Two-step freezing procedure for cryopreservation of rumen ciliates, an effective tool for creation of a frozen rumen protozoa bank

Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective

Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at -20 °C and (2) frozen at -20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using -20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO-20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at -20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.

- 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 medium-chain fatty acids (MCFAs) on in vitro rumen fermentation, methane production, and nutrient digestibility under low- and high-concentrate diets

This experiment was conducted to investigate the effects of different dosages and types of medium-chain fatty acids (MCFAs) on rumen fermentation in vitro under low- and high-concentrate diets. For this purpose, two in vitro experiments (Exp.) were conducted. In Exp. 1, the concentrate-roughage ratio of the fermentation substrate [total mixed rations (TMR), dry matter (DM) basis] was 30:70 (low-concentrate diet), while in Exp. 2, it was 70:30 (high-concentrate diet). Three types of MCFAs with octanoic acid (C₈ ), capric acid (C₁₀ ), and lauric acid (C₁₂ ) were added accounting for 1.5%, 6%, 9%, and 15% of the in vitro fermentation substrate weight (200 mg or 1 g, DM basis) based on control group, respectively. The results showed that the addition of MCFAs all could significantly reduce methane (CH₄ ) production and the number of rumen protozoa, methanogens, and methanobrevibacter under the two diets with the dosages increased (p < 0.05). In addition, MCFAs had a certain degree of improvement on rumen fermentation and influenced in vitro digestibility under low- and high-concentrate diets, and their effects were related to the dosages and types of MCFAs. This study provided a theoretical basis for the selection of types and dosages of MCFAs in ruminants production.

Preservation Method of Rumen Fluid Collected From Harvested Cattle Alters in vitro Digestibility of Reference Feedstuffs

The objective of our experiment was to evaluate preservation and revitalization strategies for rumen inoculum anticipating research and veterinary applications. Rumen fluid samples were collected from 12 harvested cattle. Liquid samples were divided into five 500-mL aliquots which were randomly allocated to one of five treatments in a 2 × 2 + 1 augmented factorial design. Factors included preservation method [freezing (FZN) or lyophilization (LYO)] and preservative (glycerol; + or –). A fresh control (CON) was maintained from each sample. Feedstuffs used in this experiment were alfalfa hay, Coastal bermudagrass hay, cracked maize, rice bran, and soybean meal. Reference feedstuffs were subjected to batch culture in vitro true digestibility (IVTD) and in vitro NDF digestibility (IVNDFD) assays using inoculum from each of the five treatments. There was an effect (P &lt; 0.05) of preservation method, preservative, and their interaction for both IVTD and IVNDFD of each of the five references feedstuffs. Freezing or lyophilization of rumen inoculum reduced (P &lt; 0.05) IVTD and IVNDFD of reference feeds relative to the CON. Despite lower degradation of feeds when frozen or lyophilized rumen fluid was used rather than fresh, differences between them in IVTD and IVNDFD suggest that, in the absence of fresh inoculum, preserved rumen fluid may be a viable option for veterinary applications, such as transfaunation, but likely will not be viable for research applications.

Effects of preservation of rumen inoculum on volatile fatty acids production and the community dynamics during batch fermentation of fruit pomace

Rumen fluid (RF) as inocula is useful for evaluating biomass digestibility and has potential for producing volatile fatty acids (VFA) via the carboxylate platform. However, RF is not readily available, necessitating evaluation of potential preservation methods. Glycerol (50% v/v) and DMSO (5% v/v) were used to preserve rumen inocula for 3 months at -80 °C. Effects of cryo-preservation on digestibility, VFA production and community composition with β-diversity distance metrics were compared to fresh RF using apple, citrus and grape pomace as substrates. For all substrates, DMSO cryo-preserved rumen digestibility parameters, VFA yield and product distribution were more significantly comparable to fresh RF (P > 0.05) than was glycerol cryo-preserved RF. Similarly, β-diversity coefficient (unweighted unifrac) between DMSO cryo-preserved RF and fresh RF was 0.250 while the coefficient was 0.359 for the glycerol cryo-preserved RF compared to fresh RF. This showed that a DMSO cryo-preserved RF is less affected by preservation effects and is a more promising alternative to fresh RF.

In vitro assessment of the factors that determine the activity of the rumen microbiota for further applications as inoculum

BACKGROUND

The rumen microbiota has been used as inoculum for in vitro studies and as a probiotic to improve productivity in young animals. However, great variability across studies has been noted depending on the inoculum considered. The present study aims to assess the relevance of different factors (microbial fraction, collection time, donor animal diet, fermentation substrate and inoculum preservation method) to maximize the rumen inoculum activity and set the standards for further in vitro and in vivo applications.

RESULTS

Rumen inoculum sampled at 3 h after feeding led to greater microbial growth and activity [+12% volatile fatty acid (VFA), +17% ammonia] compared to before feeding. Similar results were noted when rumen liquid or rumen content were used as inocula. Rumen inoculum adapted to concentrate diets increased microbial activity (+19% VFA) independently of the substrate used in vitro. Freezing-thawing the inoculum, in comparison to fresh inoculum, decreased microbial activity (-14% VFA, -96% ammonia), anaerobic fungi and protozoa, with holotrichs protozoa being particularly vulnerable. Inoculum lyophilization had a stronger negative effect on microbial activity (-51% VFA) and delayed re-activation of the microbes, leading to lower levels of methanogens and anaerobic fungi, as well as almost complete wipe out of rumen protozoa.

CONCLUSIONS

Fresh rumen fluid sampled at 3 h after feeding from donor animals that were fed concentrate diets should be chosen when the aim is to provide the most diverse and active rumen microbial inoculum. © 2018 Society of Chemical Industry.

Protocol for cryopreservation of the turbot parasite Philasterides dicentrarchi (Ciliophora, Scuticociliatia)

Philasterides dicentrarchi is a free-living marine ciliate that can become an endoparasite that causes a severe disease called scuticociliatosis in cultured fish. Long-term maintenance of this scuticociliate in the laboratory is currently only possible by subculture, with periodic passage in fish to maintain the virulence of the isolates. In this study, we developed and optimized a cryopreservation protocol similar to that used for the long-term storage of scuticociliates of the genus Miamiensis. The cryogenic medium comprised ATCC medium 1651 and a combination of 11% dimethylsulfoxide and 5% glycerol. We have verified that the most important factor ensuring the efficiency of the cryopreservation procedure is the growth phase of the culture, and that ciliates should be cryopreserved at the stationary phase (around the sixth day of culture). The cryopreservation protocol described here can be used for all strains of P. dicentrarchi as well as commercial strains of Miamiensis and enables the virulence of the strains to be maintained. Finally, this cryopreservation protocol has been shown to be more effective than others routinely applied to scuticociliates, yielding a higher survival rate with a lower initial concentration of ciliates. The results obtained indicate that the cropreservation protocol enables the long-term storage of scuticociliate parasites while maintaining the virulence of the isolates. The protocol is therefore suitable for use in vaccine production and related studies.

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.

Effect of high DMSO concentration on albumin during freezing and vitrification

This is a light microscopy image taken of the frozen solution at −20 °C during equilibrium freezing. The freeze concentrate surrounding the ice crystals, comprises unfrozen water and solutes (DMSO and albumin). The bright rectangle is the IR aperture.

Rumen microbial communities influence metabolic phenotypes in lambs

The rumen microbiota is an essential part of ruminants shaping their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

Survival and morphologic changes of entodiniomorphid ciliate Troglodytella abrassarti in chimpanzee feces

Entodiniomorphid ciliates occur in the hindgut of both captive and wild African great apes. These ciliates do not form cysts, and therefore they are more susceptible for degradation. This present study focused on the survival, quantification, and decomposition processes of Troglodytella abrassarti trophozoites in the feces of captive chimpanzees. Fecal samples were examined using wet mounts and the merthiolate-iodine-formaldehyde concentration method, and the number of ciliates was expressed as ciliates per gram, which did not differ when examined from three different samples of the same feces. Trophozoites of T. abrassarti survived 5-15 hr after defecation at 25 degrees C under aerobic conditions. Decomposition of trophozoites began immediately after defecation; however, most of the trophozoites had a compact shape and visible cilia. Trophozoites, although without cilia, can be detected in the feces 55-65 hr after defecation, although most of the trophozoites were fragmented. The total number of ciliates in the sample started to decrease 35-55 hr after defecation. The absence of entodiniomorphid ciliates in fecal samples could not be caused by delayed feces fixation; instead, the absence was due to low sensitivity of coproscopic techniques. However, because of quick morphologic changes of trophozoites, accurate identification of ciliates in older samples may be difficult or even impossible.

Improved in vitro procedure for maintaining stock cultures of three genera of rumen protozoa

To maintain stock cultures of rumen protozoa, studies were initiated to explore possible methods for keeping the protozoa viable without feeding every day. Cultures of Entodinium caudatum, Epidinium caudatum, Enoploplastron triloricatum, and Entodinium exiguum were used to study the effect of not feeding for 1 or 2 d. The study lasted 88 d, and although bacterial concentrations decreased when cultures were not fed for 2 d (over the weekend), they recovered quickly with subsequent daily feedings. The exception was Enoploplastron triloricatum, which showed a gradual decline over the entire study. Addition of streptomycin to the media had little effect on maintaining bacterial concentrations in all cultures except Entodinium caudatum, in which the overall mean concentration was greater (P < 0.01). No differences in pH or bacterial concentrations were found between cultures fed daily and those held without feed for 2 d, with or without streptomycin. For maintaining protozoal cultures (10-mL volumes) over a long period without feeding on weekends, the following schedule is proposed: transfer and feed 0.12 mL of 1.5% ground wheat-1% orchardgrass on Monday; feed 0.12 mL of 1.5% ground wheat-1% orchardgrass on Tuesday, Wednesday, and Thursday; transfer and feed 0.5 mL of 1.5% ground wheat-1% orchardgrass on Friday; do not feed on Saturday and Sunday.

Effect of the cryopreservation conditions on the viability of the rumen ciliate Diploplastron (Metadinium) affine

AIMS

To study the viability of Diploplastron (Metadinium) affine after its cryopreservation at two cooling rates, and the effect of procedure conditions on viability.

METHODS AND RESULTS

There were differences in viability between cooling rates (1 and 4 degrees C min(-1)) at 15 or 5 degrees C, but not after thawing. When the equilibrium temperature (25 or 5 degrees C), the cryopreservant (glycerol or dimethyl sulfoxide [DMSO]) and the use of membrane protector were tested, there were no differences caused by the cryopreservant or the membrane protector. However, the equilibrium at 25 degrees C increased the viability (P = 0.005) compared with 5 degrees C.

CONCLUSIONS

Viability after thawing was 0.10-0.19. Adding the cryopreservant (either glycerol or DMSO) at 25 degrees C instead of 5 degrees C improves viability of D. affine after thawing.

SIGNIFICANCE AND IMPACT OF THE STUDY

Conditions of cryopreservation are largely dependent on the species of rumen protozoa. Number of viable cells after thawing would indicate the possibility of culture recovery for D. affine.

Regeneration of cryoresistance of in vitro rumen ciliate cultures

The purpose of this study was to investigate factors affecting mechanical- and cryo-resistance of the rumen ciliates Entodinium caudatum (E.c.), Entodinium furca monolobum (E.f.m.), Entodinium simplex (E.s.), Diplodinium denticulatum (two clones, D.d.01 and D.d.02), Diploplastron affine (D.a.) and Epidinium ecaudatum forma caudatum (E.e.c.) after long-term in vitro cultivation. Following prolonged in vitro cultivation (more than six months), the ciliates were very sensitive to both centrifugation and 5% (v/v) dimethylsulphoxide, with motility decreased to: 39 and 23% for E.c., 66 and 32% for E.f.m., 46 and 27% for D.d. 01, 64 and 41% for D.a., and 44 and 28% for E.e.c., respectively. Thus, cryopreservation was unsuccessful. The effect of supplementing the ciliate growth medium with rumen fluid, glycine-betaine, proline, myo-inositol, linoleic acid, Sel-Plex or insulin, together with the effect of the source of rumen fluid on ciliate resistance to centrifugation, dimethylsulphoxide and freezing was also tested. The omission of rumen fluid from the growth medium resulted in the loss of cryoresistance after one-month cultivation. Supplementing the growth environment with a combination of glycine-betaine, proline, linoleic acid, Sel-Plex, insulin plus improved quality rumen fluid significantly enhanced survival of the ciliates after the freezing-thawing procedure (from 1 to 33% survival in un-supplemented vs. supplemented for E.c., P<0.01; 4-40% E.f.m., P<0.01; 0-17% D.d., P<0.05; 5-7% D.a. and 4-36% E.e.c., P<0.01).

Parasite cryopreservation by vitrification

Parasitic protozoa and helminths and parasitic/vector insects each have distinct requirements for cryopreservation. Most parasitic protozoa respond to cryopreservation stresses similarly to other single cell suspensions, but few species are currently routinely cryopreserved by protocols specifically designed for vitrification. With slow equilibrium cooling, some protozoa osmotically dehydrated by solutes concentrated in the residual unfrozen fraction will survive by vitrifying. Several species of helminths, together with insect embryos cannot be cryopreserved by slow cooling protocols and have an absolute requirement for vitrification. Studies incorporating slow cooling and stepped cooling of both protozoa and helminths, particularly the intraerythrocytic stages of malaria and the schistosomula larvae of Schistosoma mansoni have aided in the design of vitrification protocols for parasites. For helminths, the most widely used cryopreservation protocol, originally successful for cryopreserving S. mansoni schistosomula, consists of the addition of ethanediol in two steps, followed by rapid cooling (approximately 5100 degrees C min(-1)) to -196 degrees C. This technique exploits the temperature-dependent differential in permeability of the cryoprotectant additive (CPA) to first permeate into the organism at 37 degrees C followed by a dehydration-mediated internal CPA increase in concentration resulting from incubation in a second higher CPA concentration at 0 degree C. Samples are rapidly warmed/diluted (approximately 14,000 degrees C min(-1)) to recover the organisms from liquid nitrogen storage. Variations on this technique have also been successful in cryopreserving the larvae and adult worms of filariae, muscle stage larvae of Trichinella spp., the infective stages of gastro-intestinal nematode parasites and insect embryos. Other protocols where the dehydration step precedes CPA addition have been used to cryopreserve entomogenous nematode larvae by vitrification. Techniques that utilize high concentrations of CPA cocktails and slower cooling, developed for the vitrification of mammalian embryos, have been applied to the cryopreservation of parasitic protozoa, but with limited success to date. Where cryopreservation by classical slow cooling methods is possible, vitrification has enhanced the levels of survival obtained. And vitrification has enabled the successful cryopreservation of those parasitic species not able to be cryopreserved by traditional methods. Since a limited number of parasitic organisms has been cryopreserved using vitrification protocols, there is considerable scope for further improvement in the cryopreservation techniques used for many parasitic species.

A cryopreservation procedure for the rumen protozoon Entodinium caudatum: estimation of its viability by fluorescence microscopy

AIMS

To study the viability of a culture of the rumen protozoon Entodinium caudatum after a cryopreservation procedure by a fluorescence microscopy staining method.

METHODS AND RESULTS

Fluorescence method is based on the different colour of cells depending on their membrane integrity. When the temperature effect was studied either by fluorescence or motility, the techniques were correlated (r = 0.727) and their slopes and intercepts were not different (P > 0.05). However, motility showed a higher variation coefficient (0.40 vs 0.12). There were no differences between cooling rates at cryopreservation (1 and 4 degrees C min-1) at 38, 15 or 5 degrees C, nor after thawing.

CONCLUSIONS

Fluorescence staining is more accurate than motility for assessing protozoal viability. Viability after thawing was 0.50, and the number of viable cells per 250 microl straw was 320 and 420 for 1 and 4 degrees C min-1.

SIGNIFICANCE AND IMPACT OF THE STUDY

This cryopreservation procedure seems to ensure culture recovery for E. caudatum.