Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome

Review: Mechanism, effectiveness, and the prospects of medicinal plants and their bioactive compounds in lowering ruminants' enteric methane emission

Animal nutritionists continue to investigate new strategies to combat the challenge of methane emissions from ruminants. Medicinal plants (MPs) are known to be beneficial to animal health and exert functional roles in livestock due to their phytogenic compounds with antimicrobial, immunostimulatory, antioxidative, and anti-inflammatory activities. Some MP has been reported to be anti-methanogenic and can effectively lower ruminants' enteric methane emissions. This review overviews trends in MP utilization in ruminants, their bioactivity and their effectiveness in lowering enteric methane production. It highlights the MP regulatory mechanism and the gaps that must be critically addressed to improve its efficacy. MP could reduce enteric methane production by up to 8-50% by regulating the rumen fermentation pathway, directing hydrogen toward propionogenesis, and modifying rumen diversity, structure, and population of the methanogens and protozoa. Yet, factors such as palatability, extraction techniques, and economic implications must be further considered to exploit their potential fully.

Dissecting the association between gut microbiota and hypertrophic scarring: a bidirectional Mendelian randomization study

Hypertrophic scars affect a significant number of individuals annually, giving rise to both cosmetic concerns and functional impairments. Prior research has established that an imbalance in the composition of gut microbes, termed microbial dysbiosis, can initiate the progression of various diseases through the intricate interplay between gut microbiota and the host. However, the precise nature of the causal link between gut microbiota and hypertrophic scarring remains uncertain. In this study, after compiling summary data from genome-wide association studies (GWAS) involving 418 instances of gut microbiota and hypertrophic scarring, we conducted a bidirectional Mendelian randomization (MR) to investigate the potential existence of a causal relationship between gut microbiota and the development of hypertrophic scar and to discern the directionality of causation. By utilizing MR analysis, we identified seven causal associations between gut microbiome and hypertrophic scarring, involving one positive and six negative causal directions. Among them, Intestinimonas, Ruminococcus2, Barnesiella, Dorea, Desulfovibrio piger, and Ruminococcus torques act as protective factors against hypertrophic scarring, while Eubacterium rectale suggests a potential role as a risk factor for hypertrophic scars. Additionally, sensitivity analyses of these results revealed no indications of heterogeneity or pleiotropy. The findings of our MR study suggest a potential causative link between gut microbiota and hypertrophic scarring, opening up new ways for future mechanistic research and the exploration of nanobiotechnology therapies for skin disorders.

Acetate and succinate benefit host muscle energetics as exercise-associated post-biotics

Recently, the gut microbiome has emerged as a potent modulator of exercise-induced systemic adaptation and appears to be crucial for mediating some of the benefits of exercise. This study builds upon previous evidence establishing a gut microbiome-skeletal muscle axis, identifying exercise-induced changes in microbiome composition. Metagenomics sequencing of fecal samples from non-exercise-trained controls or exercise-trained mice was conducted. Biodiversity indices indicated exercise training did not change alpha diversity. However, there were notable differences in beta-diversity between trained and untrained microbiomes. Exercise significantly increased the level of the bacterial species Muribaculaceae bacterium DSM 103720. Computation simulation of bacterial growth was used to predict metabolites that accumulate under in silico culture of exercise-responsive bacteria. We identified acetate and succinate as potential gut microbial metabolites that are produced by Muribaculaceae bacterium, which were then administered to mice during a period of mechanical overload-induced muscle hypertrophy. Although no differences were observed for the overall muscle growth response to succinate or acetate administration during the first 5 days of mechanical overload-induced hypertrophy, acetate and succinate increased skeletal muscle mitochondrial respiration. When given as post-biotics, succinate or acetate treatment may improve oxidative metabolism during muscle hypertrophy.

A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins

There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role in discovering new plastizymes. Here, we combined 66 whole metagenomic data from plastic-contaminated environment samples from four previously collected metagenome data with our new sample. In this study, an integrated plastic-contaminated environment gene, protein, taxa, and plastic degrading enzyme catalog (PDEC) was constructed. These catalogs contain 53,300,583 non-redundant genes and proteins, 691 metagenome-assembled genomes, and 136,654 plastizymes. Based on KEGG and eggNOG annotations, 42% of recognized genes lack annotations, indicating their functions remain elusive and warrant further investigation. Additionally, the PDEC catalog highlights hydrolases, peroxidases, and cutinases as the prevailing plastizymes. Ultimately, following multiple validation procedures, our effort focused on pinpointing enzymes that exhibited the highest similarity to the introduced plastizymes in terms of both sequence and three-dimensional structural aspects. This encompassed evaluating the linear composition of constituent units as well as the complex spatial conformation of the molecule. The resulting catalog is expected to improve the resolution of future multi-omics studies, providing new insights into plastic-pollution related research.

Potential use of garlic products in ruminant feeding: A review

The addition of antibiotics as growth promoters to ruminant feed can result in bacterial resistance and antibiotic residues in ruminant products. Correspondingly, there is serious public concern regarding the presence of antibiotic residue in ruminant products and the consequent threat to human health. As a result, the addition of plants and their products to ruminant feeds, as an alternative to antibiotics, has received much attention recently. Garlic and its products are rich in organosulphur compounds, which have a variety of biological activities and have been widely used as natural additives in animal production. This review presents recent knowledge on the addition of garlic products (powder, skin, oil, leaf and extracts) to the diets of ruminants. In this paper, garlic products are evaluated with respect to their chemical composition, bioactive compounds, and their impacts on the rumen ecosystem, antioxidant status, immune response, parasitic infection, growth performance and product quality of ruminants. This review provides valuable guidance and a theoretical basis for the development of garlic products as green, highly efficient and safe additives, with the aims of promoting ruminant growth and health, reducing methane emissions and improving ruminant product quality. Garlic extracts have the potential to control parasite infections by decreasing the faecal egg count. Garlic powder, oil and allicin are able to reduce the methane emissions of ruminants. Organosulphur compounds such as allicin, which is present in garlic products, have the potential to inhibit membrane lipid synthesis of the archaeal community, thus influencing the population of methanogenic archaea and resulting in a reduction in methane emissions. Some garlic products are also able to increase the average daily gain (garlic skin, water extract, and leaf) and the feed conversion ratio (garlic skin and leaf) of ruminants. Garlic stalk silage fed to sheep has the potential to improve the nutritional value of mutton by increasing the concentrations of linoleic and linolenic acids and essential amino acids. Sheep fed a diet containing garlic powder or oil are able to produce milk with higher concentrations of the conjugated linoleic acids and n-3 fatty acids, which has health benefits for consumers, due to the widely recognized positive impact of n-3 polyunsaturated fatty acids and conjugated linoleic acids on human heart health, improving platelet aggregation, vasodilation and thrombotic tendency. Overall, garlic products have the potential to enhance growth performance and product quality and reduce parasite infections, as well as methane emissions of ruminants.

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.

Management of Enteric Methane Emissions in Ruminants Using Feed Additives: A Review

In ruminants' metabolism, a surplus of hydrogen is removed from the reduction reaction of NAD⁺ (nicotinamide adenine dinucleotide) by the formation of methane by methanogenic bacteria and archaea methanogens. The balance of calculations between VFA (volatile fatty acids), CO₂, and CH₄ indicates that acetate and butyrate play a role in methane production, while the formation of propionate maintains hydrogen and therefore reduces methane production. CH₄ formation in ruminant livestock is not desired because it reduces feed efficiency and contributes to global warming. Therefore, numerous strategies have been investigated to mitigate methane production in ruminants. This review focuses on feed additives which have the capability of reducing methane emissions in ruminants. Due to the environmental importance of methane emissions, such studies are needed to make milk and meat production more sustainable. Additionally, the additives which have no adverse effects on rumen microbial population and where the reduction effects are a result of their hydrogen sink property, are the best reduction methods. Methane inhibitors have shown such a property in most cases. More work is needed to bring methane-reducing agents in ruminant diets to full market maturity, so that farmers can reap feed cost savings and simultaneously achieve environmental benefits.

Simulated seasonal diets alter yak rumen microbiota structure and metabolic function

Yak is the only ruminant on the Qinghai-Tibetan Plateau that grazes year-round. Although previous research has shown that yak rumen microbiota fluctuates in robust patterns with seasonal foraging, it remains unclear whether these dynamic shifts are driven by changes in environment or nutrient availability. The study examines the response of yak rumen microbiota (bacteria, fungi, and archaea) to simulated seasonal diets, excluding the contribution of environmental factors. A total of 18 adult male yaks were randomly divided into three groups, including a nutrition stress group (NSG, simulating winter pasture), a grazing simulation group (GSG, simulating warm season pasture), and a supplementation group (SG, simulating winter pasture supplemented with feed concentrates). Volatile fatty acids (VFAs) profiling showed that ruminal acetate, propionate and total VFA contents were significantly higher (p < 0.05) in GSG rumen. Metagenomic analysis showed that Bacteroidetes (53.9%) and Firmicutes (37.1%) were the dominant bacterial phyla in yak rumen across dietary treatments. In GSG samples, Actinobacteriota, Succinivibrionaceae_UCG-002, and Ruminococcus albus were the most abundant, while Bacteroides was significantly more abundant in NSG samples (p < 0.05) than that in GSG. The known fiber-degrading fungus, Neocallimastix, was significantly more abundant in NSG and SG samples, while Cyllamyces were more prevalent in NSG rumen than in the SG rumen. These findings imply that a diverse consortium of microbes may cooperate in response to fluctuating nutrient availability, with depletion of known rumen taxa under nutrient deficiency. Archaeal community composition showed less variation between treatments than bacterial and fungal communities. Additionally, Orpinomyces was significantly positively correlated with acetate levels, both of which are prevalent in GSG compared with other groups. Correlation analysis between microbial taxa and VFA production or between specific rumen microbes further illustrated a collective response to nutrient availability by gut microbiota and rumen VFA metabolism. PICRUSt and FUNGuild functional prediction analysis indicated fluctuation response of the function of microbial communities among groups. These results provide a framework for understanding how microbiota participate in seasonal adaptations to forage availability in high-altitude ruminants, and form a basis for future development of probiotic supplements to enhance nutrient utilization in livestock.

A critical assessment of gene catalogs for metagenomic analysis

MOTIVATION

Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses.

RESULTS

As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research.

AVAILABILITY AND IMPLEMENTATION

All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Ruminal microbiota is associated with feed-efficiency phenotype of fattening bulls fed high-concentrate diets

Abstract Context Improving feed efficiency in livestock production is of great importance to reduce feeding costs. Aims To examine the relationship between ruminal microbiota and variation in feed efficiency in beef cattle fed concentrate-based diets. Methods Residual feed intake of 389 fattening bulls, supplied with corn-based concentrate and forage ad libitum, was used to estimate animals’ feed efficiency. Faeces and ruminal fluid samples, from 48 bulls chosen at random, were collected to estimate their forage intake and to determine their apparent digestibility, ruminal fermentation and microbiota. Those animals with extreme values of feed efficiency (high-efficiency (HE, n = 12) and low-efficiency (LE, n = 13)) were subjected to further comparisons. Alpha biodiversity was calculated on the basis of the normalised sequence data. Beta diversity was approached through performing a canonical correspondence analysis based on log-transformed sequence data. Genera differential abundance was tested with an ANOVA-like differential expression analysis and genera interactions were determined applying the sparse correlations for compositional data technique. Key results No differences in dry matter intake were found between the two categories of feed efficiency (P = 0.699); however, HE animals had higher apparent digestibility of dry matter (P = 0.002), organic matter (P = 0.003) and crude protein (P = 0.043). The concentration of volatile fatty acids was unaffected by feed efficiency (P = 0.676) but butyrate proportion increased with time in LE animals (P = 0.047). Ruminal microbiota was different between HE and LE animals (P = 0.022); both α biodiversity and genera network connectance increased with time in LE bulls (P = 0.005 for Shannon index and P = 0.020 for Simpson index), which suggests that LE animals hosted a more robust ruminal microbiota. Certain genera usually related to high energy loss through methane production were found to establish more connections with other genera in LE animals’ rumen than in HE ones. Microbiota function capability suggested that methane metabolism was decreased in HE finishing bulls. Conclusions Rumen microbiota was associated with feed efficiency phenotypes in fattening bulls fed concentrate-based diets. Implications The possible trade-off between feed efficiency and robustness of ruminal microbiota should be taken into account for the optimisation of cattle production, especially in systems with intrinsic characteristics that may constitute a disturbance to rumen microbial community.

A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions

A better understanding of rumen microbial interactions is crucial for the study of rumen metabolism and methane emissions. Metagenomics-based methods can explore the relationship between microbial genes and metabolites to clarify the effect of microbial function on the host phenotype. This study investigated the rumen microbial mechanisms of methane metabolism in cattle by combining metagenomic data and network-based methods. Based on the relative abundance of 1461 rumen microbial genes and the main volatile fatty acids (VFAs), a multilayer heterogeneous network was constructed, and the functional modules associated with metabolite-microbial genes were obtained by heat diffusion algorithm. The PLS model by integrating data from VFAs and microbial genes explained 72.98% variation of methane emissions. Compared with single-layer networks, more previously reported biomarkers of methane prediction can be captured by the multilayer network. More biomarkers with the rank of top 20 topological centralities were from the PLS models of diffusion subsets. The heat diffusion algorithm is different from the strategy used by the microbial metabolic system to understand methane phenotype. It inferred 24 novel biomarkers that were preferentially affected by changes in specific VFAs. Results showed that the heat diffusion multilayer network approach improved the understanding of the microbial patterns of VFAs affecting methane emissions which represented by the functional microbial genes.