Why don't ruminal bacteria digest cellulose faster?

Enhancing biogas generation from lignocellulosic biomass through biological pretreatment: Exploring the role of ruminant microbes and anaerobic fungi

Biogas production from Lignocellulosic Biomass (LB) via anaerobic digestion (AD) has gained attention for its potential in self-sustainability. However, the recalcitrance of LB cell walls pose a challenge to its degradability and biogas generation. Therefore, pretreatment of LB is necessary to enhance lignin removal and increase degradability. Among the different approaches, environmentally friendly biological pretreatment ispromising as it avoids the production of inhibitors. The ruminal microbial community, including anaerobic fungi, bacteria, and protozoa, has shown an ability to effectively degrade LB through biomechanical and microbial penetration of refractory cell structures. In this review, we provide an overview of ruminant microbes dominating LB's AD, their degradation mechanism, and the bioaugmentation of the rumen. We also explore the potential cultivation of anaerobic fungi from the rumen, their enzyme potential, and their role in AD. The rumen ecosystem, comprising both bacteria and fungi, plays a crucial role in enhancing AD. This comprehensive review delves into the intricacies of ruminant microorganisms' adhesion to plant cells, elucidates degradation mechanisms, and explores integrated pretreatment approaches for the effective utilization of LB, minimizing the impact of inhibitors. The discussion underscores the considerable potential of ruminant microbes in pretreating LB, paving the way for sustainable biogas production. Optimizing fungal colonization and ligninolytic enzyme production, such as manganese peroxidase and laccase, significantly enhances the efficiency of fungal pretreatment. Integrating anaerobic fungi through bioaugmentation during mainstream processing demonstrably increases methane production. This study opens promising avenues for further research and development of these microorganisms for bioenergy production.

Optimization of Fermented Maize Stover for the Fattening Phase of Geese: Effect on Production Performance and Gut Microflora

To optimize the utilization of fermented maize stover (FMS) feed during the fattening phase of Xianghai flying geese (XFG), a total of 300 XFG at 125 days of age were randomly assigned to four dietary treatment groups with three replicates of 25 in each set. Group A was fed the basal fattening diet, while the B, C, and D groups were fed the basic fattening diet and diets supplemented with 5%, 10% or 15% FMS, respectively. The findings indicate that the production performance indicators (especially the dressed, eviscerated and breast muscle yield) of Group D closely resembled Group A more than Groups B and C. Intestinal morphometry found that the jejunal villus height and the villus height/crypt depth were significantly increased in Group D compared to Group A. Next, 16S rRNA amplicon sequencing of the extracted DNA revealed that beneficial microbiota (Coprococcus and Victivallis) showed increased abundance in Group D. Cecal flora function analysis further revealed that some amino acid and glycerol biosynthesis were found to be associated with growth performance in geese. These findings suggest that incorporating 15% FMS as a substitute for a portion of the feed during the fattening phase of XFG can effectively sustain their production performance, optimize the gut microbial community and morphometrical traits, provide new insight into using non-conventional feed resources to reduce feed cost and improve economic benefits in the breeding industry.

Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity

Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.

Supplementing Proteolytic Enzymes Increased the In Vitro Nutrient Effective Degradability and Fermentation Characteristics of Pineapple Waste Silage

Pineapple waste silage (PAS) is an abundant agro-industrial by-product characterized by its high fiber content posing a high potential feed value as roughage for ruminants. Studies on its supplementation with proteolytic enzyme (PE) will help extend its utilization as an alternative nutritive feed source for cattle nutrition. Thus, this study aimed to determine the in vitro nutrient degradability and fermentation characteristics of fiber-rich but low-protein PAS supplemented with different levels of PE. Seven treatments were evaluated in this study: PAS without PE and PAS1 to PAS6, which corresponds to incremental levels of PAS supplementation as follows: 0.1%, 0.2%, 0.3%, 1%, 2%, and 4%. The nutrient disappearance, nutrient effective degradability, and fermentation characteristics such as total gas production, ammonia-nitrogen, and pH values were evaluated in vitro. PAS without added PE showed a comparably good nutritive value (dry matter: 94.30%, neutral detergent fiber: 63.66%, acid detergent fiber: 34.78%) to that of commonly used corn silage in South Korea. With the supplementation of PE in PAS, the PE increased the effective degradability of different nutrients such as dry matter (DM), neutral detergent fiber (NDF), acid detergent fiber (ADF), organic matter (OM), and crude protein (CP). The effect of PE supplementation on the degradation of nutrients was consistent with improvements in in vitro rumen fermentation characteristics. Supplementing PAS with PE increased the total gas production and decreased the pH values, which are characteristics of heightened fiber degradation and fermentation. The ammonia-N concentration of the in vitro-incubated PAS was moderated by the addition of PE, which is likely due to the decrease in pH or in vitro acidosis and has shown a synergistic protease activity effect on nutrient degradation. Overall, supplementing PAS with PE increased the effective degradability of DM, NDF, ADF, OM, and CP, with the most dramatic effects observed in PAS3 and PAS6 (0.3% and 4%, respectively).

A buffalo rumen-derived probiotic (SN-6) could effectively increase simmental growth performance by regulating fecal microbiota and metabolism

Microorganisms play a key role in ruminal digestion, some of which can be used as probiotics to promote growth in ruminants. However, which potential bacteria are responsible for ruminant growth and how they potentiate the basic mechanism is unclear. In this study, three bacterial strains, Bacillus pumilus (SN-3), Bacillus paralicheniformis (SN-6), and Bacillus altitudinis (SN-20) with multiple digestive enzymes were isolated from the rumen of healthy buffaloes. Among these strains, SN-6 secreted cellulase, laccase, and amylase, and significantly inhibited Staphylococcus aureus ATCC25923 and Escherichia coli K99 in vitro. In addition, SN-6 exhibited strong tolerance to artificial gastric juice, intestinal juice, and high temperature. Antibiotic resistance test, virulence gene test, and mouse toxicity test confirmed the safety of SN-6. Further, SN-6 significantly increased the body weight (p < 0.01), affects the intestinal microbiota structure, and alters the metabolomic patterns of Simmental. There was a remarkable difference in the β diversity of fecal microflora between SN-6 and control groups (p < 0.05). Furthermore, SN-6 significantly increased the abundance of Clostridium_sensu_stricto_1, Bifidobacterium, Blautia, and Cellulolyticum, decreased the relative abundance of Monoglobus and norank_f_Ruminococcacea. Moreover, SN-6 feeding significantly enriched intestinal metabolites (i.e., 3-indoleacrylic acid, kynurenic acid) to maintain intestinal homeostasis. Finally, the microbial and metabolic functional analysis indicated that SN-6 could enhance amino acid metabolism (mainly tryptophan metabolism) and lipid metabolism pathways. Overall, these findings indicated that SN-6 could be used as a probiotic in ruminants.

Ruminal Microbiome Manipulation to Improve Fermentation Efficiency in Ruminants

The rumen is an integrated dynamic microbial ecosystem composed of enormous populations of bacteria, protozoa, fungi, archaea, and bacteriophages. These microbes ferment feed organic matter consumed by ruminants to produce beneficial products such as microbial biomass and short-chain fatty acids, which form the major metabolic fuels for ruminants. The fermentation process also involves inefficient end product formation for both host animals and the environment, such as ammonia, methane, and carbon dioxide production. In typical conditions of ruminal fermentation, microbiota does not produce an optimal mixture of enzymes to maximize plant cell wall degradation or synthesize maximum microbial protein. Well-functioning rumen can be achieved through microbial manipulation by alteration of rumen microbiome composition to enhance specific beneficial fermentation pathways while minimizing or altering inefficient fermentation pathways. Therefore, manipulating ruminal fermentation is useful to improve feed conversion efficiency, animal productivity, and product quality. Understanding rumen microbial diversity and dynamics is crucial to maximize animal production efficiency and mitigate the emission of greenhouse gases from ruminants. This chapter discusses genetic and nongenetic rumen manipulation methods to achieve better rumen microbial fermentation including improvement of fibrolytic activity, inhibition of methanogenesis, prevention of acidosis, and balancing rumen ammonia concentration for optimal microbial protein synthesis.

Effect of Feeding Discarded Durian Peel Ensiled with Lactobacillus casei TH14 and Additives in Total Mixed Rations on Digestibility, Ruminal Fermentation, Methane Mitigation, and Nitrogen Balance of Thai Native–Anglo-Nubian Goats

The objective of this study was to evaluate the effect of fermented discarded durian peel with Lactobacillus casei TH14, cellulase, and molasses separately or in combination in total mixed rations on feed utilization, digestibility, ruminal fermentation, and nitrogen utilization in growing crossbreed Thai Native–Anglo-Nubian goats. Five crossbreed Thai Native–Anglo-Nubian goats (50%) at 9 to 12 months of age and 20 ± 1 of body weight (BW) were assigned to a 5 × 5 Latin square design. Evaluated treatments were fermented discarded durian peel without additives (FDP), fermented discarded durian peel with 5% of molasses (FDPM), fermented discarded durian peel with 2% of cellulase (FDPC), fermented discarded durian peel with 1.0 × 105 cfu/g fresh matter of L. casei TH14 (FDPL), and fermented discarded durian peel with 5% of molasses and 1.0 × 105 cfu/g fresh matter of L. casei TH14 (FDPML). This study showed that acid detergent fiber intake was different (p < 0.05) between goats fed FDP and those fed FDPLM, 0.24 g/d and 0.20 g/d, respectively. The FDPML ration had significantly (p < 0.05) greater apparent nutrient digestibility and a better propionate concentration compared with other treatments. FDPML treatment significantly (p < 0.05) decreased the acetate-to-propionate ratio, methane production, and urinary nitrogen. Therefore, treated discarded durian peel with molasses and L. casei TH14 in combination could add 25% of dry matter into the diet for growing goats without a negative impact.

Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?

Agriculture is responsible for a great share of the anthropogenic sources of greenhouse gases that, by warming the earth, threaten its biodiversity. Among greenhouse gas emissions, enteric CH4 from livestock is an important target to slow down climate changes. The CH4 is originated from rumen fermentation and its concentration is affected by several factors, including genetics and nutrition. Ruminants have an extraordinary symbiosis with microorganisms (bacteria, fungi, and protozoa) that ferment otherwise indigestible carbohydrates, from which they obtain energy to grow and continue actively producing, among other products, volatile fatty acids, CO2 and H2. Detrimental ruminal accumulation of H2 is avoided by methanogenesis carried out by Archaea methanogens. Importantly, methanogenesis is not the only H2 sink pathway. In fact, other bacteria can reduce substrates using metabolic hydrogen formed during carbohydrate fermentation, namely propionate production and reductive acetogenesis, thus lowering the CH4 produced. Although the complexity of rumen poses challenges to mitigate CH4 production, the emergence of sequencing techniques that allow the study of microbial communities, gene expression, and metabolome are largely contributing to unravel pathways and key players in the rumen. Indeed, it is now recognized that in vivo emissions of CH4 are correlated to microbial communities, and particularly with the abundance of methanogens, several bacterial groups, and  their genes. The goal of CH4 mitigation is to work in favor of the natural processes, without compromising rumen function, animal health, and productivity. Notwithstanding, the major challenge continues to be the feasibility and affordability of the proposed solutions.

Gut Microbiota and Their Role in Health and Metabolic Disease of Dairy Cow

Ruminants are mostly herbivorous animals that employ rumen fermentation for the digestion of feed materials, including dairy cows. Ruminants consume plant fibre as their regular diet, but lack the machinery for their digestion. For this reason, ruminants maintain a symbiotic relation with microorganisms that are capable of producing enzymes to degrade plant polymers. Various species of microflora including bacteria, protozoa, fungi, archaea, and bacteriophages are hosted at distinct concentrations for accomplishing complete digestion. The ingested feed is digested at a defined stratum. The polysaccharic plant fibrils are degraded by cellulolytic bacteria, and the substrate formed is acted upon by other bacteria. This sequential degradative mechanism forms the base of complete digestion as well as harvesting energy from the ingested feed. The composition of microbiota readily gets tuned to the changes in the feed habits of the dairy cow. The overall energy production as well as digestion is decided by the intactness of the resident communal flora. Disturbances in the homogeneity gastrointestinal microflora has severe effects on the digestive system and various other organs. This disharmony in communal relationship also causes various metabolic disorders. The dominance of methanogens sometimes lead to bloating, and high sugar feed culminates in ruminal acidosis. Likewise, disruptive microfloral constitution also ignites reticuloperitonitis, ulcers, diarrhoea, etc. The role of symbiotic microflora in the occurrence and progress of a few important metabolic diseases are discussed in this review. Future studies in multiomics provides platform to determine the physiological and phenotypical upgradation of dairy cow for milk production.

Potential Valorization of Organic Waste Streams to Valuable Organic Acids through Microbial Conversion: A South African Case Study

The notion of a “biobased economy” in the context of a developing country such as South Africa (SA) necessitates the development of technologies that utilize sustainable feedstocks, have simple and robust operations, are feasible at small scale and produce a variety of valuable bioproducts, thus fitting the biorefinery concept. This case study focuses on the microbial production of higher-value products from selected organic waste streams abundant in the South African agricultural sector using microbes adapted to utilize different parts of biomass waste streams. A ruminant-based carboxylate platform based on mixed or undefined anaerobic co-cultures of rumen microorganisms can convert the carbohydrate polymers in the lignocellulosic part of organic waste streams to carboxylic acids that can be upgraded to biofuels or green chemicals. Furthermore, yeast and fungi can convert the simpler carbohydrates (such as the sugars and malic acid in grape and apple pomace) to ethanol and high-value carboxylic acids, such as lactic, fumaric, succinic and citric acid. This review will discuss the combinational use of the ruminal carboxylate platform and native or recombinant yeasts to valorize biomass waste streams through the production of higher-value organic acids with various applications.

Rumen microbiota and its relation to fermentation in lactose-fed calves

In our previous studies, we revealed the effect of lactose inclusion in calf starters on the growth performance and gut development of calves. We conducted the present study as a follow-up study to identify the shift in rumen microbiota and its relation to rumen fermentation when calves are fed a lactose-containing starter. Thirty Holstein bull calves were divided into 2 calf starter treatment groups: texturized calf starter (i.e., control; n = 15) or calf starter in which starch was replaced with lactose at 10% (i.e., LAC10; n = 15) on a dry matter basis. All calves were fed their respective treatment calf starter ad libitum from d 7, and kleingrass hay from d 35. Rumen digesta were collected on d 80 (i.e., 3 wk after weaning) and used to analyze rumen microbiota and fermentation products. There was no apparent effect of lactose feeding on the α-diversity and overall composition of rumen microbiota. Amplicon sequencing and real-time PCR quantification of the 16S rRNA gene confirmed that the abundance of butyrate-producing bacteria (i.e., Butyrivibrio group and Megasphaera elsdenii) did not differ between the control and LAC10 groups. Conversely, the relative abundance of Mitsuokella spp., which produce lactate, succinate, and acetate, was significantly higher in the rumen of calves that were fed lactose, whereas the lactate concentration did not differ between the control and LAC10 groups. These findings suggest that the lactate production can be elevated by an increase of Mitsuokella spp. and then converted into butyrate, not propionate, since the proportion of propionate was lower in lactose-fed calves. In addition, we observed a higher abundance of Coriobacteriaceae and Pseudoramibacter-Eubacterium in the LAC10 group. Both these bacterial taxa include acetate-producing bacteria, and a positive correlation between the acetate-to-propionate ratio and the abundance of Pseudoramibacter-Eubacterium was observed. Therefore, the higher abundance of Coriobacteriaceae, Mitsuokella spp., and Pseudoramibacter-Eubacterium in the rumen of lactose-fed calves partially explains the increase in the proportion of rumen acetate that was observed in our previous study.

Effects of lactic acid bacteria in a silage inoculant on ruminal nutrient digestibility, nitrogen metabolism, and lactation performance of high-producing dairy cows

Silage treated with lactic acid bacteria inoculants has been reported to increase ruminal microbial biomass when tested in vitro. Therefore, we tested if alfalfa silage inoculated with Lactobacillus plantarum MTD-1 would improve ruminal N metabolism and increase milk production in high-producing dairy cows. Twenty-eight early lactation Holstein cows (8 ruminally cannulated) were blocked by DIM and milk production; animals were used in a double crossover design consisting of four 28-d periods. Animals in each block were randomly assigned to 2 treatments: a diet containing uninoculated alfalfa silage (control) and a diet containing alfalfa silage inoculated with L. plantarum MTD-1 (LP). Diets were formulated to contain 50% of alfalfa silage, 16% crude protein, and 25% neutral detergent fiber (dry matter basis). Milk production and dry matter intake were recorded in the last 14 d of each period. Milk samples were collected twice at both daily milkings on d 20, 21, 27, and 28 of each period. On d 22, omasal samples were collected from the cannulated animals over a period of 3 d to quantify ruminal digestibility and nutrient flows. Data were analyzed using mixed models of SAS 9.4 (SAS Institute). Compared to the control, cows receiving the LP treatment had greater milk production (40.4 vs. 39.6 kg/d) and lower milk urea nitrogen concentration (11.6 vs. 12.7 mg/dL), despite minor changes in energy-corrected milk. Milk lactose concentration was greater in the milk produced by cows fed the LP treatment, which reflected a tendency for increased milk lactose yield. Although milk true protein concentration was lower for cows in the LP treatment, milk true protein yield was the same on both control and LP treatments. Improvements in milk production of animals under the LP treatment were associated with greater organic matter truly digested in the rumen, especially ruminal neutral detergent fiber digestion. Minor changes were observed in total omasal microbial nonammonia N flow in cows receiving the LP treatment. Therefore, alfalfa silage treated with L. plantarum MTD-1 may improve ruminal fermentation and milk production; however, because of a lack of response in ruminal N metabolism, these changes did not result in greater energy-corrected milk in high-producing dairy cows.

Effect of Oats and Wheat Genotype on In Vitro Gas Production Kinetics of Straw

Simple Summary

Increases in cereal grain yields cause the accumulation of large amounts of straw on the soils after grain harvest. Straw is usually burned in the field to help soil preparation for the next crop, a practice resulting in local and global pollution, erosion, loss of soil carbon, and wildfires. An alternative is feeding straw to ruminants, but straw has poor nutritive value, making this option unattractive to Chilean farmers. Oats and wheat have been bred for greater grain yield and improved agronomic traits, but it is unknown whether the straw of different varieties and breeding lines differs in nutritive quality. To investigate this possibility, we incubated the straws from 49 different varieties and breeding lines of oats and 24 of wheat with rumen microorganisms, and studied gas production as an indication of the extent of straw digestion. We found moderate differences among varieties and breeding lines of oats and wheat in gas production, which were not detrimental to agronomic characteristics of importance. If these results can be confirmed in animal experiments, gas production of straw incubated in rumen microbial cultures may be used to identify cereal genotypes whose straw has a better nutritive quality for ruminants.

Abstract

Increases in cereals grain yield in the last decades have increased the accumulation of straw on the soil after harvest. Farmers typically open burn the straw to prepare the soil for the next crop, resulting in pollution, emission of greenhouse gases, erosion, loss of soil organic matter, and wildfires. An alternative is feeding straw to ruminants, but straw nutritive value is limited by its high content of lignocellulose and low content of protein. Cereal breeding programs have focused on improving grain yield and quality and agronomic traits, but little attention has been paid to straw nutritive value. We screened straw from 49 genotypes of oats and 24 genotypes of wheat from three cereal breeding trials conducted in Chile for in vitro gas production kinetics. We found moderate effects of the genotype on gas production at 8, 24, and 40 h of incubation, and on the maximum extent and rate of gas production. Gas production was negatively associated with lignin and cellulose contents and not negatively associated with grain yield and resistance to diseases and lodging. Effects observed in vitro need to be confirmed in animal experiments before gas production kinetics can be adopted to identify cereal genotypes with more digestible straw.

Evaluation of the Nutrient Composition, In Vitro Fermentation Characteristics, and In Situ Degradability of Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hypochondriacus in Cattle

Simple Summary

The amaranth plants, one of the crops that can grow in poor soil and areas with extreme weather conditions—high temperature and limited rainfall—showed high potential feed value as forage for ruminants. An extensive study will help extend its utilization as an alternative protein and fiber feed source in cattle feeding. In this study, the nutrient compositions of the three different species of amaranth, Amaranthus caudatus, A. cruentus, and A. hypochondriacus, were evaluated. Rumen fluid was incubated with the amaranth plants to evaluate fermentation characteristics (total gas production, total volatile fatty acids concentration, pH, and ammonia concentration). There were no differences among the different amaranth species, but all amaranth showed favorable fermentation values. The effective degradabilities of dry matter and crude protein of the amaranth forages were also determined. Compared to other studies, the effective degradabilities of dry matter (33–56%) and crude protein (27–59%) of the amaranth were lower; these results could be due to the maturity stage at which the forages were harvested. In terms of chemical composition, the amaranth forages showed better nutritive value than the locally produced forages in Chungcheong province of Korea. The amaranth forages showed 11.95–14.19% crude protein (CP), 45.53–70.88% neutral detergent fiber (NDF), and 34.17–49.83% acid detergent fiber (ADF) contents. The high nutrient composition, highly effective degradability of dry matter, and crude protein coupled with the favorable fermentation characteristics suggest that the amaranth forages showed good to excellent feed quality to cattle.

Abstract

The amaranth plants showed high potential feed value as forage for ruminants. An in-depth study of this plant, particularly in cattle, will help extend its utilization as an alternative protein and fiber feed source in cattle feeding. In this study, the nutrient compositions of three different species of amaranth, Amaranthus caudatus L., Amaranthus cruentus L., and Amaranthus hypochondriacus L.—two varieties for each species, A.ca 74, A.ca 91, A.cu 62, A.cu 66, A. hy 30, and A. hy 48—were evaluated. The in vitro technique was used to evaluate the fermentation characteristics such as total gas production, total volatile fatty acids (VFA) concentration, pH, and ammonia concentration of the rumen fluid. Moreover, the effective degradabilities of dry matter (EDDM) and crude protein (EDCP) of the amaranth forages were determined through in situ bag technique. The amaranth forages: A. caudatus, A. cruentus, and A. hypochondriacus showed better nutritive value than the locally produced forages in Chungcheong province of Korea. The CP of the amaranth ranged from 11.95% to 14.19%, and the neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents ranged from 45.53% to 70.88% and 34.17% to 49.83%, respectively. Among the amaranth varieties, A. hypochondriacus 48 showed the most excellent ruminant feed nutrient quality (CP, 14.19%; NDF, 45.53%; and ADF, 34.17%). The effective degradabilities of dry matter (EDDM; 33–56%) and crude protein EDCP (27–59%) of the amaranth were lower compared to other studies, which could be due to the maturity stage at which the forages were harvested. Nonetheless, A. hypochondriacus 48 showed the highest EDDM (56.73%) and EDCP (59.09%). The different amaranth species did not differ greatly in terms of total VFA concentration or molar proportions, total gas production, or ammonia-N concentration. The high nutrient composition, and highly effective degradability of dry matter and crude protein, coupled with the favorable fermentation characteristics, suggest that the amaranth forages showed good to excellent feed quality for cattle.

Dynamic role of single-celled fungi in ruminal microbial ecology and activities

In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; (i) to prevent rumen microflora disorders, (ii) to improve and sustain higher production of milk and meat, (iii) to reduce rumen acidosis and bloat which adversely affect animal health and performance, (iv) to decrease the risk of ruminant-associated human pathogens and (v) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fibre digestibility and lower faecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants.

Diversity-triggered deterministic bacterial assembly constrains community functions

A growing body of evidence suggests that microbial α-diversity (local species richness) may have positive effects on ecosystem function. However, less attention has been paid to β-diversity (the variation among local microbial assemblages). Here we studied the impact of microbial α-diversity on stochastic/deterministic microbial community assembly processes, which are related to β-diversity, and the consequences for community function. Bacterial communities differing in α-diversity were generated and their structures and potential community functional traits were inferred from DNA sequencing. Phylogenetic null modeling analysis suggests that stochastic assembly processes are dominant in high-diversity communities. However, in low-diversity communities, deterministic assembly processes are dominant, associating with the reduction of specialized functions that are correlated with specific bacterial taxa. Overall, we suggest that the low-diversity-induced deterministic community assembly processes may constrain community functions, highlighting the potential roles of specialized functions in community assembly and in generating and sustaining the function of soil ecosystems.

The role of microbial β-diversity in soil ecosystem function is not well-studied. Here, the authors use genetic data to show that microbial α-diversity levels may have impacts on stochastic/deterministic assembly processes and functions of soil microbiome.

Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem

The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.

Nutrient composition and in vitro fermentability of corn grain and stover harvested at different periods in Goesan, a mountainous area

With South Korea's limited capability of feed production because of its relatively small cultivable area, the country is pushed to depend on foreign feed imports despite the immensely fluctuating price of corn. Hence, intensive efforts to increase the total cultivable area in Korea like extending of farming to mountainous area is being practiced. Corn was planted in Goesan County, a mountainous area in the country. Grain and stover were harvested separately in three harvest periods: early-harvest (Aug 8), mid-harvest (Aug 18), and late-harvest (Aug 28). The nutrient composition such as dry matter (DM), crude protein (CP), crude fat (EE), organic matter (OM), neutral detergent fiber (NDF), acid detergent fiber (ADF), and non-fibrous carbohydrates (NFC) was determined after harvest. Effective degradability (ED) of the major nutrients (DM, NDF, ADF, and CP) were measured through in vitro fermentation of rumen fluid from Hanwoo (Korean cattle). pH, ammonia-N concentration, volatile fatty acid (VFA) concentration, and gas production were periodically measured at 0, 3, 6, 12, 24, 48, and 72 h. Corn grain showed higher nutrient content and ED than stover. It also had higher gas production but its pH, ammonia-N, and total VFA concentration were lower than corn stover. The best nutrient composition of corn grain was observed in early-harvest (high CP, EE, NDF, OM, NFC, and low ADF). Early-harvest of corn grain also had high effective degradability of dry matter (EDDM), effective degradability of neutral detergent fiber (EDNDF), effective degradability of acid detergent fiber (EDADF), and total VFA concentration. On the other hand, the best nutrient composition of stover was observed in mid-harvest (high DM, CP, NDF, and low ADF). EDDM, EDNDF, and EDADF were pronounced in early-harvest and mid-harvest of stover but the latter showed high total VFA concentration. Hence, early and mid-harvested corn stover and grain in a mountainous area preserved their nutrients, which led to the effective degradation of major nutrients and high VFA production.

Altering undigested neutral detergent fiber through additives applied in corn, whole barley crop, and alfalfa silages, and its effect on performance of lactating Holstein dairy cows

OBJECTIVE

We hypothesized that silage additives may alter the undigested neutral detergent fiber (uNDF) content through ensiling. Therefore, urea and formic acid were applied to corn, whole barley crop (WBC) and alfalfa to change uNDF content of the ensiled forages.

METHODS

Six experimental diets at two groups of high uNDF (untreated corn and alfalfa silages [CSAS] and untreated whole barley and alfalfa silages [BSAS]) and low uNDF (urea-treated corn silage+untreated alfalfa silage [CSUAS], urea-treated whole barley silage+untreated alfalfa silage [BSUAS], untreated corn silage+formic acid-treated alfalfa silage [CSASF], and untreated whole barley silage+formic acid-treated alfalfa silage [BSASF]), were allocated to thirty-six multiparous lactating Holstein dairy cows.

RESULTS

The untreated silages were higher in uNDF than additive treated silages, but the uNDF concentrations among silages were variable (corn silage0.05). Milk yield tended to increase in the cows fed high uNDF diets than those fed low uNDF (p = 0.10). The cows fed diet based on urea-treated corn silage had higher milk yield than those fed other silages (p = 0.05). The substitution of corn silage with the WBC silage tended to decrease milk production (p = 0.07). Changing the physical source of NDF supply and the uNDF content from the corn silage to the WBC silage caused a significant increase in ruminal NH3-N concentration, milk urea-N and fat yield (p< 0.05). The cows fed diets based on WBC silage experienced greater rumination time than the cows fed corn silage (p<0.05).

CONCLUSION

Administering additives to silages to reduce uNDF may improve the performance of Holstein dairy cows.

Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites

Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.

The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential

Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F. succinogenes strain S85 and F. intestinalis strain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed among Fibrobacter phylotypes. F. succinogenes genomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those of F. intestinalis strains. Moreover, genomes of F. succinogenes phylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes of F. succinogenes phylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of the Fibrobacter genomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology of Fibrobacter spp. in the herbivore gut.IMPORTANCE The herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genus Fibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolated Fibrobacter strains, to identify a robust association between carbohydrate-active enzyme gene content and the Fibrobacter phylogeny. Our results provide the strongest evidence reported to date for functional differences among Fibrobacter phylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.

Identification of novel enzymes to enhance the ruminal digestion of barley straw

Crude enzyme extracts typically contain a broad spectrum of enzyme activities, most of which are redundant to those naturally produced by the rumen microbiome. Identification of enzyme activities that are synergistic to those produced by the rumen microbiome could enable formulation of enzyme cocktails that improve fiber digestion in ruminants. Compared to untreated barley straw, Viscozyme® increased gas production, dry matter digestion (P < 0.01) and volatile fatty acid production (P < 0.001) in ruminal batch cultures. Fractionation of Viscozyme® by Blue Native PAGE and analyses using a microassay and mass-spectrometry revealed a GH74 endoglucanase, GH71 α-1,3-glucanase, GH5 mannanase, GH7 cellobiohydrolase, GH28 pectinase, and esterases from Viscozyme® contributed to enhanced saccharification of barley straw by rumen mix enzymes. Grouping of these identified activities with their carbohydrate active enzymes (CAZy) counterparts enabled selection of similar CAZymes for downstream production and screening. Mining of these specific activities from other biological systems could lead to high value enzyme formulations for ruminants.

Improving the Yield and Nutritional Quality of Forage Crops

Despite being some of the most important crops globally, there has been limited research on forages when compared with cereals, fruits, and vegetables. This review summarizes the literature highlighting the significance of forage crops, the current improvements and some of future directions for improving yield and nutritional quality. We make the point that the knowledge obtained from model plant and grain crops can be applied to forage crops. The timely development of genomics and bioinformatics together with genome editing techniques offer great scope to improve forage crops. Given the social, environmental and economic importance of forage across the globe and especially in poorer countries, this opportunity has enormous potential to improve food security and political stability.

Biochanin A improves fibre fermentation by cellulolytic bacteria

AIMS

The objective was to determine the effect of the isoflavone biochanin A (BCA) on rumen cellulolytic bacteria and consequent fermentative activity.

METHODS AND RESULTS

When bovine microbial rumen cell suspensions (n = 3) were incubated (24 h, 39°C) with ground hay, cellulolytic bacteria proliferated, short-chain fatty acids were produced and pH declined. BCA (30 μg ml^-1 ) had no effect on the number of cellulolytic bacteria or pH, but increased acetate, propionate and total SCFA production. Addition of BCA improved total digestibility when cell suspensions (n = 3) were incubated (48 h, 39°C) with ground hay, Avicel, or filter paper. Fibrobacter succinogenes S85, Ruminococcus flavefaciens 8 and Ruminococcus albus 8 were directly inhibited by BCA. Synergistic antimicrobial activity was observed with BCA and heat killed cultures of cellulolytic bacteria, but the effects were species dependent.

CONCLUSIONS

These results indicate that BCA improves fibre degradation by influencing cellulolytic bacteria competition and guild composition.

SIGNIFICANCE AND IMPACT OF THE STUDY

BCA could serve as a feed additive to improve cellulosis when cattle are consuming high-fibre diets. Future research is needed to evaluate the effect of BCA on fibre degradation and utilization in vivo.

Effect of sugarcane fiber digestibility, conservation method and concentrate level on the ruminal ecosystem of beef cattle

The aim of this study was to investigate the effects of sugarcane neutral detergent fiber digestibility (NDFD), conservation method, and concentrate level on the ruminal microbial population of steers. Eight ruminal-cannulated Nellore steers were distributed in two contemporary 4 × 4 Latin Square design with a 2 × 2 factorial arrangement of treatments. Experiment 1: diets were formulated with 60% of concentrate level, and two sugarcane genotypes (high or low NDFD) either freshly cut or as silage. Experiment 2: diets were formulated with two levels of concentrate (60 or 80%), and two sugarcane genotypes (high or low NDFD) offered as freshly cut. Each experimental period lasted for 14 d, with the last 4 d used for ruminal fluid collection. Three cellulolytic bacteria (Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens), two amylolytic (Streptococcus bovis, Ruminobacter amylophilus), and a lactate fermenting microorganism (Megasphaera elsdenii) were quantified by qPCR. Experiment 1: diets with fresh sugarcane increased the population of S. bovis, and M. elsdenii. Sugarcane with high NDFD increased F. succinogenes population only when sugarcane was offered as freshly cut. Experiment 2: increasing concentrate in the diet decreased S. bovis population, and increased R. amylophilus. Sugarcane with high NDFD increased the population of cellulolytic bacteria only at the 60% concentrate diet. Providing sugarcane with high NDFD favored the growth of fibrolytic bacteria, and this effect were dependent on the conservation method and on diet concentrate level. In addition, sucrose appears to have great effect on the composition of ruminal microflora, especially S. bovis.

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats

We used 16S rRNA gene sequencing to examine the posteffects of antibiotic treatment on the structure and metabolism of rumen microbiota. Twelve goats were randomly assigned into two groups, with one group receiving intramuscular streptomycin injection at 40 mg/kg bodyweight daily for 10 days. At 4 weeks after treatment with antibiotic, three goats were randomly selected from each group and switched to a 35% concentrate diet. The remaining six goats continued with the 10% concentrate diet. At 4 weeks after dietary shift, ruminal fluid and epithelium were collected to analyze the microbiota composition and short‐chain fatty acid (SCFA) concentrations of the rumen. We found that antibiotic administration led to increases in the diversity and richness of recovered mucosal microbiota and to decreases in those of recovered fluid microbiota. When dietary modulation was performed after antibiotic intake, both communities showed little difference in structure from premodulated states. Additionally, antibiotic pretreatment reduced the basal lines of individual SCFAs but did not affect the increased percentages of SCFAs. Overall, our results indicate that antibiotic administration affects the structure of both rumen fluid and mucosal microbiota and reduces the functional redundancy of rumen microbiota.

Growth performance, rumen fermentation, bacteria composition, and gene expressions involved in intracellular pH regulation of rumen epithelium in finishing Hu lambs differing in residual feed intake phenotype

The objective of this study was to evaluate the effect of residual feed intake (RFI) on rumen function in finishing lambs. A total of 60 male Hu lambs (average initial BW = 25.2 ± 2.5kg) were used and were offered a pelleted high-concentrate diet, of which the forage to concentrate ratio was 25:75. Individual feed intake was recorded over a period of 42 d, then 10 lambs with the lowest RFI and the highest RFI were selected, respectively. The rumen fluid used for fermentation variables and relative abundance of bacteria measurement was obtained on d 10 and 20 after RFI measurement. At the end of this experiment, the selected lambs were slaughtered and rumen epithelium and liver tissues were collected for RNA extraction. Low-RFI lambs had lower ( < 0.01) DMI and greater ( < 0.05) G:F than the high-RFI ones, while the RFI groups did not differ in ADG and BW ( > 0.05). Additionally, RFI was positively ( = 0.57; < 0.01) correlated with DMI and negatively ( = -0.53; < 0.05) correlated with G:F. Total VFA and individual VFA decreased ( < 0.05) over time. The concentrations of total VFA, acetate, valerate, isobutyrate, isovalerate, and rumen pH ( > 0.05) were not affected by RFI classification. Nonetheless, low-RFI group lambs had a greater ( < 0.05) concentration of propionate, a lower ( < 0.05) concentration of butyrate, and a lower ( < 0.05) acetate to propionate ratio compared with the high-RFI group. There was a significant ( < 0.05) effect of RFI on the relative abundance of and . The relative abundance of , , and decreased ( < 0.05) over time in high-RFI group. And the relative abundance of in high-RFI group was greater ( < 0.05) than its low-RFI counterpart. Furthermore, RFI had no effect ( > 0.05) on gene expression associated with intracellular pH regulation (, , , , , , , and ) in rumen epithelium and β-hydroxybutyrate metabolism () in both rumen epithelium and liver tissues. In conclusion, even though low-RFI lambs had lower DMI, however, the number of was lower. Additionally, there was no difference in gene expressions level associated with intracellular pH regulation in rumen epithelium between RFI groups.

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats

BACKGROUND

Diet-derived short-chain fatty acids (SCFAs) in the rumen have broad effects on the health and growth of ruminants. The microbe-G-protein-coupled receptor (GPR) and microbe-histone deacetylase (HDAC) axes might be the major pathway mediating these effects. Here, an integrated approach of transcriptome sequencing and 16S rRNA gene sequencing was applied to investigate the synergetic responses of rumen epithelium and rumen microbiota to the increased intake of dietary non-fiber carbohydrate (NFC) from 15 to 30% in the goat model. In addition to the analysis of the microbial composition and identification of the genes and signaling pathways related to the differentially expressed GPRs and HDACs, the combined data including the expression of HDACs and GPRs, the relative abundance of the bacteria, and the molar proportions of the individual SCFAs were used to identify the significant co-variation of the SCFAs, clades, and transcripts.

RESULTS

The major bacterial clades promoted by the 30% NFC diet were related to lactate metabolism and cellulose degradation in the rumen. The predominant functions of the GPR and HDAC regulation network, under the 30% NFC diet, were related to the maintenance of epithelium integrity and the promotion of animal growth. In addition, the molar proportion of butyrate was inversely correlated with the expression of HDAC1, and the relative abundance of the bacteria belonging to Clostridum_IV was positively correlated with the expression of GPR1.

CONCLUSIONS

This study revealed that the effects of rumen microbiota-derived SCFA on epithelium growth and metabolism were mediated by the GPR and HDAC regulation network. An understanding of these mechanisms and their relationships to dietary components provides better insights into the modulation of ruminal fermentation and metabolism in the promotion of livestock production.

Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen

The genus Fibrobacter contains cellulolytic bacteria originally isolated from the rumen. Culture-independent investigations have since identified Fibrobacter populations in the gastrointestinal tracts of numerous hindgut-fermenting herbivores, but their physiology is poorly characterized due to few representative axenic cultures. To test the hypothesis that novel Fibrobacter diversity exists in hindgut fermenters, we performed culturing and 16S rRNA gene amplicon sequencing on samples collected from phylogenetically diverse herbivorous hosts. Using a unique approach for recovering axenic Fibrobacter cultures, we isolated 45 novel strains from 11 different hosts. Full-length 16S rRNA gene sequencing of these isolates identified nine discrete phylotypes (cutoff = 0.03%) among them, including several that were only isolated from hindgut-fermenting hosts, and four previously unrepresented by axenic cultures. Our phylogenetic analysis indicated that six of the phylotypes are more closely related to previously described subspecies of Fibrobacter succinogenes, while the remaining three were more closely related to F. intestinalis. Culture-independent bacterial community profiling confirmed that most isolates were representative of numerically dominant phylotypes in their respective samples and strengthened the association of certain phylotypes with either ruminants or hindgut-fermenters. Despite considerable phylogenetic diversity observed among the Fibrobacter strains isolated here, phenotypic characterization suggests a conserved specialization for growth on cellulose.

Biofilms, bubbles and boundary layers - A new approach to understanding cellulolysis in anaerobic and ruminant digestion

Anaerobic digestion of plant biomass to hydrocarbons could play a major part in meeting the needs of a modern low carbon society, but the cost reductions needed to make it an economically viable technology have been slower to arrive than in other renewable technologies. This is notwithstanding the observation that ruminants carry out the rate limiting hydrolysis step up to 30 times faster than an AD plant, and that bio-mimicry of ruminants could be an important source of innovation. This paper examines a number of factors which may, by focusing emphasis on the physical and chemical environment within cellulolytic biofilms, help accelerate development in the arena. It examines the process of cellulolysis from the perspective of a bacterium attached within a biofilm to a piece of insoluble cellulosic substrate to illustrate the extent of chemical heterogeneity that exists in the film, and between the film and the supernatant, and how this might control the rate of cellulolysis. It suggests several strategies used by ruminants to manage this heterogeneity that may be significant contributors to their effectiveness, and could provide a useful guide to more effective anaerobic digestion.

Live yeasts enhance fibre degradation in the cow rumen through an increase in plant substrate colonization by fibrolytic bacteria and fungi

AIMS

To monitor the effect of a live yeast additive on feedstuff colonization by targeted fibrolytic micro-organisms and fibre degradation in the cow rumen.

METHODS AND RESULTS

Abundance of adhering fibrolytic bacteria and fungi on feedstuffs incubated in sacco in the cow rumen was quantified by qPCR and neutral detergent fibre (NDF) degradation was measured. Saccharomyces cerevisiae I-1077 (SC) increased the abundance of fibre-associated Fibrobacter succinogenes on wheat bran (WB) and that of Ruminococcus flavefaciens on alfalfa hay (AH) and wheat silage (WS). The greatest effect was observed on the abundance of Butyrivibrio fibrisolvens on AH and soya hulls (SH) (P < 0·001). Fungal biomass increased on AH, SH, WS and WB in the presence of SC. NDF degradation of AH and SH was improved (P < 0·05) with SC supplementation.

CONCLUSIONS

Live yeasts enhanced microbial colonization of fibrous materials, the degree of enhancement depended on their nature and composition. As an effect on rumen pH was not likely to be solely involved, the underlying mechanisms could involve nutrient supply or oxygen scavenging by the live yeast cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

Distribution of this microbial additive could be an interesting tool to increase fibre digestion in the rumen and thereby improve cow feed efficiency.

Maximizing efficiency of rumen microbial protein production

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen.

Effects of a spoilage yeast from silage on in vitro ruminal fermentation

Feeding silages with high concentrations of yeasts from aerobic spoilage is often implicated as a cause of poor animal performance on dairies. Our objective was to determine if a commonly found spoilage yeast, isolated from silage, had the potential to alter in vitro ruminal fermentations. A single colony of Issatchenkia orientalis, isolated from high-moisture corn, was grown in selective medium. The yeast culture was purified and added to in vitro culture tubes containing a total mixed ration (43% concentrate, 43% corn silage, 11% alfalfa haylage, and 3% alfalfa hay on a dry matter basis), buffer, and ruminal fluid to achieve added theoretical final concentrations of 0 (CTR), 4.40 (low yeast; LY), 6.40 (medium yeast; MY), and 8.40 (high yeast; HY) log10 cfu of yeast/mL of in vitro fluid. Seven separate tubes were prepared for each treatment and each time point and incubated for 12 and 24h at 39 °C. At the end of the incubation period, samples were analyzed for pH, yeast number, neutral detergent fiber (NDF) digestibility, volatile fatty acids (VFA), and fatty acids (FA). We found that total viable yeast counts decreased for all treatments in in vitro incubations but were still relatively high (5.3 log10 cfu of yeasts/mL) for HY after 24h of incubation. Addition of HY resulted in a lower pH and higher concentration of total VFA in culture fluid compared with other treatments. Moreover, additions of MY and HY decreased in vitro NDF digestibility compared with CTR, and the effect was greatest for HY. Overall, the biohydrogenation of dietary unsaturated FA was not altered by addition of I. orientalis and decreased over time with an increase in the accumulation of saturated FA, especially palmitic and stearic acids. We conclude that addition of I. orientalis, especially at high levels, has the potential to reduce in vitro NDF digestion and alter other aspects of ruminal fermentations.

Cinética de fermentação ruminal in vitro de silagens de híbridos de sorgo

Objetivou-se com esta pesquisa avaliar as silagens de 23 híbridos de sorgo por meio da técnica in vitro semiautomática de produção de gases. Foi utilizado o delineamento inteiramente ao acaso, com 23 tratamentos e três repetições, sendo os tratamentos as silagens de híbridos de sorgo. Os híbridos foram cultivados na estação experimental do Instituto Nacional do Semiárido (INSA), no município de Campina Grande - PB. A produção de gases foi estimada por intermédio do modelo logístico bicompartimental, ajustado às curvas de produção cumulativa de gases. Com relação ao volume final de carboidratos fibrosos (VfCF), houve efeito de híbrido (P<0,05), com resultados variando de 105,99 a 144,53mL/g de MS. Os valores de taxa de degradação dos carboidratos fibrosos (KdCF) variaram (P<0,05), e o híbrido 866041 apresentou o maior resultado 0,015h-1. Os valores de volume final total (VfT) variaram (P<0,05), e os híbridos 870085, Volumax e XBS 60329 apresentaram maiores (P<0,05) valores de VfT em relação aos demais. Pela análise multivariada, foram formados seis grupos distintos. O grupo 2, composto pelos híbridos 22 (Volumax) e 23 (XBS60329), apresentou os maiores valores médios para os volumes de gás, tanto para os carboidratos fibrosos quanto para os não fibrosos. O grupo 4, composto pelo híbrido 1 (866005), apresentou as menores médias para volume de gás produzido e o maior lag time (3,15 horas). Todos os híbridos estudados apresentam potencial para ensilagem, de acordo com a cinética de fermentação ruminal.

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H₂) transfer, a process during which bacterially generated H₂ is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H₂ transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H₂ was metabolized into CH₄ by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.