Inhibition of the Rumen Ciliate Entodinium caudatum by Antibiotics

Culture techniques for ciliate protozoa from the rumen: Recent advances and persistent challenges

Ciliate protozoa are key members of the microbial community of the rumen. Their study is important to the health and productivity of cattle, which are their hosts. However, there have been persistent challenges in culturing this microbial group in the laboratory. This review will sum up recent advances along with these persistent challenges. Protozoa have been maintained in three types of cultures (ex vivo, in vitro batch, in vitro continuous). Ex vivo cultures are prepared readily from rumen contents by washing away contaminating cells (e.g., bacteria). They have been useful in making basic observations of metabolism, such as which types of fermentation products protozoa form. However, these cultures can be maintained for only short periods (minutes or hours). In vitro batch and in vitro continuous cultures can be used in longer experiments (weeks or longer). However, it is not currently possible to maintain protozoa in these cultures unless bacteria are also present. We conclude the review with a protocol for preparing ex vivo cultures of protozoa. Our protocol has been standardized and used successfully across animal diets, users, and institutions. We anticipate this review will prepare others to culture rumen ciliate protozoa and reach new insights into this important microbial group.

Rumen protozoa and viruses: The predators within and their functions-A mini-review

The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion and fermentation, but as predators, they affect the microbiome and its function by regulating the abundance and activities of other rumen microbes both in a top-down (by directly killing the prey) and bottom-up (by affecting the metabolism of other microbes) manner. Rumen viruses (or phages, used interchangeably below) are diverse and abundant but the least understood. They are also predators (intracellular "predators") because of their lytic lifecycle, although they can co-exist peacefully with their hosts and reprogram host metabolism, buttressing host ecological fitness. In doing so, rumen viruses also affect the rumen microbiome in both a top-down and a bottom-up manner. Here we review the recent advancement in understanding both types of predators, focusing on their potential impact on the rumen microbiome and functions.

Turning weeds into feed: Ensiling Calotropis gigantea (Giant milkweed) reduces its toxicity and enhances its palatability for dairy cows

Calotropis gigantea (Giant milkweed, GM) has the potential to be utilized as a new feed additive for ruminants, however, the presence of unpalatable or toxic compounds decreases animal feed intake. This study aimed to valorize GM as a potential new feed resource through the chemical and microbial biotransformation of toxic compounds that will henceforth, make the plant palatable for cows. After GM's ensiling using fermentative bacteria, the plant was sampled for UHPLC-MS/MS to analyse the metabolomic changes. Illumina Miseq of the 16 S rRNA fragment genes and ITS1 were used to describe the microbial composition and structure colonizing GM silage and contributing to the biodegradation of toxic compounds. Microbial functions were predicted from metataxonomic data and KEGG pathways analysis. Eight Holstein dairy cows assigned in a cross-over design were supplemented with GM and GM silage to evaluate palatability and effects on milk yield and milk protein. Cows were fed their typical diet prior to the experiment (positive control). After ensiling, 23 flavonoids, 47 amino acids and derivatives increased, while the other 14 flavonoids, 9 amino acids and derivatives decreased, indicating active metabolism during the GM ensiling process. Lactobacillus buchneri, Bacteroides ovatus, and Megasphaera elsdenii were specific to ensiled GM and correlated to functional plant metabolites, while Sphingomonas paucimobilis and Staphylococcus saprophyticus were specific to non-ensiled GM and correlated to the toxic metabolite 5-hydroxymethylfurfural."Xenobiotics biodegradation and metabolism", "cancer overview" and "neurodegenerative disease" were the highly expressed microbial KEGG pathways in non-ensiled GM. Non-ensiled GM is unpalatable for cows and drastically reduces the animal's feed intake, whereas ensiled GM does not reduce feed intake, milk yield and milk protein. This study provides essential information for sustainable animal production by valorizing GM as a new feed additive.

- 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.

Metabolic influence of core ciliates within the rumen microbiome

Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.

Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates

Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.

Identification of Bioactive Phytochemicals from Six Plants: Mechanistic Insights into the Inhibition of Rumen Protozoa, Ammoniagenesis, and α-Glucosidase

Simple Summary

Rumen protozoa have some contribution to feed digestibility in the rumen, but Entodinium, the most predominant genus, is the main culprit of inefficient nitrogen utilization in ruminants. Using chemical drugs, many studies have attempted to inhibit the rumen protozoa, but few of the approaches are either effective or practical. In this study, we investigated the nutritional and functional properties of Adansonia digitata (baobab), Flemingia macrophylla (waras tree), Kalimeris indica (Indian aster),Brassica rapa subsp. chinensis (bok choy), Portulaca oleracea (common purslane), and Calotropis gigantea (giant milkweed) for their potential as feed additives in animal husbandry. The plants were also analyzed for their major phytochemicals using reversed phase-high performance liquid chromatography (HPLC) and then evaluated for their ability to inhibit rumen protozoa, ammoniagenesis, and microbial α-glucosidase activity in vitro. C. gigantea inhibited the rumen protozoa and reduced the wasteful ammoniagenesis, thereby indicating improved nitrogen utilization. A. digitata also reduced the microbial α-glucosidase activity that can potentially contribute to rumen acidosis. The tested plants, especially C. gigantea and A. digitata, could be used as potential alternatives to chemicals or antibiotics to ensure sustainable and green animal husbandry.

Abstract

Rumen protozoa prey on feed-degrading bacteria synthesizing microbial protein, lowering nitrogen utilization efficiency in ruminants. In this in vitro study, we evaluated six plants (Adansonia digitata, Flemingia macrophylla, Kalimeris indica,Brassica rapa subsp. chinensis, Portulaca oleracea, and Calotropis gigantea) for their potential to inhibit rumen protozoa and identified the phytochemicals potentially responsible for protozoa inhibition. Rumen protozoa were anaerobically cultured in vitro in the presence of each plant at four doses. All of the tested plants reduced total rumen protozoa (p ≤ 0.05), but C. gigantea and B. rapa were the most inhibitory, inhibiting rumen protozoa by 45.6 and 65.7%, respectively, at the dose of 1.1 mg/mL. Scanning electron microscopy revealed a disruption of the extracellular structure of protozoa cells. Only C. gigantea also decreased the wasteful ammoniagenesis (p ≤ 0.05). Moreover, the A. digitata extract inhibited α-glucosidase activity by about 70% at 100 µg/mL. Reversed-phase high-performance liquid chromatography analysis detected quercetin, anthraquinone, 3-hydroxybenzoic acid, astragaloside, and myricetin in the tested plant leaves. These plants may hold potential as feed additives to reduce rumen protozoa and α- glucosidase activity. Future research is needed to identify the specific anti-protozoal compound(s), the effects on the rumen microbiome, and its fermentation characteristics.

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.

Nitrate supplementation of rations based on rice straw but not Pangola hay, improves growth performance in meat goats

Objective

Supplemental nitrate is known to be an effective tool to mitigate methane emission by ruminants. Based on theoretical considerations, supplemental nitrate can improve but also deteriorate the growth performance. The overall effect of supplemental nitrate on growth performance, however, is not yet known. The objective of the current study was therefore to evaluate the effect of a higher dose of NO₃⁻ on overall growth performance when feeding either Pangola grass hay or rice straw.

Methods

Thirty-two crossbred, 3-month-old Thai native×Anglo-Nubian crossbred male goats were used. The experiment had a 2×2 factorial design with an experimental period of 60 days. Eight goats were randomly allocated to each dietary treatment, i.e. a ration containing either Pangola hay (Digitaria eriantha Steud) or rice straw (Oryza Sativa) as a source of roughage, supplemented with a concentrate containing either 3.2% or 4.8% potassium nitrate. The rations were formulated to be isonitrogenous. The animals were weighed at the start of the experiment and at days 30 and 60. Feces were collected during the last five days of each 30-day period.

Results

High-nitrate increased overall DM intake by approximately 3%, irrespective the source of roughage, but only the goats fed a rice straw-based ration responded with an increase in body weight (BW). Thus, the overall feed conversion ratio (kg feed/kg BW gain) was influenced by roughage source ×nitrate and decreased by almost 60% when the goats were fed rice straw in combination with a high versus a low dietary nitrate content. The digestibility of macronutrients was only affected by the source of roughage and the digestibility of organic matter, crude protein, and neutral detergent fibre was greater when the goats were fed Pangola hay.

Conclusion

It was concluded that the replacement of soybean meal by nitrate improves the growth performance of meat goats fed rations based on rice straw, but not Pangola hay.

Extending Burk Dehority's Perspectives on the Role of Ciliate Protozoa in the Rumen

Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ciliated protozoa. We have summarized many of the advancements in knowledge from his work but also in his scientific way of thinking about interactions of ruminal ciliates with the entire rumen microbial community and animal host. As a dedication to his legacy, an electronic library of high-resolution images and video footage catalogs numerous species and techniques involved in taxonomy, isolation, culture, and ecological assessment of ruminal ciliate species and communities. Considerable promise remains to adapt these landmark approaches to harness eukaryotic cell signaling technology with genomics and transcriptomics to assess cellular mechanisms regulating growth and responsiveness to ruminal environmental conditions. These technologies can be adapted to study how protozoa interact (both antagonism and mutualism) within the entire ruminal microbiota. Thus, advancements and limitations in approaches used are highlighted such that future research questions can be posed to study rumen protozoal contribution to ruminant nutrition and productivity.

The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features

Background

Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. However, they remain poorly understood due to the lack of definitive direct evidence without influence by prokaryotes (including symbionts) in co-cultures or the rumen. In this study, we used RNA-Seq to characterize the transcriptome of Entodinium caudatum, the most predominant and representative rumen ciliate species.

Results

Of a large number of transcripts, > 12,000 were annotated to the curated genes in the NR, UniProt, and GO databases. Numerous CAZymes (including lysozyme and chitinase) and peptidases were represented in the transcriptome. This study revealed the ability of E. caudatum to depolymerize starch, hemicellulose, pectin, and the polysaccharides of the bacterial and fungal cell wall, and to degrade proteins. Many signaling pathways, including the ones that have been shown to function in E. caudatum, were represented by many transcripts. The transcriptome also revealed the expression of the genes involved in symbiosis, detoxification of reactive oxygen species, and the electron-transport chain. Overall, the transcriptomic evidence is consistent with some of the previous premises about E. caudatum. However, the identification of specific genes, such as those encoding lysozyme, peptidases, and other enzymes unique to rumen ciliates might be targeted to develop specific and effective inhibitors to improve nitrogen utilization efficiency by controlling the activity and growth of rumen ciliates. The transcriptomic data will also help the assembly and annotation in future genomic sequencing of E. caudatum.

Conclusion

As the first transcriptome of a single species of rumen ciliates ever sequenced, it provides direct evidence for the substrate spectrum, fermentation pathways, ability to respond to various biotic and abiotic stimuli, and other physiological and ecological features of E. caudatum. The presence and expression of the genes involved in the lysis and degradation of microbial cells highlight the dependence of E. caudatum on engulfment of other rumen microbes for its survival and growth. These genes may be explored in future research to develop targeted control of Entodinium species in the rumen. The transcriptome can also facilitate future genomic studies of E. caudatum and other related rumen ciliates.

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.

Do Ruminal Ciliates Select Their Preys and Prokaryotic Symbionts?

Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal microbiota for their survival. However, it remains elusive if they have selectivity over their preys or symbionts. In the present study, we investigated the above selectivity by identifying and comparing the free-living prokaryotes (FLP) and the ciliate-associated prokaryotes (CAP) using Illumina MiSeq sequencing of 16S rRNA gene amplicons. We used single ciliates cells of both monocultures of Entodinium caudatum and Epidinium caudatum and eight different ciliate genera isolated from fresh rumen fluid of dairy cows. Irrespective of the source (laboratory monocultures vs. fresh isolates) of the single ciliate cells, the CAP significantly differed from the FLP in microbiota community profiles. Many bacterial taxa were either enriched or almost exclusively found in the CAP across most of the ciliate genera. A number of bacteria were also found for the first time as ruminal bacteria in the CAP. However, no clear difference was found in methanogens between the CAP and the FLP, which was confirmed using methanogen-specific qPCR. These results suggest that ruminal ciliates probably select their preys and symbionts, the latter of which has rarely been found among the free-living ruminal prokaryotes. The bacteria enriched or exclusively found in the CAP can be target bacteria to detect and localize using specific probes designed from their 16S rRNA sequences, to characterize using single-cell genomics, or to isolate using new media designed based on genomic information.