Invited review: adhesion mechanisms of rumen cellulolytic bacteria

A concise review on waste biomass valorization through thermochemical conversion

Due to an increase in industrialization and urbanization, massive amounts of solid waste biomass are speedily accumulating in our environment, which poses several adverse effects on habitat and human health thus becoming a matter of discussion in the environmental community. With reference to the circular economy, continuous efforts have been put forward for setting up an organised management approach in combination with an efficient treatment technique for increasing the profitable utilization of solid waste. This review aims to provide a systematic discussion on the recent thermochemical technologies employed for converting waste biomass generated from different sources into valuable products like biochar, bio-oil, heat, energy and syngas. The article further focuses on a few important aspects of thermochemical conversion of waste biomass to useful products like technical factors affecting thermochemical processes, applications of by-products of thermochemical conversion, and biological pretreatment of waste biomass. The review assists interesting recent and scientific trends for boosting up the systematic management and valorization of solid waste through low-cost, efficient, environment-friendly and sustainable technologies.

Coping with extremes: the rumen transcriptome and microbiome co-regulate plateau adaptability of Xizang goat

The interactions between the rumen microbiota and the host are crucial for the digestive and absorptive processes of ruminants, and they are heavily influenced by the climatic conditions of their habitat. Owing to the harsh conditions of the high-altitude habitat, little is known about how ruminants regulate the host transcriptome and the composition of their rumen microbiota. Using the model species of goats, we examined the variations in the rumen microbiota, transcriptome regulation, and climate of the environment between high altitude (Lhasa, Xizang; 3650 m) and low altitude (Chengdu, Sichuan, China; 500 m) goats. The results of 16 S rRNA sequencing revealed variations in the abundance, diversity, and composition of rumen microbiota. Papillibacter, Quinella, and Saccharofermentans were chosen as potential microbes for the adaptation of Xizang goats to the harsh climate of the plateau by the Spearman correlation study of climate and microbiota. Based on rumen transcriptome sequencing analysis, 244 genes were found to be differentially expressed between Xizang goats and low-altitude goats, with 127 genes showing up-regulation and 117 genes showing down-regulation. SLC26A9, GPX3, ARRDC4, and COX1 were identified as potential candidates for plateau adaptation in Xizang goats. Moreover, the metabolism of fatty acids, arachidonic acids, pathway involving cytokines and their receptors could be essential for adaptation to plateau hypoxia and cold endurance. The expression of GPX3, a gene linked to plateau acclimatization in Xizang goats, was linked to the abundance of Anaerovibrio, and the expression of SLC26A9 was linked to the quantity of Selenomonas, according to ruminal microbiota and host Spearman correlation analysis. Our findings imply that in order to adapt harsh plateau conditions, Xizang goats have evolved to maximize digestion and absorption as well as to have a rumen microbiota suitable for the composition of their diet.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

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.

Effects of Dietary Fiber Level and Forage Particle Size on Growth, Nutrient Digestion, Ruminal Fermentation, and Behavior of Weaned Holstein Calves under Heat Stress

This experiment was designed to investigate the effects of feeding diets with different fiber content and forage particle size on the performance, health, nutrient digestion, rumen fermentation, and behavioral and sorting activity of Holstein dairy calves kept under elevated environmental temperature. Sixty weaned Holstein female calves (age = 96.7 ± 7.62 days old; body weight = 82.4 ± 10.4 kg) were randomly assigned to one of 4 treatments arranged in a 2-by-2 factorial design in a 70-day experiment. Dietary forage content (moderate, 22.5%; or high, 40.0% on DM basis) and alfalfa hay particle size (short, 4.39 mm; or long, 7.22 mm as geometric mean) were the experimental factors, resulting in the following combinations: (1) high-fiber (HF) diets with forage-to-concentrate ratio of 40:60 and long particle-sized alfalfa hay (LPS; HF-LPS); (2) HF diets with short particle-sized alfalfa hay (SPS; HF-SPS); (3) moderate-fiber (MF) diets with forage-to-concentrate ratio of 22.5:77.5 with LPS (MF-LPS); and (4) MF diets with SPS (MF-SPS). The temperature-humidity index averaged 73.0 ± 1.86, indicating that weaned calves experienced a moderate extent of heat stress. Fiber level and AH particle size interacted and affected dry matter intake, with the greatest intake (4.83 kg/d) observed in MF-SPS-fed calves. Final body weight was greater in calves receiving MF vs. HF diets (164 vs. 152 kg; p < 0.01). Respiration rate decreased when SPS vs. LPS AH was included in HF but not MF diet. Lower rectal temperature was recorded in calves fed MF vs. HF diet. Digestibility of dry matter and crude protein was greater in calves fed MF than HF diets, resulting in lower ruminal pH (6.12 vs. 6.30; p = 0.03). Fiber digestibility was greater in calves fed SPS compared with those fed LPS alfalfa hay. Feeding HF compared with MF diet increased acetate but lowered propionate molar proportions. The inclusion of SPS vs. LPS alfalfa hay decreased lying time in HF diet (920 vs. 861 min; p < 0.01). Calves fed MF vs. HF diets spent less time eating but more time lying, which is likely indicative of better animal comfort. Dietary fiber level and forage particle size interacted and affected sorting against 19 mm particles, the extent of which was greater in HF-SPS diet. Overall, dietary fiber level had a stronger effect than forage particle size on the performance of weaned calves exposed to a moderate degree of heat stress as feeding MF vs. HF diet resulted in greater feed intake, final body weight, structural growth measures, nutrient digestion, as well as longer lying behavior. The inclusion of SPS alfalfa hay in MF diets increased feed consumption.

Potential of dietary hemp and cannabinoids to modulate immune response to enhance health and performance in animals: opportunities and challenges

Cannabinoids are a group of bioactive compounds abundantly present in Cannabis sativa plant. The active components of cannabis with therapeutic potential are known as cannabinoids. Cannabinoids are divided into three groups: plant-derived cannabinoids (phytocannabinoids), endogenous cannabinoids (endocannabinoids), and synthetic cannabinoids. These compounds play a crucial role in the regulation various physiological processes including the immune modulation by interacting with the endocannabinoid system (A complex cell-signaling system). Cannabinoid receptor type 1 (CB1) stimulates the binding of orexigenic peptides and inhibits the attachment of anorexigenic proteins to hypothalamic neurons in mammals, increasing food intake. Digestibility is unaffected by the presence of any cannabinoids in hemp stubble. Endogenous cannabinoids are also important for the peripheral control of lipid processing in adipose tissue, in addition to their role in the hypothalamus regulation of food intake. Regardless of the kind of synaptic connection or the length of the transmission, endocannabinoids play a crucial role in inhibiting synaptic transmission through a number of mechanisms. Cannabidiol (CBD) mainly influences redox equilibrium through intrinsic mechanisms. Useful effects of cannabinoids in animals have been mentioned e.g., for disorders of the cardiovascular system, pain treatment, disorders of the respiratory system or metabolic disorders. Dietary supplementation of cannabinoids has shown positive effects on health, growth and production performance of small and large animals. Animal fed diet supplemented with hemp seeds (180 g/day) or hemp seed cake (143 g/kg DM) had achieved batter performance without any detrimental effects. But the higher level of hemp or cannabinoid supplementation suppress immune functions and reduce productive performance. With an emphasis on the poultry and ruminants, this review aims to highlight the properties of cannabinoids and their derivatives as well as their significance as a potential feed additive in their diets to improve the immune status and health performance of animals.

Physical, Metabolic, and Microbial Rumen Development in Goat Kids: A Review on the Challenges and Strategies of Early Weaning

The digestive system of newborn ruminant functions is similar to monogastric animals, and therefore milk flows into the abomasum instead of rumen for digestion. The rumen undergoes tremendous changes over time in terms of structure, function, and microbiome. These changes contribute to the smooth transition from the dependence on liquid diets to solid diets. Goat kids are usually separated at early ages from their dams in commercial intensive systems. The separation from dams minimizes the transfer of microbiota from dams to newborns. In this review, understanding how weaning times and methodologies could affect the normal development and growth of newborn goats may facilitate the development of new feeding strategies to control stress in further studies.

Polyclonal antibodies inhibit growth of key cellulolytic rumen bacterial species

Antibodies targeting specific bacterial species could allow for modification of the rumen microbial population to enhance rumen fermentation. However, there is limited knowledge of targeted antibody effects on rumen bacteria. Therefore, our objective was to develop efficacious polyclonal antibodies to inhibit the growth of targeted cellulolytic bacteria from the rumen. Egg-derived, polyclonal antibodies were developed against pure cultures of Ruminococcus albus 7 (anti-RA7), Ruminococcus albus 8 (anti-RA8), and Fibrobacter succinogenes S85 (anti-FS85). Antibodies were added to a cellobiose-containing growth medium for each of the three targeted species. Antibody efficacy was determined via inoculation time (0 h and 4 h) and dose response. Antibody doses included: 0 (CON), 1.3 × 10^-4 (LO), 0.013 (MD), and 1.3 (HI) mg antibody per ml of medium. Each targeted species inoculated at 0 h with HI of their respective antibody had decreased (P < 0.01) final optical density and total acetate concentration after a 52 h growth period when compared with CON or LO. Live/dead stains of R. albus 7 and F. succinogenes S85 dosed at 0 h with HI of their respective antibody indicated a decrease (≥ 96%; P < 0.05) in live bacterial cells during the mid-log phase compared with CON or LO. Addition of HI of anti-FS85 at 0 h in F. succinogenes S85 cultures reduced (P < 0.01) total substrate disappearance over 52 h by at least 48% when compared with CON or LO. Cross-reactivity was assessed by adding HI at 0 h to non-targeted bacterial species. Addition of anti-RA8 or anti-RA7 to F. succinogenes S85 cultures did not affect (P ≥ 0.45) total acetate accumulation after 52 h incubation, indicating that antibodies have less of an inhibitory effect on non-target strains. Addition of anti-FS85 to non-cellulolytic strains did not affect (P ≥ 0.89) OD, substrate disappearance, or total VFA concentrations, providing further evidence of specificity against fiber-degrading bacteria. Western blotting with anti-FS85 indicated selective binding to F. succinogenes S85 proteins. Identification by LC-MS/MS of 8 selected protein spots indicated 7 were outer membrane proteins. Overall, polyclonal antibodies were more efficacious at inhibiting the growth of targeted cellulolytic bacteria than non-targeted bacteria. Validated polyclonal antibodies could serve as an effective approach to modify rumen bacterial populations.

Biofilm-Mediated Fragmentation and Degradation of Microcrystalline Cellulose by Cellulomonas flavigena KU (ATCC 53703)

Cellulomonas flavigena KU (ATCC 53703) produces an extracellular matrix involved in the degradation of microcrystalline cellulose. This extracellular material is primarily composed of the gel-forming, β-1,3-glucan known as curdlan and associated, cellulose-degrading enzymes. In this study, the effects of various forms of nutrient limitation on cellulose attachment, cellular aggregation, curdlan production, and biofilm formation were investigated throughout a 7-day incubation period by using phase-contrast microscopy. Compared to cultures grown in non-limiting media, nitrogen-limitation promoted early attachment of C. flavigena KU cells to the cellulose surface, and cellulose attachment was congruent with cellular aggregation and curdlan production. Over the course of the experiment, microcolonies of attached cells grew into curdlan-producing biofilms on the cellulose. By contrast, bacterial cells grown on cellulose in non-limiting media remained unattached and unaggregated throughout most of the incubation period. By 7 days of incubation, bacterial aggregation was ninefold greater in N-limited cultures compared to nutritionally complete cultures. In a similar way, phosphorus- and vitamin-limitation (i.e., yeast extract-limitation) also resulted in early cellulose attachment and biofilm formation. Furthermore, nutrient limitation promoted more rapid and efficient fragmentation and degradation of cellulose, with cellulose fragments in low-N media averaging half the size of those in high-N media after 7 days. Two modes of cellulose degradation are proposed for C. flavigena KU, a "planktonic mode" and a "biofilm mode". Similar observations have been reported for other curdlan-producing cellulomonads, and these differing cellulose degradation strategies may ultimately prove to reflect sequential stages of a multifaceted biofilm cycle important in the bioconversion of this abundant and renewable natural resource.

Characterization of the Dynamic Changes of Ruminal Microbiota Colonizing Citrus Pomace Waste during Rumen Incubation for Volatile Fatty Acid Production

Rumen microorganisms are promising for efficient bioconversion of lignocellulosic wastes to biofuels and industrially relevant products. Investigating the dynamic changes of the rumen microbial community colonizing citrus pomace (CtP) will advance our understanding of the utilization of citrus processing waste by rumen fluid. Citrus pomace in nylon bags was incubated in the rumen of three ruminally cannulated Holstein cows for 1, 2, 4, 8, 12, 24, and 48 h. Results showed that total volatile fatty acids concentrations and proportions of valerate and isovalerate were increased over time during the first 12 h. Three major cellulose enzymes attached to CtP rose initially and then decreased during the 48-h incubation. Primary colonization happened during the initial hours of CtP incubation, and microbes compete to attach CtP for degrading easily digestible components and/or utilizing the waste. The 16S rRNA gene sequencing data revealed the diversity and structure of microbiota adhered to CtP were distinctly different at each time point. The increased abundance of Fibrobacterota, Rikenellaceae_RC9_gut_group, and Butyrivibrio may explain the elevated volatile fatty acids concentrations. This study highlighted key metabolically active microbial taxa colonizing citrus pomace in a 48-h in situ rumen incubation, which could have implications for promoting the biotechnological process of CtP. IMPORTANCE As a natural fermentation system, the rumen ecosystem of ruminants can efficiently degrade plant cellulose, indicating that the rumen microbiome offers an opportunity for anaerobic digestion to utilize biomass wastes containing cellulose. Knowledge of the response of the in situ microbial community to citrus pomace during anaerobic fermentation will help improve the current understanding of citrus biomass waste utilization. Our results demonstrated that a highly diverse rumen bacterial community colonized citrus pomace rapidly and continuously changed during a 48-h incubation period. These findings may provide a deep understanding of constructing, manipulating, and enriching rumen microorganisms to improve the anaerobic fermentation efficiency of citrus pomace.

Understanding the microbial fibre degrading communities & processes in the equine gut

The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 36-48 h through the synergistic activities of bacteria, fungi, and methanogenic archaea. Anaerobic gut dwelling bacteria and fungi break down complex plant polysaccharides through combined mechanical and enzymatic strategies, and notably possess some of the greatest diversity and repertoire of carbohydrate active enzymes among characterized microbes. In addition to the production of enzymes, some equid-isolated anaerobic fungi and bacteria have been shown to possess cellulosomes, powerful multi-enzyme complexes that further enhance break down. The activities of both anaerobic fungi and bacteria are further facilitated by facultatively aerobic yeasts and methanogenic archaea, who maintain an optimal environment for fibrolytic organisms, ultimately leading to increased fibrolytic microbial counts and heightened enzymatic activity. The unique interactions within the equine gut as well as the novel species and powerful mechanisms employed by these microbes makes the equine gut a valuable ecosystem to study fibrolytic functions within complex communities. This review outlines the primary taxa involved in fibre break down within the equine gut and further illuminates the enzymatic strategies and metabolic pathways used by these microbes. We discuss current methods used in analysing fibrolytic functions in complex microbial communities and propose a shift towards the development of functional assays to deepen our understanding of this unique ecosystem.

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.

Starch and Cellulose Degradation in the Rumen and Applications of Metagenomics on Ruminal Microorganisms

Simple Summary

Starch and cellulose are the principal components in diets for dairy cows worldwide, providing the primary energy to the rumen microorganisms as well as the host. Starch and cellulose degradation in the rumen have always been of key importance for dairy cows to obtain high production performance. To improve the starch- and cellulose-degrading activities in the rumen, the amylolytic and cellulolytic microbes and the related enzymes need to be well understood. As the rapid development of sequencing technologies, bioinformatic tools and reference databases, the rumen metagenomics have made great progress in mining the rumen microbial community for novel enzymes, such as the carbohydrate active enzymes (CAZymes). This review will summarize the ruminal microbes and enzymes involved in starch and cellulose degradation. Recent studies with metagenomics techniques on CAZymes related to starch and cellulose degradation will be discussed.

Abstract

Carbohydrates (e.g., starch and cellulose) are the main energy source in the diets of dairy cows. The ruminal digestion of starch and cellulose is achieved by microorganisms and digestive enzymes. In order to improve their digestibility, the microbes and enzymes involved in starch and cellulose degradation should be identified and their role(s) and activity known. As existing and new analytical techniques are continuously being developed, our knowledge of the amylolytic and cellulolytic microbial community in the rumen of dairy cows has been evolving rapidly. Using traditional culture-based methods, the main amylolytic and cellulolytic bacteria, fungi and protozoa in the rumen of dairy cows have been isolated. These culturable microbes have been found to only account for a small fraction of the total population of microorganisms present in the rumen. A more recent application of the culture-independent approach of metagenomics has acquired a more complete genetic structure and functional composition of the rumen microbial community. Metagenomics can be divided into functional metagenomics and sequencing-based computational metagenomics. Both approaches have been applied in determining the microbial composition and function in the rumen. With these approaches, novel microbial species as well as enzymes, especially glycosyl hydrolases, have been discovered. This review summarizes the current state of knowledge regarding the major amylolytic and cellulolytic microorganisms present in the rumen of dairy cows. The ruminal amylases and cellulases are briefly discussed. The application of metagenomics technology in investigating glycosyl hydrolases is provided and the novel enzymes are compared in terms of glycosyl hydrolase families related to amylolytic and cellulolytic activities.

Effect of the Combining Corn Steep Liquor and Urea Pre-treatment on Biodegradation and Hydrolysis of Rice Straw

A novel pre-treatment using corn steep liquor (CSL) and urea was developed to enhance the enzymatic saccharification and degradability of rice straw (RS). We used RS (1) without (Con) or with additives of (2) 5% urea (U), (3) 9% CSL and 2.5% urea (CU), and (4) 9% CSL and 5% urea (C5U). The result showed that the water-soluble carbohydrate (WSC) conversion of RS reached 69.32% after C5U pre-treatment. Scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and X-ray diffraction analysis (XRD) confirmed that the surface of pre-treated RS exposed more cellulose and hemicellulose due to the disruption of the resistant structure of lignocellulose. Pre-treated RS significantly decreased neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents and increased crude protein (CP) content, microbial colonization, and induction of Carnobacterium and Staphylococcus attachment. Altogether, we concluded that pre-treatment of a combination of CSL and urea has the potential to improve the nutritive value of RS.

Effects of Chlortetracycline Rumen-Protected Granules on Rumen Microorganisms and Its Diarrhea Therapeutic Effect

Chlortetracycline is a broad-spectrum antibiotic used as an oral medication in ruminants. However, this antibiotic affects the rumen microbial population, thereby upsetting the normal microbiota of ruminants. This study determined whether our newly developed chlortetracycline rumen-protected granules are relatively harmless to rumen microorganisms while effective against lamb E. coli diarrhea. We used a qPCR assay to quantify selected rumen microorganisms from lambs treated with or without oral chlortetracycline. We also assessed bacterial diversity in the rumen by 16S rRNA gene sequencing. Lambs were divided into three groups: one group given with oral chlortetracycline granules for 7 days; one group with chlortetracycline premix; and one without treatment. Rumen fluid was collected on 0 d, 7 d, and 14 d of the experiment. In the therapeutic effect trial, cases of naturally E. coli-infected lamb with diarrhea were selected and divided into low, medium, and high dose groups of granules, premix, infection control, and healthy control groups. Treatments were continuously administered for 7 days, and animals were observed for 14 days after drug withdrawal to score and evaluate the treatment effect. Results of qPCR and 16S rRNA gene sequencing showed that the granules could diminish the impact of chlortetracycline on rumen microorganisms compared with the premix. The diarrhea therapeutic effect trial showed that the oral administration of the chlortetracycline rumen-protected granules at the dose of 30 mg/kg·bw/d for 7 days could effectively treat lamb diarrhea caused by E. coli. In conclusion, we provide a new drug preparation of chlortetracycline that can diminish the effect on the rumen microbiota while treating diarrhea caused by E. coli.

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.

Comparing Antibiotic Pastes with Electrospun Nanofibers as Modern Drug Delivery Systems for Regenerative Endodontics

Nanomaterials have various features that make these types of materials able to be applied in different biomedical applications like, diagnosis, treatment, and drug delivery. Using such materials in endodontic filed both to face the challenges that occur during treatment processes and to make these materials have an antibacterial effect without showing any harm on the host cells. The approach of nanofibers loaded with various antibacterial drugs offers a potential treatment method to enhance the elimination procedure of intracanal biofilms. Clinically, many models of bacterial biofilms have been prepared under in vitro conditions for different aims. The process of drug delivery from polymeric nanofibers is based on the principle that the releasing ratio of drug molecules increases due to the increase in the surface area of the hosted structure. In our review, we discuss diverse approaches of loading/releasing drugs on/from nanofibers and we summarized many studies about electrospun nanofibers loaded various drugs applied in the endodontic field. Moreover, we argued both the advantages and the limitations of these modern endodontic treatment materials comparing them with the traditional ones.

Changes in the Fermentation and Bacterial Community by Artificial Saliva pH in RUSITEC System

The purpose of the study was to assess the artificial saliva (AS) pH on ruminal fermentation and rumen bacteria community in the rumen simulation technique (RUSITEC) system. The experiment was performed in two treatments (low AS pH vs. high AS pH) with four replicates. The low AS pH was sustained by altering the composition of the AS (NaHCO₃ from 9.8 to 1.96 g/L, Na₂HPO₄ from 9.3 to 1.86 g/L) according to McDougall's method. The diets were supplemented with 16 g basic diets with forage to the concentrate ratio of 50:50. The experiments were conducted over 13-day incubation periods, with 9 days adaption and 4 days sample collection. The results showed low AS pH decreased dry matter (DM) degradability (64.37 vs. 58.67%), organic matter (OM) degradability (64.38 vs. 59.32%), neutral detergent fiber (NDF) degradability (46.87 vs. 39.94%), acid detergent fiber (ADF) degradability (38.16 vs. 31.13%), and crude protein (CP) degradability (70.33 vs. 62.99%), respectively. Compared with the high AS pH, the low AS pH increased the proportion of butyrate (P = 0.008) and decreased the proportion of propionate (P < 0.001). At the bacteria community, the low AS pH increased the abundances of Spirochaetes (P = 0.001) and Synergistetes (P = 0.004) and decreased the Verrucomicrobia abundance (P = 0.004) in solid-associated bacteria. At the genus level, the low AS pH increased the abundance of Lactobacillus (P = 0.050) and decreased the abundance of Schwartzia (P = 0.002) in solid-associated bacteria. The abundances of Prevotellaceae_YAB2003_group (P = 0.040), Schwartzia (P = 0.002), and Ruminobacter (P = 0.043) were lower in the low AS pH group compared with the high AS pH group in liquid-associated bacteria. Low AS pH decreased the number of Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes (P < 0.001) both in the solid- and liquid-associated bacteria, respectively. The results of the present study included three groups of bacteria communities according to the different sensitives to rumen pH: the abundances of Lactobacillus, Succinivibrio, and Prevotella_7 are increased with decreasing AS pH; the amounts of R. albus, R. flavefaciens, F. succinogenes as well as the abundances of Schwartzia and Ruminobacter decreased with the reducing AS pH; the abundances of Selenomonas_1, Rikenellaceae_RC9_gut_group, and Succiniclasticum were not affected by the AS pH in RUSTITEC.

A novel ammoniation treatment of barley as a strategy to optimize rumen pH, feed degradability and microbial protein synthesis in sheep

BACKGROUND

Meeting the energy and nitrogen (N) requirements of high-performing ruminants at the same time as avoiding digestive disturbances (i.e. rumen acidosis) is a key priority in ruminant nutrition. The present study evaluated the effect of a cereal ammoniation treatment, in which barley grains are combined with urea and enzymes that catalyze the conversion of urea to ammonia to optimize rumen function. Twelve rumen cannulated sheep were randomly divided into two groups and fed a diet containing 60% of ammoniated barley (AMM) or untreated barley supplemented with urea (CTL) to investigate the impact on rumen fermentation and feed utilization.

RESULTS

AMM had higher total N content and effective rumen degradable N than untreated barely. AMM sheep had a consistently higher rumen pH throughout the day (6.31 versus 6.03) and tended to have a lower post-prandial ammonia peak and higher acetate molar proportion (+5.1%) than CTL sheep. The rumen environment in AMM sheep favored the colonization and utilization of agro-industrial by-products (i.e. orange pulp) by the rumen microbes leading to a higher feed degradability. AMM sheep also had higher total tract apparent N digestibility (+21.7%) and urinary excretion of purine derivatives (+34%), suggesting a higher N uptake and microbial protein synthesis than CTL sheep.

CONCLUSION

The inclusion of AMM in the diet of ruminants represents a valid strategy for maintaining rumen pH within a physiological range and improving N utilization by the rumen microbes, which could have positive effects on the health and productivity of animals in intensive production systems. These findings warrant further studies under conventional farm conditions. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Recent Progress and Trends in the Development of Microbial Biofuels from Solid Waste—A Review

This review covers the recent progress in the design and application of microbial biofuels, assessing the advancement of genetic engineering undertakings and their marketability, and lignocellulosic biomass pretreatment issues. Municipal solid waste (MSW) is a promising sustainable biofuel feedstock due to its high content of lignocellulosic fiber. In this review, we compared the production of fatty alcohols, alkanes, and n-butanol from residual biogenic waste and the environmental/economic parameters to that of conventional biofuels. New synthetic biology tools can be used to engineer fermentation pathways within micro-organisms to produce long-chain alcohols, isoprenoids, long-chain fatty acids, and esters, along with alkanes, as substitutes to petroleum-derived fuels. Biotechnological advances have struggled to address problems with bioethanol, such as lower energy density compared to gasoline and high corrosive and hygroscopic qualities that restrict its application in present infrastructure. Biofuels derived from the organic fraction of municipal solid waste (OFMSW) may have less environmental impacts compared to traditional fuel production, with the added benefit of lower production costs. Unfortunately, current advanced biofuel production suffers low production rates, which hinders commercial scaling-up efforts. Microbial-produced biofuels can address low productivity while increasing the spectrum of produced bioenergy molecules.

Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles

Greater understanding of the spatial relationships between members of the human gut microbiota and available nutrients is needed to gain deeper insights about community dynamics and expressed functions. Therefore, we generated a panel of artificial food particles with each type composed of microscopic paramagnetic beads coated with a fluorescent barcode and one of 60 different dietary or host glycan preparations. Analysis of 160 Bacteroides and Parabacteroides strains disclosed diverse strain-specific and glycan-specific binding phenotypes. We identified carbohydrate structures that correlated with binding by specific bacterial strains in vitro and noted strain-specific differences in the catabolism of glycans that mediate adhesion. Mixed in vitro cultures revealed that these adhesion phenotypes are maintained in more complex communities. Additionally, orally administering glycan beads to gnotobiotic mice confirmed specificity in glycan binding. This approach should facilitate analyses of how strains occupying the same physical niche interact, and it should advance the development of synbiotics, more nutritious foods, and microbiota-based diagnostics.

A comparative study of artificial cow and sheep rumen fermentation of corn straw and food waste: Batch and continuous operation

To optimize the artificial rumen microorganism sources and develop a stable artificial rumen system, batch and continuous operation were investigated with corn straw and food waste as substrates. The batch trials evaluated the volatile fatty acid (VFA) yield, biogas production, and lignocellulose degradation efficiency. The continuous test evaluated the performance of the artificial cow and sheep rumen systems using a dynamic membrane bioreactor (DMBR) with a stepwise organic loading rate at mesophilic temperature. The anaerobic digestion (AD) of the lignocellulose biomass after rumen fermentation pretreatment and of the permeate from the artificial rumen system were also evaluated for CH₄ production. The results indicated that the cow rumen microorganisms were more suitable than sheep rumen microorganisms for lignocellulosic biomass pretreatment and maximized the CH₄ yield through the AD process without inhibition. After approximately four months of continuous operation, a stable and continuous artificial rumen system for lignocellulosic biomass degradation was achieved with cow rumen fluid as inoculum. Based on analysis of the core lignocellulose-degrading enzyme levels and gel filtration chromatography, the cow rumen microorganisms could secrete more extracellular multienzyme complexes to hydrolyze lignocellulosic biomass than the sheep rumen microorganisms in vitro. During the batch and continuous operations, a high diversity and similar richness of bacteria and fungi demonstrated that the cow rumen microorganisms can be used as a preferred inoculum for the artificial rumen system. The use of an artificial cow rumen system with a DMBR is a promising way to construct a stable and continuous artificial rumen system to biodegrade lignocellulosic biomass for biogas production.

Pretreatment of Rapeseed Meal Increases Its Recalcitrant Fiber Fermentation and Alters the Microbial Community in an in vitro Model of Swine Large Intestine

The aim of current study was to investigate in an in vitro study how enzymatic and chemical pretreated rapeseed meal (RSM) influences the fiber fermentation and microbial community in the swine large intestine. RSM was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. 16S rRNA gene sequencing data was performed to evaluate changes in the gut microbiota composition, whereas short-chain fatty acid (SCFA) production (ion-chromatography) and non-starch polysaccharides (NSP) composition (using monoclonal antibodies; mAbs) were used to assess fiber degradation. The results showed that ALK, CELL, PECT1, and PECT2 changed microbial community composition, increased the predicted abundance of microbial fiber-degrading enzymes and pathways, and increased acetic acid, propionic acid, butyric acid, and total SCFA production. The increased microbial genera positively correlated with SCFA production. Monoclonal antibody analyses showed that the cell wall polysaccharide structures of RSM shifted after ALK, CELL, PECT1, and PECT2 treatment. The degradation of NSP during the fermentation period was dynamic, and not continuous based on the epitope recognition by mAbs. This study provides the first detailed analysis of changes in the swine intestinal microbiota due to RSM modified by ALK, CELL, PECT1, and PECT2, which altered the microbial community structure, shifted the predicted functional metagenomic profile and subsequently increased total SCFA production. Our findings that ALK, CELL, PECT1, and PECT2 increased fiber degradability in RSM could help guide feed additive strategies to improve efficiency and productivity in swine industry. The current study gave insight into how enzymatic treatment of feed can alter microbial communities, which provides good opportunity to develop novel carbohydrase treatments, particularly in swine feed.

Tibetan Sheep Adapt to Plant Phenology in Alpine Meadows by Changing Rumen Microbial Community Structure and Function

The rumen microbiota is strongly associated with host health, nutrient absorption, and adaptability. However, the composition, functioning and adaptability of rumen microbiota in Tibetan sheep (TS) across different phenological periods are unclear. In this study we used sequencing of the V4-V5 region of 16S rRNA, qPCR technology and metagenomics to investigate the adaption of rumen microbiota to forage in different stages of phenology. In a grassy period, due to the high nutritional quality of the forage, TS can produce high concentrations of NH₃-N and short fatty acids by increasing the content of key bacteria in the rumen, such as Bacteroidetes, Prevotella, Succiniclasticum, Treponema, Butyrivibrio fibrisolvens, Fibrobacter succinogenes, Prevotella ruminicola, Ruminococcus albus, and Ruminococcus flavefaciens to aid in growth. In the withering period, there was a positive correlation between microorganisms which indicated the closely cooperation between microorganisms, and metagenomic analysis showed that the high genes (GHs and CBMs) and subtribe (GH8, GH12, GH45, GH6, GH9, GH5, GH10, GH3, GH52, GH11, GH57, CBM1, CBM4, CBM6, CBM16, CBM37, CBM13, CBM35, CBM42, CBM32, and CBM62) that encode cellulolytic enzymes were significantly increased when the host faced low quantity and quality of forage. Genes involved in metabolic pathways, fatty acid biosynthesis and biosynthesis of antibiotics were significantly enriched, which indicated that rumen microbiota could improve plant biomass deconstruction and energy maintenance in the face of nutritional deficiencies. In the regreen period, both the composition and function of rumen microbiota had obvious disadvantages, therefore, to improve the competitiveness of microorganisms, we suggest TS should be supplemented with high-protein feed. This study is of great significance for exploring the high altitude adaptability of TS.

Dihydropyridine Enhances the Antioxidant Capacities of Lactating Dairy Cows under Heat Stress Condition

Simple Summary

Additives contribute to improving the health of dairy cows, enhancing antioxidative capacities, and/or increasing milk production, etc. To alleviate the harmful effects of heat stress on dairy cows, a few feed additives studies have been conducted. Dihydropyridine has been used as a feed additive in dairy cow diets. However, the underlying mechanisms of its beneficial effects still remain unclear. In the present study, dairy cows were randomly divided into a control group and a dihydropyridine treatment group under heat stress in summer. The rumen and blood samples of dairy cows were collected to determine the changes in their antioxidative capacities. Meanwhile, the effects of dihydropyridine on ruminal microbial communities were also analyzed. Our data demonstrated that dihydropyridine enhanced the antioxidative capacities of dairy cows under heat stress conditions.

Abstract

Heat stress (HS), a nonspecific response to environmental heat, can seriously affect dairy cow health. Feed additives may alleviate HS in dairy cows by improving rumen fermentation efficacy, stimulating feed consumption, enhancing vasodilation, and/or improving antioxidant capacity. The temperature–humidity index (THI) indicates that spring is a non-HS season, and summer is an HS season. HS results in the decrease in dairy cow antioxidant capacities. Our results indicated the decrease in superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), and total antioxidation (T-AOC) levels and the increase in malondialdehyde (MDA) level during HS season. Meanwhile, antioxidant indexes (SOD, GSH-Px, and T-AOC) were positively correlated with milk yield (p < 0.01), whereas MDA exhibited a significant negative correlation with milk yield (p < 0.05). In addition, the effects of dihydropyridine (DHP) on antioxidant capacity and ruminal microbial communities in dairy cows under HS were investigated. During summer, dairy cows were randomly assigned into two groups under HS, including a standard diet (S-ND) group and standard diet with 3 g/day/cow DHP (S-D) group. DHP treatment significantly restored SOD and GSH-Px levels under HS. Denaturing gradient gel electrophoresis results indicated that the DHP altered ruminal bacterial community mainly composed Proteobacteria and Firmicutes in dairy cows under HS. Our results suggest that DHP can enhance the antioxidant abilities of dairy cows with favorable effects on ruminal microbial communities under HS, further alleviating HS on dairy cows.

Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits

The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi. Collectively, rumen microbial populations interact closely in order to degrade and ferment complex plant material into nutrients for host metabolism, a process which also produces other by-products, such as methane gas. Our understanding of the rumen microbiome and its functions are of both scientific and industrial interest, as the metabolic functions are connected to animal health and nutrition, but at the same time contribute significantly to global greenhouse gas emissions. While many of the major microbial members of the rumen microbiome are acknowledged, advances in modern culture-independent meta-omic techniques, such as metaproteomics, enable deep exploration into active microbial populations involved in essential rumen metabolic functions. Meaningful and accurate metaproteomic analyses are highly dependent on representative samples, precise protein extraction and fractionation, as well as a comprehensive and high-quality protein sequence database that enables precise protein identification and quantification. This review focuses on the application of rumen metaproteomics, and its potential towards understanding the complex rumen microbiome and its metabolic functions. We present and discuss current methods in sample handling, protein extraction and data analysis for rumen metaproteomics, and finally emphasize the potential of (meta)genome-integrated metaproteomics for accurate reconstruction of active microbial populations in the rumen.

Fermented soybean meal affects the ruminal fermentation and the abundance of selected bacterial species in Holstein calves: a multilevel analysis

The effect of soybean meal (SBM) replacement with fermented SBM (FSBM) on ruminal fermentation and bacterial abundance in Holstein calves was investigated in this study. Thirty nine calves were randomized to: (1) control: 27% SBM + 0% FSBM (FSBM0, n = 13); (2) 18% SBM + 9% FSBM (FSBM9, n = 13); and (3) 13.5% SBM + 13.5% FSBM (FSBM13, n = 13). SBM contained a greater amount of large peptides containing 3 to 10 amino acids (AAs), while FSBM had a greater amount of ammonia nitrogen (NH3-N), free AAs, and small peptides containing 2 to 3 AAs. The calves fed FSBM13 had the lowest acetic acid, NH3-N, and the ratio of acetate to propionate, with the greatest concentration of caproic acid, valeric acid and isovaleric acid in ruminal fluid. Compared to those fed FSBM9 or FSBM13, the calves fed FSBM0 had the greatest proportion of Butyrivibrio fibrisolvens and Ruminococcus albus in rumen fluid. However, the ruminal abundance of Prevotella ruminicola in calves fed FSBM13 was greater than in calves fed FSBM0. Network analysis showed that the abundance of the Ruminococcus albus was associated with large peptides, and butyric acid was correlated with small peptide. Taken together, our findings suggest that FSBM may have the potential to boost calf performance by changing the fermentation products and the relative abundance of some members of the bacterial community in the rumen.

Cosubstrate strategy for enhancing lignocellulose degradation during rumen fermentation in vitro: Characteristics and microorganism composition

To enhance the degradation of wheat straw (WS) and corn straw (CS) in rumen fermentation, characterization of degradation and ruminal microorganisms of monosubstrate (WS/CS) groups and a cosubstrate strategy with food waste (FW) group was performed. The cellulose, hemicellulose, and lignin degradation efficiency of WS and CS; soluble chemical oxygen demand; volatile fatty acid yields; and activity of ligninolytic, cellulolytic, and hemicellulolytic enzymes for the cosubstrate group were improved compared with those for the corresponding monosubstrate groups. An accurate and a good of fit of the Weibull kinetic model, decreased crystallinity index values, and characteristic absorbance bands in the Fourier transform-infrared spectra further confirmed that cosubstrate addition with FW decreased the resistance of cellulose and hemicellulose to biodegradation. High-throughput sequencing results suggested that the bacterial diversity in CS rumen fermentation and fungal diversity and richness in WS rumen fermentation were promoted with FW as a cosubstrate. The cosubstrate addition with FW significantly affected the composition of the ruminal bacteria and fungi in rumen fermentation. The relative abundances (RAs) of rumen bacteria were increased in the cosubstrate CS/WS and FW fermentation conditions, and the enhancement of CS degradation with FW supplementation was stronger than that of WS rumen fermentation with FW supplementation. The RAs of the ruminal fungal genera Ustilago and Fusarium were promoted in CS and WS fermentation with FW, respectively. Moreover, the fermentation properties and rumen flora in the FW rumen fermentation also provided some evidence to suggest an enhancement of the cosubstrate strategy compared with the monosubstrate strategy.

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep

The tolerance of ruminants to gossypol, a natural phenolic compound derived from the cotton plant, is greater than that of monogastric animals, partially because of the gossypol-degrading bacteria in the rumen of the ruminants. In this study, we aimed to examine the effect of gossypol supplementation on fermentation characteristics, bacterial α-diversity and community structure in the rumen fluid of sheep to analyse the change of bacterial in response to gossypol. 8 sheep with permanent fistula were randomly divided into 2 groups, a control and gossypol acetate supplementation groups. Sheep in the latter group were supplemented with gossypol acetate at the levels of 600 mg and 1,200 mg/animal per day during the first (S1, days 1 to 27) and subsequent (S2, days 28 to 47) stages. Gossypol supplementation significantly increased the molar proportion of acetate, and decreased the molar proportion of isobutyric acid, butyric acid, and isovaleric acid in the rumen fluid. Gossypol supplementation have no significant effect on bacterial diversity in the rumen fluid. At the phylum level, gossypol had no effect on bacterial community. At the genus level, gossypol supplementation significantly increased the relative abundance of Treponema_2. However, there were no significant differences in the relative abundance of dominant bacterial genera. In conclusion, gossypol supplementation had an effect on molar proportion of acetate, isobutyric acid, butyric acid, and isovaleric acid, but had no significant effect on the bacterial diversity and relative abundance of dominant bacteria in rumen fluid of sheep.

Persistent action of cow rumen microorganisms in enhancing biodegradation of wheat straw by rumen fermentation

Rumen fermentation is known to be effective for lignocellulosic-wastes biodegradation to certain extent but it is still unclear if there exists a termination of the microorganisms' action to further degrade the bio-refractory fractions. In order to illuminate the related microbiological characteristics, experiments were conducted in a prolonged duration of rumen fermentation of mechanically ruptured wheat straw, with inoculation of cow rumen microorganisms in vitro. Although the organic wastes could not be biodegraded quickly, continuous conversion of the lignocellulosic contents to volatile fatty acids and biogas proceeded in the duration of more than three months, resulting in 96-97% cellulose and hemicellulose decomposition, and 42% lignin decomposition. X-ray diffraction and Fourier transform infrared spectroscopy further demonstrated the characteristics of lignocellulosic structure decomposition. Under the actions of cow rumen microorganisms, stable pH was maintained in the fermentation liquid, along with a steady NH₄⁺-N, volatile fatty acids accumulation, and a large buffering ability. It was identified by enzyme analysis and Illumina MiSeq sequencing that the rich core lignocellulolytic enzymes secreted by the abundant and diverse rumen bacteria and fungi contributed to the persistent degradation of lignocellulosic wastes. Members of the Clostridiales order and Basidiomycota phylum were found to be the dominant lignocellulolytic bacteria and fungi, respectively. It could thus be inferred that the main lignocellulose degradation processes were a series of catalytic reactions under the actions of lignocellulolytic enzymes secreted from bacteria and fungi. The dominant hydrogenotrophic methanogens (Methanomassiliicoccus, Methanobrevibacter, Methanosphaera, and Methanoculleus) in the rumen could also assist CH₄ production if the rumen fermentation was followed with anaerobic digestion.

Effect of combinations of feed-grade urea and slow-release urea in a finishing beef diet on fermentation in an artificial rumen system

This study evaluated the effect of combinations of feed-grade urea and slow-release urea (SRU) on fermentation and microbial protein synthesis within two artificial rumens (Rusitec) fed a finishing concentrate diet. The experiment was a completely randomized, dose-response design with SRU substituted at levels of 0% (control), 0.5%, 1%, or 1.75% of dry matter (DM) in place of feed-grade urea, with four replicate fermenters per dosage. The diet consisted of 90% concentrate and 10% forage (DM basis). The experiment was conducted over 15 d, with 8 d of adaptation and 7 d of sampling. Dry matter and organic matter disappearances were determined after 48 h of incubation from day 9 to 12, and daily ammonia (NH₃) and volatile fatty acid (VFA) production were measured from day 9 to 12. Microbial protein synthesis was determined on days 13-15. Increasing the level of SRU quadratically affected total VFA (Q, P = 0.031) and ammonia (Q, P = 0.034), with a linear increment in acetate (L, P = 0.01) and isovalerate (L, P = 0.05) and reduction in butyrate (L, P = 0.05). Disappearance of neutral detergent fiber (NDF) and acid detergent fiber (ADF) was quadratically affected by levels of SRU, plateauing at 1% SRU. Inclusion of 1% SRU resulted in the highest amount of microbial nitrogen associated with feed particles (Q, P = 0.037). Responses in the efficiency of microbial protein synthesis fluctuated (L, P = 0.002; Q, P = 0.001) and were the highest for 1% SRU. In general, the result of this study showed that 1% SRU in combination with 0.6% urea increased NDF and ADF digestibility and total volatile fatty acid (TVFA) production.

Biofilm formation as a microbial strategy to assimilate particulate substrates

In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

Effect of diet quality and shearing on feed and water intake, in vitro ruminal methane production, and blood parameters of Omani sheep

The aim of this study was to evaluate the effect of diet and animal shearing on the feed and nutrient intakes, water intake, in vitro ruminal methane production, and blood parameters of Omani sheep. A pens trial was carried out for 16 days each in March and June of 2017 using 20 Omani non-castrated yearling rams selected from the sheep herd in the research station and randomly assigned to four groups with 5 animals per group. Group 1: sheared animals fed a high concentrate (HC) diet, group 2: fleeced animals fed a HC diet, group 3: sheared animals fed a low concentrate (LC) diet, group 4: fleeced animals fed a LC diet. Furthermore, a metabolic crates trial was carried out in July of 2017 on three animals from each group over a 10-day period. The effect of diet and shearing on the tested parameters was evaluated using the mixed linear model, where animals were fitted as a random effect to account for the individual animal deviation from the overall mean. Results showed that rams fed on the high concentrate diet had a significantly increased organic matter intake of the total diet (62 g/kg ^0.75 Live Weight (LW) in HC group to 54 g/kg ^0.75 LW in LC group), an increased water intake (6.3 L/day vs 4.8 L/day in LC group), and a reduced in vitro methane production (i.e. the invitro ruminal CH₄ was measured and converted to daily CH₄ using the daily feed intake data and was 20.4 g CH₄ per head/day in HC group vs 27.3 g CH₄ per head/day in LC group), compared with rams fed on the low concentrate diet. Furthermore, shearing had a significant effect (P < 0.01) on increased feed and nutrients intake. The apparent and organic matter digestibility was significantly different (P < 0.01) between the experimental groups and was greater for those rams fed on the HC diet. Partial substitution of low-quality Rhodes grass hay by high-quality concentrate significantly improved the total diet organic matter digestibility (P < 0.01) and nutrients digestibility, whereas no significant effects on biochemical blood parameters or animal health were observed. These results show the importance of utilizing effective feeding and shearing plans to improve the productivity and reduce the methane emission of Omani sheep.

Effect of steam explosion of oil palm frond and empty fruit bunch on nutrient composition and ruminal fermentation characteristics

In this study, we evaluated the effect of steam explosion of oil palm frond (OPF) and oil palm empty fruit bunch (EFB) on nutrient composition and ruminal fermentation characteristics in vitro. The results showed that steam explosion decreased NDF (P < 0.01), ADF (P < 0.01), and hemicellulose content (P < 0.01) in OPF and EFB. Steam explosion improved the effective energy value of OPF and EFB. In vitro fermentation results revealed that 72-h gas production capacity of OPF and EFB increased by 12.60and 85.06% (P < 0.01), respectively, after steam explosion. Steam explosion had a tendency to improve the concentration of total volatile fatty acids (TVFA) (P = 0.082). In conclusion, steam explosion of OPF and EFB reduced NDF, ADF, and hemicellulose content and increased gas production and TVFA concentration.

Exogenous fibrolytic enzymes and recombinant bacterial expansins synergistically improve hydrolysis and in vitro digestibility of bermudagrass haylage

Four experiments were conducted to examine the effects of a recombinant bacterial expansin-like protein (BsEXLX1) from Bacillus subtilis and a commercial exogenous fibrolytic enzyme (EFE) preparation for ruminants on hydrolysis of pure substrates (cellulose and xylan) and in vitro digestibility of bermudagrass haylage (BMH). Recombinant Escherichia coli BL21 strain was used to express BsEXLX1; the protein was purified using an affinity column. In experiment 1, carboxymethylcellulose, Whatman #1 filter paper (General Electric, Boston, MA) and oat-spelt xylan substrates were subjected to 4 treatments (1) sodium citrate buffer (control), (2) BsEXLX1 (162 µg/g of substrate), (3) EFE (2.3 mg/g of substrate), and (4) EFE + BsELX1 in 3 independent runs. Samples were incubated at optimal conditions for both additives (pH 5 and 50°C) or at ruminal (pH 6 and 39°C) or ambient (pH 6 and 25°C) conditions for 24 h and sugar release was measured. In experiment 2, digestibility in vitro of BMH was examined after treatment with the following: (1) control (buffer only), (2) BsEXLX1 (162 µg/g of dry matter), (3) EFE (2.2 mg/g of dry matter), and (4) EFE + BsEXLX1 in 3 independent runs at 39°C for 24 h. Experiment 3 examined effects of EFE and BsEXLX1 on simulated preingestive hydrolysis and profile of released sugars from BMH after samples were suspended in deionized water with sodium azide at 25°C for 24 h in 2 independent runs. In experiment 4, the sequence of the BsEXLX1 purified protein was compared with 447 ruminal bacterial genomes to identify similar proteins from the rumen. In experiment 1, compared with EFE alone, EFE and BsEXLX1 synergistically increased sugar release from carboxymethylcellulose and Whatman #1 filter paper under all simulated conditions; however, hydrolysis of xylan was not improved. In experiment 2, compared with EFE alone, treatment with EFE and BsEXLX1 increased neutral detergent fiber and acid detergent fiber digestibility of bermudagrass haylage (by 5.5 and 15%, respectively) and total volatile fatty acid concentrations, and decreased acetate-propionate ratio. In experiment 3, compared with EFE alone. The EFE and BsEXLX1 synergistically reduced concentrations of neutral detergent fiber and acid detergent fiber and increased release of sugars by 9.3%, particularly cellobiose (72.5%). In experiment 4, a similar sequence to that of BsEXLX1 was identified in Bacillus licheniformis, and similar hypothetical protein sequences were identified in Ruminococcus flavefaciens strains along with different protein structures in E. xylanophilum and Lachnospiraceae. This study showed that an expansin-like protein synergistically increased the hydrolysis of pure cellulose substrates and the hydrolysis and digestibility in vitro of BMH.

Early Feeding Regime of Waste Milk, Milk, and Milk Replacer for Calves Has Different Effects on Rumen Fermentation and the Bacterial Community

Simple Summary

The postnatal period may be the most critical window for rumen manipulation, and the early feeding regime may lead to permanent changes in the rumen microbial composition. The objective of this research was to investigate the effects of the most common liquid feeds (whole milk, waste milk, and milk replacer) on growth performance, rumen development, and the ruminal bacterial community during the weaning period, and to then follow calves to up to six months of age to determine the persistence of any ruminal imprinting effects. The results demonstrate that the early feeding regime impacts rumen development not only by dry matter intake, but also the type of liquid feed. Calves fed waste milk had a distinctly structured bacterial community at two months of age, but this difference diminished at six months of age. Calves fed milk replacer had a different rumen fermentation pattern at two months of age, which may induce a long-lasting effect on the rumen environment.

Abstract

We investigated the effects of different types of early feeding on rumen fermentation parameters and the bacterial community in calves. Fifty-four Holstein calves were assigned to three treatments and fed whole milk (M), pasteurized waste milk (WM), or milk replacer (MR). Male calves were slaughtered at the age of two months to measure the stomach masses. The female calves were followed for six months to determine the body weight, blood indices, rumen fermentation, and ruminal bacterial community. At the age of two months, the average daily gain was lower, but the concentration of total volatile fatty acids was greater in the MR group. Starter intake and stomach mass were lower, but the isovalerate molar proportion was greater in the WM group. The blood indices and ruminal bacterial community of the WM group differed from those of the other groups. At the age of six months, the ruminal propionate molar proportion was lower, but the ruminal pH and acetate/propionate ratio were greater in the MR group. In conclusion, calves fed WM had different rumen fermentation and bacterial community during the weaning period, whereas feeding MR produced a long-lasting effect on the rumen environment.

Seasonal differences in rumen bacterial flora of wild Hokkaido sika deer and partial characterization of an unknown bacterial group possibly involved in fiber digestion in winter

Rumen digesta was obtained from wild Hokkaido sika deer to compare bacterial flora between summer and winter. Bacterial flora was characterized with molecular-based approaches and enrichment cultivation. Bacteroidetes was shown as a major phylum followed by Firmicutes, with similar proportions in both seasons. However, two phylogenetically unique groups in Bacteroidetes were found in each season: unknown group A in winter and unknown group B in summer. The ruminal abundance of unknown group A was the highest followed by Ruminococcus flavefaciens in winter. Moreover, the abundance of these two was higher in winter than in summer. In contrast, the abundance of unknown group B was higher in summer than in winter. In addition, this group showed the highest abundance in summer among the bacteria quantified. Unknown group A was successfully enriched by cultivating with oak bark and sterilized rumen fluid, particularly that from deer. Bacteria of this group were distributed in association with the solid rather than the liquid rumen fraction, and were detected as small cocci. Accordingly, unknown group A is assumed to be involved in degradation of fibrous materials. These results suggest that wild Hokkaido sika deer develop a rumen bacterial flora in response to changes in dietary conditions.

Effects of exogenous fibrolytic and amylolytic enzymes on ruminal fermentation and performance of mid-lactation dairy cows

Lactation diets are composed mostly of carbohydrates that are not fully fermented by rumen microbes. The aim of this study was to evaluate exogenous fibrolytic (Fibrozyme, Alltech Inc., Nicholasville, KY) and amylolytic (Amaize, Alltech Inc.) enzymes on nutrient intake, sorting index, total-tract apparent digestibility, ruminal fermentation, nitrogen utilization, milk yield, and composition of dairy cows in mid-lactation. Thirty-two multiparous Holstein cows (181 ± 35 d in milk, 571 ± 72.7 kg of body weight, and 29.6 ± 5.24 kg/d of milk yield at the start of experiment) were blocked according to milk yield and randomly allocated to treatments in a 4 × 4 Latin square design. Treatments were (1) control, basal diet without exogenous enzymes; (2) fibrolytic enzyme (FIB), dietary supplementation of Fibrozyme at 12 g/d (51 IU of xylanase activity/kg of diet dry matter); (3) amylolytic enzyme (AMY), dietary supplementation of Amaize at 8 g/d (203 fungal amylase units/kg of diet dry matter); and (4) both fibrolytic and amylolytic enzymes (FIB+AMY) added at the same dose of the individual treatments. Enzyme products were added to the concentrate during its preparation (once a week). The supply of FIB and AMY had no effect on nutrient intake and digestibility. However, an interaction effect was observed on sorting index of feed particle size between 8 and 19 mm. Amylolytic enzyme increased the sorting for feed particles between 8 and 19 mm, only when fed without FIB. In addition, AMY decreased the sorting for feed with particle size greater than 19 mm. An interaction effect was observed between FIB and AMY for ruminal butyrate concentration and N excretion. Amylolytic enzyme increased ruminal butyrate concentration in cows treated with FIB. Further, FIB decreased milk protein production and feed efficiency only in cows not fed AMY. Amylolytic enzyme reduced urinary N excretion. Exogenous enzymes had no effect on milk production and composition of dairy cows. This study lacks evidence that fibrolytic and amylolytic enzymes can affect nutrient digestibility, ruminal fermentation, and performance of mid-lactation cows.

Evaluation of the digestibility of steam-exploded wheat straw by ruminal fermentation, sugar yield and microbial structurein vitro

Wheat straw is considered an abundant lignocellulosic biomass source in China. However, its recalcitrance hinders the degradation of wheat straw by enzymes and microbes. In this study, we investigated the optimum steam explosion conditions of pretreated wheat straw by response surface methodology to improve its nutrition level as a feedstuff for the ruminant industry or as a feedstock for biofuel production. The highest volatile fatty acid (VFA) yield (30.50 mmol L⁻¹) was obtained at 2.3 MPa, 90 s and a moisture content of 36.46%. Under optimal conditions, steam explosion significantly altered the fermentation parameters in vitro. Ionic chromatography showed that pretreating wheat straw could improve the production of fermentable sugar, which was ascribed to the degradation of cellulose and hemicellulose. In addition, high throughput 16S rRNA amplicon sequencing analysis revealed that steam explosion changed the microbial community and enhanced the colonization of cellulolytic bacteria. Our findings demonstrated that steam explosion pretreatment could greatly improve the digestibility of wheat straw by facilitating sugar production and microbial colonization.

Wheat straw is considered an abundant lignocellulosic biomass source in China.

Using 'Omic Approaches to Compare Temporal Bacterial Colonization of Lolium perenne, Lotus corniculatus, and Trifolium pratense in the Rumen

Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

Steam explosion enhances digestibility and fermentation of corn stover by facilitating ruminal microbial colonization

The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradation of corn stover by ruminal microbiome. The steam explosion conditions were first optimized, and then the efficacy of steam explosion was evaluated both in vitro and in vivo. Steam explosion altered the physical and chemical structure of corn stover as revealed by scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, respectively, and increased its cellulose content while decreasing hemicellulose content. Steam-exploded corn stover also increased release of reducing sugars, rate of fermentation, and production of volatile fatty acids (VFAs) in vitro. The steam explosion treatment increased microbial colonization and in situ degradation of cellulose and hemicellulose of corn stover in the rumen of dairy cows. Steam explosion may be a useful pretreatment of corn stover to improve its nutritional value as forage for cattle, or as feedstock for biofuel production.

RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production

The microbes inhabiting the rumen convert low-quality, fibrous, plant material into useable energy for the host ruminant. Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency of the host ruminant. Robert Hungate laid the foundation for rumen microbiome research. This area of research has expanded immensely with advances in methodology and technology that have not only improved the ability to describe microbes in taxonomic and density terms but also characterize populations of microbes, their functions, and their interactions with each other and the host. The interplay between the rumen microbiome and the host contributes to variation in many phenotypic traits expressed by the host animal. A better understanding of how the rumen microbiome influences host health and performance may lead to novel strategies and treatments for trait improvement. Furthermore, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance. The potential for these tiny but mighty rumen microbes to play a role in improving livestock production is appreciated despite being relatively obscure.