In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses

Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.

Effects of the Interaction between Rumen Microbiota Density-VFAs-Hepatic Gluconeogenesis on the Adaptability of Tibetan Sheep to Plateau

During the adaptive evolution of animals, the host and its gut microbiota co-adapt to different elevations. Currently, there are few reports on the rumen microbiota-hepato-intestinal axis of Tibetan sheep at different altitudes. Therefore, the purpose of this study was to explore the regulatory effect of rumen microorganism-volatile fatty acids (VFAs)-VFAs transporter gene interactions on the key enzymes and genes related to gluconeogenesis in Tibetan sheep. The rumen fermentation parameters, rumen microbial densities, liver gluconeogenesis activity and related genes were determined and analyzed using gas chromatography, RT-qPCR and other research methods. Correlation analysis revealed a reciprocal relationship among rumen microflora-VFAs-hepatic gluconeogenesis in Tibetan sheep at different altitudes. Among the microbiota, Ruminococcus flavefaciens (R. flavefaciens), Ruminococcus albus (R. albus), Fibrobactersuccinogenes and Ruminobacter amylophilus (R. amylophilus) were significantly correlated with propionic acid (p < 0.05), while propionic acid was significantly correlated with the transport genes monocarboxylate transporter 4 (MCT4) and anion exchanger 2 (AE2) (p < 0.05). Propionic acid was significantly correlated with key enzymes such as pyruvate carboxylase, phosphoenolpyruvic acid carboxylase and glucose (Glu) in the gluconeogenesis pathway (p < 0.05). Additionally, the expressions of these genes were significantly correlated with those of the related genes, namely, forkhead box protein O1 (FOXO1) and mitochondrial phosphoenolpyruvate carboxykinase 2 (PCK2) (p < 0.05). The results showed that rumen microbiota densities differed at different altitudes, and the metabolically produced VFA contents differed, which led to adaptive changes in the key enzyme activities of gluconeogenesis and the expressions of related genes.

Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs

Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner-Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes.

Evaluating the dose-dependent effects of curcumin nano-micelles on rumen fermentation, nitrogen metabolism, and nutrient digestibility in heat-stressed fattening lambs: Implications for climate change and sustainable animal production

Global warming threatens livestock production, especially in hot climates. This study evaluated the dose-dependent impacts of dietary curcumin nano-micelles (CNM) on rumen fermentation, nitrogen metabolism, and nutrient digestibility in heat-stressed fattening lambs. Thirty-two crossbred male lambs [ˆIle-de-France × (Dalagh × Romanov)] were utilized within the current study. The initial weight of lambs was documented as averaged by 31.2 ± 1.55 kg, while they were in their 4th to 5th months of age. Animals were fed increasing doses of dietary CNM (0, 20, 40, and 80 mg/day) over 97 days, under severe heat stress conditions with average temperature-humidity index (THI) of 24.5. Quadratic improvements (p < 0.01) occurred in weight gain, average daily gain (ADG), and feed conversion ratio (FCR) by 28.7%, 27.4%, and 23.9%, respectively, in the T40 group compared to the control. Additionally, T40 increased fiber digestion by 2.8% (p < 0.05). Furthermore, T40 quadratically improved parameters of rumen fermentation, including concentrations of NH3-N (p < 0.05), total volatile fatty acids (TVFA; p < 0.01), acetate (p < 0.05), and iso-valerate (p < 0.05), by 13.9%, 12.5%, 15.0%, and 43.5%, respectively, compared to the control. Quadratic increases were also observed in nitrogen balance (p < 0.05) and microbial protein synthesis (p < 0.01) by 19.8% and 37.6%, respectively, in the T40 group. Quadratic models estimated optimal CNM levels between 41.5 and 48.6 mg/day for multiple parameters. These findings indicate CNM at dose level of 40 mg/day could benefit heat-stressed lambs through enhanced rumen function and microbiota. Further research should refine ideal dosing for various species and production phases as higher levels adversely impacted fiber digestibility. Overall, CNM shows promise as a sustainable nutritional intervention for livestock production facing global warming.

Isolation and characterization of strictly anaerobic cellulolytic rumen bacterial species from Sahiwal cattle

Objective

To isolate and characterize cellulolytic rumen bacteria from the rumen of Sahiwal cattle using rumen bacterial inoculum to increase the nutritional value of rice bran used as broiler feed.

Materials and Methods

The ruminal liquid was kept at an optimal pH of 6.9 and a redox potential of less than -300 mV while being incubated anaerobically at 39°C in a medium containing rumen fluid glucose cellobiose agar. By using the Hungate technique, the organisms were detected based on their morphological, physiological, biochemical, and molecular testing.

Results

The findings revealed that the isolated Ruminococcus albus, and Ruminococcus flavifaciens were obligate anaerobic, generally Gram-positive, nonmotile cocci or rod, single or pair, occasionally short chain, producing yellow pigment when grown on cellulose, and having a clear zone around the colonies. Both isolate fermented sugars such as cellobiose, glucose, and lactose, as well as decomposed xylan. The results also showed that the isolates recognized as Ruminococcus spp., a cellulolytic rumen bacterium, were catalase-negative, indole-negative, and gelatin liquefaction-positive.

Conclusion

Isolation and characterization of Ruminococcus spp. may be helpful for Bangladesh in reducing the cost of producing poultry feed and circumventing restrictions on rice bran use. We can also develop more efficient and long-lasting plans to enhance poultry performance and feed efficiency, as well as increase the nutritional value of rice bran used as broiler feed, by understanding how various Ruminococcus spp. function in this process.

- Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation

Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids

BACKGROUND

The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.

RESULTS

In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.

CONCLUSIONS

Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.

Tropical tree foliage supplementation in ruminants improves rumen fermentation and the bacterial profile and decreases methane production

The main of this study was to evaluate the effect of supplementation of tropical tree foliage in ruminant diets on the in vitro fermentation, bacterial population, volatile fatty acids (VFAs), and enteric CH4 production. Seven experimental diets were evaluated: a control treatment of Pennisetum purpureum (T7) and six treatments of P. purpureum supplemented (30%) with the foliage of Neomillspaughia emargiata (T1), Tabernaemontana amygdalifolia (T2), Caesalpinia gaumeri (T3), Piscidia piscipula (T4), Leucaena leucocephala (T5), and Havardia albicans (T6). The T2, T7, and T5 treatments had the highest (p < 0.05) digestibility of dry matter. Overall, supplementation increased (p < 0.05) the concentrations of propionic and butyric acid and decreased acetic acid. Methanogenic bacteria decreased (p < 0.05) in T1, T2, T5, and T6. Ruminococcus albus decreased in T1, T2, T3, and T5 and Selenomonas ruminiantum increased in T3. Fibrobacter succinogenes increased, except in T5. Methane production decreased (p < 0.05) in T1, T4, T5, and T6. The supplementation with Leucaena leucocephala, Tabernaemontana amygdalifolia, Neomillspaughia emargiata, Piscidia piscipula, Havardia albicans, and Caesalpinia gaumeri is a potential alternative nutritional strategy for ruminants that results in positive changes in VFAs profile, a decrease on CH4 production and methanogenic bacteria, and changes on fibrolytic and non-fibrolytic bacteria composition.HIGHLIGHTSTropical tree foliage supplementation increased propionic and butyric acid and decreased acetic acid concentrations.Fibrolytic, non-fibrolytic, and Methanogenic bacteria were selectively modulated with the supplementation of tropical tree foliage.The enteric methane (CH4) production decreased with the supplementation of tree foliage.The supplementation of Tabernaemontana amygdalifolia and Leucaena leucocephala had the highest digestibility and is a potential alternative nutritional strategy for ruminants.

The epithelial transcriptome and mucosal microbiota are altered for goats fed with a low-protein diet

Introduction

Feeding low protein (LP) diet to animals impose severe challenge to animals' immune homeostasis. However, limited knowledge about the underlying adaption mechanism of host and ruminal microbiota responding to LP diet were well understood. Herein, this study was performed to examine the changes in relative abundance of ruminal microbiota and host ruminal mucosal transcriptome profiles in response to a LP diet.

Methods

A total of twenty-four female Xiangdong balck goats with similar weight (20.64 ± 2.40 kg) and age (8 ± 0.3 months) were randomly assigned into two groups, LP (5.52% crude protein containing diet) and CON (10.77% crude protein containing diet) groups. Upon completion of the trial, all goats were slaughtered after a 16-hour fasting period in LiuYang city (N 28°15', E 113°63') in China. HE staining, free amino acids measurement, transcriptome analysis and microbiome analysis were applied to detect the morphology alterations, free amino acids profile alterations and the shift in host ruminal mucosal transcriptome and ruminal microbiota communities.

Results

Firstly, the results showed that feeding LP diet to goats decreased the rumen papilla width (P = 0.043), surface area (P = 0.013) and total ruminal free amino acids concentration (P = 0.016). Secondly, microbiome analysis indicated that 9 microbial genera, including Eubacterium and Prevotella, were enriched in LP group while 11 microbial genera, including Butyrivibrio and Ruminococcus, were enriched in CON group. Finally, in terms of immune-related genes, the expression levels of genes involved in tight junction categories (e.g., MYH11, PPP2R2C, and MYL9) and acquired immunity (e.g., PCP4 and CXCL13) were observed to be upregulated in the LP group when compared to the CON group.

Conclusion

Under the LP diet, the rumen exhibited increased relative abundance of pathogenic microbiota and VFA-degrading microbiota, leading to disruptions in immune homeostasis within the host's ruminal mucosa. These findings indicate that the ruminal microbiota interacts with host results in the disruption in animals' immune homeostasis under LP diet challenge.

Winery by-products as a feed source with functional properties: dose-response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC

BACKGROUND

Grape and winery by-products have nutritional values for cattle and also contain functional compounds like phenols, which not only bind to protein but can also directly affect microbiota and their function in the rumen. We characterized the nutritional and functional effects of grape seed meal and grape pomace as well as an effective dosage of grape phenols on ruminal microbiota and fermentation characteristics using a rumen simulation technique.

RESULTS

Six diets (each n = 8) were compared including a control diet (CON, no by-product), a positive control diet (EXT, CON + 3.7% grape seed extract on a dry matter (DM) basis), two diets with grape seed meal at 5% (GS-low) and 10% (GS-high), and two diets with grape pomace: at 10% (GP-low) and 20% (GP-high), on a DM basis. The inclusion of the by-product supplied total phenols at 3.4%, 0.7%, 1.4%, 1.3%, and 2.7% of diet DM for EXT, GS-low, GS-high, GP-low, and GP-high, respectively. Diets were tested in four experimental runs. All treatments decreased ammonia concentrations and the disappearances of DM and OM (P < 0.05) compared to CON. EXT and GP-high lowered butyrate and odd- and branch-chain short-chain fatty acids while increased acetate compared to CON (P < 0.05). Treatments did not affect methane formation. EXT decreased the abundance of many bacterial genera including those belonging to the core microbiota. GP-high and EXT consistently decreased Olsenella and Anaerotipes while increased Ruminobacter abundances.

CONCLUSION

The data suggest that the inclusion of winery by-products or grape seed extract could be an option for reducing excessive ammonia production. Exposure to grape phenols at a high dosage in an extract form can alter the rumen microbial community. This, however, does not necessarily alter the effect of grape phenols on the microbial community function compared to feeding high levels of winery by-products. This suggests the dominant role of dosage over the form or source of the grape phenols in affecting ruminal microbial activity. In conclusion, supplementing grape phenols at about 3% of diet DM is an effective dosage tolerable to ruminal microbiota.

Invited review: Rumen modifiers in today's dairy rations

Our aim was to review feed additives that have a potential ruminal mechanism of action when fed to dairy cattle. We discuss how additives can influence ruminal fermentation stoichiometry through electron transfer mechanisms, particularly the production and usage of dihydrogen. Lactate accumulation should be avoided, especially when acidogenic conditions suppress ruminal neutral detergent fiber digestibility or lead to subclinical acidosis. Yeast products and other probiotics are purported to influence lactate uptake, but growing evidence also supports that yeast products influence expression of gut epithelial genes promoting barrier function and resulting inflammatory responses by the host to various stresses. We also have summarized methane-suppressing additives for potential usage in dairy rations. We focused on those with potential to decrease methane production without decreasing fiber digestibility or milk production. We identified some mitigating factors that need to be addressed more fully in future research. Growth factors such as branched-chain volatile fatty acids also are part of crucial cross-feeding among groups of microbes, particularly to optimize fiber digestibility in the rumen. Our developments of mechanisms of action for various rumen-active modifiers should help nutrition advisors anticipate when a benefit in field conditions is more likely.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Animal Age Affects the Gut Microbiota and Immune System in Captive Koalas (Phascolarctos cinereus)

Gut microbiota is one of the major elements in the control of host health. However, the composition of gut microbiota in koalas has rarely been investigated. Here, we performed 16S rRNA gene sequencing to determine the individual and environmental determinants of gut microbiota diversity and function in 35 fecal samples collected from captive koalas. Meanwhile, blood immune-related cytokine levels were examined by quantitative reverse transcription-PCR to initially explore the relationship between the gut microbiota and the immune system in koalas. The relative abundance of many bacteria, such as Lonepinella koalarum, varies at different ages in koalas and decreases with age. Conversely, Ruminococcus flavefaciens increases with age. Moreover, bacterial pathways involved in lipid metabolism, the biosynthesis of other secondary metabolites, and infectious disease show a significant correlation with age. Age affects the relationship between the microbiota and the host immune system. Among them, the gut microbiota of subadult and aged koalas was closely correlated with CD8β and CD4, whereas adult koalas were correlated with CLEC4E. We also found that sex, reproductive status, and living environment have little impact on the koala gut microbiota and immune system. These results shed suggest age is a key factor affecting gut microbiota and immunity in captive koalas and thus provide new insight into its role in host development and the host immune system. IMPORTANCE Although we have a preliminary understanding of the gut microbiota of koalas, we lack insight into which factors potentially impact captive koalas. This study creates the largest koala gut microbiota data set in China to date and describes several factors that may affect gut microbiota and the immune system in captive koalas, highlighting that age may be a key factor affecting captive koalas. Moreover, this study is the first to characterize the correlation between gut microbiota and cytokines in koalas. Better treatment strategies for infectious disorders may be possible if we can better understand the interactions between the immune system and the microbiota.

The claim of primacy of human gut Bacteroides ovatus in dietary cellobiose degradation

A demonstration of cellulose degrading bacterium from human gut changed our view that human cannot degrade the cellulose. However, investigation of cellulose degradation by human gut microbiota on molecular level has not been completed so far. We showed here, using cellobiose as a model that promoted the growth of human gut key members, such as Bacteroides ovatus (BO), to clarify the molecular mechanism. Our results showed that a new polysaccharide utilization locus (PUL) from BO was involved in the cellobiose capturing and degradation. Further, two new cellulases BACOVA_02626GH5 and BACOVA_02630GH5 on the cell surface performed the degradation of cellobiose into glucose were determined. The predicted structures of BACOVA_02626GH5 and BACOVA_02630GH5 were highly homologous with the cellulase from soil bacteria, and the catalytic residues were highly conservative with two glutamate residues. In murine experiment, we observed cellobiose reshaped the composition of gut microbiota and probably modified the metabolic function of bacteria. Taken together, our findings further highlight the evidence of cellulose can be degraded by human gut microbes and provide new insight in the field of investigation on cellulose.

Insights to improve the activity of glycosyl phosphorylases from Ruminococcus albus 8 with cello-oligosaccharides

The phosphorolysis of cello-oligosaccharides is a critical process played in the rumen by Ruminococcus albus to degrade cellulose. Cellodextrins, made up of a few glucosyl units, have gained lots of interest by their potential applications. Here, we characterized a cellobiose phosphorylase (RalCBP) and a cellodextrin phosphorylase (RalCDP) from R. albus 8. This latter was further analyzed in detail by constructing a truncated mutant (Ral∆N63CDP) lacking the N-terminal domain and a chimeric protein by fusing a CBM (RalCDP-CBM37). RalCBP showed a typical behavior with high activity on cellobiose. Instead, RalCDP extended its activity to longer soluble or insoluble cello-oligosaccharides. The catalytic efficiency of RalCDP was higher with cellotetraose and cellopentaose as substrates for both reaction directions. Concerning properties of Ral∆N63CDP, results support roles for the N-terminal domain in the conformation of the homo-dimer and conferring the enzyme the capacity to catalyze the phosphorolytic reaction. This mutant exhibited reduced affinity toward phosphate and increased to glucose-1-phosphate. Further, the CBM37 module showed functionality when fused to RalCDP, as RalCDP-CBM37 exhibited an enhanced ability to use insoluble cellulosic substrates. Data obtained from this enzyme's binding parameters to cellulosic polysaccharides agree with the kinetic results. Besides, studies of synthesis and phosphorolysis of cello-saccharides at long-time reactions served to identify the utility of these enzymes. While RalCDP produces a mixture of cello-oligosaccharides (from cellotriose to longer oligosaccharides), the impaired phosphorolytic activity makes Ral∆N63CDP lead mainly toward the synthesis of cellotetraose. On the other hand, RalCDP-CBM37 remarks on the utility of obtaining glucose-1-phosphate from cellulosic compounds.

Insight into CAZymes of Alicyclobacillus mali FL18: Characterization of a New Multifunctional GH9 Enzyme

In the bio-based era, cellulolytic and hemicellulolytic enzymes are biocatalysts used in many industrial processes, playing a key role in the conversion of recalcitrant lignocellulosic waste biomasses. In this context, many thermophilic microorganisms are considered as convenient sources of carbohydrate-active enzymes (CAZymes). In this work, a functional genomic annotation of Alicyclobacillus mali FL18, a recently discovered thermo-acidophilic microorganism, showed a wide reservoir of putative CAZymes. Among them, a novel enzyme belonging to the family 9 of glycosyl hydrolases (GHs), named AmCel9, was identified; in-depth in silico analyses highlighted that AmCel9 shares general features with other GH9 members. The synthetic gene was expressed in Escherichia coli and the recombinant protein was purified and characterized. The monomeric enzyme has an optimal catalytic activity at pH 6.0 and has comparable activity at temperatures ranging from 40 °C to 70 °C. It also has a broad substrate specificity, a typical behavior of multifunctional cellulases; the best activity is displayed on β-1,4 linked glucans. Very interestingly, AmCel9 also hydrolyses filter paper and microcrystalline cellulose. This work gives new insights into the properties of a new thermophilic multifunctional GH9 enzyme, that looks a promising biocatalyst for the deconstruction of lignocellulose.

Tannic acid supplementation in the diet of Holstein bulls: Impacts on production performance, physiological and immunological characteristics, and ruminal microbiota

This study was conducted to evaluate the influences of supplementing tannic acid (TA) at different doses on the production performance, physiological and immunological characteristics, and rumen bacterial microbiome of cattle. Forty-eight Holstein bulls were randomly allocated to four dietary treatments: the control (CON, basal diet), the low-dose TA treatment [TAL, 0.3% dry matter (DM)], the mid-dose TA treatment (TAM, 0.9% DM), and the high-dose TA treatment (TAH, 2.7% DM). This trial consisted of 7 days for adaptation and 90 days for data and sample collection, and samples of blood and rumen fluid were collected on 37, 67, and 97 d, respectively. The average daily gain was unaffected (P > 0.05), whilst the ruminal NH3-N was significantly decreased (P < 0.01) by TA supplementation. The 0.3% TA addition lowered (P < 0.05) the levels of ruminal isobutyrate, valerate, and tumor necrosis factor alpha (TNF-α), and tended to (P < 0.1) increase the gain to feed ratio. The digestibility of DM, organic matter (OM), and crude protein, and percentages of butyrate, isobutyrate, and valerate were lower (P < 0.05), while the acetate proportion and acetate to propionate ratio in both TAM and TAH were higher (P < 0.05) than the CON. Besides, the 0.9% TA inclusion lessened (P < 0.05) the concentrations of glucagon and TNF-α, but enhanced (P < 0.05) the interferon gamma (IFN-γ) level and Simpson index of ruminal bacteria. The 2.7% TA supplementation reduced (P < 0.05) the intake of DM and OM, and levels of malondialdehyde and thyroxine, while elevated (P < 0.05) the Shannon index of the rumen bacterial populations. Moreover, the relative abundances of the phyla Fibrobacteres and Lentisphaerae, the genera Fibrobacter and Bradyrhizobium, and the species Bradyrhizobium sp., Lachnospiraceae bacterium RM29, and Lachnospiraceae bacterium CG57 were highly significantly (q < 0.01) or significantly (q < 0.05) raised by adding 2.7% TA. Results suggested that the TA addition at 0.3% is more suitable for the cattle, based on the general comparison on the impacts of supplementing TA at different doses on all the measured parameters.

Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon)

The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.

Silymarin Modulates Microbiota in the Gut to Improve the Health of Sow from Late Gestation to Lactation

Inflammatory responses reduce milk production in lactating sows. Silymarin may modulate inflammatory reactions. Here, we aimed to verify whether dietary silymarin supplementation could alleviate inflammatory responses in lactating sows through microbiota change in the gut. We also investigated how silymarin impacts inflammatory response in lactating sows. One hundred and ten sows were randomly assigned to a control diet (basal diet) or treatment diet (basal diet and 40 g/d silymarin) from the 108th day of gestation to weaning. Blood, milk, and feces from sows were collected for analysis. It was shown in the results that dietary silymarin supplementation decreased the level of pro-inflammatory cytokine IL-1β (p < 0.05) on the 18th day of lactation in the blood of the sows. Dietary silymarin supplementation tended to decrease (p = 0.06) somatic cell count in the colostrum of sows. Dietary silymarin supplementation reduced the gut bacterial community and the richness of the gut microbial community (p < 0.01) using 16S rRNA gene sequencing. The fecal microbes varied at different taxonomic levels in the lactating sows with silymarin supplementation. The most representative changes included an increase in the relative abundance of Fibrobacteres and Actinobacteria (p < 0.05) and tended to reduce the relative abundance of Spirochaetaes and Tenericutes (p = 0.09, 0.06) at the phylum level. It is suggested that dietary silymarin supplementation in late gestation until lactation has anti-inflammatory effects in lactation sow, which could be associated with the modulation of gut microbiota.

Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates

Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.

Optimizing Anthocyanin-Rich Black Cane (Saccharum sinensis Robx.) Silage for Ruminants Using Molasses and Iron Sulphate: A Sustainable Alternative

Anthocyanin-rich black cane (aBC) is a grass rich in lignin and carbohydrates, with an abundance of anthocyanins. Silages of aBC produced with molasses (MS) and/or ferrous sulphate (FS) mixtures may have beneficial effects on silage quality and animal performance in ruminants. However, the addition of MS and FS to ensiled grass is relatively unexplored. Therefore, this study systematically evaluated the effect of their administration at different doses to select an effective treatment to modulate the ensiling characteristics of aBC. In the first trial, fresh or pre-ensiled materials (PBC) were compared with ensiled PBC treated with: 0% MS 0% FS, 4% MS, 8% MS, 0.015% FS, 0.030% FS, 4% MS + 0.015% FS, 4% MS + 0.030% FS, 8% MS + 0.015% FS, and 8% MS + 0.030% FS on a fresh matter basis. The quality of ensiling characteristics was determined in laboratory-scale silos after 42 d of preservation. Based on these results, the second trial was further conducted in rumen cultures to ensure that the selected treatment would not impair rumen fermentation. For this, ruminal biogases, rumen fermentation profiles, and microbial communities were evaluated. Ensiled PBC with the incremental addition of MS and FS resulted in the observations for anthocyanin contents and the ensiling characteristics of the aBC silages. The combination of MS (4%) and FS (0.030%) incorporated into silages had the highest silage production effect among the experimental treatments. This combination demonstrated the sustainable mitigation of the ruminal biogases of methane and carbon dioxide without impairment of total gas production. Concurrently, this combination improved total volatile fatty acid concentrations, modulated cellulolytic bacteria, and suppressed methanogenic bacteria in rumen fluids. The results presented here indicated that addition of a mixture of 4% MS and 0.030% FS to aBC resulted in an optimal balance of ensiling characteristics and is suitable for use in ruminants.

Silage Fermentation Quality, Anthocyanin Stability, and in vitro Rumen Fermentation Characteristic of Ferrous Sulfate Heptahydrate-Treated Black Cane (Saccharum sinensis R.)

Pretreatment of lignocellulose agricultural biomass with iron prior to ensiling is required to accelerate biomass breakdown during fermentation, which could result in functional microorganisms and chemicals that reduce nutrition loss, harmful substances, and improve animal performance. The objective of this study was to investigate the effects of increasing dilutions of ferrous sulfate heptahydrate (FS) pretreatment at fresh matter concentrations of 0, 0.015, and 0.030% on the fermentation quality of black cane (BC) silage, anthocyanin stability, ruminal biogas, rumen fermentation profile, and microbial community. Pre-ensiled and silage materials were evaluated. High moisture, fiber, anthocyanin, and lignification of biomass, as well as undesirable ensiling microorganisms, were found in BC' pre-ensiled form. Increasing dilutions of FS incorporated into silages were observed to linearly decrease dry matter, anthocyanin, and nutritive value losses. The lignin values decreased linearly as the percentage of FS increased up to 0.030%. Given that the ruminants were fed pre-ensiled materials, BC silage treated with 0.030% FS dilution had comparable results to pre-ensiled BC in terms of increasing in vitro volatile fatty acid concentrations, maintaining total gas production, and reducing methane production, when compared to other FS-treated silages. In addition, BC silage treated with a 0.030% FS dilution inhibited methanogenic bacteria and regulated cellulolytic bacteria in rumen fluid. Overall, the anthocyanin content of BC remained constant throughout the rumen fermentation process after increasing dilutions of FS, indicating that BC is a viable ruminant feedstock and that pretreatment of BC with dilute FS-assisted ensiling at 0.030% could be used to generate ruminant diets.

A composite polyphenol-rich extract improved growth performance, ruminal fermentation and immunity, while decreasing methanogenesis and excretion of nitrogen and phosphorus in growing buffaloes

The effects of a composite polyphenolic-rich extract (CPRE) on ruminal fermentation, nutrient utilisation, growth performance, excretion of nitrogen and phosphorus and methane emission were studied in growing buffaloes. Four herbal dry extracts prepared from Acacia arabica (babul; bark), Acacia catechu (cutch; bark), Punica granatum (pomegranate; peel) and Eugenia jambolana (Indian blackberry; seeds) were mixed in an equal proportion (1:1:1:1) to prepare the CPRE that contained mainly phenolic compounds (146 g/kg), flavonoids (41.7 g/kg) and saponins (40.5 g/kg). First, in vitro tests were performed for ruminal fermentation and feed degradability using ruminal fluid as inocula and CPRE at 0 to 40 g/kg substrate to decide an optimal dose of CPRE for an in vivo study on buffaloes. In the animal study, 20 buffaloes were randomly assigned to two groups (n = 10)-a control diet and a CPRE diet (control diet added with extra 20 g/kg of CPRE). The in vitro tests suggested that addition of CPRE at 20 g/kg substrate increased degradability of substrate, short-chain fatty acid concentration and propionate proportion, and reduced methane production, acetate proportion, acetate:propionate ratio and ammonia concentration in fermentation media, which were also noted in the rumen of buffaloes. Feeding CRPE to buffaloes did not affect feed intake, but increased daily body weight gain, dry matter and crude protein digestibility and nitrogen and phosphorus retention in the body. Total bacteria, methanogens and protozoal numbers were similar between two groups, but Fibrobacter succinogenes increased in the rumen of buffaloes fed CPRE. Concentrations of total, essential, non-essential and glucogenic amino acids were greater in the plasma of CPRE-fed buffaloes. Cell-mediated immune response improved in the CPRE-fed buffaloes compared with the control group. Estimated methane production and excretion of nitrogen and phosphorus per unit of body weight gain decreased in the CPRE group. The comprehensive results of this study clearly suggested that the composite polyphenol-rich feed additive at 20 g/kg diet improved growth performance, ruminal fermentation, immunity and plasma amino acids profile, whereas it reduced indicators of environmental impacts of buffalo production.

Glycan processing in gut microbiomes

Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and nutrition. In this review, we describe recent insights into nutrient processing in microbiomes across three exemplary yet contrasting gastrointestinal ecosystems (humans, ruminants and insects), with focus on bacterial mechanisms for the utilization of common and atypical dietary glycans as well as host-derived mucus glycans. In parallel, we discuss findings from multi-omic studies that have provided new perspectives on understanding glycan-dependent interactions and the complex food-webs of microbial populations in their natural habitat. Using key examples, we emphasize how increasing understanding of glycan processing by gut microbiomes can provide critical insights to assist 'microbiome reprogramming', a growing field that seeks to leverage diet to improve animal growth and host health.

Evaluation of gallnut tannin and Lactobacillus plantarum as natural modifiers for alfalfa silage: Ensiling characteristics, in vitro ruminal methane production, fermentation profile and microbiota

AIMS

The potential of gallnut tannin (GT) and Lactobacillus plantarum (LP) on fermentation characteristics, in vitro ruminal methane (CH₄ ) production and microbiota of alfalfa silage was investigated.

METHODS AND RESULTS

Alfalfa was ensiled with GT (20 and 50 g kg^-1 dry matter [DM]) and LP (3 × 10⁸  CFU per gram fresh matter) alone or in combination for 60 days. The GT and LP alone or in combination decreased DM losses, pH and non-protein nitrogen contents of alfalfa silage. All additive treatments decreased ruminal CH₄ production, and increased propionic acid molar proportions and Fibrobacter succinogenes numbers. The LP treatment increased nutrient degradation, cellobiase, pectinase and protease activities, and Prevotella ruminicola abundance, whereas high-dose GT treatment inhibited these variables. Importantly, LP together with GT alleviated the adverse effects of high-dose GT supply alone by enhancing pectinase and protease activities as well as Rumincoccus flavefaciens and P. ruminicola growth.

CONCLUSIONS

Combination of GT and LP can be used as an efficient additive to improve silage quality and utilization by ruminants.

SIGNIFICANCE AND IMPACT OF THE STUDY

Using GT-LP combination has practical implications, particularly concerning effects of tannins on ruminal CH₄ mitigation, which may alleviate inhibitory effects of tannins on feed digestion through modulating ruminal microbiota.