Rumen ciliates: their metabolism and relationships with bacteria and their hosts

Effect of Agro-Industrial by Products Derived from Volatile Fatty Acids on Ruminant Feed In Vitro Digestibility

The growing demand for sustainable ruminant feed alternatives has motivated the application of bioconversion approaches for the valorization of agro-food byproducts (AFB) into feed additives and supplements. The present study thoroughly investigated substituting volatile fatty acids (VFAs) obtained from acidogenic fermentation (AF) of AFB as an energy source in ruminant feed. Rumen in vitro digestibility assays were conducted utilizing the gas production method, wherein the VFAs obtained from AF of apple pomace and potato protein liquor was substituted with partial silage and concentrate energy at levels of 10%, 20%, and 30%. The results indicate that substituting 20% of the concentrate's energy with VFA mixture significantly reduced methane production and had no adverse effect on the production and accumulation of VFAs in the simulated rumen media. Conversely, replacing 10% of the silage energy with VFAs led to a decrease in methane production and further enhanced the production of VFAs. Readily digestible VFAs in ruminant feed have the potential to enhance energy availability and sustainability in ruminant farming practices, aligning with the principles of circular economy and waste valorization.

Effects of biotin and coated cobalamin on lactation performance, nutrient digestion and rumen fermentation in Holstein dairy cows

Biotin (BI) and cobalamin (CA) are essential for rumen propionate production and hepatic gluconeogenesis. The study evaluated the influence of BI or/and coated CA (CCA) on milk performance and nutrient digestion in cows. Sixty Holstein dairy cows were assigned in a 2 × 2 factorial arrangement and randomised block design to four groups. The factors were BI at 0 or 20 mg/day and CCA at 0 or 9 mg CA/day. Dry matter intake increased with BI addition but was unchanged with CCA supply. Addition of BI or CCA increased fat-corrected milk, milk fat and milk protein yields and feed efficiency. Moreover, lactose yield was increased by CCA addition. Dry matter, organic matter, crude protein and acid detergent fibre total-tract digestibility increased for BI or CCA supply. When CCA was supplemented, positive response of neutral detergent fibre digestibility to BI addition was enhanced. Supplementing BI did not affect pH, propionate content and acetate to propionate ratio, but increased total volatile fatty acids (VFA) and acetate contents. Supplementing CCA decreased pH and acetate to propionate ratio, but increased total VFA, acetate and propionate contents. Rumen protease and carboxymethyl-cellulase activities and fungi, bacteria and Butyrivibrio fibrisolvens numbers increased for BI or CCA supply. In addition, protozoa increased for BI addition, and protease activity and Prevotella ruminicola increased for CCA supply. When CCA was supplemented, positive responses of R. albus and Ruminobacter amylophilus numbers to BI addition were enhanced. Blood glucose concentration was unchanged with BI supply, but increased for CCA supply. Blood nonesterified fatty acids and β-hydroxybutyrate contents reduced with BI or CCA supply. Supplementation with BI or CCA increased blood BI or CA content. The results showed that supplementing BI or/and CCA improved lactation performance and nutrient digestion, and CCA supply did not enhance the lactation performance response to BI supply.

- Invited Review - Ruminal ciliates as modulators of the rumen microbiome

Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes.

Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study

The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH₄ produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH₄ emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH₄ emission.

Effects of folic acid and riboflavin on growth performance, nutrient digestion and rumen fermentation in Angus bulls

This study examined the influences of coated folic acid (CFA) and coated riboflavin (CRF) on bull performance, nutrients digestion and ruminal fermentation. Forty-eight Angus bulls based on a randomised block and 2 × 2 factorial design were assigned to four treatments. The CFA of 0 or 6 mg of folic acid/kg DM was supplemented in diets with CRF 0 or 60 mg riboflavin (RF)/kg DM. Supplementation of CRF in diets with CFA had greater increase in daily weight gain and feed efficiency than in diets without CFA. Supplementation with CFA or CRF enhanced digestibility of DM, organic matter, crude protein, neutral-detergent fibre and non-fibre carbohydrate. Ruminal pH and ammonia N content decreased and total volatile fatty acids concentration and acetate to propionate ratio elevated for CFA or CRF addition. Supplement of CFA or CRF increased the activities of fibrolytic enzymes and the numbers of total bacteria, protozoa, fungi, dominant fibrolytic bacteria and Prevotella ruminicola. The activities of α-amylase, protease and pectinase and the numbers of Butyrivibrio fibrisolvens and Ruminobacter amylophilus were increased by CFA but were unaffected by CRF. Blood concentration of folate elevated and homocysteine decreased for CFA addition. The CRF supplementation elevated blood concentrations of folate and RF. These findings suggested that CFA or CRF inclusion had facilitating effects on performance and ruminal fermentation, and combined addition of CFA and CRF had greater increase in performance than CFA or CRF addition alone in bulls.

Effect of Dietary Inclusion of Riboflavin on Growth, Nutrient Digestibility and Ruminal Fermentation in Hu Lambs

The study evaluated the influences of riboflavin (RF) supply on the growth performance, nutrient digestibility and ruminal fermentation in lambs. Forty-eight Hu lambs were randomly assigned into four groups receiving RF of 0, 15, 30 and 45 mg/kg dry mater (DM), respectively. Increasing RF supply did not affect the DM intake, but quadratically increased the average daily gain and linearly decreased feed conversion ratio. Total-tract DM, neutral detergent fibre, acid detergent fibre and crude protein digestibility increased quadratically. Rumen pH and propionate molar percentage decreased linearly, total volatile fatty acids concentration, acetate proportion and the ratio of acetate to propionate increased linearly, but ammonia nitrogen concentration was unchanged with increasing RF supply. Linear increases were observed on the activities of carboxymethyl-cellulase, xylanase, pectinase and protease, and the populations of bacteria, fungi, protozoa, dominant cellulolytic bacteria, Ruminobacter amylophilus and Prevotella ruminicola. Methanogens population was not affected by RF supplementation. The microbial protein amount and urinary total purine derivatives excretion increased quadratically. The results indicated that 30 mg/kg DM RF supply improved growth performance, rumen fermentation and nutrient digestion in lambs.

Effects of different protein sources on nutrient disappearance, rumen fermentation parameters and microbiota in dual-flow continuous culture system

Scarce high-quality protein feed resources has limited the development of animal husbandry. In this study, we used a dual-flow continuous culture system to evaluate effects of difference dietary protein sources including soybean meal (SBM), cottonseed meal (CSM), and rapeseed meal (RSM), on nutrient disappearance, rumen fermentation, and microbiota of XiongDong black goats. Dietary proteins of either CSM, RSM or SBM had no effect on nutrient disappearance (P > 0.05). CSM or RSM significantly reduced (P < 0.01) the pH and enhanced (P < 0.01) the ammonia nitrogen (NH₃-N) concentration in fermentation liquid compared to SBM. The short-chain fatty acids (SCFAs) contents were greater (P = 0.05) and acetate was lower (P < 0.01) in SBM than those in RSM and CSM, whereas propionate was greater (P < 0.01) in RSM than that in SBM, consequently reducing the acetate to propionate ratio (A/P) in RSM. Bacteroidetes, Firmicutes, and Proteobacteria were detected as the dominant phyla, and the relative abundances of Spirochaetae (P < 0.01) and Chlorobi (P < 0.05) declined in the CSM and RSM groups as compared to those in the SBM group. At the genus level, Prevotella_1 was the dominant genus; as compared to SBM, its relative abundance was greater (P < 0.01) in CSM and RSM. The abundances of Prevotellaceae_Ga6A1 and Christensenellaceae_R7 were lower (P < 0.05) in CSM, whereas Eubacterium_oxidoreducens_group, and Treponema_2 were lower (P < 0.01) in both CSM and RSM, and other genera were not different (P > 0.10). Although the bacterial community changed with different dietary protein sources, the disappearances of nutrients were not affected, suggesting that CSM and RSM could be used by rumen bacteria, as in case with SBM, and are suitable protein sources for ruminant diets.

Effects of riboflavin supplementation on performance, nutrient digestion, rumen microbiota composition and activities of Holstein bulls

To investigate the influences of dietary riboflavin (RF) addition on nutrient digestion and rumen fermentation, eight rumen cannulated Holstein bulls were randomly allocated into four treatments in a repeated 4 × 4 Latin square design. Daily addition level of RF for each bull in control, low RF, medium RF and high RF was 0, 300, 600 and 900 mg, respectively. Increasing the addition level of RF, DM intake was not affected, average daily gain tended to be increased linearly and feed conversion ratio decreased linearly. Total tract digestibilities of DM, organic matter, crude protein (CP) and neutral-detergent fibre (NDF) increased linearly. Rumen pH decreased quadratically, and total volatile fatty acids (VFA) increased quadratically. Acetate molar percentage and acetate:propionate ratio increased linearly, but propionate molar percentage and ammonia-N content decreased linearly. Rumen effective degradability of DM increased linearly, NDF increased quadratically but CP was unaltered. Activity of cellulase and populations of total bacteria, protozoa, fungi, dominant cellulolytic bacteria, Prevotella ruminicola and Ruminobacter amylophilus increased linearly. Linear increase was observed for urinary total purine derivatives excretion. The data suggested that dietary RF addition was essential for rumen microbial growth, and no further increase in performance and rumen total VFA concentration was observed when increasing RF level from 600 to 900 mg/d in dairy bulls.

The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment

Entodinium caudatum is an anaerobic binucleated ciliate representing the most dominant protozoal species in the rumen. However, its biological features are largely unknown due to the inability to establish an axenic culture. In this study, we primally sequenced its macronucleus (MAC) genome to aid the understanding of its metabolism, physiology, ecology. We isolated the MAC of E. caudatum strain MZG-1 and sequenced the MAC genome using Illumina MiSeq, MinION, and PacBio RSII systems. De novo assembly of the MiSeq sequence reads followed with subsequent scaffolding with MinION and PacBio reads resulted in a draft MAC genome about 117 Mbp. A large number of carbohydrate-active enzymes were likely acquired through horizontal gene transfer. About 8.74% of the E. caudatum predicted proteome was predicted as proteases. The MAC genome of E. caudatum will help better understand its important roles in rumen carbohydrate metabolism, and interaction with other members of the rumen microbiome.

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing

In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.

Inhibition of Rumen Protozoa by Specific Inhibitors of Lysozyme and Peptidases in vitro

Defaunation studies have shown that rumen protozoa are one of the main causes of low nitrogen utilization efficiency due to their bacterivory and subsequent intraruminal cycling of microbial protein in ruminants. In genomic and transcriptomic studies, we found that rumen protozoa expressed lysozymes and peptidases at high levels. We hypothesized that specific inhibition of lysozyme and peptidases could reduce the activity and growth of rumen protozoa, which can decrease their predation of microbes and proteolysis and subsequent ammoniagenesis by rumen microbiota. To test the above hypothesis, we evaluated three specific inhibitors: imidazole (IMI), a lysozyme inhibitor; phenylmethylsulphonyl fluoride (PMSF), a serine protease inhibitor; and iodoacetamide (IOD), a cysteine protease inhibitor; both individually and in combinations, with sodium dodecyl sulfate (SDS) as a positive control. Rumen fluid was collected from two Jersey dairy cows fed either a concentrate-based dairy ration or only alfalfa hay. Each protozoa-enriched rumen fluid was incubated for 24 h with or without the aforementioned inhibitors and fed a mixture of ground wheat grain, alfalfa, and grass hays to support microbial growth. Live protozoa cells were morphologically identified and counted simultaneously at 3, 6, 12, and 24 h of incubation. Fermentation characteristics and prokaryotic composition were determined and compared at the end of the incubation. Except for IOD, all the inhibitors reduced all the nine protozoal genera identified, but to different extents, in a time-dependent manner. IOD was the least inhibitory to protozoa, but it lowered ammoniagenesis the most while not decreasing feed digestibility or concentration of volatile fatty acids (VFA). ANCOM analysis identified loss of Fibrobacter and overgrowth of Treponema, Streptococcus, and Succinivibrio in several inhibitor treatments. Functional prediction (from 16S rRNA gene amplicon sequences) using the CowPI database showed that the inhibitors decreased the relative abundance of the genes encoding amino acid metabolism, especially peptidases, and lysosome in the rumen microbiota. Overall, inhibition of protozoa resulted in alteration of prokaryotic microbiota and in vitro fermentation, and peptidases, especially cysteine-peptidase, may be targeted to improve nitrogen utilization in ruminants.

Preservation of rumen fluid for the pretreatment of waste paper to improve methane production

It is necessary to preserve rumen fluid for transport from slaughterhouses to the pretreatment facilities for use in treating lignocellulosic biomass. In this study, we investigated how the preservation of rumen fluid at various temperatures affects its use in hydrolysis of waste paper. Rumen fluid was preserved anaerobically at 4, 20, and 35 °C for 7 days. The number of protozoa and fibrolytic enzyme activity after preservation at 4 °C were significantly higher than that after preservation at either 20 or 35 °C. Waste paper was subsequently treated with preserved rumen fluid at 37 °C for 48 h. Preservation at 20 °C remarkedly decreased the hydrolysis of waste paper. Xylanase activity in rumen fluid preserved at 35 °C increased during the treatment, which enhanced the solubilization of waste paper as comparable to the control and preservation at 4 °C. Pretreatment of waste paper with rumen fluid preserved at 4 °C showed that the fluid retained high fibrolytic activity, and reduced the loss of organic carbon as substrate for methanogens. Our results suggest that preservation of rumen fluid at 4 °C is most suitable for efficient pretreatment and methane fermentation of waste paper.

Co-existence of multiple bacterivorous clevelandellid ciliate species in hindgut of wood-feeding cockroaches in light of their prokaryotic consortium

The hindgut of wood-feeding Panesthia cockroaches harbours a diverse microbial community, whose most morphologically prominent members are bacterivorous clevelandellid ciliates. Co-occurrence and correlation patterns of prokaryotes associated with these endosymbiotic ciliates were investigated. Multidimensional scaling based on taxa interaction-adjusted index showed a very clear separation of the hindgut ciliate samples from the ciliate-free hindgut samples. This division was corroborated also by SparCC analysis which revealed strong negative associations between prokaryotic taxa that were relatively more abundant in the ciliate-free hindgut samples and prokaryotic taxa that were more abundant in the ciliate samples. This very likely reflects the grazing behaviour of hindgut ciliates which prefer Proteobacteria, Firmicutes and Actinobacteria, causing their abundances to be increased in the ciliate samples at the expense of abundances of Euryarchaeota and Bacteroidetes which prevail in the hindgut content. Ciliate species do not distinctly differ in the associated prokaryotes, indicating that minute variations in the proportion of associated bacteria might be sufficient to avoid competition between bacterivorous ciliate species and hence enable their co-occurrence in the same host. The nearest free-living relatives of hindgut ciliates have a different pattern of associations with prokaryotes, i.e., alphaproteobacteria are predominantly associated with free-living ciliates while gammaproteobacteria with hindgut ciliates.

In vitro investigation of the ruminal digestion kinetics of different nitrogen fractions of 15N-labelled timothy forage

An in vitro method based on ¹⁵N-labelled forage nitrogen (N) was developed to study ruminal N metabolism of soluble N (SN), insoluble N (ISN) and neutral detergent insoluble N (NDIN) fractions of timothy forage. Timothy grass was grown on replicated experimental plots with one plot receiving ¹⁵N-labelled and the other unlabelled N fertilizer. Harvested grass was preserved as dried grass or as formic acid treated or untreated silage. The intact forages and their corresponding N fractions were incubated in buffered rumen fluid in vitro to determine degradation parameters based on the ¹⁵N fluxes between labelled feed N and ammonia N pools. A high percentage (25–38%) of ¹⁵N-labelled ammonia disappeared from ammonia N pool during the first 15 min of incubation. Microbial uptake of dried grass SN fraction was higher than of silage SN fractions. Fractional degradation rates of SN from formic acid treated silage, untreated silage and dried grass during the first 6 hours of incubation were 0.145, 0.125 and 0.115 /h, respectively. By the end of the incubation period (28 h), 69, 66 and 43%, of the SN fraction of formic acid treated silage, untreated silage and dried grass, respectively were recovered as ammonia. The percentage of ISN fractions degraded to ammonia N were 9, 34 and 27%, respectively. Based on the changes in ¹⁵N-labelled ammonia N pool in blank incubation and appearance of ¹⁵N to ammonia N pool from ¹⁵N-labelled NDIN fractions, it was estimated that a significant portion of microbial lysis occurred when incubations were carried out for longer than 20 hours. With dried grass the contribution of ammonia N for microbial N synthesis was greater than with silages. Use of ¹⁵N-labelled forages together with this in vitro method is a promising technique for determining soluble N degradation parameters, but it requires further development to be used for determining degradation parameters of insoluble N fractions and work with whole feeds.

Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split

Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.

Diagnosis and Management of Rumen Acidosis and Bloat in Feedlots

Ruminal acidosis and ruminal bloat represent the most common digestive disorders in feedlot cattle. Ruminants are uniquely adapted to digest and metabolize a large range of feedstuffs. Although cattle have the ability to handle various feedstuffs, disorders associated with altered ruminal fermentation can occur. Proper ruminal microorganism adaptation and a consistent substrate (ration) help prevent digestive disorders. Feed bunk management, sufficient ration fiber, consistent feed milling, and appropriate response to abnormal weather are additional factors important in prevention of digestive disorders. When digestive disorders are suspected, timely diagnosis is imperative.

Inhibition of the Rumen Ciliate Entodinium caudatum by Antibiotics

Axenic cultures of free-living aerobic ciliates, such as Tetrahymena thermophila and Paramecium aurelia, have been established and routinely used in laboratory research, greatly facilitating, or enabling characterization of their metabolism, physiology, and ecology. Ruminal protozoa are anaerobic ciliates, and they play important roles in feed digestion and fermentation. Although, repeatedly attempted, no laboratory-maintainable axenic culture of ruminal ciliates has been established. When axenic ciliate cultures are developed, antibiotics are required to eliminate the accompanying bacteria. Ruminal ciliates gradually lose viability upon antibiotic treatments, and the resultant axenic cultures can only last for short periods of time. The objective of this study was to evaluate eight antibiotics that have been evaluated in developing axenic cultures of ruminal ciliates, for their toxicity to Entodinium caudatum, which is the most predominant ruminal ciliate species. Scanning and transmission electron microscopy (TEM) showed that the antibiotics damaged both the cell surface and nuclei of E. caudatum and increased accumulation of intracellular glycogen. Combinations of the three least toxic antibiotics failed to eliminate the bacteria that are present in the E. caudatum culture. The combination of ampicillin, carbenicillin, streptomycin, and oxytetracycline was able to eliminate all the bacteria, but the resultant axenic E. caudatum culture gradually lost viability. Adding the bacterial fraction (live) separated from an untreated E. caudatum culture reversed the viability decline and recovered the growth of the treated E. caudatum culture, whereas feeding nine strains of live bacteria isolated from E. caudatum cells, either individually or in combination, could not. Nutritional and metabolic dependence on its associated bacteria, accompanied with direct and indirect inhibition by antibiotics, makes it difficult to establish an axenic culture of E. caudatum. Monoxenic or polyxenic cultures of E. caudatum could be developed if the essential symbiotic partner(s) can be identified.

Effects of physical form of diet on nutrient digestibility, rumen fermentation, rumination, growth performance and protozoa population of finishing lambs

This study was conducted to compare effects of 3 physical forms of feed including mash (diet 1), pellet (diet 2) and complete feed block (CFB; diet 3) on digestion, fermentation and performance of lambs. Twenty-one lambs with an initial average body weight of 26 ± 2.5 kg and 6 ± 1.5 months of age were assigned through a completely randomized design to 3 treatments and 7 replicates. The experimental treatments had the same formulation. The results of present experiment showed that CFB significantly increased feed intake and nutrient digestibility (P < 0.05). There was no significant difference among the diets for rumen fluid pH, blood glucose, concentration of volatile fatty acids (P > 0.05), except acetic acid (P < 0.05). The rumen ammonia nitrogen (NH₃—N), mixed rumen protozoa population (RPP), Entodiniums spp., Epidiniums spp., blood urea nitrogen (BUN) concentration, rumination time adjusted for dry matter (DM), neutral detergent fiber (NDF), acid detergent fiber (ADF) intake, and total body weight gain of lambs in CFB diet were the highest among all diets (P < 0.05). Feed conversion ratio at days 31 to 45 and whole experimental period were better in CFB than in other diets (P < 0.05). Overall, according to the findings of the present study, among 3 physical forms of the diets, CFB had the best efficiency due to improvement of nutrient digestibility, rumen fermentation and performance of lambs. Therefore, the CFB diet offers the best result in lambs compared with mash and pellet diets.

The effect of rumen ciliates on chitinolytic activity, chitin content and the number of fungal zoospores in the rumen fluid of sheep

The objective of this study was to investigate the effect of selected protozoa on the degradation and concentration of chitin and the numbers of fungal zoospores in the rumen fluid of sheep. Three adult ewes were fed a hay-concentrate diet, defaunated, then monofaunated with Entodinium caudatum or Diploplastron affine alone and refaunated with natural rumen fauna. The average density of the protozoa population varied from 6.1 · 10(4) (D. affine) to 42.2 · 10(4) cells/ml rumen fluid (natural rumen fauna). The inoculation of protozoa in the rumen of defaunated sheep increased the total activity of chitinolytic enzymes from 2.9 to 3.6 μmol N-acetylglucosamine/g dry matter (DM) of rumen fluid per min, the chitin concentration from 6.3 to 7.2 mg/g DM of rumen fluid and the number of fungal zoospores from 8.1 to 10.9 · 10(5) cells/ml rumen fluid. All examined indices showed diurnal variations. Ciliate population density was highest immediately prior to feeding and lowest at 4 h thereafter. The opposite effects were observed for the numbers of fungal zoospores, the chitin concentration and chitinolytic activity. Furthermore, it was found that chitin from zoospores may account for up to 95% of total microbial chitin in the rumen fluid of sheep. In summary, the examined ciliate species showed the ability of chitin degradation as well as a positive influence on the development of the ruminal fungal population.

Phylogeny of intestinal ciliates, including Charonina ventriculi, and comparison of microscopy and 18S rRNA gene pyrosequencing for rumen ciliate community structure analysis

The development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates, Charonina ventriculi, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescence in situ hybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence, Charonina ventriculi was positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.

In vitro Evaluation of Different Feeds for Their Potential to Generate Methane and Change Methanogen Diversity

Optimization of the dietary formulation is the most effective way to reduce methane. Nineteen feed ingredients (brans, vegetable proteins, and grains) were evaluated for their potential to generate methane and change methanogen diversity using an in vitro ruminal fermentation technique. Feed formulations categorized into high, medium and low production based on methane production of each ingredient were then subjected to in vitro fermentation to determine the real methane production and their effects on digestibility. Methanogen diversity among low, medium and high-methane producing groups was analyzed by PCR-DGGE. The highest methane production was observed in Korean wheat bran, soybean and perilla meals, and wheat and maize of brans, vegetable protein and cereal groups, respectively. On the other hand, corn bran, cotton seed meal and barley led to the lowest production in the same groups. Nine bacteria and 18 methanogen 16s rDNA PCR-DGGE dominant bands were identified with 83% to 99% and 92% to 100% similarity, respectively. Overall, the results of this study showed that methane emissions from ruminants can be mitigated through proper selection of feed ingredients to be used in the formulation of diets.

The ability of rumen ciliates, Eudiplodinium maggii, Diploplastron affine, and Entodinium caudatum, to use the murein saccharides

Murein polysaccharides may contribute to a considerable part of the dry matter of bacterial cells. Their utilization by protozoa inhabiting the rumen is, however, poorly recognized. The objective of this study was to examine the ability of three species of ciliates, i.e., Eudiplodinium maggii, Diploplastron affine, and Entodinium caudatum of digest, and ferment these saccharides. The cultivation experiments showed that the enrichment of growth medium with bacterial cell wall β-glycans increased the ciliate number (p < 0.05). A statistically significant increase (p < 0.01) was followed by a continuous decrease (p < 0.01) in the percentage of individuals containing β-glycans particles after 4- and 24-h incubation of ciliates with this substrate, respectively. The enzymatic experiments confirmed the ability of the examined protozoa to digest murein. E. caudatum exhibited the highest activity (8.2 unit (U)/mg protein per min), and E. maggii, the lowest (3.0 U/mg protein per min). The production rates of volatile fatty acids by starved and fed ciliate species were 0.7 and 1.6 (E. caudatum) pmol/ciliate cell per h, 30.5 and 42.5 (E. maggii) pmol/ciliate cell per h, and 8.3 and 19.2 (D. affine) pmol/ciliate cell per h (p < 0.05).

Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC)

A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N.

Effect of rumen protozoa on Escherichia coli O157:H7 in the rumen and feces of specifically faunated sheep

The effects of rumen protozoal populations on ruminal populations and fecal shedding of Escherichia coli O157:H7 were evaluated by using specifically faunated sheep. Nine fauna-free sheep (three animals per treatment) were inoculated with Dasytricha spp. (DAS sheep); with mixed population A (PopA) comprising Entodinium spp., Isotricha spp., Diplodinium spp., and Polyplastron spp.; or with mixed population B (PopB) comprising Entodinium spp., Isotricha spp., Dasytricha spp., and Epidinium spp.; six sheep were maintained fauna-free (FF sheep) to serve as controls. Sheep were fed barley silage-based diets, and treatment groups were housed in isolated rooms. Sheep were inoculated orally with 10(10) CFU of a four-strain mixture of nalidixic acid-resistant E. coli O157:H7. Samples of ruminal fluid and feces were collected over 77 days. Polyplastron spp. were detected in only one sheep in PopA, and Dasytricha spp. were detected only once within the PopB cohort. Sheep in the DAS group were 2.03 times more likely (P < 0.001) to shed E. coli O157:H7 than were those in the other three treatments, whereas the PopB sheep were less likely (0.65; P < 0.05) to shed this bacterium. The likelihood of harboring ruminal E. coli O157:H7 also tended (P = 0.06) to be higher in DAS and was lower (P < 0.01) in FF than in other cohorts. Possibly, Dasytricha spp. had a hosting effect, and Epidinium spp. had a predatory relationship, with E. coli O157:H7. Additional study into predator-prey and hosting relationships among rumen protozoa and E. coli O157:H7 is warranted.

Ruminal acidosis in beef cattle: the current microbiological and nutritional outlook

Ruminal acidosis continues to be a common ruminal digestive disorder in beef cattle and can lead to marked reductions in cattle performance. Ruminal acidosis or increased accumulation of organic acids in the rumen reflects imbalance between microbial production, microbial utilization, and ruminal absorption of organic acids. The severity of acidosis, generally related to the amount, frequency, and duration of grain feeding, varies from acute acidosis due to lactic acid accumulation, to subacute acidosis due to accumulation of volatile fatty acids in the rumen. Ruminal microbial changes associated with acidosis are reflective of increased availability of fermentable substrates and subsequent accumulation of organic acids. Microbial changes in the rumen associated with acute acidosis have been well documented. Microbial changes in subacute acidosis resemble those observed during adaptation to grain feeding and have not been well documented. The decrease in ciliated protozoal population is a common feature of both forms of acidosis and may be a good microbial indicator of an acidotic rumen. Other microbial factors, such as endotoxin and histamine, are thought to contribute to the systemic effects of acidosis. Various models have been developed to assess the effects of variation in feed intake, dietary roughage amount and source, dietary grain amount and processing, step-up regimen, dietary addition of fibrous byproducts, and feed additives. Models have been developed to study effects of management considerations on acidosis in cattle previously adapted to grain-based diets. Although these models have provided useful information related to ruminal acidosis, many are inadequate for detecting responses to treatment due to inadequate replication, low feed intakes by the experimental cattle that can limit the expression of acidosis, and the feeding of cattle individually, which reduces experimental variation but limits the ability of researchers to extrapolate the data to cattle performing at industry standards. Optimal model systems for assessing effects of various management and nutritional strategies on ruminal acidosis will require technologies that allow feed intake patterns, ruminal conditions, and animal health and performance to be measured simultaneously in a large number of cattle managed under conditions similar to commercial feed yards. Such data could provide valuable insight into the true extent to which acidosis affects cattle performance.

Acidosis in Feedlot Cattle

Mortality from digestive diseases in feedlot cattle is second only to that from respiratory diseases. Acidosis is a major digestive disorder and is likely to continue because of ongoing attempts to improve the efficiency of beef production by feeding more grain and less roughage. Subacute acidosis is the most prevalent form of acidosis in feedlots but is difficult to diagnose because of the absence of overt clinical signs. Control of acidosis is achieved largely by sound nutritional management. No single strategy or solution exists; however, an effective management strategy should factor in dietary formulation, a consistent feeding program, prudent bunk management, use of nonstarch by-products, and feed additives to minimize pen-to-pen and animal-to-animal variations in feed intake.

The effect of absence of protozoa on rumen biohydrogenation and the fatty acid composition of lamb muscle

The effects of the absence of protozoa in the rumen of lambs on animal growth, rumen fermentation, microbial diversity and fatty acid profiles in abomasal fluid and intramuscular fat were measured in ten control and ten protozoa-free (PF) lambs. PF lambs were prepared by isolating them from ewes within the first 24 h after birth. The PF and control lambs were kept for 4 months in two different fields and received a daily supplement of 250 g concentrate. The bacterial populations visualised by denaturing gradient gel electrophoresis differed between the two groups of animals and showed a higher bacterial diversity in control lambs than in PF lambs. Abomasal contents from control lambs contained higher concentrations of 22 : 5n-3 and 22 : 6n-3 and lower concentrations of vaccenic acid (trans-11–18 : 1) and 20 : 3n-6 than PF lambs. The rest of the fatty acids, including the conjugated linoleic acid (CLA) isomers, were present at the same concentrations in abomasal contents from both experimental groups. Fatty acid composition in intramuscular fat showed differences between the groups. PF lambs had higher proportions of 18 : 0, 18 : 3,trans-10,cis-12-CLA and total SFA than control lambs. Control lambs had higher proportions ofcis-9–18 : 1,cis-9,cis-12–18 : 2, 20 : 3n-6, 22 : 6n-3 (DHA) and MUFA. In conclusion, rumen defaunation led to higher tissue levels of thetrans-10,cis-12-CLA isomer and SFA and lower PUFA:SFA ratio andn-3 PUFA in lamb muscle.

Pre- and postweaning attributes in faunated and ciliate-free calves fed calf starter with or without fish meal

In a 2 x 2 factorial design, 24 newborn, crossbred (Bos indicus x Bos taurus) calves were distributed in 4 equal groups involving dietary treatments of prestarter diets with (FM) or without fish meal (NFM) in a faunated (F) or ciliate-free (D) ruminal environment to study the ruminal fermentative development in pre-and postweaning periods. Defaunation was achieved by rearing calves in isolation and its effect was studied after first appearance of ciliate protozoa (observed after 8 wk of age) in the faunated animals. Calves were fed colostrum for 24 h and whole milk until weaning at 8 wk of age. Ruminal content samples were collected on d 4, 1 wk, weekly to 8 wk, and then biweekly at 9, 11, and 13 wk of age. The samples were analyzed for fermentation products [pH, total volatile fatty acids (VFA) and ammonia N] and enzyme [carboxymethyl (CM) cellulase, xylanase, beta-glucosidase, alpha-amylase, beta-galactosidase, proteases, and urease] activities. Weekly feed intake increased with age, but was similar in both groups. Ruminal pH declined steadily during 0 to 4 wk of age and then stabilized. The total VFA concentration increased with the age. The ammonia N (mg/dL) concentration increased from 14.9 on d 4 to 32.4 at 4 wk, decreased to 17.6 at 8 wk, and then steadied during the postweaning period. Samples collected on d 4 had no fibrolytic activity. Xylanase (U/dL) appeared first (1 wk) followed by beta-glucosidase (U/dL) and CM cellulase (U/dL), which increased steadily from a low of 4.69, 0.08, and 2.95 to 31.8 (6 wk), 5.92 (7 wk), and 19.8 (8 wk), respectively, and the concentrations showed nonsignificant alterations during postweaning periods. The concentration of alpha-amylase (U/dL) increased from 34.3 on d 4 to 87.2 at 8 wk, and then decreased to 56.6 (13 wk). beta-Galactosidase increased up to 6 wk then decreased to trace level (0.20 U/dL) at 13 wk of age. The concentrations of proteases and urease reached a steady state after 1 wk of age. The effect of diet type on ruminal fermentation products and enzyme parameters was nonsignificant. However, a steady and proportional alteration in both parameters in response to dry feed intake with the advancement of age was seen in all calves. Defaunation increased total VFA (97.3 vs. 75.8 mM/L) and alpha-amylase activity (80.3 vs. 61.4 U/dL) and decreased ammonia N (16.4 vs. 21.1 mg/dL), whereas the effect on other parameters was nonsignificant. Ruminal fermentative changes responded to dry feed intake, but did not differ in response to animal protein in prestarter diet.

Efeitos da defaunação em ovinos alimentados com cana-de-açúcar (Saccharum officinarum, L.) adicionada de uréia

Em delineamento inteiramente ao acaso, estudou-se o efeito da defaunação em ovinos que receberam cana-de-açúcar e uréia sobre o consumo e digestibilidade aparente de nutrientes, dinâmica da fase sólida, parâmetros de fermentação ruminal e de degradação in situ. As taxas de passagem no rúmen foram, respectivamente, de 3,05 e 1,97%/h, para ovinos faunados e defaunados. Valores mais elevados para taxa (5,4%/h) e extensão (46,7%) da digestão ruminal e de degradabilidade efetiva da FDN da cana (31,5%) foram obtidos nos ovinos faunados. Seus consumos diários (57,7 e 32,3 g/kg0,75, respectivamente para MS e FDN) foram superiores (P<0,06) aos dos ovinos defaunados. Em função do tempo de amostragem observaram-se maiores (P<0,05) concentrações de AGV total, acetato e propionato para os cordeiros faunados. Nos defaunados ocorreu queda pós-prandial mais acentuada (P<0,04) no pH. Para digestibilidade aparente diferença (P<0,05) entre tratamentos foi verificada apenas para matéria seca.

Phytase activity of anaerobic ruminal bacteria

Phytase catalyses the release of phosphate from phytate (myo-inositol hexakisphosphate), the predominant form of phosphorus in cereal grains, oilseeds and legumes. The presence of phytase activity was investigated in 334 strains of 22 species of obligately anaerobic ruminal bacteria. Measurable activities were demonstrated in strains of Selenomonas ruminantium, Megasphaera elsdenii, Prevotella ruminicola, Mitsuokella multiacidus and Treponema spp. Strains isolated from fermentations with cereal grains proved to have high activity, and activity was particularly prevalent in S. ruminantium, with over 96% of the tested strains being positive. The measured phytase activity was found exclusively associated with the bacterial cells and was produced in the presence of approximately 14 mM phosphate. The most highly active strains were all S. ruminantium, with the exception of the one Mitsuokella multiacidus strain examined. Phytase activity varied greatly among positive strains but activities as high as 703 nmol phosphate released (ml culture)-1 were measured for a S. ruminantium strain and 387 nmol phosphate released (ml culture)-1 for the Mitsuokella multiacidus strain.

Enzyme activities of rumen particles and feed samples incubated in situ with differing types of cloth

Three ruminally cannulated non-lactating dairy cows were used to investigate the effects of six different bag cloth types with pore size (microns): free surface area (%) ratios of 200:45, 41:33, 16:5, 10:2, 6:5 and 1:2 respectively on the disappearance of grass silage DM and neutral-detergent fibre (NDF), and on particle-associated carboxymethylcellulase (EC 3.2.1.4; CMCase) and xylanase (EC 3.2.1.8) activities extracted from feed residues. Another objective was to compare microbial activity inside the bags and in rumen ingesta. Rumen incubation periods were 3, 6, 12, 24, 48 and 96 h. DM and NDF disappearance and particle-associated enzyme activities were greatly reduced with the smaller pore size and/or open surface area. Re-analysing some of the data as a 2 x 2 factorial (pore size x free surface area) indicated that, generally, free surface area rather than pore size affected the disappearance of feed components and particle-associated enzyme activities. Enzyme activities were highly correlated with NDF disappearance at 6-48 h of incubation. Cumulative area under CMCase and xylanase activity curves explained 0.79 and 0.88 of the variation in NDF disappearance when different cloth type and 6-48 h incubation data were combined. Weighted mean enzyme activities inside the bags were less than 0.35 those in rumen ingesta. The highest activity values inside the bags (24 or 48 h) were less than 0.50 those found in rumen ingesta. The lower microbial activity inside the bags explains the slower rates of NDF digestion reported with in situ techniques than with rumen evacuation techniques. The general assumption of similar microbial activity inside the bags and in rumen ingesta is not justified by the present results, and caution must be taken in interpreting in situ results quantitatively for feed evaluation systems.