eight calves were randomly assigned to each diet, with four animals per treatment. Rumen epithelium and liver tissues were collected at 17 weeks of age right after euthanasia. Total RNAs were extracted and followed by whole transcriptome sequencing. Microbial RNA reads were enriched bioinformatically and used for microbial taxonomy classification using Kraken2.

Results

AC Calves showed significantly less weight gain over the course of the experiment, in addition to significantly lower ruminal pH, and rumen degradation comparison to the control group (p < 0.05). In the liver, a total of 29 genera showed a significant (p < 0.05) abundance change (> 2-fold) between the treatments at 17-week of age. Among these, Fibrobacter, Treponema, Lactobacillus, and Olsenella have been reported in abscessed liver in cattle. Concurrent abundance changes in 9 of the genera were observed in both the liver and rumen tissues collected at 17-week of age, indicating potential crosstalk between the liver and rumen epithelial microbial communities. Significant association was identified between host liver gene and its embedded microbial taxa. Aside from identifying previously reported microbial taxa in cattle abscessed liver, new repertoire of actively transcribed microbial taxa was identified in this study.

Discussion

By employing metatranscriptome sequencing, our study painted a picture of liver microbiome in young calves with or without feed induced acidosis. Our study suggested that liver microbiome may have a critical impact on host liver physiology. Novel findings of this study emphasize the need for further in-depth analysis to uncover the functional roles of liver resident microbiome in liver metabolic acidosis resultant from feed-related ruminal acidosis.

Effects of milk replacer allowances and levels of starch in pelleted starter on nutrient digestibility, whole gastrointestinal tract fermentation, and pH around weaning

The objectives of this study were to examine the effects of pelleted starter diets differing in starch and neutral detergent fiber (NDF) content when fed differing levels of milk replacer (MR) on nutrient digestibility, whole gastrointestinal tract fermentation, pH, and inflammatory markers in dairy calves around weaning. Calves were randomly assigned to 1 of 4 dietary treatments (n = 12 per treatment) in a 2 × 2 factorial design based on daily MR allowance and amount of starch in pelleted starter (SPS): 0.691 kg of MR per day [dry matter (DM) basis] with starter containing low or high starch (12.0% and 35.6% starch on DM basis, respectively), and 1.382 kg of MR per day (DM) with starter containing low or high starch. All calves were housed in individual pens with straw bedding until wk 5 when bedding was covered. Calves were fed MR twice daily (0700 and 1700 h) containing 24.5% crude protein (DM) and 19.8% fat (DM), and had access to pelleted starter (increased by 50 g/d if there were no refusals before weaning and then 200 g/d during and after weaning) and water starting on d 1. Calves arrived between 1 and 3 d of age and were enrolled into an 8-wk study, with calves undergoing step-down weaning during wk 7. Starting on d 35, an indwelling pH logger was inserted orally to monitor rumen pH until calves were dissected at the end of the study in wk 8. Higher SPS calves showed an increase in rumen pH magnitude (1.46 ± 0.07) compared with low SPS calves (1.16 ± 0.07), a decrease in rumen pH in wk 8 (high SPS: 5.37 ± 0.12; low SPS: 5.57 ± 0.12), and a decrease in haptoglobin in wk 8 (high SPS: 0.24 ± 0.06 g/L; low SPS: 0.49 ± 0.06 g/L). The majority of differences came from increased starter intake in general, which suggests that with completely pelleted starters the differences in starch and NDF do not elicit drastic changes in fermentation, subsequent end products, and any resulting inflammation in calves around weaning.

Starch-protein interaction in the rumen of weaned dairy calves

The objectives of this study were to investigate the effect of starch and protein interaction on rumen environment, in situ digestion, and total-tract digestibility of nutrients in weaned dairy calves between 8 and 16 wk of age. Sixteen rumen-cannulated calves were randomly divided into 4 dietary treatment groups with 4 calves fed in each treatment. The treatment diets had 2 levels of starch [18%, low starch (LS), or 38%, high starch (HS)] and 2 levels of protein [16%, low protein (LP), or 22%, high protein (HP)] on a dry matter (DM) basis in calf grower: (1) LPLS, (2) LPHS, (3) HPLS, and (4) HPHS. Calves were fed for ad libitum intake (95% assigned grower and 5% grass hay), and refusals were collected weekly. Total-tract digestibility collection and in situ digestibility procedures were performed for each calf at 11 and 15 wk. Samples for in situ digestibility, grass hay (GH), soybean hulls (SBH), wheat middlings (WM), ground corn (GrC), and soybean meal (SBM) were incubated for 9 and 24 h. There was no starch and protein interaction on total-tract digestibility of calves. Total-tract DM, neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility, and feed efficiency were affected by both protein and starch inclusion level in calf diet. Total-tract starch digestibility was lower for LS diets. Dry matter digestibility and feed efficiency were greater in calves fed HP and HS diets compared with calves fed LP and LS diets, respectively. Fiber digestibility (NDF and ADF) was less in calves fed HS diets compared with calves fed LS diets but was greater in calves fed HP diets compared with calves fed LP diets. Level of protein did not affect in situ DM and NDF disappearance of GH, but HP increased in situ DM and NDF disappearance of SBH. High-starch diets decreased DM and NDF disappearance of both GH and SBH. At 20 h after feeding, ruminal pH was 0.51 unit higher in calves fed HPHS compared with calves fed LPHS. Total ruminal VFA and proportion of propionate was greater with HS versus LS, whereas proportion of acetate was greater with LS versus HS. The DM disappearance of SBM and WM and NDF disappearance of WM was greater for calves fed HPHS compared with calves fed LPHS at 11 wk of age. In our study, when HP was fed with HS, rumen pH, in situ digestion of WM and SBM, and total-tract digestion of DM, NDF, and ADF increased. This provides evidence for starch-protein interaction in the rumen of recently weaned dairy calves. Improvements in total-tract and in situ digestibility suggest that both protein and starch levels are important for 8- to 16-wk-old calves.

Nutrient digestibility and endogenous protein losses in the foregut and small intestine of weaned dairy calves fed calf starters with conventional or enzyme-treated soybean meal

The aims of this experiment were (1) to compare the effects of a soybean meal with an enzymatic treatment (ESBM) to reduce the concentration of antinutritional factors versus a standard soybean meal (SBM) on foregut and small intestine digestion in weaned dairy calves and (2) to estimate the endogenous losses of crude protein (CP) in the small intestine. Our hypothesis was that a diet containing ESBM instead of SBM would improve ruminal and small intestine digestion and absorption of nutrients. A T-cannula was placed in the duodenum, and a second T-cannula was installed in the distal ileum of 12 Holstein calves at approximately 3 wk of age. Calves were weaned on d 42, and on d 50 they were assigned randomly to a quadruplicated 3 × 3 Latin square with 10-d periods. Digesta samples were collected on d 7 and 8 from the ileum and d 9 and 10 from the duodenum. The diets were fed for ad libitum intake and consisted of a calf starter (CS) of 20% CP with SBM as the main source of protein (CTRL), and an isonitrogenous CS with an ESBM instead of SBM (ENZT). A third diet with a low content of CP (10%) and no soy protein was fed to estimate endogenous N losses and digestibilities of test ingredients. Flows and digestibilities of nutrients were compared between CTRL and ENZT and their test ingredients (SBM vs. ESBM, respectively). Duodenal net flows of CP and total AA as well as ruminal microbial protein synthesis per kilogram of digested CP were greater, and flow of nonprotein N and CP true (corrected by endogenous and microbial flows) foregut digestibility were lower with ENZT than CTRL. The apparent small intestine digestibilities of CP and total AA were greater for ESBM than SBM, but there were no differences between the CTRL and ENZT diets. We observed no differences in digestibilities at the duodenum or ileum of starch or NDF, but true small intestine digestibilities of CP and all AA were greater with ENZT than CTRL. Total endogenous protein losses in the small intestine estimated from calves fed the low-CP with no soy protein diet were 37 ± 1.5 g of CP and 29 ± 1.4 g of AA/kg of DMI. These values may be considered the basal endogenous losses as they are similar to values obtained with the regression method, which estimates N losses when dietary N is null. Our results indicated that the inclusion of an ESBM improved the efficiency of ruminal microbial protein synthesis per digested kilogram of organic matter and CP, and increased CP and AA absorption in the small intestine despite a greater proportion of undigested dietary protein entering the duodenum.

Replacing soybean hulls with grass hay on growth, intake, total tract digestibility, and rumen microbial nitrogen production of weaned Holstein dairy calves from 8 to 16 weeks of age

The objective of this experiment was to determine the effects of replacing soybean hull (SBH) pellets with grass hay (GH) on growth, intake, total-tract digestibility, and rumen microbial nitrogen production of weaned dairy calves from 8 to 16 wk of age. Holstein calves (n = 16) were randomly assigned to 1 of 4 rations containing, on a dry matter (DM) basis, 76% grower with the remaining 24% being made up of different amounts of SBH pellets and GH [0% GH, 24% SBH (0GH); 8% GH, 16% SBH (8GH); 16% GH, 8% SBH (16GH); and 24% GH, 0% SBH (24GH)]. Calves were weaned at 6 wk, housed individually, and studied from 8 to 16 wk of age. From 8 to 9 wk of age calves were offered a ration consisting of 50% of texturized starter (20% CP and 35% starch), which was offered from 3 d of age, and 50% of their assigned ration. From 9 wk until the end of the study, calves were offered 100% of their assigned ration. Intake and body weight were measured weekly, and frame measurements were taken at the beginning and end of the study. Animal behavior observations were recorded every 5 min over a 24-h period at 10 and 14 wk of age. Total fecal and urine collection was conducted for 4 d consecutively at 11 and 15 wk of age. Feed and feces were evaluated for DM, N, neutral detergent fiber, acid detergent fiber, and starch to determine total-tract digestibility. Feces were evaluated for geometric mean particle length (Xgm) and particle size distribution. Urine was evaluated for N, creatinine, urea, and total purine derivatives to estimate microbial N yield. Calves offered 0GH and 8GH had a 20% increase in intake, average daily gain (1.23, 1.27, 0.89, and 0.71 kg/d for 0GH, 8GH, 16GH, and 24GH, respectively), and feed efficiency compared with 16GH and 24GH. Calves offered 8GH had the greatest levels of neutral detergent fiber and acid detergent fiber digestibility, as well as the greatest estimated microbial N yields. Inclusion of forage increased rumination time (2.75, 6.89, 7.18, and 8.16 h/d for 0GH, 8GH, 16GH, and 24GH, respectively) and decreased fecal Xgm by ~35% compared with calves offered 0GH. In the current study, increasing the replacement of SBH with GH beyond 8% was detrimental to weaned calf performance. These results indicate that when diets containing 8% GH and 16% SBH were fed to recently weaned calves, rumen functionality and feed efficiency were optimized compared with the other GH-SBH combinations.

Effect of increasing the amount of hay fed on Holstein calf performance and digestibility from 2 to 4 months of age

A good transition from a mainly liquid diet to a solid diet of concentrates and forages is important considering the small size and development of the calf's rumen. However, the optimal amount of hay or other high-fiber ingredients in the diet of recently weaned calves is not well defined. The objective of this trial was to determine the effects of feeding 0, 5, or 10% chopped grass hay (6.5% crude protein, 64.6% neutral detergent fiber) with a textured, high-starch starter (20.5% crude protein, 38.4% starch, 14.1% neutral detergent fiber; protein pellet, whole corn, and oats) on performance and digestion in Holstein steer calves between 2 and 4 mo of age. Forty-eight calves (initial body weight = 90.7 ± 2.15 kg) were housed in group pens (4 per pen) and fed diets and water for ad libitum intake. Feed offered and refused was measured daily. Calf body weight, hip width, and body condition score (1-5 scale) were measured initially and at 28 and 56 d. Fecal samples were collected from the pen floor with care not to sample bedding material and composited by pen during d 5-9, 26-30, and 47-51 to estimate apparent total-tract digestibility using acid-insoluble ash. Data were analyzed as a completely randomized design with repeated measures and pen as the experimental unit. As grass hay increased, dry matter intake (kg/d) decreased linearly but tended to change quadratically. Dry matter intake as a % of body weight changed quadratically with increasing hay, increasing from 0 to 5%, and decreasing from 5 to 10% hay. Average daily gain (1.15, 1.12, and 0.95 kg/d), feed efficiency (0.336, 0.319, and 0.309 kg of average daily gain/kg of dry matter intake), and hip width change (4.6, 4.7, and 4.1) decreased linearly with 0, 5, and 10% hay, respectively. Overall estimates of dry matter, organic matter, neutral detergent fiber, acid detergent fiber, and crude protein digestibility changed quadratically with hay, increasing from 0 to 5%, and decreasing from 5 to 10% hay, whereas digestibility of starch, sugar, and fat decreased linearly with increasing hay. Digestibility of dry matter, organic matter, neutral detergent fiber, and acid detergent fiber increased from 2 to 3 mo of age, and decreased from 3 to 4 mo of age. Digestibility of starch decreased linearly and digestibility of fat and crude protein increased linearly with age. Digestive capacity did not appear mature by 4 mo of age. Feeding 5% chopped hay supported optimal digestion and growth in calves 2 to 4 mo of age, which agrees with previously published research.

Effects of rumen-protected methionine or methionine analogs in starter on plasma metabolites, growth, and efficiency of Holstein calves from 14 to 91 d of age

During weaning, methionine (Met) supply decreases as liquid feed intake is reduced and ruminal function is developing. During this transition, the calf starter should both promote ruminal development and provide adequate nutrients post-ruminally. In mature ruminants, rumen-protected Met (RPM) and the Met analogs, 2-hydroxy-4-(methylthio)-butanoic acid (HMTBa) and HMTBa isopropyl ester (HMBi), are used to increase Met supply, stimulate ruminal fermentation, or exert both effects, respectively. To evaluate the effects of these forms of Met on calf performance during development of ruminal function, 74 Holstein calves were raised until 91 d of age, in 2 enrollment periods. Calves were individually housed from birth and, at 14 d of age, balanced for sex and randomly assigned to receive a starter with no added Met (CTRL, n = 20) or one supplemented with RPM (Smartamine M, Adisseo USA Inc., Alpharetta, GA; n = 16), HMTBa (RumenSmart, Adisseo; n = 19), or HMBi (MetaSmart, Adisseo; n = 19). Milk replacer [28% crude protein (CP), 15% fat] was offered up to 1.6 kg of dry matter (DM)/d and fed 3 times daily. Weaning was facilitated from d 49 to 63. The 4 starters (25% CP, 2.5 Mcal of metabolizable energy/kg of DM) were offered ad libitum, and supplement inclusion was set to provide an additional 0.16% DM of Met equivalents, and equal amounts of HMTBa within the analogs. Body weight and stature were measured, and blood was collected and analyzed for plasma urea nitrogen, β-hydroxybutyrate, and free AA on a weekly basis. Supplementation of RPM and HMBi increased free plasma Met, but no differences in growth or feed efficiency compared with calves fed the CTRL starter could be attributed to the additional Met supply alone. The addition of HMBi in the starter increased feed intake and body weight during the last weeks of the experiment. On the contrary, HMTBa failed to increase plasma Met and depressed intake and growth after weaning, likely because the level included in the diet was too high and intake was greater than previous studies, exacerbating the level of HMTBa ingested. No differences were observed in stature, feed efficiency, or non-AA plasma measurements among groups. These results demonstrate that RPM and HMBi are effective sources of metabolizable Met; however, Met was apparently not limiting calves fed the basal diet in this study. The increased feed intake observed with the inclusion of HMBi in the starter during the weaning and early postweaning period might be mediated by its metabolism in the rumen, and further research is needed to determine the mechanisms involved.

Effects of conditioner retention time during pelleting of starter feed on nutrient digestibility, ruminal fermentation, blood metabolites, and performance of Holstein female dairy calves

This study evaluated the effects of conditioner retention time during the pelleting process of starter feed on intake, nutrient digestibility, ruminal fermentation, blood metabolites, and growth performance of dairy calves. A total of 30 Holstein female dairy calves [40 ± 1.93 kg of body weight (BW)] were randomly assigned to 1 of 3 treatments: (1) pelleted starter conditioned for 0 min (CON), (2) pelleted starter conditioned for 2 min, and (3) pelleted starter conditioned for 4 min. Three pelleted starter feeds had similar nutritional composition, and the starters were blended with 3% chopped wheat straw and fed to individually housed calves from d 3 to 70 of age. All calves were fed 4 L/d of pasteurized whole milk twice daily at 0800 and 1600 h from d 3 to 50 of calf age, followed by 2 L/d of morning feeding from 51 to 56 d of age. All calves were weaned on d 56 of age and remained in the study until d 70 of age. With the increase of conditioner retention time during pellet processing for 0, 2, and 4 min, the gelatinized starch content of pelleted starter feed linearly increased from 14, 30, and 45%, respectively. Additionally, the pellet durability and hardness also linearly increased with increasing conditioner retention time during pelleting. Feeding pelleted feed prepared using different conditioner retention time did not affect feed dry matter intake, metabolizable energy intake, weaning BW, final BW, or feed efficiency during the study. We observed no differences in the total-tract apparent digestibility of organic matter, neutral detergent fiber, and crude protein around weaning (d 49 to 56 of age) and after weaning (d 63 to 70 of calf cage); however, the digestibility of dry matter and starch after weaning was increased with increasing conditioner retention time during pelleting of starter feed. No difference was found in overall average daily gain (ADG) or growth rates of hip height, withers height, and heart girth. Ruminal volatile fatty acid profile was not affected by pelleting under different conditioner retention times. The ruminal ammonia concentration tended to be lower for calves fed the 4-min diet compared with those fed the CON diet during the postweaning period. The postweaning (d 57-70 of age) ADG was greater for calves fed the 4-min diet compared with those fed the CON diet. In conclusion, the conditioning time during the pelleting process of starter feed increased the gelatinization of starch, durability, and hardness of the pellets but did not influence feed intake, feed efficiency, and skeletal growth during the first 70 d of age. Increasing conditioning time during the pelleting process improved postweaning ADG; however, the final BW of calves was similar among treatments.

Effect of converting weaned dairy calves from a component-fed diet to a total mixed ration on growth and nutrient digestibility

The objective was to determine the effects of converting calves from a component-fed ration to a total mixed ration (TMR) at 8, 10, or 12 wk of age on intake, growth, and nutrient digestibility. Holstein calves (n = 40) were randomly assigned to 1 of 4 groups (no TMR, TMR conversion at 8, 10 or 12 wk; T0, T8, T10, and T12, respectively). Calves were weaned at 6 wk of age, housed individually, and studied from 7 to 14 wk of age. Rations, consisting of a 20% crude protein texturized starter and grass hay, were offered ad libitum as separate components or as a TMR with 85% starter and 15% grass hay on a dry matter (DM) basis. Intakes and body weights (BW) were measured weekly. Component intake for TMR was calculated from the proportion of grass hay and starter contained in the TMR. Fecal grab samples were collected every 9 h over 3 d for a total of 8 samples that formed a composite at 9, 11, and 13 wk of age from the same 4 calves per group. Rumen fluid samples were collected via esophageal tube at -1, 0, 3, and 7 d relative to conversion from component to TMR. Feed and feces were evaluated for DM, neutral detergent fiber, acid detergent fiber, and acid detergent lignin (internal flow marker) to estimate digestibility. Average daily gain and final BW tended to be least for T8. Empty BW gain was significantly less for T8 than for T0 but not different from T10 or T12 (T0 = 1.07, T8 = 0.93, T10 = 1.02, T12 = 1.04 kg/d). Hip growth tended to be least for T8 and resulted in lower final hip width (T0 = 25.9, T8 = 25.2, T10 = 25.6, T12 = 25.8 cm). Intake tended to be reduced for calves converted to TMR earlier. Throughout the study, calves fed TMR ate more hay and less starter than component-fed calves. Metabolizable energy intake was less for T8 versus T0 but not different from T10 or T12 (T0 = 8.46, T8 = 7.55, T10 = 8.01, T12 = 8.23 Mcal/d). We observed no differences in feed efficiency for the duration of the study. Differences in DM digestibility were not observed, but fiber digestibility was greater for calves fed TMR at 9, 11, and 13 wk of age. Conversion to TMR increased rumen pH. These results indicate that TMR conversion increased hay consumption and subsequently decreased starter and total DM intake. This led to reduced weight and structural growth; however, calves that were converted to TMR as early as 8 wk still achieved adequate growth. The increase in rumen pH and subsequent increase in fiber digestibility allowed for calves to be converted to a 15% grass hay TMR as early as 8 wk and still achieve desirable growth goals.

Physiological effects of starter-induced ruminal acidosis in calves before, during, and after weaning

The objectives were to nutritionally induce or blunt ruminal acidosis in young calves and to compare indicators of rumen and systemic health. Ten bull calves (n = 5/diet) were ruminally cannulated at 3 wk of age and received milk replacer and 1 of 2 calf starter diets that were designed to cause (AC; pelleted, 42.7% starch, 15.1% neutral detergent fiber, 57.8% nonfiber carbohydrates) or blunt (BL; texturized, 35.3% starch, 25.3% neutral detergent fiber, 48.1% nonfiber carbohydrates) ruminal acidosis. Mean birth weight was 38.7 ± 1.3 kg. Body weight and calf starter intake were measured weekly. Rumen contents were sampled at -8, -4, 0, 2, 4, 8, 12, and 24 h relative to starter feeding during wk 6, 8, 10, 12, 14, and 16 of age. Blood was collected from the jugular vein during the same weeks for complete blood cell count, blood pH, and partial pressures of oxygen and carbon dioxide. Rate of starter consumption was assessed during wk 16. Marker systems were used to estimate liquid passage and volatile fatty acid absorption rates. Calves were slaughtered at 17 wk, and rumen tissue was collected and assessed for papillae length, width, and degree of tissue degradation. Mean ruminal pH ± standard error was 5.37 ± 0.24 and 5.63 ± 0.24 for AC and BL calves, respectively. Lowest pH values were observed the week after weaning. Total ruminal volatile fatty acid concentrations were 131.5 and 124.8 ± 2.4 mM in AC and BL calves, respectively, and increased with age and time after feeding. Dry matter intake was lower in AC calves at wk 4 and remained lower through wk 16. Rate of starter consumption was also lower in AC calves at wk 16. Body weight also was also lower for AC calves from wk 5 through 16. Blood hemoglobin and hematocrit were lower in AC calves, but other blood characteristics were not different. Rumen volume increased with age and tended to be greater in BL calves. Passage rate and papillae length and width were not different between diets, but AC calves experienced a greater degree of tissue degradation. Ruminal acidosis symptoms in calves appear similar to those in adult cattle, and the etiology of the disease seems to follow similar mechanisms. It is clear from this study that symptoms can be moderated by diet, but further research is needed to determine whether symptoms can be nutritionally prevented or whether calves that experience ruminal acidosis are more susceptible to the disease as adults.

Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis

The common management practices of dairy calves leads to increased starch concentration in feed, which subsequently may cause rumen acidosis while on milk and during weaning. Until recently, few attempts were undertaken to understand the health risks of prolonged ruminal acidosis in post weaning calves. Resultantly, the molecular changes in the digestive tracts in post-weaning calves with ruminal acidosis remain largely unexplored. In this study, we investigated the liver transcriptome changes along with its correlation with the rumen microbial rRNA expression changes in young calves using our model of feed induced ruminal acidosis. In this model, new born calves were fed a highly processed, starch-rich diet starting from one week of age through 16 weeks. A total of eight calves were involved in this study. Four of them were fed the acidosis-inducing diet (Treated) and the rest of the four were fed a standard starter diet (Control). Liver and rumen epithelial tissues were collected at necropsy at 17 weeks of age. Transcriptome analyses were carried out in the liver tissues and rRNA meta-transcriptome analysis were done using the rumen epithelial tissues. The correlation analysis was performed by comparing the liver mRNA expression with the rumen epithelial rRNA abundance at genus level. Calves with induced ruminal acidosis had significantly lower ruminal pH in comparison to the control group, in addition to significantly less weight-gain over the course of the experiment. In liver tissues, a total of 428 differentially expressed genes (DEGs) (fold-change, FC ≥ 1.5; adjusted P ≤ 0.1) were identified in treated group in comparison to control. Biological pathways enriched by these DEGs included cellular component organization, indicating the impact of ruminal acidosis on liver development in young calves. Specifically, the up-regulated genes were enriched in acute phase response (P < 0.01), pyruvate metabolic process (P < 0.01) and proton-acceptors (P ≪ 0.001), indicating the liver's response to feed induced acidosis at the transcriptome level. Twelve transferase activity related genes had significant correlation with rumen microbial rRNA expression changes. Among these genes, two up-regulated genes were reported with involvement in lipid metabolism in the liver, implying the direct effect of feed-induced acidosis on both the rumen microbial community and liver metabolism. Our study provides insight into the physiological remodeling in the liver resultant from the prolonged acidosis in post weaning calves, which may facilitate future RNA-seq based diagnosis and precision management of rumen acidosis in dairy calves.

Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis

Many common management practices used to raise dairy calves while on milk and during weaning can cause rumen acidosis. Ruminal pH has long been used to identify ruminal acidosis. However, few attempts were undertaken to understand the role of prolonged ruminal acidosis on rumen microbial community or host health in young calves long after weaning. Thus, the molecular changes associated with prolonged rumen acidosis in post weaning young calves are largely unknown. In this study, we induced ruminal acidosis by feeding a highly processed, starch-rich diet to calves starting from one week of age through 16 weeks. Rumen epithelial tissues were collected at necropsy at 17 weeks of age. Transcriptome analyses on the rumen epithelium and meta-transcriptome analysis of rumen epimural microbial communities were carried out. Calves with induced ruminal acidosis showed significantly less weight gain over the course of the experiment, in addition to substantially lower ruminal pH in comparison to the control group. For rumen epithelial transcriptome, a total of 672 genes (fold-change, FC ≥ 1.5; adjusted-p ≤ 0.05) showed significant differential expression in comparison to control. Biological pathways impacted by these differentially expressed genes included cell signaling and morphogenesis, indicating the impact of ruminal acidosis on rumen epithelium development. rRNA read-based microbial classification indicated significant increase in abundance of several genera in calves with induced acidosis. Our study provides insight into host rumen transcriptome changes associated with prolonged acidosis in post weaning calves. Shifts in microbial species abundance are promising for microbial species-based biomarker development and artificial manipulation. Such knowledge provides a foundation for future more precise diagnosis and preventative management of rumen acidosis in dairy calves.