Comparison of duodenal flow and digestibility in fauna-free sheep inoculated with Holotrich protozoa, Entodinium monofauna or total mixed protozoa population

- 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.

Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats

Introduction

This study explores if promoting a complex rumen microbiota represents an advantage or a handicap in the current dairy production systems in which ruminants are artificially reared in absence of contact with adult animals and fed preserved monophyte forage.

Methods

In order to promote a different rumen microbial diversity, a total of 36 newborn goat kids were artificially reared, divided in 4 groups and daily inoculated during 10 weeks with autoclaved rumen fluid (AUT), fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate (RFC) diets, or absence of inoculation (CTL). At 6 months of age all animals were shifted to an oats hay diet to determine their ability to digest a low quality forage.

Results and discussion

Early life inoculation with fresh rumen fluid promoted an increase in the rumen overall microbial diversity which was detected later in life. As a result, at 6 months of age RFF and RFC animals had higher bacterial (+50 OTUs) and methanogens diversity (+4 OTUs) and the presence of a complex rumen protozoal community (+32 OTUs), whereas CTL animals remained protozoa-free. This superior rumen diversity and presence of rumen protozoa had beneficial effects on the energy metabolism allowing a faster adaptation to the forage diet, a higher forage digestion (+21% NDF digestibility) and an energetically favourable shift of the rumen fermentation pattern from acetate to butyrate (+92%) and propionate (+19%) production. These effects were associated with the presence of certain rumen bacterial taxa and a diverse protozoal community. On the contrary, the presence of rumen protozoa (mostly Entodinium) had a negative impact on the N metabolism leading to a higher bacterial protein breakdown in the rumen and lower microbial protein flow to the host based on purine derivatives urinary excretion (-17% to -54%). The inoculation with autoclaved rumen fluid, as source of fermentation products but not viable microbes, had smaller effects than using fresh inoculum. These findings suggest that enhancing rumen microbial diversity represents a desirable attribute when ruminants are fed forages in which the N supply does not represent a limiting factor for the rumen microbiota.

Effect of rumen microbiota transfaunation on the growth, rumen fermentation, and microbial community of early separated Japanese Black cattle

This study aimed to investigate the effect of rumen microbiota transfaunation on the growth, rumen fermentation, and the microbial community of Japanese Black cattle that were separated early from their dams. Here, 24 calves were separated from their dams immediately after calving, 12 of which were transfaunated via inoculation with rumen fluid from adult cattle at the age of 2 months while the remaining 12 were kept unfaunated (not-inoculated). Feed efficiency monitoring was performed during 7-10 months of age. Body weight and feed intake were not significantly different between the transfaunated and unfaunated cattle. Transfaunation increased the relative levels of acetate and butyrate but decreased those of propionate, which increased the non-glucogenic/glucogenic short-chain fatty acid ratio. Microbial 16S, 18S, and ITS ribosomal RNA gene amplicon analysis showed that rumen microbial diversity and composition differed between transfaunated and unfaunated cattle; transfaunation increased the abundance of acetate- and butyrate-producing bacteria, and decreased the abundance of bacterial genera associated with propionate production. Transfaunation also increased the abundance of Methanomassiliicoccaceae_group10 (1.94% vs. 0.05%) and Neocallimastix (27.1% vs. 6.8%) but decreased that of Methanomicrobium (<0.01% vs. 0.06%). Our findings indicate that rumen microbiota transfaunation shifts rumen fermentation toward acetate and butyrate production through a change in the rumen microbial composition in Japanese Black cattle.

Role of Chitin and Chitosan in Ruminant Diets and Their Impact on Digestibility, Microbiota and Performance of Ruminants

The slow progress in the development of the subsector, particularly of alternative feed sources such as agro-industrial byproducts and unconventional feed resources, has deepened the gap in the availability of and accessibility to animal feed. Production of animal feed is highly resource demanding. Recently, it has been shown that increasing climate change, land degradation, and the recurrence of droughts have worsened the feed gap. In the backdrop of these challenges, there has been attention to food-not-feed components, which have great potential to substitute human-edible components in livestock feeding. Chitosan, a non-toxic polyglucosamine, is widely distributed in nature and used as a feed additive. Chitosan is obtained from the de-acetylation process of the chitin and is mostly present in shrimp, crabs, and insect exoskeletons, and has antimicrobial and anti-inflammatory, anti-oxidative, antitumor, and immune-stimulatory hypo-cholesterolemic properties. This review article discusses the results of recent studies focusing on the effects of chitosan and chitin on the performance of dairy cows, beef steers, sheep, and goats. In addition, the effects of chitosan and chitin on feed intake, feed digestibility, rumen fermentation, and microbiota are also discussed. Available evidence suggests that chitosan and chitin used as a feed additive for ruminants including dairy cows, beef steers, sheep, goats, and yaks have useful biological effects, including immune-modulatory, antimicrobial, and other important properties. These properties of chitosan and chitin are different from the other feed additives and have a positive impact on production performance, feed digestibility, rumen fermentation, and bacterial population in dairy cows, beef steers, sheep, goats, and yaks. There is promising evidence that chitosan and chitin can be used as additives in livestock feed and that well-designed feeding interventions focusing on these compounds in ruminants are highly encouraged.

Effect of Chitosan Inclusion and Dietary Crude Protein Level on Nutrient Intake and Digestibility, Ruminal Fermentation, and N Excretion in Beef Heifers Offered a Grass Silage Based Diet

Nitrogen (N) use efficiency in beef cattle is low (10-20%), resulting in large amounts of N excreted into the environment. The objective of this study was to evaluate the effects of chitosan inclusion and dietary crude protein (CP) level on nutrient intake and digestibility, ruminal fermentation, and N excretion in beef heifers. Eight Belgian Blue × Holstein Friesian cross beef heifers (752 ± 52 kg BW) were used in a 4 × 4 Latin square with a 2 × 2 factorial design. Factors were dietary CP concentration-high CP, 16% (HP) or low CP, 12% (LP)-and chitosan inclusion-0 or 10 g kg^-1 dry matter (DM) offered at 50:50 forage concentrate ratio on a dry matter (DM) basis. Apparent total tract digestibility of DM, organic matter (OM), and CP were reduced (p < 0.001) with chitosan inclusion, whereas offering the HP diets increased apparent total tract digestibility of CP (p < 0.001). Offering the HP diets increased urinary N excretion (p < 0.001), while chitosan inclusion increased N excretion in faeces (p < 0.05). Ruminal pH was increased with chitosan inclusion (p < 0.01). There was a CP × chitosan interaction for rumen ammonia (NH₃) concentrations (p < 0.05). Including chitosan in the HP diets increased ruminal NH₃ concentration while having no effect on the LP diets. Urinary N excretion was increased with increased levels of CP, but chitosan inclusion increased the quantity of N excreted in the faeces.

The Role of Ciliate Protozoa in the Rumen

First described in 1843, Rumen protozoa with their striking appearance were assumed to be important for the welfare of their host. However, despite contributing up to 50% of the bio-mass in the rumen, the role of protozoa in rumen microbial ecosystem remains unclear. Phylogenetic analysis of 18S rDNA libraries generated from the rumen of cattle, sheep, and goats has revealed an unexpected diversity of ciliated protozoa although variation in gene copy number between species makes it difficult to obtain absolute quantification. Despite repeated attempts it has proven impossible to maintain rumen protozoa in axenic culture. Thus it has been difficult to establish conclusively a role of ciliate protozoa in rumen fiber degradation. The development of techniques to clone and express ciliate genes in λ phage, together with bioinformatic indices to confirm the ciliate origin of the genes has allowed the isolation and characterization of fibrolytic genes from rumen protozoa. Elimination of the ciliate protozoa increases microbial protein supply by up to 30% and reduces methane production by up to 11%. Our recent findings suggest that holotrich protozoa play a disproportionate role in supporting methanogenesis whilst the small Entodinium are responsible for much of the bacterial protein turnover. As yet no method to control protozoa in the rumen that is safe and practically applicable has been developed, however a range of plant extract capable of controlling if not completely eliminating rumen protozoa have been described.

Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions

Rumen methanogenesis represents an energy waste for the ruminant and an important source of greenhouse gas; thus, integrated studies are needed to fully understand this process. Eight fauna-free sheep were used to investigate the effect of successive inoculation with holotrich protozoa then with total fauna on rumen methanogenesis. Holotrichs inoculation neither altered rumen fermentation rate nor diet digestibility, but increased concentrations of acetate (+15%), butyrate (+57%), anaerobic fungi (+0.82 log), methanogens (+0.41 log) and methanogenesis (+54%). Further inoculation with total fauna increased rumen concentrations of protozoa (+1.0 log), bacteria (+0.29 log), anaerobic fungi (+0.78 log), VFA (+8%), ammonia and fibre digestibility (+17%) without affecting levels of methanogens or methanogenesis. Rumen methanogens population was fairly stable in terms of structure and diversity, while the bacterial community was highly affected by the treatments. Inoculation with holotrich protozoa increased bacterial diversity. Further inoculation with total fauna lowered bacterial diversity but increased concentrations of certain propionate and lactate-producing bacteria, suggesting that alternative H2 sinks could be relevant. This experiment suggests that holotrich protozoa have a greater impact on rumen methanogenesis than entodiniomorphids. Thus, further research is warranted to understand the effect of holotrich protozoa on methane formation and evaluate their elimination from the rumen as a potential methane mitigation strategy.

Rumen fermentation and microbial population in lactating dairy cows receiving diets containing oilseeds rich in C-18 fatty acids

Sixteen Holstein rumen-cannulated primiparous milking dairy cows were fed a control diet (CN) based on maize silage and soyabean meal during a 4-week period before the start of a 21-d experiment with oilseeds containing high concentration of linoleic acid (Linola™) or linolenic acid (NuLin™). Thereafter, four cows received ad libitum one of each of four dietary treatments comprising of CN, Linola (LN), NuLin (NL) and LN/NL (50/50 % combination). Each LN, NL and LN/NL treatment contained 6 % oil of DM. Rumen digesta samples were collected on days 6, 11, 16 and 21 and milk samples on days 13, 15 and 17. There were no effects (P>0.05) of the oilseeds on pH and concentrations of NH3-N and total volatile fatty acids, while the acetate:propionate ratio was decreased (P< 0.05). The oilseeds also decreased (P< 0.05) protozoa and increased (P< 0.1) total cellulolytic bacteria in rumen fluid, especially when containing high dietary linoleic acid (P< 0.05). The milk protein concentration was increased (P< 0.1) by the dietary linoleic acid, which produced most beneficial results. It was concluded that supplements of linoleic acid in diets of ruminants might contribute to better digestion of dietary fibre and increased quality of milk.

Effect of the rumen ciliates Entodinium caudatum, Epidinium ecaudatum and Eudiplodinium maggii, and combinations thereof, on ruminal fermentation and total tract digestion in sheep

The quantitative importance of individual ciliate species and their interaction in the rumen is still unclear. The present study was performed to test whether there are species differences in the influence on ruminal fermentation in vivo and if combinations of ciliates act additive in that respect. Six adult wethers fed a hay-concentrate diet were defaunated, then refaunated either with Entodinium caudatum (EC), Epidinium ecaudatum (EE) or Eudiplodinium maggii (EM) alone, then progressively with all possible species combinations. Feed, faeces, urine, ruminal fluid and gas were sampled for eight days always after at least 21 days of adaptation. With a linear mixed model, accounting for the 2 x 2 x 2 full factorial study design, mean marginal effect sizes, i.e., the magnitude of change in variables as caused by the presence of each ciliate species or of combinations of them, were estimated. The apparent digestibility of organic matter and neutral detergent fibre remained unaffected. The apparent N digestibility increased by 0.054 with EM (0.716 with defaunation). Ruminal ammonia increased by 1.6, 4.0 and 8.7 mmol/l in the presence of EM, EC and EE, respectively, compared to defaunation (6.9 mmol/l). In the EM + EE combination, ruminal ammonia was lower than would have been expected from an additive effect. With EE, total short-chain fatty acids increased by 23 mmol/l (100 mmol/l with defaunation), but not when EE was combined with EM. The acetate-to-propionate ratio decreased by 0.73 units in the presence of EE (4.0 with defaunation), but only when EE was the sole ciliate species in the rumen. In the presence of any ciliate species, the 16S rDNA copies of total Bacteria and major fibrolytic species decreased to 0.52- and 0.22-fold values, respectively of that found without protozoa. Total Archaea were unaffected; however, Methanobacteriales copies increased 1.44-fold with EC. The CH4-to-CO2 ratio of ruminal gas decreased by 0.036 with EM and 0.051 with EE (0.454 with defaunation). In conclusion, individual ciliates affected ruminal fermentation differently and, when different species were combined, sometimes in a non-additive manner. From the ciliates investigated, EE affected ruminal fermentation most and might play a dominant role in mixed ciliate populations.