Effects of Saccharomyces cerevisiae and Bacillus subtilis on in vitro fermentation in the rumen of Hu sheep

BACKGROUND

The demand for animal products is increasing in developing countries due to population growth. However, livestock production contributes significantly to global warming, accounting for 25%. Probiotics can help improve livestock efficiency by enhancing gut microbes and fat metabolism. They can modify rumen populations, enhance fermentation, reduce methane emissions and improve feed digestion. In this study, the goal was to determine the most effective method of reducing methane emissions in the rumen of sheep in vitro by adding different concentrations of Saccharomyces cerevisiae and Bacillus subtilis.

RESULTS

Adding 8 × 106 CFU g-1 S. cerevisiae during fermentation reduced pH levels after 48 h. This also increased the concentrations of NH3-N, microbial protein and total gas production. At the same time, it decreased methane emissions. Furthermore, adding 20 × 106 CFU g-1 B. subtilis to the mixture increased total gas production (TGP) and methane production, with the highest production observed after 48 h. However, it did not affect pH levels after 48 h.

CONCLUSION

It can be concluded that S. cerevisiae had significantly increased microbial protein and NH3-N concentrations after fermentation without altering pH. Additionally, the addition of S. cerevisiae enhanced TGP and reduced methane emissions. It is worth noting that TGP increased because B. subtilis was added at a concentration of 20 × 106 CFU g-1, with no significant differences between concentrations. Therefore, we recommend adding S. cerevisiae and B. subtilis to the diet at doses of 8 and 20 × 106 CFU g-1, as it resulted in higher TGP and reduced methane emissions. © 2024 Society of Chemical Industry.

Molecular detection of ruminal micro-flora and micro-fauna in Saudi Arabian camels: Effects of season and region

This study investigated and explored the availability of micro-flora and micro-fauna in the ruminal contents of Arabian camel (Camelus dromedarius) from three different regions in Saudi Arabia along with two seasons. Samples were prepared and tested by conventional polymerase chain reaction (PCR). This study confirmed that the bacterial flora were dominating over other microbes. Different results of the availability of each microbe in each region and season were statistically analyzed and discussed. There was no significant effect of season on the micro-flora or micro-fauna however, the location revealed a positive effect with Ruminococcus flavefaciens (p < 0 0.03) in the eastern region. This study was the first to investigate the abundance of micro-flora and micro-fauna in the ruminal contents of camels of Saudi Arabia. This study underscores the significance of camel ruminal micro-flora and micro-fauna abundance, highlighting their correlation with both seasonality and geographic location. This exploration enhances our comprehension of camel rumination and digestion processes. The initial identification of these microbial communities serves as a foundational step, laying the groundwork for future in-depth investigations into camel digestibility and nutritional requirements.

Evaluation of Increasing Dietary Concentrations of a Multi-Enzyme Complex in Feedlot Lambs' Rations

The objective of this study was to evaluate the effects of increasing levels of the M-E complex (xylanase, glucanase, cellulase, and invertase) Optimax E® on the performance of growing lambs, their digestibility, and their rumen microbiota, and to estimate NEm, NEg, and ruminal methane levels. Forty lambs (Katahdin x Dorset; 22.91 ± 4.16 kg) were randomly assigned to dietary concentrations of ME (0, 0.2, 0.4, and 0.8% DM) and fed individually for 77 days. Increasing M-E improved feed conversion (p < 0.05) as well as NEm and NEg (p < 0.05), which were associated with increased in vivo DM and NDF digestion (linear and quadratic p < 0.01). Few microbial families showed abundancy changes (Erysipelotrichaceae, Christensenellaceae, Lentisphaerae, and Clostridial Family XIII); however, the dominant phylum Bacteroidetes was linearly reduced, while Firmicutes increased (p < 0.01), resulting in a greater Firmicutes-to-Bacteroidetes ratio. Total Entodinium showed a quadratic response (p < 0.10), increasing its abundancy as the enzyme dose was augmented. The daily emission intensity of methane (per kg of DMI or AGD) was reduced linearly (p < 0.01). In conclusion, adding the M-E complex Optimax E® to growing lambs' diets improves their productive performance by acting synergistically with the rumen microbiota, modifying the Firmicutes-to-Bacteroidetes ratio toward more efficient fermentation, and shows the potential to reduce the intensity of greenhouse gas emissions from lambs.

Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet

A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies

BACKGROUND

Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle.

RESULTS

The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host.

CONCLUSIONS

This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.

New insights in improving sustainability in meat production: opportunities and challenges

Treating livestock as senseless production machines has led to rampant depletion of natural resources, enhanced greenhouse gas emissions, gross animal welfare violations, and other ethical issues. It has essentially instigated constant scrutiny of conventional meat production by various experts and scientists. Sustainably in the meat sector is a big challenge which requires a multifaced and holistic approach. Novel tools like digitalization of the farming system and livestock market, precision livestock farming, application of remote sensing and artificial intelligence to manage production and environmental impact/GHG emission, can help in attaining sustainability in this sector. Further, improving nutrient use efficiency and recycling in feed and animal production through integration with agroecology and industrial ecology, improving individual animal and herd health by ensuring proper biosecurity measures and selective breeding, and welfare by mitigating animal stress during production are also key elements in achieving sustainability in meat production. In addition, sustainability bears a direct relationship with various social dimensions of meat production efficiency such as non-market attributes, balance between demand and consumption, market and policy failures. The present review critically examines the various aspects that significantly impact the efficiency and sustainability of meat production.

Interaction between genetics and inulin affects host metabolism in rainbow trout fed a sustainable all plant-based diet

Inulin affects nutrition and metabolism in many animals. Although inulin is widely used in the diet of teleosts, its mechanism of action is unknown. Here, we investigated the effect of inulin (2 %) on the intestinal microbiome and metabolism in rainbow trout (Oncorhynchus mykiss) selected for growth and survival when fed a 100 % plant-based diet (suave) and a control line (temoin). Metabolic responses to the two factors (line and inulin) in liver, intestine, muscle and adipose were tissue-specific, with line and interaction between the two factors influencing overall expression in liver. In the intestine, inulin and line and in muscle, line influenced the expression of metabolic genes. Microbiota between the mucus and digestive contents was significantly different, with genera from Proteobacteria being more abundant in the mucus, whereas genera from the Firmicutes and Planctomycetes being more abundant in contents. Effect of inulin and interaction between factors on the microbiome was evident in contents. The significant taxa of control and inulin-fed groups differed greatly with Streptococcus and Weissella being significantly abundant in the inulin-fed group. There was a general trend showing higher levels of all SCFA in temoin group with propionic acid levels being significantly higher. An operational taxonomic unit (OTU) belonging to the Ruminococcaceae was significantly abundant in suave. The tissue-specific correlations between OTU and gene expression may indicate the link between microbiome and metabolism. Together, these results suggest that line and inulin impact the gene expression in a tissue-specific manner, possibly driven by specific OTUs enriched in inulin-fed groups and suave.

Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird

Background

The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela.

Methods

Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO.

Results

The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences.

Conclusion

Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.

Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology

The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.

Feeding incremental amounts of ground flaxseed: effects on diversity and relative abundance of ruminal microbiota and enteric methane emissions in lactating dairy cows

We evaluated the effects of incremental amounts of ground flaxseed (GFX) on diversity and relative abundance of ruminal microbiota taxa, enteric methane (CH₄) emissions, and urinary excretion of purine derivatives (PD) in lactating dairy cows in a replicated 4 × 4 Latin square design. Twenty mid-lactation Jersey cows were used in the study. Of these 20 cows, 12 were used for ruminal sampling, 16 for enteric CH₄ measurements, and all for spot urine collection. Each period lasted 21 d with 14 d for diet adaptation and 7 d for data and sample collection. Diets were formulated by replacing corn meal and soybean meal with 0%, 5%, 10%, and 15% of GFX in the diet's dry matter. Ruminal fluid samples obtained via stomach tubing were used for DNA extraction. Enteric CH₄ production was measured using the sulfur hexafluoride tracer technique. Diets had no effect on ruminal microbiota diversity. Similarly, the relative abundance of ruminal archaea genera was not affected by diets. In contrast, GFX decreased or increased linearly the relative abundance of Firmicutes (P < 0.01) and Bacteroidetes (P < 0.01), respectively. The relative abundance of the ruminal bacteria Ruminococcus (P < 0.01) and Clostridium (P < 0.01) decreased linearly, and that of Prevotella (P < 0.01) and Pseudobutyrivibrio (P < 0.01) increased linearly with feeding GFX. A tendency for a linear reduction (P = 0.055) in enteric CH₄ production (from 304 to 256 g/d) was observed in cows fed increasing amounts of GFX. However, neither CH₄ yield nor CH₄ intensity was affected by treatments. Diets had no effect on the urinary excretion of uric acid, allantoin, and total PD. Overall, feeding GFX decreased linearly the relative abundance of the ruminal bacterial genera Ruminococcus and Clostridium and enteric CH₄ production, but no change was seen for CH₄ yield and CH₄ intensity, or urinary excretion of total PD, suggesting no detrimental effect of GFX on microbial protein synthesis in the rumen.

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

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

Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray-Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow's 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.

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

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.

The gastrointestinal microbiome of browsing goats (Capra hircus)

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

Association between body weight and distal gut microbes in Hainan black goats at weaning age

Gut microbiota plays a critical role in the healthy growth and development of young animals. However, there are few studies on the gut microbiota of young Hainan black goats. In this study, 12 three-month-old weaned lambs with the same birth date were selected and divided into the high body weight group (HW) and low body weight group (LW). The microbial diversity, composition, and predicted function in the feces of HW and LW groups were analyzed by collecting fecal samples and sequencing the 16S rRNA V3-V4 region. The results indicated that the HW group exhibited higher community diversity compared with the LW group, based on the Shannon index. The core phyla of the HW and LW groups were both Firmicutes and Bacteroidetes. Parabacteroides, UCG-005, and Bacteroides are the core genera of the HW group, and Bacteroides, Escherichia-Shigella, and Akkermansia are the core genera of the LW group. In addition, genera such as Ruminococcus and Anaerotruncus, which were positively correlated with body weight, were enriched in the HW group; those genera, such as Akkermansia and Christensenellaceae, which were negatively correlated with body weight, were enriched in the LW group. Differential analysis of the KEGG pathway showed that Amino Acid Metabolism, Energy Metabolism, Carbohydrate Metabolism, and Nucleotide Metabolism were enriched in the HW group, while Cellular Processes and Signaling, Lipid Metabolism, and Glycan Biosynthesis and Metabolism were enriched in the LW group. The results of this study revealed the gut microbial characteristics of Hainan black goats with different body weights at weaning age and identified the dominant flora that contributed to their growth.

Carbohydrate active enzyme system in rumen fungi: a review

Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.

A Combination of Novel Microecological Agents and Molasses Role in Digestibility and Fermentation of Rice Straw by Facilitating the Ruminal Microbial Colonization

In this study, we evaluated the effect of microecological agents (MA) combined with molasses (M) on the biodegradation of rice straw in the rumen. Rice straw was pretreated in laboratory polyethylene 25 × 35 cm sterile bags with no additive control (Con), MA, and MA + M for 7, 15, 30, and 45 days, and then the efficacy of MA + M pretreatment was evaluated both in vitro and in vivo. The scanning electron microscopy, X-ray diffraction analysis, and Fourier-transform infrared spectroscopy results showed that the MA or MA + M pretreatment altered the physical and chemical structure of rice straw. Meanwhile, the ruminal microbial attachment on the surface of rice straw was significantly increased after MA+M pretreatment. Furthermore, MA + M not only promoted rice straw fermentation in vitro but also improved digestibility by specifically inducing rumen colonization of Prevotellaceae_UCG-001, Butyrivibrio, and Succinimonas. Altogether, we concluded that microecological agents and molasses could be the best choices as a biological pretreatment for rice straw to enhance its nutritive value as a ruminant's feed.

Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses

There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan

The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes.

Brittle Culm 15 mutation alters carbohydrate composition, degradation and methanogenesis of rice straw during in vitro ruminal fermentation

Brittle Culm 15 (BC15) gene encodes a membrane-associated chitinase-like protein that participates in cellulose synthesis, and BC15 gene mutation affects cell wall composition in plant, such as cellulose or hemicellulose. The present study was designed to investigate the changes of carbohydrates composition in bc15 mutant straw, and the resulting consequence on rumen fermentation, methanogenesis, and microbial populations (qPCR) during in vitro ruminal fermentation process. Two substrates, bc15 mutant and wild-type (WT) rice straws, were selected for in vitro rumen batch culture. The first experiment was designed to investigate the kinetics of total gas and CH₄ production through 48-h in vitro ruminal fermentation, while the second experiment selected incubation time of 12 and 48 h to represent the early and late stage of in vitro ruminal incubation, respectively, and then investigated changes in biodegradation, fermentation end products, and selected representative microbial populations. The bc15 mutant straw had lower contents of cellulose, neutral detergent fiber (NDF) and acid detergent fiber (ADF), and higher contents of water-soluble carbohydrates, neutral detergent solubles (NDS) and monosaccharides. The bc15 mutant straw exhibited a distinct kinetics of 48-h total gas and CH₄ production with faster increases in early incubation when compared with WT straw. The bc15 mutant straw had higher DM degradation, NDF degradation and total volatile fatty acid concentration at 12 h of incubation, and lower NDF degradation and CH₄ production at 48 h of incubation, together with lower acetate to propionate ratio and ADF degradation and higher butyrate molar percentage and NDS degradation at both incubation times. Furthermore, the bc15 mutant straw resulted in greater 16S gene copies of F. succinogenes, with lower 18S gene copies of fungi at both incubation times. These results indicated that the BC15 gene mutation decreased fibrosis of cell wall of rice straw, enhanced degradation at the early stage of rumen fermentation, and shifts fermentation pattern from acetate to propionate and butyrate production, leading to the decreased volume and fractional rate of CH₄ production. However, BC15 gene mutation may enhance hardenability of cell wall structure of rice straw, which is more resistant for microbial colonization with decreased fiber degradation. Thus, this study modified rice straw by manipulating a cell wall biosynthesis gene and provides a potential strategy to alter degradation and CH₄ production during in vitro ruminal fermentation process.

Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing

This study aimed to determine the taxonomic and functional characteristics of the Japanese Black (JB) steer rumen microbiome. The rumen microbiomes of six JB steers (age 14.7 ± 1.44 months) and six JB sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 months), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the JB and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the JB steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the JB steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the JB steer rumen. Although Prevotella spp. were predominant both in the JB and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between JB and F1.

Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.

Manipulation of In Vitro Ruminal Fermentation and Feed Digestibility as Influenced by Yeast Waste-Treated Cassava Pulp Substitute Soybean Meal and Different Roughage to Concentrate Ratio

Cassava pulp (CS) is high in fiber and low in protein; hence, improving the nutritive value of CS is required to increase its contribution to enhancing ruminant production. The present work hypothesized that CS quality could be enhanced by fermentation with yeast waste (YW), which can be used to replace soybean meal (SBM), as well as lead to improved feed utilization in ruminants. Thus, evaluation of in vitro ruminal fermentation and feed digestibility, as influenced by YW-treated CS and different roughage (R) to concentrate (C) ratios, was elucidated. The design of the experiment was a 5 × 3 factorial arrangement in a completely randomized design. Each treatment contained three replications and three runs. The first factor was replacing SBM with CS fermented with YW (CSYW) in a concentrate ratio at 100:0, 75:25, 50:50, 25:75, and 0:100, respectively. The second factor was R:C ratios at 70:30, 50:50, and 30:70. The level of CSYW showed significantly higher (p < 0.01) gas production from the insoluble fraction (b), potential extent of gas production (a + b), and cumulative gas production at 96 h than the control group (p < 0.05). There were no interactions among the CSYW and R:C ratio on the in vitro digestibility (p > 0.05). Furthermore, increasing the amount of CSYW to replace SBM up to 75% had no negative effect on in vitro neutral detergent fiber degradability (IVNDFD) (p > 0.05) while replacing CSWY at 100% could reduce IVNDFD (p > 0.05). The bacterial population in the rumen was reduced by 25.05% when CSYW completely replaced SBM (p < 0.05); however, 75% of CSWY in the diet did not change the bacterial population (p > 0.05). The concentration of propionate (C3) decreased upon an increase in the CSYW level, which was lowest with the replacement of SBM by CSYW up to 75%. However, various R:C ratios did not influence total volatile fatty acids (VFAs), and the proportion of VFAs (p > 0.05), except the concentration of C3, increased when the proportion of a concentrate diet increased (p < 0.05). In conclusion, CSYW could be utilized as a partial replacement for SBM in concentrate diets up to 75% without affecting gas kinetics, ruminal parameters, or in vitro digestibility.

Effect of pine-based biochars with differing physiochemical properties on methane production, ruminal fermentation, and rumen microbiota in an artificial rumen (RUSITEC) fed barley silage

This study investigated the effects of three pine-based biochar products on nutrient disappearance, total gas and methane (CH4) production, rumen fermentation, microbial protein synthesis, and rumen microbiota in a rumen simulation technique (RUSITEC) fed a barley-silage-based total mixed ration (TMR). Treatments consisted of 10 g TMR supplemented with no biochar (control) and three different biochars (CP016, CP024, and CP028) included at 20 g·kg−1 DM. Treatments were assigned to 16 fermenters (n = 4 per treatment) in two RUSITEC units in a randomized block design for a 17 d experimental period. Data were analyzed using MIXED procedure in SAS, with treatment and day of sampling as fixed effects and RUSITEC unit and fermenters as random effects. Biochar did not affect nutrient disappearance (P > 0.05), nor total gas or CH4, irrespective of unit of expression. The volatile fatty acid, NH3-N, total protozoa, and microbial protein synthesis were not affected by biochar inclusion (P > 0.05). Alpha and beta diversity and rumen microbiota families were not affected by biochar inclusion (P > 0.05). In conclusion, biochar did not reduce CH4 emissions nor affect nutrient disappearance, rumen fermentation, microbial protein synthesis, or rumen microbiota in the RUSITEC.

Analysis of gut microbiota in three species belonging to different genera (Hemitragus, Pseudois, and Ovis) from the subfamily Caprinae in the absence of environmental variance

This study aimed to identify the effects of host species on the gut microbial flora in three species (Hemitragus jemlahicus, Pseudois nayaur, and Ovis orientalis) from the subfamily Caprinae, by excluding the impact of environment factors. We investigated the differences in intestinal flora of three species belonging to Caprinae, which were raised in identical conditions. Fecal samples were collected from tahr, mouflon, and bharal, and the V3-V4 region of the 16S ribosomal RNA gene was analyzed by high-throughput sequencing. The analysis of 16S rRNA gene sequences reveals that fecal samples were mainly composed of four phyla: Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria. The most abundant phyla included Firmicutes and Bacteroidetes accounting for >90% of the bacteria, and a higher Firmicutes/Bacteroidetes ratio was observed in tahrs. Moreover, significant differences existed at multiple levels of classifications in the relative abundance of intestinal flora, differing greatly between species. Phylogenetic analyses based on 16S rRNA gene indicated that mouflon is closely related to bharal, and it is inconsistent with previous reports in the species evolutionary relationships. In this study, we demonstrated that the gut microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host-microbiome interactions were not significant.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. II: Relation with solid passage rate and pH on neutral detergent fiber degradation and microbial function in continuous culture

To support improving genetic potential for increased milk production, intake of digestible carbohydrate must also increase to provide digestible energy and microbial protein synthesis. We hypothesized that the provision of exogenous branched-chain volatile fatty acids (BCVFA) would improve both neutral detergent fiber (NDF) degradability and efficiency of microbial protein synthesis. However, BCVFA should be more beneficial with increasing efficiency of bacterial protein synthesis associated with increasing passage rate (k_p). We also hypothesized that decreasing pH would increase the need for isobutyrate over 2-methylbutyrate. To study these effects independent from other sources of variation in vivo, we evaluated continuous cultures without (control) versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate), low versus high k_p of the particulate phase (2.5 vs. 5.0%/h), and high versus low pH (ranging from 6.3 to 6.8 diurnally vs. 5.7 to 6.2) in a 2 × 2 × 2 factorial arrangement of treatments. Diets were 50% forage pellets and 50% grain pellets administered twice daily. Without an interaction, NDF degradability tended to increase from 29.7 to 35.0% for main effects of control compared with BCVFA treatments. Provision of BCVFA increased methanogenesis, presumably resulting from improved NDF degradability. Decreasing pH decreased methane production. Total volatile fatty acid (VFA) and acetate production were decreased with increasing k_p, even though true organic matter degradability and bacterial nitrogen flow were not affected by treatments. Decreasing pH decreased acetate but increased propionate and valerate production, probably resulting from a shift in bacterial taxa and associated VFA stoichiometry. Decreasing pH decreased isobutyrate and isovalerate production while increasing 2-methylbutyrate production on a net basis (subtracting doses). Supplementing BCVFA improved NDF degradability in continuous cultures administered moderate (15.4%) crude protein diets (excluding urea in buffer) without major interactions with culture pH and k_p.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. I: Comparison with branched-chain amino acids and forage source in ruminal batch cultures

Three experiments assessed branched-chain volatile fatty acid (BCVFA) stimulation of neutral detergent fiber (NDF) disappearance after 24 h of incubation in batch cultures derived from ruminal fluid inocula that were enriched with particulate-phase bacteria. In experiment 1, a control was compared with 3 treatments with isomolar doses of all 3 BCVFA (plus valerate), all 3 branched-chain AA (BCAA), or half of each BCVFA and BCAA mix with either alfalfa or grass hays (50%) and ground corn grain (50%). A portion of the BCAA and BCVFA doses were enriched with ¹³C, and valerate (also enriched with ¹³C) was added with BCVFA. Although BCAA yielded a similar production of BCVFA compared with dosing BCVFA, equimolar substitution of BCVFA for BCAA decreased the percentage of N in bacterial pellets when alfalfa hay was fed but increased N when grass hay was fed. Substituting BCVFA for BCAA increased total fatty acid (FA) concentration with alfalfa hay. Dosing of BCAA or BCVFA did not affect total branched-chain FA, iso-FA, or anteiso-FA percentages in bacterial total FA, whereas numerous individual FA isomers and their ¹³C enrichments were affected by these treatments. Increasing recovery of the ¹³C dose from respective labeled BCVFA primers indicated facilitated BCVFA uptake and incorporation into FA compared with BCAA, whereas increased recovery of ¹³C from labeled BCAA in the bacteria pellet but not in the FA fraction suggested direct assimilation into bacterial protein. The BCVFA and valerate were dosed in varying combinations that either summed to 4 mM (experiment 2) or had only 1 mM no matter what combination (experiment 3). In general, grass hay was more responsive to stimulation in NDF digestibility by BCVFA than was alfalfa hay, which was attributed to the higher degradable protein in the latter. The net production of the BCVFA (after subtracting dose) was affected by source and combination of BCVFA. Isovalerate dosing tended to increase its own net production; in contrast, isobutyrate seemed to be used more when it was added alone, but 2-methylbutyrate seemed to be preferred over isobutyrate when 2-methylbutyrate was added. Results supported potential interactions, including potential feedback in production from feed BCAA or increased concentration-dependent competition for dosed BCVFA into cellular products. Under our conditions, the BCVFA appear to be more readily available than BCAA, probably because of regulated BCAA transport and metabolism. Valerate consistently provided no benefit. Using nonparametric ranking, all 3 BCVFA or either isovalerate or isobutyrate (both yielding iso-FA) should be combined with 2-methylbutyrate (yielding anteiso-FA) as a potential opportunity to improve NDF digestibility when rumen-degraded BCAA are limited in diets to decrease environmental impact from N in waste.

Strategies to improve the efficiency of beef cattle production

Globally, there are approximately one billion beef cattle, and compared with poultry and swine, beef cattle have the poorest conversion efficiency of feed to meat. However, these metrics fail to consider that beef cattle produce high-quality protein from feeds that are unsuitable for other livestock species. Strategies to improve the efficiency of beef cattle are focusing on operational and breeding management, host genetics, functional efficiency of rumen and respiratory microbiomes, and the structure and composition of feed. These strategies must also consider the health and immunity of the herd as well as the need for beef cattle to thrive in a changing environment. Genotyping can identify hybrid vigor with positive consequences for animal health, productivity, and environmental adaptability. The role of microbiome–host interactions is key in efficient nutrient digestion and host health. Microbial markers and gene expression patterns within the rumen microbiome are being used to identify hosts that are efficient at fibre digestion. Plant breeding and processing are optimizing the feed value of both forages and concentrates. Strategies to improve the efficiency of cattle production are a prerequisite for the sustainable intensification needed to satisfy the future demand for beef.

Molecular speciation and aromaticity of biochar-manure: Insights from elemental, stable isotope and solid-state DPMAS 13C NMR analyses

The use of biochar (BC) in feedlot cattle diets has recently been explored as an approach to simultaneously improving animal production and reducing enteric methane (CH₄) emissions. This study examines the impact of BC on manure properties and whether BC affects manure composition and carbon (C) and nitrogen (N) outputs from feedlot steers offered a barley-based diet with BC at 0.0, 0.5, 1.0 and 2.0% (BC₀, BC_0.5, BC₁ and BC₂) of diet dry matter. Manure was sampled three times over a 235 day feeding trial conducted in southern Alberta, Canada. Results showed that BC₂ increased total C and the C/N ratio by 5.7 and 6.6% relative to BC₀, respectively (P < 0.05), while total N exhibited a quadratic response from BC₀ to BC₂ (P = 0.005). Manure ¹⁵δN signatures, ranging from +3.83 to +7.34‰, were not affected (P > 0.05) by BC treatment. DPMAS ¹³C NMR revealed similar structural features among BC₀ and BC₂; indigestible BC had a minor impact on the bulk-C speciation of manure organic matter (OM). Compositional changes were limited to the aromatic-C region of the ¹³C NMR spectra. Fused-ring domains, mainly pyrogenic-C, were increased by 1.56-fold at BC₂ relative to BC₀. Overall, results demonstrated that BC stabilizes recalcitrant-C in manure OM, potentially sequestering soil-C when applied to croplands. This approach provides an added value to its use in ruminant diets, mainly from a nutrient cycling perspective. However, whole-farm studies are further required to validate the incorporation of BC into beef production systems.

Gene function adjustment for carbohydrate metabolism and enrichment of rumen microbiota with antibiotic resistance genes during subacute rumen acidosis induced by a high-grain diet in lactating dairy cows

The high-grain diets fed to ruminants generally alters the structure and function of rumen microbiota, resulting in variations of rumen fermentation patterns and the occurrence of subacute rumen acidosis (SARA). To clarify the microbial mechanism for carbohydrate metabolism during SARA, 8 ruminally cannulated Holstein cows in mid lactation were selected for a 3-wk experiment. The cows were randomly divided into 2 groups, fed either a conventional diet (CON; 40% concentrate; dry matter basis) or a high-grain diet (HG; 60% concentrate; dry matter basis). Compared with the CON diet, the HG diet reduced average daily pH (5.71 vs. 6.13), acetate concentration (72.56 vs. 78.44 mM), acetate ratio (54.81 vs. 65.24%), and the ratio of the concentrations of acetate to propionate (1.87 vs. 3.21) but increased the concentrations of total volatile fatty acids (133.03 vs. 120.22 mM), propionate (41.32 vs. 24.71 mM), and valerate (2.46 vs. 1.68 mM) and the propionate ratio (30.51 vs. 20.47%). Taxonomic analysis indicated that the HG cows had a higher relative abundance of Ruminococcus, Eubacterium, Selenomonas, Ruminobacter, Succinimonas, Methanomicrobium, and Methanocaldococcus accompanied by a lower relative abundance of unclassified Firmicutes, unclassified Bacteroidetes, Bacteroides, Fibrobacter, Alistipes, Candidatus Methanoplasma, Methanomassiliicoccus, and Methanolobus. Carbohydrate-active enzyme annotation suggested that there was enriched abundance of glycosyltransferases (GT) 2, glycoside hydrolase (GH) 13, GH24, carbohydrate-binding module (CBM) 26, GH73, GH25, CBM12, GH23, GT8, CBM50, and GT9 and reduced abundance of GH78, GH31, S-layer homology, GH109, carbohydrate esterase 1, GH3, carbohydrate esterase 10, and GH43 in the HG group. Functional profiling revealed that the HG feeding mainly downregulated the pentose phosphate pathway of carbohydrate catabolism, acetate metabolism, propionate metabolism (succinate pathway), and methane metabolism, whereas it upregulated the Embden-Meyerhof-Parnas and Entner-Doudoroff pathways of glycolysis and the citrate cycle. Additionally, the HG feeding promoted the abundance of various antibiotic resistance genes and antimicrobial resistance gene families. These results elucidated the structure and function adjustment of rumen microbiota for carbohydrate metabolism and summarized the enrichment of rumen antibiotic resistance genes under the HG feeding, which expands our understanding of the mechanism underlying the response of rumen microbiota to SARA in dairy cattle.

Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites

BACKGROUND

Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet, and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories.

RESULTS

Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly, 0.18% of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts.

CONCLUSIONS

Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass. Video Abstract.

Pretreatment of crop residues by ammonia fiber expansion (AFEX) alters the temporal colonization of feed in the rumen by rumen microbes

This study examines the colonization of barley straw (BS) and corn stover (CS) by rumen bacteria and how this is impacted by ammonia fiber expansion (AFEX) pre-treatment. A total of four ruminally cannulated beef heifers were used to investigate in situ microbial colonization in a factorial design with two crop residues, pre-treated with or without AFEX. Crop residues were incubated in the rumen for 0, 2, 4, 8 and 48 h and the colonizing profile was determined using 16 s rRNA gene sequencing. The surface colonizing community clustered based on incubation time and pre-treatment. Fibrobacter, unclassified Bacteroidales, and unclassified Ruminococcaceae were enriched during late stages of colonization. Prevotella and unclassified Lachnospiraceae were enriched in the early stages of colonization. The microbial community colonizing BS-AFEX and CS was less diverse than the community colonizing BS and CS-AFEX. Prevotella, Coprococcus and Clostridium were enriched in both AFEX crop residues, while untreated crop residues were enriched with Methanobrevibacter. Several pathways associated with simple carbohydrate metabolism were enriched in the primary colonizing community of AFEX crop residues. This study suggests that AFEX improves the degradability of crop residues by increasing the accessibility of polysaccharides that can be metabolized by the dominant taxa responsible for primary colonization.

Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments

Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.

High fibre selection by roe deer (Capreolus capreolus): evidence of ruminal microbiome adaption to seasonal and geographical differences in nutrient composition

Context. The European roe deer owes its ability to digest fibre to its microbiome. This is made up of many different species at different levels of abundance and with different differentiations. In Europe, the roe deer is often classified as a so-called ‘concentrate selector’. This term has often been interpreted by different researchers to mean a selector of either protein- or energy-rich food. According to various studies, this selection behaviour is due to the low abundance of fibre-degrading microorganisms. Aims. The aim of the present study was to determine the concentration of crude nutrients in the rumen of roe deer, with the focus on the fibre fractions, and to show changes among seasons and between habitats. Furthermore, the aim was to find out how far the composition of the ruminal microbiota adapts to these changes. Methods. From 2011 to 2014, we collected the rumens of 245 roe deer in two Bavarian habitat types, a forest and an agricultural habitat. The crude nutrient contents and the size of the total microbiome and the proportions of individual genera were determined in the rumen content. Key results. The average annual concentration of crude fibre in the ingested food is 26–30% and this rises to 38% in certain months. The forest roe deer had the highest proportions of crude fibre in their food and the concentrations of other nutrients were also highly dependent on the season and habitat. Furthermore, the animals also have far less protein in their rumen content than often assumed. The total number of microorganisms in the rumens of the forest deer is significantly higher than in animals living in the agricultural area. The number of microorganisms was highest in the forest roe deer in winter, and in the roe deer from the agricultural area in summer. Clear connections can also be seen between individual groups of microorganisms and particular crude nutrients. The high crude-fibre concentration leads to a high number of fibre-degrading microorganisms, such as, for example, anaerobic fungi or the Ruminococcus flavefaciens. Conclusions. The results showed a high adaptability of the animals to a fibre-rich diet. The microbiome adapts very well to the respective nutrient availabilities. This, in turn, is what allows the roe deer to adapt so readily to diverse habitats and environmental conditions. Implications. Due to the generally high concentrations of fibre, combined with the high numbers of fibre-degraders in the rumen, we suggest that, from now on, we should talk of a roe deer as being a ‘selector’ or ‘browser’ rather than a ‘concentrate selector’.