Rumen Microbial Profiles Research Articles

Programming rumen microbiome development in calves with the anti-methanogenic compound 3-NOP

The aim of this study was to establish a distinctive rumen microbial and fermentation profile using the anti-methanogenic compound 3-NOP to assess dam effect, and nutritional intervention of the juvenile offspring on microbial structure and function of rumen up to 12 months of age, once the treatment was withdrawn. Forty-eight pregnant heifers (H) and their future offspring (C) were allocated to either Control (-) or 3-NOP (+) treatment resulting in four experimental groups: H+/C+, H+/C-, H-/C + and H-/C-. Animals were treated from 6 weeks prior to calving until weaning, with the offspring monitored until 12 months of age. Rumen fluid samples and methane measurements using the Greenfeed system were collected during the trial. Results supported the mode of action of the compound, with a shift in fermentation from acetate to propionate, increases in branched chain fatty acids and formic acid in the 3-NOP treated animals. Similar shifts in microbial populations occurred in 3-NOP treated animals with lower abundances of rumen methanogen populations, increases of bacterial groups Succiniclasticum spp, Candidatus Saccharimonas. Fibrobacter and the families Prevotellaceae and Succinivibrioacea. and the protozoa Entodinium. Early life intervention had an enduring impact on the rumen microbial structure of young animals up to 28 weeks post weaning, however the effect was diminished once 3-NOP was withdrawn. Interestingly, a group of young animals emitted significantly less methane (15%) than the animals that did not receive the treatment during their juvenile stage. Our results suggest a higher resemblance of the young calf microbiome to a low methane adult and that early life colonisation of the rumen persists through to later life with the pre-weaning microbiome comprising ~ 65% of the yearling animal. Further research needs to be performed to determine the timing and dose of 3-NOP for new-born calves that can sustain a reduction in methane emissions after the treatment is withdrawn, under extensive grazing or controlled conditions.

Effects of Formaldehyde-Treated Feed on Rumen Metabolism and Blood Biochemistry in Lambs: A Review

This review evaluates the impact of formaldehyde treatment on feed for lambs, focusing on its effects on rumen metabolism and blood biochemical indicators. Formaldehyde is commonly used as a feed additive to improve nutritional efficiency and preserve feed quality. This review synthesizes data from various studies to assess how formaldehyde-treated feed influences rumen fermentation parameters, including volatile fatty acid (VFA) production, rumen pH, and microbial activity. Additionally, the review examines the effects of formaldehyde treatment on key blood biochemical markers such as glucose, urea nitrogen, and liver enzymes. Studies indicate that formaldehyde treatment can enhance the stability and digestibility of feed, potentially improving nutrient utilization and overall animal performance. The preservation of protein and reduction in feed spoilage are highlighted as significant benefits, contributing to more consistent rumen function and metabolic efficiency. However, the impact on rumen microbial populations and VFA profiles shows mixed results, with some studies reporting improved microbial efficiency and others noting minimal changes. The review also discusses potential adverse effects, including alterations in blood biochemical parameters. While formaldehyde treatment generally maintains or improves key indicators like blood glucose and protein levels, excessive use may lead to concerns such as elevated urea nitrogen levels and potential liver enzyme disruptions, the review concludes that formaldehyde-treated feed can be a valuable tool in optimizing feed efficiency and lamb health, provided it is used judiciously. Future research is recommended to further elucidate the long-term effects on rumen microbiota and metabolic processes, ensuring balanced benefits without compromising animal welfare.

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.

Study of Fauna and Ecology of Species Belonging to Entodynimorpha in the Regions of Nakhchivan Autonomous Republic

Rumen Protozoa are strictly anaerobic and highly specialized ciliates and can live only in the rumen and similar habitats. These Ciliata play an important role in feed utilization and indicate the environmental impact (methane emissions and nitrogen excretion) of ruminant production. Digestion of feed in ruminants depends on the life activity of microorganisms. Without their help, ruminants could not assimilate cellulose with simple non-protein compounds. These microorganisms located in rumen decompose the organic substances in the feed and form volatile fatty acids, ammonia, amino acids, which animals use for their development and reproduction. In the rumen of domesticated cattle and sheep, rumen cilia constitute 20-50% of the total microbial biomass. Rumen Ciliata develop symbiotic relationships with their animal hosts and both symbiotic and predator-prey relationships with other members of the rumen microbiota. The lack of axenic cultures of rumen Ciliata has forced researchers to use other methods to determine the metabolism and functions of rumen Protozoa, such as comparing rumen fermentation and microbial profiles of faunal and non-ciliated cattle or sheep or using in vitro cultures.

Diurnal shifts of rumen fermentation and microbial profiles revealed circadian rhythms of rumen bacteria, methanogens, and protozoa under high-grain and high-forage diets

In this study, we investigated how the composition and population of rumen microbiota shifted in response to diurnal oscillations under 2 different diets (high grain vs high forage). Five multiparous Holstein dairy cows with similar body weight, days in milk, and parity were enrolled in this study. The cows were fed high-grain (HG) diet for 21 d and then shifted to high-forage (HF) diet in the next 21 d (7-d washout and 14-d experimental period). During the experimental period, dry matter intake (DMI) and rumination activity were recorded, and rumen fluid was collected 8 times post-feeding every 6 h during the last 2 d of each dietary feeding period. The rumen microbial (bacterial, archaeal, and protozoal) population and composition were assessed using quantitative PCR and amplicon sequencing respectively. The daily dynamic of measurements was assessed using cosinor model. The associations between microbial taxa and rumen fermentation profiles were assessed using linear mixed model, in which the cows were termed as random intercept effects. Daily rhythmicity was observed for DMI, rumination activity, and rumen fermentation profiles under both diets. Additionally, rumination time, rumen pH, and acetate/propionate ratio had a higher mesor (the average level of diurnal fluctuations) under HF diet than in HG diet. The amplitude (the distance between the peak and mesor) of DMI, rumen pH, ammonia nitrogen, and total volatile acid concentration were higher under HG diet than in HF diet. Although no significant diurnal oscillation was observed in rumen microbial population, the relative abundance of 14 bacterial genera, one protozoal genus, and 2 archaeal species had significant diurnal oscillations under both HF and HG diets. Among them, the bacterial genera Ruminococcus and Colidextribacter had time at peak of rhythm within 0 to12 h after feeding, which were also negatively associated with the rumen acetate/propionate ratio. The bacterial genus Rikenellaceae_RC9_gut_group had time at peak of rhythm within 12 to 24 h after feeding, which was also positively associated with the rumen acetate/propionate ratio. Our study illustrated the daily dynamic on the rumen microbiota population and composition under different diets, and also identified the feeding-responsive rumen microbiota, highlighting a more targeted approach is needed to manipulate rumen microbiota.

218 Methane and Carbon Dioxide Emissions from Crossbred Beef Cattle Fall-Grazed on Native Aspen Parkland Pastures

Abstract Over 20 M ha of grazing land is utilized for beef production in western Canada, significantly contributing to the Canadian economy. Cattle are recognized for contributing to methane (CH4) and carbon dioxide (CO2), and individual animal contribution varies with several factors, one of them being feed efficiency as measured using residual feed intake adjusted for off-test backfat thickness (RFIfat). Given that commercial cattle spend a large portion of their production lifecycle grazing on diverse pastures in western Canada, understanding whether and how RFIfat measured in drylot and CH4 emissions reflect animal performance on pasture remains essential. This study quantified CH4 and CO2 production from beef cattle while grazing diverse diets on open-range aspen parkland pastures during fall. Cattle had been previously measured for RFIfat in drylot. Production of CH4 and CO2 (g/day) from crossbred beef cows (n = 22, with a range of -2.2 to +1.3 kg DM/day in RFIfat) and replacement heifers (n = 15; with a range of -2.6 to + 3.0 kg DM/day in RFIfat) were monitored using the GreenFeed emissions monitoring system over 40 days while grazing on native rangeland (70 ha) in the fall of 2022. Fall grazing was divided into two 20 ± 1 day' grazing periods; 20 days in September (SEP) vs. 20 days in October (OCT). Total spot measurements of CH4 and CO2 emissions in SEP and OCT were 1,096 vs. 1,054 for cows and 644 vs. 571 for heifers, respectively. The average number of daily visits per animal to the GreenFeed unit for cows and heifers were 2.8 ± 0.1 vs. 2.5 ± 0.1 in SEP, and 2.5 ± 0.1 vs. 2.0 ± 0.1 in OCT, respectively. Cows had greater average daily CH4 (SEP: 268.4 ± 6.1 vs. 196.1 ± 4.3; OCT: 243.9 ± 6.1 vs. 185.0 ± 4.3 g/day) and CO2 emission (SEP: 9,105.0 ± 143.1 vs. 6,485.3 ± 108.6; OCT: 8,544.3 ± 143.2 vs. 6,308.7 ± 108.9 g/day) than heifers (all P < 0.01). A negative relationship was evident between the CH4 emission and RFIfat in heifers (SEP: R2 = 0.043 vs. OCT: R2 = 0.014; P < 0.01), as well as CO2 emission and RFIfat (SEP: R2 = 0.083 vs. OCT: R2 = 0.020; P < 0.01), although the amount of variation explained by RFIfat is very small and is in disagreement with previous data. We speculate that the decline in CH4 and CO2 emissions from cattle in Oct might be due to various factors, including but not limited to changes in overall intake, daylight hours, air temperature, plant community, feeding and ruminating patterns, and rumen microbial profiles. Further analysis of forage quality, step counts, and GPS location, as well as rumen bacterial community, may shed more light on methane production in the fall.

"Get the best out of what comes in" - adaptation of the microbiota of chamois (Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps.

As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.

Effect of Tea Seed Oil on In Vitro Rumen Fermentation, Nutrient Degradability, and Microbial Profile in Water Buffalo.

Tea seed oil (TSO) was investigated for its effects on rumen fermentation and in vitro parameters of bacterial communities in water buffalo diets containing Siraitia grosvenorii and soybean residues. TSO was added at rates of 0% (control group (CT)), 0.5% (T1), 1% (T2), and 2% (T3) of the in vitro fermentation substrate weight (dry matter (DM) basis). T2 and T3 had significantly lower acetate and total volatile fatty acid contents but a significantly higher microbial crude protein content than CT. The lowest NH3-N content was observed in T1 and T2. Treatment significantly increased DM digestibility, with the highest percentage observed in T2. T2 showed significantly higher crude protein digestibility than CT. TSO supplementation significantly increased the C18:2n6c, C18:2 trans-10, cis-12, and C20:4n6 concentrations compared to those in CT. The total number of bacteria was significantly lower in T2 than in CT. TSO supplementation decreased the total bacteria, fungi, and methanogen populations but increased rumen microorganism diversity and richness. In conclusion, TSO can regulate the number and flora of rumen microorganisms through antimicrobial activity, thereby affecting rumen fermentation patterns, reducing methane production, and improving nutrient digestibility, and an optimal supplementation rate appears to be achieved with 1% TSO (DM basis).

Use of milk proteins as biomarkers of changes in the rumen metaproteome of Holstein cows fed low-fiber, high-starch diets

Dietary levels of undegraded neutral detergent fiber (uNDF240) and rumen-fermentable starch (RFS) can affect the rumen microbiome and milk composition. The objective of the study is to investigate the use of milk proteins as biomarkers of rumen microbial activity through a comparative evaluation of the rumen microbial and milk protein profiles produced by Holstein cows fed diets with varying contents of physically effective uNDF240 (peuNDF240) and RFS. Eight ruminally cannulated lactating Holstein cows were included in a larger study as part of a 4 × 4 Latin square design with 4 28-d periods to assess 4 diets varying in peuNDF240 and RFS content. For this experiment, cows received one of 2 dietary treatments: (1) low-peuNDF240, high-RFS (LNHR) diet or (2) high-peuNDF240, low-RFS (HNLR) diet. Within each period, rumen fluid samples were collected from each cow on d 26 (1400 h) and d 27 (0600 h and 1000 h), and milk samples were collected from each cow on d 25 (2030 h), d 26 (0430 h, 1230 h, and 2030 h), and d 27 (0430 h and 1230 h). Microbial proteins were isolated from each rumen fluid sample. For milk samples, milk proteins were fractionated, and the whey fraction was subsequently isolated. Isolated proteins within each rumen fluid or milk sample were isobarically labeled and analyzed by liquid chromatography-tandem mass spectrometry. Product ion spectra acquired from rumen fluid samples were searched using SEQUEST against 71 composite databases. In contrast, product ion spectra acquired from milk samples were searched against the Bos taurus database. Data were analyzed using the PROC MIXED procedure in SAS 9.4 to assess the effect of diet and time of sampling. To increase stringency, the false discovery rate-adjusted P-value (PFDR) was also calculated to account for multiple comparisons. Using the mixed procedure, a total of 129 rumen microbial proteins were quantified across 24 searched microbial species. Of these, the abundance of 14 proteins across 9 microbial species was affected due to diet and diet × time interaction, including 7 proteins associated with energetics pathways. Among the 159 quantified milk proteins, the abundance of 21 proteins was affected due to the diet and diet × time interaction. The abundance of 19 of these milk proteins was affected due to diet × time interactions. Of these, 16 proteins had the disparity across diets at the 0430 h sampling time, including proteins involved in host defense, nutrient synthesis, and transportation, suggesting that biological shifts resulting from diet-induced rumen changes are not diurnally uniform across milkings. The concentration of lipoprotein lipase (LPL) was statistically higher in the milk from the cows fed with the LNHR diet, which was numerically confirmed with an ELISA. Further, as determined by ELISA, the LPL concentration was significantly higher in the milk from the cows fed with the LNHR diet at 0430 h sampling point, suggesting that LPL concentration may indicate dietary carbohydrate-induced ruminal changes. The results of this study suggest that diet-induced rumen changes can be reflected in milk in a diurnal pattern, further highlighting the need to consider sampling time points for using milk proteins as a representative biomarker of rumen microbial activity.

Effect of Supplementation of Tinospora cordifolia on Nutrient Utilization, Blood Biochemical Profile, Cell Mediated Immune Response and Rumen Microbial Profile in Beetal Goat Kids

Background: Tinospora cordifolia is a common climbing shrub that grows on other trees. It is native to India. Its root, stems and leaves are used in Ayurvedic medicine. Methods: Experimental animals (n=10) were equally divided into two groups of five animals each (average body weight 16.53 kg), designated as control (C) and treatment (C + T. cordifolia) group. A 60 day growth trial was conducted after giving adaptation period of 20 days. A 7-day metabolic trial was conducted towards the end of the experiment using standard protocol. Blood samples were collected at the end of study to determine biochemical and antioxidant profile. Rumen liquor samples were collected by oral intubation and used for quantification of microbial population. Result: T. cordifolia supplemented at the rate of 2% of DM intake in the total mixed ration of goat kids reduced the relative abundance of methanogens in the rumen, without any significant effect on nutrient digestibility, N balance, blood biochemical profile, cell mediated immune response and growth performance.

Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas.

Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.

Effect of Unsaturated Fatty Acid Ratio In Vitro on Rumen Fermentation, Methane Concentration, and Microbial Profile

It is well known that dairy cows are fed diets with high fat content, which can adversely affect rumen fermentation. However, whether the effects of high fat content on rumen fermentation are related to the composition of fatty acids (FA) is for further study. We explored the effects of unsaturated fatty acid (UFA) ratios in vitro on rumen, methane concentration and microbial composition under the same fat levels. The experiment included a low-unsaturated group (LU, UFA proportion: 42.8%), a medium-unsaturated group (MU, UFA proportion: 56.9%), and a high-unsaturated group (HU, UFA proportion: 70.9%). The incubation fluid pH and NH3-N levels were not significantly different in the three groups. Total volatile fatty acid (TVFA), acetate, propionate, butyrate, and valerate in the MU group had a decreased trend compared to the LU group (0.05 < p < 0.1), and no difference was found in other volatile fatty acids (VFAs) among the three groups. Furthermore, gas production kinetic parameters among the three groups did not differ significantly. The LU group’s CH4 concentration was significantly higher than the HU group (p < 0.05). The CO2 concentration in the LU group was also significantly higher than the MU and LU groups (p < 0.05). Additionally, 16S rRNA microbial sequencing results showed that the Shannon diversity value significantly increased in the MU group (p < 0.05) compared to the LU group. Other alpha diversity indices (Chao 1, observed species, and ACE) did not differ among the three groups. The increased proportion of UFA significantly decreased the relative abundance of Succinivibrionaceae_UCG_001 and Fibrobacter (p < 0.05). Meanwhile, the multiple Lachnospiraceae bacteria significantly increased in the MU group (p < 0.05). Overall, our findings indicated that the microbial community in the incubation system could be affected by elevating proportions of UFA, affecting the yield of VFA, whereas the CH4 concentration was reduced.

Implications of phyto-feed additives supplementation in buffalo calves on rumen fermentation pattern and microbial population

Natural phyto-feed additives have been identified as a potential rumen fermentation modifier by in vitro studies and by few short-term in vivo trials. However, information on impact on animal performance by their long-term administration is still inadequate. In light of this, the present study was undertaken to examine the rumen fermentation pattern, rumen microbial enzymes and microbial profiles as influenced by long term supplementation of phyto-feed additives to buffalo calves. A six months feeding trial was conducted on 20 male buffaloes (165±4 kg body weight), divided into four groups and fed on diet supplemented with no additive (T0, control), with feed additive FAI @ 1% of dry matter intake (DMI) (T1), with FAII @ 1 ml/kg DMI (T2) and with FAI and FAII switched alternatively after every 15 days (T3). No significant effect was observed on rumen fermentation pattern as well as carboxymethylcellulase, avicelase, xylanase, acetyl esterase, and protease activities in the rumen of buffalo calves. The population density of methanogens, fungi, Ruminococcus flavefaciens, and R. albus decreased significantly in T3 where FAI and FAII were fed alternately, but Fibrobacter succinogenes decreased significantly in T2 where FAII was fed. When compared to the control, the microscopic count of protozoa decreased in all the three supplemented groups. It can be concluded that rumen fermentation, including rumen metabolites and microbial enzymes, were unaffected; however, phyto-feed additives exhibited changes in rumen microbes.

Influence of dietary carbohydrate profile on the dairy cow rumen meta-proteome.

Diet starch and fiber contents influence the rumen microbial profile and its fermentation products, yet no information exists about the effects of these dietary carbohydrate fractions on the metabolic activity of these microbes. The objective of this experiment was to evaluate the effects of dietary carbohydrate profile changes on the rumen meta-proteome profile. Eight cannulated Holstein cows were assigned to the study as part of a 4 × 4 Latin square design with a 2 × 2 factorial treatment arrangement including four 28-d periods. Cows received 1 of 4 dietary treatments on a dry matter (DM) basis. Diets included different concentrations of rumen fermentable starch (RFS) and physically effective undigested NDF (peuNDF240) content in the diet: (1) low peuNDF240, low RFS (LNLS); (2) high peuNDF240, low RFS (HNLS); (3) low peuNDF240, high RFS (LNHS); and (4) high peuNDF240, high RFS (HNHS). Rumen fluid samples were collected from each cow on the last 2 d of each period at 3 time points (0600, 1000, and 1400 h). The microbial protein fraction was isolated, isobarically labeled, and analyzed using liquid chromatography combined with tandem mass spectrometry techniques. Product ion spectra were searched using the SEQUEST search on Proteome Discoverer 2.4 (Thermo Scientific) against 71 curated microbe-specific databases. Data were analyzed using PROC MIXED procedure in SAS 9.4 (SAS Institute Inc.). A total of 138 proteins were characterized across 26 of the searched microbial species. In total, 46 proteins were affected by treatments across 17 of the searched microbial species. Of these 46 proteins, 28 were affected by RFS content across 13 microbial species, with 20 proteins having higher abundance with higher dietary RFS and 8 proteins having higher abundance with lower dietary RFS. The majority of these proteins have roles in energetics, carbon metabolism, and protein synthesis. Examples include pyruvate, phosphate dikinase (Ruminococcus albus SY3), 30S ribosomal protein S11 (Clostridium aminophilum), and methyl-coenzyme M reductase subunit α (Methanobrevibacter ruminantium strain 35063), which had higher abundances with higher dietary RFS. Conversely, glutamate dehydrogenase (Butyrivibrio fibrisolvens) and 50S ribosomal protein L5 (Pseudobutyrivibrio ruminis) and L15 (Ruminococcus bromii) had lower abundances with higher dietary RFS content. Among the remaining 18 proteins unaffected by RFS content alone, 5 proteins were affected by peuNDF240 content, and 13 were affected by peuNDF240 × RFS interactions. Our results suggest that the RFS content of the diet may have a greater influence on rumen microbial protein abundances than dietary peuNDF240 content or peuNDF240 × RFS interactions. This research highlights that dietary carbohydrate profile changes can influence rumen microbial protein abundances. Further research is needed to fully characterize the effects of diet on the rumen meta-proteome and manipulate the various roles of rumen microbes. This will aid in designing the strategies to maximize the efficiency of nutrient use in the rumen.

Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach

Lignocellulosic biomass is a rich source of feed for cattle. Amongst them, coconut coir may be the potential source of feed supplements. To assess, the effect of various concentrations of coconut coir (0 %, 21 % and 40 %) as a feed supplement on the rumen microbiome of cattle (Kankrej breed), a metagenomic (16S rRNA gene amplicon and shotgun sequencing) study was performed. The Alpha diversity estimation from the amplicon study suggested that the group of cattle fed food without the coconut coir has a higher number of genera than the cattle fed with mixed ration. Within the liquid fraction, bacterial phyla Bacteroidetes were abundant followed by Firmicutes and Fibrobacteres, whereas the proportion of Tenericutes, TM7, SRI, Verrucomicrobia, Lentisphaerae, and Elusimicrobia had decreased with the rise in the coir concentration. While within the solid fractions, the proportion of Elusimicrobia increased, but the count of Bacteriodetes, Firmicutes, Fibrobacteres Tenericutes, TM7, SRI, Verrucomicrobia, and Lentisphaerae decreased with an increase in coir percentages. The results obtained from shotgun sequencing show similar results for bacterial diversity. The functions associated with carbohydrate metabolism were abundant in both the treatments as compared to the control. Functions related to glycoside hydrolases, glycosyltransferases and carbohydrate-binding modules were abundant in both the treatments as compared to control. Thus, the study indicates that the microbiome does alter after feeding coir as a supplement and may be used as feed for cattle.

Calf rumen microbiome from birth to weaning and shared microbial properties to the maternal rumen microbiome.

Optimization of host performance in cattle may be achieved through programming of the rumen microbiome. Thus, understanding maternal influences on the development of the calf rumen microbiome is critical. We hypothesized that there exists a shared microbial profile between the cow and calf rumen microbiomes from birth through weaning. Specifically, our objective was to relate the calf's meconium and rumen fluid microbiomes in early life to that of the cow rumen fluid prior to parturition and at weaning. Rumen fluid was collected from multiparous Angus crossbred cows (n = 10) prior to parturition and at weaning. Immediately following the parturition, meconium and rumen fluid were collected from the calf. Rumen fluid was collected again from the calf on day 2, day 28, and at weaning. The rumen fluid microbial profile and subsequent volatile fatty acid (VFA) profile were characterized using 16S rRNA sequencing and gas liquid chromatography, respectively. Microbial data was analyzed using QIIME2 and the GLM procedure of SAS was used to analyze the VFA profile. Alpha diversity was similar in the early gut microbiome (meconium, rumen fluid at birth and day 2; q ≥ 0.12) and between the cow and calf at weaning (q ≥ 0.06). Microbial composition, determined by beta diversity, differed in the early rumen microbiome (rumen fluid at birth, day 2, and day 28; q ≤ 0.04), and VFA profiles complimented these results. There were similarities in composition between meconium, rumen fluid at birth, and rumen fluid from the cow at weaning (q ≥ 0.09). These data indicate successive development of the rumen microbiome and stabilization over time. Similarities between meconium and rumen fluid at birth potentially indicates in utero colonization of the calf gastrointestinal tract. Similarities in composition between the early calf rumen microbiome and the cow at weaning prompt an interesting comparison and area for future consideration in terms of identifying at what stage of gestation might colonization begin. Overall, this study provides insight into similarities between the cow and calf microbiomes and may be helpful in developing hypotheses for the pathway of colonization and programming potential in the early gut.

Effects of medium-chain fatty acid supplementation on performance and rumen fermentation of lactating Holstein dairy cows

Medium-chain fatty acids (MCFAs) have antimicrobial properties and cause negative or positive effects on animal performance depending on its dosage. We hypothesized that MCFA supplementation at a lower dose (i.e., 0.05–0.2% of dietary DM) would increase rumen pH and milk production without decreasing nutrient digestibility which is typically observed with the higher inclusion rates (i.e., >1% of dietary DM). The objective of this study was to evaluate the effects of MCFA supplementation at a lower dose on productivity, plasma energy metabolite concentrations, apparent total tract nutrient digestibility, rumen fermentation, and rumen microbial profile of lactating dairy cows. Thirty (n = 8 primiparous, n = 22 multiparous) Holstein cows in mid-lactation (637 ± 68.5 kg of initial BW, 98.5 ± 27.4 d in milk; mean ± standard deviation) were used in a crossover design with two 28-d periods. The MCFA supplement, consisted of 25% MCFA (containing 32% C8:0, 21% C10:0, 47% C12:0 on DM basis) and 75% carrier ingredients, was fed at 0.25% of dietary DM replacing dry ground corn in control (CON). Total inclusion of MCFA was 0.063% of dietary DM. No differences were observed in DM intake, apparent total tract nutrient digestibility and BW change between MCFA and CON. Milk and milk component yields did not differ between treatment groups. The MCFA supplementation tended to have higher minimum rumen pH (5.66 vs. 5.54), and decreased daily fluctuation range of rumen pH (1.17 vs. 1.40) compared to CON. However, the duration of acidosis (pH < 5.8, min/d) did not differ between treatment groups and ruminal total volatile fatty acid concentration and its profile did not differ between treatment groups. For rumen microbiota, the Chao1 index of bacterial community tended to be lower (10.9 vs. 11.6) whereas the Shannon index did not differ (0.91 vs. 0.93) in MCFA compared to CON, and both indices did not differ for archaeal and protozoan communities between treatment groups. The relative abundance of Methanobrevibacter gottschalkii increased when supplemented with MCFA (5.14 vs. 4.92%). These results suggest that supplementation of MCFA at 0.063% dietary DM may not affect overall animal performance or total tract nutrient digestibility, but decrease the daily range of pH and the bacterial richness in the rumen.

Tannin as a modulator of rumen microbial profile, apparent digestibility and ingestive behavior of lactating goats: A preliminary metagenomic view of goats adaptability to tannin

The aim with this study was to use interdisciplinary techniques and visions in order to identify the modulating effect of tannins on adaptive factors in lactating goats with different genetic patterns, through the assessment of digestibility and nutrient intake, ingestive behavior and rumen metagenome. We used in this study 8 of the Repartida ecotype and 6 of the Canindé breed goats, on average five years old, distributed in a completely randomized design, in a 2 × 2 factorial design, with two genetic groups and two diets. The applied diets were: basal diet and inclusion of 5% commercial tannin extract in basal diet. Intake and apparent digestibility of nutrients were evaluated, based on the quantification of the offered feed and refusals, and bromatological evaluation of samples of the offered feed, refusals and feces. Behavioral data were collected in 24-h continuous visual observations. The ruminal fluid was collected and DNA extraction, sequencing, and evaluation of relative abundance of the rumen microbiome were performed. The data obtained were analyzed statistically, through analysis of variance with 5% significance and, when necessary, a comparison of means test was applied. In this preliminary findings was observed that the genetic group factor caused changes in the number of chews and the relative abundance of microorganisms (P = 0.0290 and P = 0.0051). The diet factor influenced digestibility, which better values were observed for the tannin diet (P = 0.0049), in addition, it promoted changes in the rumen microbiota, with a beneficial modulatory characteristic. The inclusion of 5% tannin extract from Acacia mearnsii modulates the rumen microbiome, improving the apparent digestibility of nutrients without affecting the feed intake of goats from the Repartida and Canindé genetic groups.

Effect of dietary sulphur supplementation at graded levels on rumen feed fermentation and microbial profile in buffaloes

Choudhary, S., Chaudhary, L.C., Kala, A., Agarwal, N. and Rahman, H. 2022. Effect of dietary sulphur supplementation at graded levels on rumen feed fermentation and microbial profile in buffaloes. Animal Nutrition and Feed Technology, 22: 543–552.

The effect of Haemonchus contortus and Trichostrongylus colubriforms infection on the ruminal microbiome of lambs

We evaluated Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC) infection on the ruminal microbial community of Santa Ines lambs to better understand the pathophysiology of parasite infections and the interactions among gastrointestinal nematodes and gut resident microbiota. In this study, 18 six months of age lambs were maintained for 34 days in individual pens divided into three treatments that included animals infected with HC and TC, and control (infection-free). Haematological, ruminal parameter and microbial nitrogen absorbed by pune derivatives, as well as enteric methane emission (CH4), were analysed, and the rumen microbial taxonomic and functional profile assessed by shotgun metagenomics. The analysis showed that total protein, albumin, urea, and butyrate level were lower in animals infected by both parasites, while HC infection also decreased the haemoglobin level. Both infected groups (TC and HC) increased the enteric methane emission (CH4). TC and HC infections increased the diversity and richness of functional microbial genes. Most alterations in the rumen microbiome composition of infected groups are associated with the suppression of microbes involved in microbial homeostasis maintenance and expansion of the archaeal community in the infected animals. Infection led to an increased abundance of nitrogen, amino acid, protein, and energy metabolism genes. Overall, TC and HC infection increased the enteric methane emission, negatively affected taxon's responsible for maintenance de rumen homeostasis and modulated some important genes related to protein and energy metabolism.