Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

Unravelling AMR dynamics in the rumenofaecobiome: Insights, challenges and implications for One Health

Antimicrobial resistance (AMR) is a critical global threat to human, animal and environmental health, exacerbated by horizontal gene transfer (HGT) via mobile genetic elements. This poses significant challenges that have a negative impact on the sustainability of the One Health approach, hindering its long-term viability and effectiveness in addressing the interconnectedness of global health. Recent studies on livestock animals, specifically ruminants, indicate that culturable ruminal bacteria harbour AMR genes with the potential for HGT. However, these studies have focused predominantly on using the faecobiome as a proxy to the rumen microbiome or using easily isolated and culturable bacteria, overlooking the unculturable population. These unculturable microbial groups could have a profound influence on the rumen resistome and AMR dynamics within livestock ecosystems, potentially holding critical insights for advanced understanding of AMR in One Health. In order to address this gap, this review of current research on the burden of AMR in livestock was undertaken, and it is proposed that combined study of the rumen microbiome and faecobiome, termed the 'rumenofaecobiome', should be performed to enhance understanding of the risks of AMR in ruminant livestock. This review discusses the complexities of the rumen microbiome and the risks of AMR transmission in this microbiome in a One Health context. AMR transmission dynamics and methodologies for assessing the risks of AMR in livestock are summarized, and future considerations for researching the impact of AMR in the rumen microbiome and the implications within the One Health framework are discussed.

Is early life programming a promising strategy for methane mitigation and sustainable intensification in ruminants?

Sustainable animal production requires lowering emissions and adapting to climate change. Numerous nutritional and management interventions that enhance adult ruminants' efficiency and resilience produce only temporary results, reducing the sustainability of the programs. This is because only short-lived changes in the host and rumen microbiome occur, which revert to the original levels when the intervention ceases. Early life programming (ELP) is a promising approach to increase sustainable livestock production, enhance efficiency and reduce greenhouse gas emissions. Early influences using ELP have profound and enduring effects on molecular pathways, physiological adaptations, and long-term phenotypic consequences later in life. These effects occur from the embryonic stage to birth (foetal programming, FP), birth to weaning, and beyond. The underlying mechanisms of ELP include the sequential development of the rumen and microbial colonisation in the rumen, orchestrated through molecular changes, including transcriptomic and epigenetic modifications. This review highlights the key mechanisms behind ELP and explores strategies across different production systems that can improve livestock performance while helping to achieve net-zero emissions. Management strategies like step-down weaning, dietary modifications including increasing solid feed and high-fibre diets and adding anti-methanogenic agents and other feed additives to target the desired rumen microbial community, such as propionate-producing Prevotella, Sharpea, Coprococcus and Megasphaera, are promising strategies for implementing ELP. Creating alternate hydrogen sinks through ELP by favouring metabolic pathways that enhance propionate production can also be targeted. Furthermore, recent innovative strategies, such as using methanotroph-methylotroph consortium as probiotics and oxidising feed additives, are worth researching for ELP.

Invited review: Interplay of rumen microbiome and the cattle host in modulating feed efficiency and methane emissions

Given that the majority of energy and protein supplied to cattle arises as a result of ruminal fermentation, the rumen microbiome plays a key role in determining host feed efficiency and methane (CH4) emissions. Some reports suggest that a less diverse rumen microbiome is associated with improved feed efficiency, whereas other studies suggest that microbial diversity does not differ between low- and high-efficiency cattle of the same breed, fed identical diets. Although reducing enteric CH4 emissions offers a dual benefit in terms of improved feed efficiency and a reduced environmental footprint, recent findings indicate that these outcomes are not always consistent in ruminants. The composition of the rumen microbiome is mainly determined by diet but is also influenced by host genetics and physiological parameters such as rumen volume, rate of passage, and rumination. Reduced microbial diversity may impair the ability of cattle to adapt to frequent changes in diet and the environment. Hydrogen exchange and capture are the energetic foundation of the rumen microbiome, and considerable resources have been invested in developing additives that redirect hydrogen flow toward alternative sinks and away from the reduction of CO2 to CH4. These additives reduce enteric CH4 emissions by 30% to 80%, yet the anticipated gains in feed efficiency remain inconsistent. Strategies to improve the feed efficiency of cattle production must consider the multifaceted interactions among the host, rumen microbiome, and diet to ensure the sustainable intensification of cattle production while maintaining the social license for milk and meat production.

Rumen metagenome profiles are heritable and rank the New Zealand national sheep flock for enteric methane emissions

BACKGROUND

Global targets to reduce greenhouse gas emissions to meet international climate change commitments have driven the livestock industry to develop solutions to reduce methane emission in ruminants while maintaining production. Research has shown that selective breeding for low methane emitting ruminants using genomic selection is one viable solution to meet methane targets at a national level. However, this requires obtaining sufficient measures of methane on individual animals across the national herd. In sheep, one affordable method for measuring methane on-farm to rank animals on their methane emissions is portable accumulation chambers (PAC), although this method is not without its challenges. An alternative is to use a proxy trait that is genetically correlated with PAC methane measures. One such trait that has shown promise is rumen metagenome community (RMC) profiles. In this study, we investigate the potential of using RMC profiles as a proxy trait for methane emissions from PAC using a large sheep dataset consisting of 4585 mixed-sex lambs from several flocks and years across New Zealand.

RESULTS

RMC profiles were generated from rumen samples collected on the animals immediately after being measured through PAC using restriction enzyme-reduced representation sequencing. We predicted methane (CH4) and carbon dioxide (CO2) emissions (grams per day), as well as the ratio CH4/(CO2 + CH4) (CH4Ratio), from the RMC profiles and SNP-array genotype data. Heritability and microbiability estimates were similar to values found in the literature for all traits. The correlation of PAC methane with predicted methane was 1.9- to 2.3-fold (CH4) and 1.2- to 1.5-fold (CH4Ratio) greater for RMC profiles compared to host genomics only. The genetic correlation between methane predicted from RMC profiles and PAC methane was 0.75 ± 0.12 for CH4 and 0.64 ± 0.11 for CH4Ratio when using a validation set consisting of the animals with the most recent year of birth in the dataset.

CONCLUSIONS

RMC profiles are predictive of, and genetically correlated, with PAC methane measures. Therefore, RMC profiles are a suitable proxy trait for determining the genetic merit of an animal's methane emissions and could be incorporated into existing breeding programs to facilitate selective breeding for low methane emitting sheep.

Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen microorganisms in Dongliu buffalo

In this study, the composition of the rumen microbiota and its functional characteristics were investigated using a metagenomic approach in Dongliu buffalo. This study compared the rumen microbial communities of six female and four male Dongliu buffaloes of similar age, weight and lifestyle. Taxonomic analysis identified 964 genera across 52 phyla, dominated by Bacteroidota (47.54%) and Bacillota (28.20%). While alpha and beta diversity showed no sex differences (PERMANOVA P = 0.82), males exhibited higher Fibrobacter at the genus level (P = 0.02). Functional profiling revealed 429 KEGG pathways, with carbohydrate metabolism (11.17%) and amino acid metabolism (9.74%) as dominant processes. Males showed enrichment in cellulose-degrading enzymes (EC2.4.1.20, EC1.2.1.90, EC2.7.1.58) and CAZymes (GH94, GT35), while females had higher Bacteroides abundance (P = 0.01) and CAZymes like CBM47. Core cellulolytic genera (Prevotella, Ruminococcus) demonstrated male-biased GH/CBM activity, linked to enhanced fiber degradation. COG annotation highlighted carbohydrate metabolism as central, with sex-specific functional partitioning in replication (female-enriched) and secondary metabolism (male-enriched). Network analysis revealed Prevotella's dominance in CAZymeme contributions and functional specialization in lignocellulose degradation pathways, suggesting sex-driven microbial adaptation to dietary fiber utilization.

Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep

BACKGROUND

Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.

RESULTS

The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.

CONCLUSIONS

In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.

Differences in rectal fecal microbes among Hu sheep, Tibetan sheep, and their hybrid breeds and their relationship with growth traits

Variety and diversity serve as the foundation for animal husbandry development. Nowadays, heterosis is often used to improve animal performance and increase economic benefits. The intestine is an important organ for nutrient absorption and is also the largest immune organ in the body. Intestinal microorganisms can be influenced by various factors such as animal growth and development stages, gender, health status, feed nutrition level, and host genetic background, among others. In this study, three strains of male sheep, with no significant differences in initial weight at 6 months old, were raised under the same conditions until they reached 9 months of age. We collected the rectal feces of these 9-month-old sheep and compared the differences in rectal fecal microorganisms among the three strains using 16S rDNA sequencing technology. The permutational multivariate analysis of variance test revealed significant differences in microorganisms among different strains. Additionally, we identified six biomarkers in Tibetan sheep and Hu sheep, respectively. Functional enrichment analysis showed that microorganisms may affect the growth traits of sheep through lipid metabolism, and the functional differences among different strains were obvious. Therefore, we believe that crossbreeding can result in the offspring obtaining intestinal microorganisms from their parents to varying degrees, and host heredity is the primary cause of the intestinal microorganism differences.

IMPORTANCE

In this study, we identified parental biomarkers by exploring the relationship between parental and hybrid offspring and concluded that these biomarkers may affect related growth traits through fat deposition or lipid metabolism pathways. We also found that hybrid sheep inherited rectal fecal microbes from their parents to varying degrees.

Exploring age-related changes in gut bacterial community composition of yak: insights from different age groups

BACKGROUND

The Qinghai-Tibetan Plateau (QTP) offers one of the most extreme environments for yaks (Bos grunniens). The yak is an indigenous species, and the wild yak was domesticated on the QTP. The gut microbiota plays a vital role in health and animal performance. However, little is known about the progression of gut microbes in different age developmental stages of domesticated yaks.

METHOD

We used the 16 S rRNA gene sequencing method to explore the progression of the fecal bacterial microbiota of 18 different confined domestic yaks at two developmental stages: 3 to 5 years (GT35) and 6 to 8 years (GT68).

RESULTS

We found significant differences in gut bacterial communities between the two age groups. The diversity of the gut bacterial community was significantly lower in the GT35 group, which reached stability with age. Bacteroidetes and Firmicutes were the two dominant phyla between the two age groups. Phylum Firmicutes was significantly higher in the GT68 group, and Proteobacteria, Spirochaetes, Tenericutes, and Actinobacteria were highly abundant in the GT35 age group. Genera Bacteroides, Alloprevotella, and Anaerovibrio were abundant in the GT35 group. The short-chain fatty acid (SCFA) producing bacteria Rikenellaceae showed higher abundance in GT35. The core bacterial microbiota of the GT68 age group was dominated by Ruminococcaceae and Rikenellaceae. The gut bacterial community has a great variation between the groups. Based on the exploration of dynamic changes in the gut bacterial community at different ages, our results illustrate that yaks undergo a process of reaching stability and maturity as they age.

Correlating the oral swab microbial community with milk production metrics in Holstein dairy cows

Oral swabs of dairy cows have been suggested as a proxy for direct ruminal sampling, and this approach can identify the presence of up to 70% of the rumen microbial community. Here, we further extend the utility of this approach by correlating the bacterial community of swabs collected from 226 dairy cows on a research farm in Wisconsin, USA, with average milk yield and days in milk, two phenotypes previously associated with differences in the ruminal microbiome. We then obtained milk production efficiency data for a subset of these animals (gross feed efficiency [GFE] and residual feed intake [RFI]) and correlated these metrics against their associated microbial data. We found that when using the oral swabs, we could identify correlations between bacterial genera and days in milk (P < 0.05). We further show that the ruminal microbiota was associated with average milk yield and days in milk for animals in their first lactation. Differential abundance testing identified amplicon sequence variants (ASVs) associated with these metrics (P < 0.05). Our comparison of bacterial communities between high and low efficiency groups, as determined by GFE and RFI, identified a significant difference in Shannon's diversity in second lactation cows (P < 0.05). We also found that RFI was significantly correlated with the bacterial community in second lactation animals (P < 0.05). Differential abundance analysis identified multiple oral- and rumen-associated ASVs correlated with GFE and RFI (P < 0.05). This study further establishes the utility of oral swabs as a ruminal proxy.IMPORTANCEImproving milk production efficiency is a key goal in the dairy industry and is traditionally pursued through genetic selection, diet optimization, and herd management practices. The ruminal microbiome, essential for digesting feed, has been linked to milk production efficiency, suggesting that microbiome modulation could improve efficiency. However, the integration of rumen microbiology into current management practices is hampered by the difficulty of large-scale rumen sampling, as proxies like fecal samples do not accurately reflect the ruminal microbiota. Traditional methods, like cannulation and stomach tubing, are labor-intensive and impractical for extensive sampling. Our research demonstrates the potential use of oral swabs as a scalable, effective method for characterizing the microbiome and its associations with milk production metrics, recapitulating established associations obtained through traditional ruminal sampling methods.

Comparative Analysis of Microbial-Short-Chain Fatty Acids-Epithelial Transport Axis in the Rumen Ecosystem Between Tarim Wapiti (Cervus elaphus yarkandensis) and Karakul Sheep (Ovis aries)

Under long-term ecological stress, the Tarim wapiti (Cervus elaphus yarkandensis) has evolved unique adaptations in digestive physiology and energy metabolism. A multi-omics comparison of three Tarim wapiti and five Karakul sheep was used to examine the synergistic mechanism between rumen bacteria, short-chain fatty acids, and host epithelial regulation in order to clarify the mechanism of high roughage digestion efficiency in Tarim wapiti. Metagenomic sequencing (Illumina NovaSeq 6000) and gas chromatography revealed that Tarim wapiti exhibited significantly higher acetate and total VFA (TVFA) concentrations compared to Karakul sheep (p < 0.01), accompanied by lower ruminal pH and propionate levels. Core microbiota analysis identified Bacteroidetes (relative abundance: 52.3% vs. 48.1%), Prevotellaceae (22.7% vs. 19.4%), and Prevotella (18.9% vs. 15.6%) as dominant taxa in both species, with significant enrichment of Bacteroidetes in wapiti (p < 0.01). Functional annotation (PICRUSt2) demonstrated enhanced glycan biosynthesis (KEGG ko00511), DNA replication/repair (ko03430), and glycoside hydrolases (GH20, GH33, GH92, GH97) in wapiti (FDR < 0.05). Transcriptomic profiling (RNA-Seq) of rumen epithelium showed upregulated expression of SCFA transporters (PAT1: 2.1-fold, DRA: 1.8-fold, AE2: 2.3-fold; p < 0.01) and pH regulators (Na+/K+ ATPase: 1.7-fold; p < 0.05) in wapiti. Integrated analysis revealed coordinated microbial-host interactions through three key modules: (1) Bacteroidetes-driven polysaccharide degradation, (2) GHs-mediated fiber fermentation, and (3) epithelial transporters facilitating short-chain fatty acids absorption. These evolutionary adaptations, particularly the Bacteroidetes-short-chain fatty acids-transporter axis, likely underpin the wapiti's superior roughage utilization efficiency, providing molecular insights for improving ruminant feeding strategies in an arid environment.

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice

The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.

Milk fatty acids and rumen composition as proxy measures of enteric methane

Genomic selection is a powerful tool to reduce methane emissions in ruminants. However, it requires large-scale on-farm phenotypic measures of methane. Current technologies to measure methane emissions have several limitations and may not be suitable for lactating animals. Because enteric methane is closely linked to the fermentation process in the rumen, which in turn affects milk composition, breeding for low-methane ruminants may change the rumen microbial and milk composition. Consequently, these compositions may provide proxy measures of methane for use in selective breeding of low-methane ruminants. We investigated the effect on rumen and milk composition in sheep bred for divergent methane yield and the potential for generating proxy measures of methane emissions from rumen or milk samples in lactating ewes. Four hundred genotyped lactating ewes from a sheep research flock bred specifically for high and low-methane emissions had methane measured and rumen and milk samples collected approximately 6 wk post-lambing across 4 lactation years. Rumen samples were processed to generate VFA and metagenomic profiles of the rumen microbial community, and fatty acid profiles and mid-infrared spectra were generated for the milk samples. Although no differences in total fat, protein, and lactose percentages in the milk were found, the milk fatty acid profiles differed between methane selection lines, with higher PUFA and branched-chain fatty acids levels, and lower total SFA contents in ewes from the low-methane line. Lower proportions of acetate relative to propionate were found in the rumen samples from the low-methane ewes. Predictions of methane were obtained from the rumen VFA and metagenomic profiles and the fatty acid profiles and mid-infrared spectra from milk. These predictions formed the proxy methane measures and were heritable (between 0.12 to 0.36) and correlated (between 0.29 and 0.42) with the measured methane values. The genetic correlation between proxies and measured methane was between 0.52 and 0.71. The estimated efficiency of indirect selection for methane was higher for the milk sample proxies (49%-75%) than the rumen metagenomic profiles (45%-47%) and rumen VFA profiles (12%-38%). These results suggest that milk fatty acid, MIR spectroscopic, and rumen microbial composition phenotypes have the potential to be used as proxy measures of methane in lactating ruminants, with the milk-based proxies showing greater promise. Results show that the number of animals with methane proxy measures could be increased substantially and will enable access to breeding technology in countries with limited methane measurement infrastructure.

Effects of different levels of chili straw supplementation on growth performance, rumen fungal community structure, function and economic benefits in sheep

Chili straw is a crop residue that can be used as an unconventional feed additive in animal production, exhibiting potential value in improving animal health. This study investigated the effects of dietary chili straw on growth performance, rumen fungal community composition, and metabolic function in sheep. Thirty finishing sheep (3-4 months old) with similar body weights were randomly divided into three groups (n = 10) and fed diets containing 0, 10, and 20% capsicum straw (CS) for 63 days, including a 7-day adaptation period. At the end of the trial, body weights were recorded, and rumen fluid samples were collected to assess growth performance, fungal diversity, and functional profiles. Dry matter intake (DMI) significantly increased in the 10% CS group (P < 0.01), which was 9.71% higher than that of CON group, while DMI and final body weight of 20% CS group (P < 0.01 or P < 0.05) decreased by 6.81 and 8.81%, respectively, compared with CON group. Final body weight and average daily gain (ADG) showed an upward trend in the 10% CS group (P > 0.05), while ADG displayed a downward trend in the 20% CS group (P > 0.05). The ACE and Chao1 indices were significantly elevated in the 20% CS group (P < 0.05). Principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) showed that compared with the control (CON) group, the representative points of the 20% CS group gathered more closely. Relative abundances of Ascomycota and Cladosporium increased, whereas Basidiomycota and Kazachstania decreased in CS-supplemented groups (P > 0.05). FUNGuild functional prediction indicated increased relative abundances of symbiotrophic and pathotrophic fungi and decreased saprotrophic fungi in CS groups (P > 0.05). The gross profit and net profit of the CS10% group were significantly higher than those of the other groups, which were 15.16 and 24.44% higher than those of the control group, respectively. Thus, adding 10% CS to sheep feed can improve the composition of rumen fungi and growth performance, thereby increasing profitability in sheep production.

Microbial insights into ruminal fiber degradation and feed efficiency of Hu sheep

Ruminal fiber degradation is essential for feed conversion efficiency in sheep; however, it remains unclear whether individual variations in ruminal fiber degradation directly affect feed conversion efficiency. Here, the relationship between ruminal fiber degradation rate and feed conversion efficiency and influence of rumen structure, function, and microbiota on fiber degradation were investigated. A total of 190 male Hu lambs were randomly selected, raised from birth to 180 days, and slaughtered. The relationships between ruminal fiber degradation rate and feed conversion efficiency, growth performance, and ruminal fermentation parameters were analyzed. Key microorganisms influencing ruminal fiber degradation were identified using multiple methods: microbial wide association study, correlation analysis, and differential abundance analysis. Both neutral detergent fiber (NDF) and acid detergent fiber (ADF) degradation rates were significantly correlated with feed conversion efficiency and intake. Seven genera were closely associated with NDF degradation rate: 6 belonged to Firmicutes (Anaerotruncus, Family_XIII_UCG-002, Lachnoclostridium_1, Moryella, Ruminococcaceae_NK4A214_group, and Veillonellaceae_UCG-001); 1, Bacteroidetes (Prevotellaceae_UCG-003). Eight genera were closely associated with ADF degradation rate: 6, Firmicutes (Lachnospiraceae_ND3007_group, Family_XIII_UCG-002, Lachnoclostridium_1, Lachnospiraceae_UCG-002, Moryella, and Ruminococcaceae_NK4A214_group); 1, Bacteroidetes (Prevotellaceae_UCG-003); and 1, Actinobacteria (Olsenella). In conclusion, high ruminal fiber degradation rates significantly enhance feed conversion efficiency, with specific microbial genera from the phylum Firmicutes and family Lachnospiraceae playing pivotal roles in fiber utilization. These findings provide a microbial basis for optimizing rumen fiber degradation efficiency in sheep and highlight the potential of uncultured taxa as future targets for improving feed conversion efficiency.

Live yeast (Saccharomyces cerevisiae) improves growth performance and liver metabolic status of lactating Hu sheep

Yeast, a natural starter culture, is widely used to improve digestion function in ruminants. However, whether yeast affects the physiological state of the liver in ruminants is currently unknown. The aim of this study was to investigate the effects of yeast on liver metabolic status and physiological functions of Hu sheep during lactation. A total of 24 lactating Hu sheep were randomly divided into 4 groups with 6 sheep in each group: the control group (normal diet) and the low-, medium-, and high-dose groups, in which each sheep was fed an additional 0.5 g, 1 g, and 2 g yeast per morning, respectively. Blood, liver, small intestine samples were collected for subsequent analysis, and milk production and BW were recorded during the experimental period. The results showed that dietary yeast supplementation mitigated BW loss, enhanced liver function, and increased milk protein and lactose contents in Hu sheep during lactation. Compared with the normal diet, dietary yeast supplementation reduced the content of lipid droplets in the liver, significantly upregulated the expression of lipid β-oxidation-related enzymes (PPARA and CPT1A), and significantly decreased the expression of lipid synthesis-related enzymes (FASN, PPARγ, DGAT1, and DGAT2) in the liver without affecting the capacity of the small intestine to absorb foodborne lipids. In addition, dietary yeast supplementation significantly decreased blood nonesterified free fatty acid content and increased blood glucose and liver expression of key enzymes involved in gluconeogenesis (PCK1α, FBP, and G6PC). These results suggest that dietary yeast supplementation may alleviate weight loss and enhance milk quality in Hu sheep during lactation. Furthermore, it can improve liver metabolic adaptability and protect liver health by regulating lipid metabolism and metabolic glucose homeostasis in the liver. Notably, adding 1 g or 2 g of yeast to the daily diet yields superior effects.

From gut microbiota to host genes: A dual-regulatory pathway driving body weight variation in dagu chicken (Gallus gallus domesticus)

During the growth and development of animals, there is an interaction between the gut microbiota and the host genotype. The host genotype can regulate the microbiota, and in turn, the microbiota can influence host gene expression, thereby affecting the animal's production performance. This study explored the dynamic interplay between the gut microbiota and host gene expression in body weight variation in Dagu chicken, an indigenous poultry genetic resource in China. We characterized mucosa-associated microbiota across four gastrointestinal segments (duodenum, jejunum, ileum, cecum) and ileocecal chyme microbiota in 12-week-old Dagu chickens stratified by divergent body weight phenotypes, while simultaneously quantifying region-specific intestinal epithelial transcriptional regulation. 16S rDNA sequencing was employed to identify Firmicutes as the predominant bacterial phylum, with notable differences in the abundance of specific genera (e.g., Ligilactobacillus and Lactobacillus) being observed between the high- or low-body-weight groups. Enhanced biosynthesis pathways were functionally predicted in heavier roosters, whereas reduced nutrient metabolism pathways were contrasted. A conserved functional concordance was observed between regionally predominant differential microbiota and the physiological specialization of corresponding intestinal niches. Functional analysis revealed that the high-body-weight group demonstrated superior capabilities in microbial biosynthesis, whereas the low-body-weight group exhibited enhanced microbial metabolic activity. NAA80 was identified as the common differentially expressed gene across all intestinal epithelial tissues. The Gene Ontology and KEGG pathway analyses revealed elevated nutrient absorption efficiency in the high-body-weight group, while the low-body-weight group demonstrated accelerated cellular renewal rates and shorter cycles. Correlation analysis identified significant associations between gut microbiota and host genes expression profiles, with the majority of correlations being positive. These results suggest a coordinated interaction between microbial communities and host genetic regulation, potentially driving phenotypic differences in body weight performance.

Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems

Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M2 = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.

Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans

Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.

Loss of Myostatin leads to low production of CH4 by altering rumen microbiota and metabolome in cattle

Myostatin (MSTN) is a protein that plays a crucial role in regulating skeletal muscle development. Despite the known benefits of MSTN mutant cattle for increasing beef production, their potential impact on CH4 emissions has not been quantified. The study comparing wild-type (WT) cattle to MSTN-knockout (MSTN-KO) cattle revealed that CH4 production was lower. Macrogenomic analysis revealed a significant decrease in rumen archaea, with reduced Richness indices (P = 0.036). The MSTN-KO cattle also showed altered archaea distribution and composition at different taxonomic levels. LEfSe results showed changes in 21 methanogenic archaea clades, with obligately hydrogen (H2)-dependent methylotrophs Candidatus Methanoplasma termitum species belonging to Methanomassiliicoccales order demonstrating the most significant decrease. Rumen metabolites revealed a decrease in the ratio of acetate to propionate, indicating a shift in rumen fermentation pattern towards propionate fermentation. Additionally, the changing trend of methanogenic archaea is consistent with the evolution of methanogens, and this is correlated with the higher levels of linoleic acid in the rumen of MSTN-KO cattle. Linoleic acid affects the utilization of H2 by methanogenic archaea, leading to a reduction in obligately H2-dependent methylotrophs. Our study suggests that MSTN-KO cattle have potential as an economically and ecologically benign breed for reducing methane emissions.

Multispecies pasture diet and cow breed affect the functional lipid profile of milk across lactation in a spring-calving dairy system

This study compared the effect of 2 pasture-based feeding systems, namely a traditional perennial ryegrass (PRG) diet, and a recently introduced, more sustainable multispecies swards (MSS) diet, on the functional lipid profile of raw milk. In addition to the 2 pasture diets, the study uniquely examined the combined effects of breed, namely Holstein Friesian (HF) or Jersey Holstein Friesian (JFX), and lactation stage in Ireland, spanning from March to November. Bulk milk samples (n = 144 yearly) for the 4 groups examined were collected for 4 wk per each of the 9 mo specified. Changes in total fatty acid (FA) and triglyceride carbon number profiles were determined by GC with a flame ionization detector, and those in polar lipids (PL) content by HPLC-evaporative light scattering-MS. Based on multivariate analysis, both diet (34.0% contribution) and breed (19.1% contribution) influenced milk FA on a yearly basis; however, in early lactation there were no differences in FA profile between the groups. In middle lactation and late lactation (LL), the MSS diet increased proportions of nutritionally beneficial n-6 and n-3 PUFA in milk, including C18:3 n-3 (ALA), C18:2 n-6 (LA) and C22:5 n-3 (DPA). Although proportions of ALA and LA increased in MSS milks, the LA/ALA ratio remained around 1 for the 2 feeding systems, confirming the beneficial modulation of LA and ALA in milks from pasture-based diets. Particularly in LL, the milk of JFX cows tended to have increased de novo FA, compared with HF, suggesting implications for techno-functional properties of dairy products such as butter. The milk of PRG HF group showed improved health-promoting properties, with lower thrombogenicity and atherogenicity indices on a yearly basis. Regarding techno-functional properties, the PRG HF group resulted in higher oleic acid reflecting in lower spreadability index, suggesting that butter made of this group would be more spreadable, compared with the one made from the other milk groups examined. The triglyceride and PL profiles were mainly affected by stage of lactation. Overall, these results show the effects of cow diet, breed, and stage of lactation on milk lipid profile, with important implications for the nutritional and techno-functional characteristics of dairy products.

The role of rumen microbiome in the development of methane mitigation strategies for ruminant livestock

Ruminants play an important role in global food security and nutrition. The rumen microbial community provides ruminants with a unique ability to convert human indigestible plant matter, into high quality edible protein. However, enteric CH4 produced in the rumen is both a potent GHG and a metabolizable energy loss for ruminants. As the rumen microbiome constitutes 15-40% of the inter-animal variation in enteric CH4 emissions, understanding the microbiological mechanisms underpinning ruminal methanogenesis and its interaction with the host animal, is crucial for developing CH4 mitigation strategies. Variation in the relative abundance of different microbial species has been observed in cattle with contrasting residual CH4 emission and CH4 yield with up to 20% of the variation in inter-animal CH4 emissions attributable to the presence of a small number of microbial species. The demonstration of ruminotypes associated with high or low CH4 emissions suggests that interactions within complex microbial consortia and with their host are a major source of variation in CH4 emissions. Consequently, microbiome-assisted genomic approaches are being developed to select low CH4 emitting cattle, with breeding values for enteric CH4 being included as part of national breeding programmes. Generating rumen microbiome data for use in selection programs is expensive, therefore, identifying microbial biomarkers in milk or plasma to develop predictive models which include microbial predictors in equations based on animal related data, is required. A better understanding of the rumen microbiome has also aided the development and refinements of anti-methanogenic feed additives. However, these strategies, which increase the amount of reducing equivalents in the rumen ecosystem, do not generally result in an enrichment of propionate or an improvement in animal performance. Current research aims to provide alternative sinks to reducing equivalents and to stimulate activity of commensal microbes or the supplementation of direct fed microbials to capture lost energy. Furthering our knowledge of the rumen microbiome and its interaction with the host, will aid in the development of CH4 mitigation strategies for ruminant livestock.

No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet

BACKGROUND

This research aimed to investigate differences in rumen fermentation characteristics between Karakul sheep and Hu sheep reared under identical conditions. The test subjects included newborn Hu and Karakul sheep, which were monitored across three stages: stage I (Weaning period: 15 ~ 30 days), stage II (Supplementary feeding period: 31 ~ 90 days), and stage III (Complete feeding period: 91 ~ 150 days). During the supplementary feeding period, cottonseed hulls were the main roughage source. To analyze the dynamics of rumen fermentation, 16S rRNA sequencing and metabolomics methods were employed, alongside measurements of rumen fermentation parameters and cellulase activity. This comprehensive approach aimed to investigate the potential impact of breed on rumen fermentation indicators, microbial community structure, and metabolites in Hu and Karakul sheep.

RESULTS

The 16S rRNA sequencing analysis revealed no significant differences in the relative abundance or dominant bacterial communities in the rumen across all stages. In stage II, rumen bacteria in both Hu and Karakul sheep were relatively stable. However, the Simpson index of Hu sheep in stage II was substantially greater than that of Karakul sheep, demonstrating similarities in the rumen microbial structure between stages II and III. Dynamic variations in fermentation parameters and cellulase activity in the rumen revealed that the indicators in both sheep breeds stabilized at 150 days. Metabolomic results revealed that the metabolic pathways in stage I were mainly concentrated in purine metabolism and lipid metabolism, while stage II was dominated by amino acid metabolism. Stage III involved mainly in pyrimidine and purine metabolism. An exploration of the relationships among rumen microbial biomarkers, key differentially abundant metabolites and rumen characteristics indicated that Karakul sheep exhibited superior lipid metabolism compared to Hu sheep.

CONCLUSION

These findings reveal that there were no interbreed differences in the rumen characteristics of Hu and Karakul sheep when fed the same cottonseed hull diet, despite differences in their metabolic pathways. The findings also indicate that the first 20 days represent the initial stage of rumen bacteria in Hu sheep, followed by a transition phase between 20 and 90 days, and a relatively stable stage from 90 to 150 days. These results provide a scientific basis for further understanding the rumen function of sheep and for optimizing their feeding strategies. Video Abstract.

The Impact of the Lactation Period Gut Microbiota of Two Different Beef Cattle Breeds on Spring-Born Calves

To investigate the impact of maternal microbiota during lactation in different beef cattle breeds on their own immune levels, milk quality, and the growth and development of their offspring, this study measured the immune parameters, intestinal microbiota diversity, and milk quality of Pingliang red cattle and Simmental cattle, and performed a correlation analysis with the growth and development of their offspring. Our study showed that during lactation, Pingliang red cattle had significantly higher IL-6 levels than Simmental cattle, while the latter exhibited higher levels of immune factors such as IgG, IgA, IgM, IL-1β, and TNFα. The analysis of the intestinal microbiota of lactating cows found that Pingliang red cattle were rich in Bacteroidetes and Fibrobacteres, while Simmental cattle had a higher proportion of Actinobacteria. This difference may be related to the different adaptation strategies in energy metabolism and immune regulation between the two breeds. In addition, the analysis of milk quality between different beef cattle breeds revealed significant differences in protein, acidity, milk fat, and total solids. The correlation analysis found that Alistipes_communis, Firmicutes_bacterium_CAG_110, Alistipes_communis, Paludibacter_propionicigenes, Alistipes_sp._58_9_plus, and Bacteroidales_bacterium_55_9 were associated with both milk quality and the growth of offspring calves, including body weight, body length, chest girth, and cannon circumference. In conclusion, this study provides new insights into the intestinal microbiota, immune characteristics, and their effects on offspring health in different beef cattle breeds, and has important implications for breed selection and management strategies in the livestock industry.

Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle

BACKGROUND

Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.

RESULTS

In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.

CONCLUSIONS

Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.

Genetic influence on the composition of the ocular microbiome in preweaned beef calves

Infectious bovine keratoconjunctivitis (IBK), commonly known as bovine pinkeye, is a disease that infects the ocular surface and surrounding tissue which is a concern to animal health and welfare as well as producer economics. Vaccinations have been shown to have variable efficacy, while limited genetics studies using either ulcer scores or binary health phenotypes have suggested that direct genetic selection for resistance would be slow. Therefore, an investigation into the host genetic component of the ocular microbiome was conducted. Animals were genotyped using either a 50K or 100K commercial genotyping array. After filtering for common markers, there were 35,374 markers available for analysis. Ocular microbiome samples were taken on approximately 600 preweaned beef calves at four time points. From these, amplicon sequence variants (ASV) were extracted and taxonomy assigned using the V4 region of the 16S rRNA gene. Four metrics of alpha diversity (observed richness, Chao1 index, Simpson index, and Shannon index) and the log-transformed relative abundance (RA) of each ASV at each sampling time point were used as phenotypes in a univariate animal model. The observed richness and Chao1 index had heritability estimates of approximately 0.15 at sample times 1 and 3 with estimates of 0 at sample times 2 and 4. Conversely, the Simpson and Shannon indices had heritability estimates ranging from approximately 0.12 to 0.03 at sample times 1 and 4, with estimates near zero for sample times 2 and 3. The RAs of 59% of ocular bacterial community were influenced by host genetics at various sampling times. Estimates of heritability ranged from 0 to 0.60, depending on time and level of taxonomic classification. A small collection of microbes previously associated with IBK (specifically Moraxella bovis, Moraxella bovoculi, and Mycoplasma bovoculi) had moderate to high heritability estimates at multiple sampling time points. This indicates selection for reduced pathogen load is possible.

Impact of dairy calf management practices on the intestinal tract microbiome pre-weaning

Introduction. Microbiota in the gastrointestinal tract (GIT) consisting of the rumen and hindgut (the small intestine, cecum and colon) in dairy calves play a vital role in their growth and development. This review discusses the development of dairy calf intestinal microbiomes with an emphasis on the impact that husbandry and rearing management have on microbiome development, health and growth of pre-weaned dairy calves.Discussion. The diversity and composition of the microbes that colonize the lower GIT (small and large intestine) can have a significant impact on the growth and development of the calf, through influence on nutrient metabolism, immune modulation, resistance or susceptibility to infection, production outputs and behaviour modification in adult life. The colonization of the calf intestinal microbiome dynamically changes from birth, increasing microbial richness and diversity until weaning, where further dynamic and drastic microbiome change occurs. In dairy calves, neonatal microbiome development prior to weaning is influenced by direct and indirect factors, some of which could be considered stressors, such as maternal interaction, environment, diet, husbandry and weaning practices. The specific impact of these can dictate intestinal microbial colonization, with potential lifelong consequences.Conclusion. Evidence suggests the potential detrimental effect that sudden changes and stress may have on calf health and growth due to management and husbandry practices, and the importance of establishing a stable yet diverse intestinal microbiome population at an early age is essential for calf success. The possibility of improving the health of calves through intestinal microbiome modulation and using alternative strategies including probiotic use, faecal microbiota transplantation and novel approaches of microbiome tracking should be considered to support animal health and sustainability of dairy production systems.

The Holobiont concept in ruminant physiology - more of the same, or something new and meaningful to food quality, food security, and animal health?

The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as impacted by the microbial communities that colonize and/or co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been "pushed" by the advent of high throughput DNA sequencing and, to a lesser extent, other "omics"-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant "holobiont" is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the "holobiont" approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinalmicrobiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. While the holobiont approach might improve food quality, food security and animal health, these benefits will be most likely achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale, as well as its generation in context with the "forgotten" knowledge of ruminant and human physiology.

Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle

Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.

The effects of different doses of compound enzyme preparations on the production performance, meat quality and rumen microorganisms of yak were studied by metagenomics and transcriptomics

Yak (Bos grunniens) is a large ruminant endemic to the Tibetan plateau. The addition of enzyme complexes to feed can significantly improve their growth performance. Therefore, studying the effects of ruminant compound enzyme preparations dosage on yak rumen microorganisms and production performance is crucial to promoting the development of the yak industry. This study aimed to determine the effects of feeding yaks with different doses of ruminant enzyme compounds on the performance, meat quality, and rumen microorganisms of yaks. Three kinds of experimental diets with doses of 0.5 g/kg (LE group), 1 g/kg (ME group), and 2 g/kg (HE group) were selected to determine the growth index, meat quality, serum biochemical indexes, rumen fluid pH and other indexes of the three experimental groups. Metagenomics studies were used to investigate the differences in rumen microbial composition and function among yak groups, and transcriptome sequencing of the longest dorsal muscle was performed to reveal the expression of differential genes among different groups. It was determined that the levels of dietary enzyme complexes significantly affected growth performance, rumen fluid pH, and serum biochemical indices. At the phylum level, the dominant phylum in all three treatment groups was Bacteroidota, Bacillota, Kiritimatiellota, and Pseudomonadota. At the genus level, Prevotella, Methanobrevibacter, Oscillibacter. Fibrobacter showed statistically significant differences in abundance (p < 0.05). CAZymes family analysis revealed significant differences in GHs, CTs, and CEs among the three groups. Genome-wide differential gene expression in the longest muscle of the yak back was analyzed by RNA-seq between the three experimental groups. Some DEGs were found to be enriched in the ECM, PI3K-Akt, PPAR, and protein digestion and absorption receptor pathways. Combined metagenomics and transcriptomics analyses revealed that some microorganisms were significantly associated with the genes COL11A1, POSTN, and PTHLH, which are involved in growth metabolism. In summary, this study investigated the effects and interrelationships of ruminant complex enzymes on yak performance, meat quality, and rumen environment. The results of this study provide a scientific basis for adding ruminant enzymes to yaks.

Metagenomics reveals the characteristics and potential spread of microbiomes and virulence factor genes in the dairy cattle production system

Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.

Connecting the ruminant microbiome to climate change: insights from current ecological and evolutionary concepts

Ruminant livestock provide meat, milk, wool, and other products required for human subsistence. Within the digestive tract of ruminant animals, the rumen houses a complex and diverse microbial ecosystem. These microbes generate many of the nutrients that are needed by the host animal for maintenance and production. However, enteric methane (CH4) is also produced during the final stage of anaerobic digestion. Growing public concern for global climate change has driven the agriculture sector to enhance its investigation into CH4 mitigation. Many CH4 mitigation methods have been explored, with varying outcomes. With the advent of new sequencing technologies, the host-microbe interactions that mediate fermentation processes have been examined to enhance ruminant enteric CH4 mitigation strategies. In this review, we describe current knowledge of the factors driving ruminant microbial assembly, how this relates to functionality, and how CH4 mitigation approaches influence ecological and evolutionary gradients. Through the current literature, we elucidated that many ecological and evolutionary properties are working in tandem in the assembly of ruminant microbes and in the functionality of these microbes in methanogenesis. Additionally, we provide a conceptual framework for future research wherein ecological and evolutionary dynamics account for CH4 mitigation in ruminant microbial composition. Thus, preparation of future research should incorporate this framework to address the roles ecology and evolution have in anthropogenic climate change.

Estimates of microbiome heritability across hosts

Microbiomes contribute to variation in many plant and animal traits, suggesting that microbiome-mediated traits could evolve through selection on the host. However, for such evolution to occur, microbiomes must exhibit sufficient heritability to contribute to host adaptation. Previous work has attempted to estimate the heritability of a variety of microbiome attributes. Here we show that most published estimates are limited to vertebrate and plant hosts, but significant heritability of microbiome attributes has been frequently reported. This indicates that microbiomes could evolve in response to host-level selection, but studies across a wider range of hosts are necessary before general conclusions can be made. We suggest future studies focus on standardizing heritability measurements for the purpose of meta-analyses and investigate the role of the environment in contributing to heritable microbiome variation. This could have important implications for the use of microbiomes in conservation, agriculture and medicine.

Intestine bacterial community affects the growth of the Pacific white shrimp (Litopenaeus vannamei)

Increasing evidence suggests that intestine microorganisms are closely related to shrimp growth, but there is no existing experiment to prove this hypothesis. Here, we compared the intestine bacterial community of fast- and slow-growing shrimp at the same developmental stage with a marked difference in body size. Our results showed that the intestine bacterial communities of slow-growing shrimp exhibited less diversity but were more heterogeneous than those of fast-growing shrimp. Uncultured_bacterium_g_Candidatus Bacilloplasma, Tamlana agarivorans, Donghicola tyrosinivorans, and uncultured_bacterium_f_Flavobacteriaceae were overrepresented in the intestines of fast-growing shrimp, while Shimia marina, Vibrio sp., and Vibrio campbellii showed the opposite trends. We further found that the bacterial community composition was significantly correlated with shrimp length, and some bacterial species abundances were found to be significantly correlated with shrimp weight and length, including T. agarivorans and V. campbellii, which were chosen as indicators for a reverse gavage experiment. Finally, T. agarivorans was found to significantly promote shrimp growth after the experiment. Collectively, these results suggest that intestine bacterial community could be important factors in determining the growth of shrimp, indicating that specific bacteria could be tested in further studies against shrimp growth retardation. KEY POINTS: • A close relationship between intestine bacterial community and shrimp growth was proven by controllable experiments. • The bacterial signatures of the intestine were markedly different between slow- and fast-growing shrimp, and the relative abundances of some intestine bacterial species were correlated significantly with shrimp body size. • Reverse gavage by Tamlana agarivorans significantly promoted shrimp growth.

Changes in Gut Microbiota in Peruvian Cattle Genetic Nucleus by Breed and Correlations with Beef Quality

This study evaluated the gut microbiota and meat quality traits in 11 healthy female cattle from the Huaral region of Peru, including 5 Angus, 3 Braunvieh, and 3 F1 Simmental × Braunvieh. All cattle were 18 months old and maintained on a consistent lifelong diet. Meat quality traits, including loin area, fat thickness, muscle depth, and marbling, were assessed in vivo using ultrasonography. Fecal samples were collected for microbiota analysis, and DNA was extracted for 16S and 18S rRNA sequencing to characterize bacterial, fungal, and protist communities. Significant correlations were observed between microbial genera and meat traits: Christensenellaceae R-7 and Alistipes were positively associated with marbling and muscle area, while Rikenellaceae RC9 showed a negative correlation with fat thickness. Among fungi, Candida positively correlated with marbling, while Trichosporon was negatively associated with muscle depth. For protists, Entodinium negatively correlated with fat thickness and marbling. Alpha diversity varied by breed, with Angus showing greater bacterial diversity, and beta diversity analyses indicated a strong breed influence on microbial composition. These findings suggest that microbial composition, shaped by breed and dietary consistency, could serve as an indicator of meat quality, offering insights into gut microbiota's role in optimizing cattle production.

Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study

Rumen microbiotas are known to influence the fat deposition (FD) in sheep, but controversy over causality remains unresolved. Here, we performed microbiome-wide association studies (MWAS), microbiome genome-wide association analysis (mbGWAS) and bidirectional mendelian randomization (MR) analyses on 1,150 sheep with genotype data from whole-genome resequencing, 16S rRNA sequencing and multilevel FD-traits data. We quantified the proportion of individual variation in FD-traits explained by host genetics, rumen microbiota, and their interaction effects. We identified 32 rumen microbiota biomarkers including Bifidobacterium that were associated with FD-traits (Padj <0.05). Further, utilizing five MR methods, we identified eight causal associations between marker genera and FD-traits (Padj <0.05), including Butyrivibrio, Olsenella, p-2534-18B5 gut group, Prevotellaceae UCG-003, and Pseudobutyrivibrio causing forward causal effects on FD, and changes in Flexilinea and Suttonella induced by FD. To our knowledge, this is the inaugural attempt to employ MR in sheep to investigate the causal relationships between gastrointestinal microbiota and complex phenotypes, underscoring the potential for developing interventions related to adipose deposition in sheep from the perspective of the rumen microbiome.

Sex-Induced Changes in Microbial Eukaryotes and Prokaryotes in Gastrointestinal Tract of Simmental Cattle

This study investigates gender-based differences in the gut microbiota of Simmental cattle, focusing on bacterial, archaeal, and fungal communities. Fecal samples were collected and analyzed using high-throughput sequencing, with taxonomic classification performed through the SILVA and UNITE databases. Alpha and beta diversity metrics were assessed, revealing significant differences in the diversity and composition of archaeal communities between males and females. Notably, females exhibited higher alpha diversity in archaea, while beta diversity analyses indicated distinct clustering of bacterial and archaeal communities by gender. The study also identified correlations between specific microbial taxa and hematological parameters, with Treponema and Methanosphaera showing gender-specific associations that may influence cattle health and productivity. These findings highlight the importance of considering gender in microbiota-related research and suggest that gender-specific management strategies could optimize livestock performance. Future research should explore the role of sex hormones in shaping these microbial differences.

The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.

Host genetic regulation of specific functional groups in the rumen microbiome of dairy cows: Implications for lactation trait

INTRODUCTION

Ruminants play a pivotal role in our society by transforming non-consumable substances from industrial by-products and plant fibers into valuable resources such as meat and milk. This remarkable conversion ability is primarily attributed to the rumen microbiota, which is influenced by various factors, including diet, climate, and geographical location. In recent years, increasing research has shown that host factors (breed, genetic variation, etc.) also play vital roles in shaping rumen microbial composition and function in cattle.

OBJECTIVE

This study aims to provide a theoretical basis and an opportunity for further investigating the regulation of lactation traits in dairy cows through host genetics and the interaction with the rumen microbiota.

METHOD

To investigate the interactions between host genotype, rumen microbiota, and animal phenotype, we curated and analyzed the dairy herd improvement data, single nucleotide polymorphisms (SNPs) genotypes, and 16S rumen microbiota data from 1,169 Holstein dairy cows. Heritability and microbiability estimation, along with genome-wide association studies, were performed to identify candidate microorganisms and host genetic loci.

RESULT

We identified thirty-one heritable taxa, whose functions were predominantly enriched in carbohydrate metabolism and energy metabolism. The genome-wide association study revealed that nine heritable bacteria were significantly associated with forty-three SNPs. Functional genes located within or near these SNPs were primarily associated with rumen epithelial development. Additionally, these nine heritable bacteria were primarily annotated as complex polysaccharide degraders and butyrate producers, such as Fibrobacter sp900143055 and Pseudoruminococcus massiliensis, which showed significant associations with milk yield and milk fat percentage. Compared to previous studies, we newly discovered the existence of a high heritability of Olsenella umbonate, Butyrivibrio hungatei, among others.

CONCLUSION

This study identified thirty-one heritable bacterial taxa in Holstein dairy cows' rumen microbiota, with nine showing significant associations with forty-three SNPs related to rumen epithelial development. The discovery of novel heritable species and their correlations with lactation traits provides valuable insights for future breeding strategies aimed at improving dairy cattle productivity through the manipulation of host genetics and rumen microbiota.

An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows

BACKGROUND

Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows.

RESULTS

The results indicated that the proportions of highly heritable subsets (h2 ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn2+ transport) (P < 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp., Prevotella_sp._E15-22, Prevotella_sp._E13-27, which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) (P < 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 (P < 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp., which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942).

CONCLUSION

Our comprehensive study revealed the distinct heritability patterns of rumen microbial composition, function, and metabolism. Additionally, we shed light on the influence of host SNP variants on the rumen microbes with carbohydrate metabolism and their subsequent effects on lactation performance. Collectively, these findings offer compelling evidence for the host-microbe interactions, wherein cows actively modulate their rumen microbiota through SNP variants to regulate their own lactation performance. Video Abstract.

Effects of Key Rumen Bacteria and Microbial Metabolites on Fatty Acid Deposition in Goat Muscle

In this study, the fatty acid composition in the muscles of Hechuan white goats was correlated with the metabolome and metagenome of their rumen contents, and potential effects of the metabolites and microorganisms in the rumen on host muscle fatty acid deposition were analyzed. The results of the correlation analysis between the rumen content's metabolome and muscle fatty acid content showed that vitamin-B-related metabolites were significantly correlated with fatty acid content (p < 0.05). Most of these metabolites were positively correlated with stearic acid and negatively correlated with palmitic acid. In accordance with the level of fatty acid content, significant differences were found in the microbial species and abundance among groups at the species level. An abundance of Bacteroides, Ruminococcaceae P7, Eubacterium ruminant, and Prevotella in the rumen was significantly correlated with fatty acid content. These results provide data support for the development of targeted feeding management strategies to improve the quality of goat meat.

Comparative Analysis of Microbiota in Jiani Yaks with Different Rib Structures

The Jiani yak is a nationally renowned species that is known for its meat which is rich in various minerals, amino acids, and proteins. The rumen microbiota plays a critical role in gastrointestinal health and feed degradation, contributing proteins, lipids, and volatile fatty acids (VFAs) essential for milk and meat production. However, there is limited knowledge about the microbiota of free-ranging Jiani yaks, especially those with 15 ribs. Rumen fluid samples were collected from yaks with 14 (PL) ribs and 15 (DL) ribs from a slaughterhouse in Jiani County, China. The total DNA of rumen fluid microorganisms was extracted for microbiota sequencing. Our results revealed 643,713 and 656,346 raw sequences in DL and PL animals, respectively, with 611,934 and 622,814 filtered sequences in these two yak groups. We identified 13,498 Amplicon Sequence Variants (ASVs), with 2623 shared between DL and PL animals. The ratio of Bacteroidota to Firmicutes differed between PL (3.04) and DL (2.35) animals. Additionally, 6 phyla and 21 genera showed significant differences between yaks with 14 and 15 ribs, leading to altered microbiota functions, with 51 and 35 notably different MetaCyc and KEGG pathways, respectively. Hence, the microbiota of yaks with 15 ribs differs from those with 14 ribs. Therefore, these microbiota-related comparative investigations will provide insights into yak husbandry practices and genetic selection strategies for their improved productivity in harsh environments.

Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation

Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.

The Rumen Microbiome Composition of Raramuri Criollo and European Cattle in an Extensive System

Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.

Revealing host genome-microbiome networks underlying feed efficiency in dairy cows

Ruminants have the ability to digest human-inedible plant materials, due to the symbiotic relationship with the rumen microbiota. Rumen microbes supply short chain fatty acids, amino acids, and vitamins to dairy cows that are used for maintenance, growth, and lactation functions. The main goal of this study was to investigate gene-microbiome networks underlying feed efficiency traits by integrating genotypic, microbial, and phenotypic data from lactating dairy cows. Data consisted of dry matter intake (DMI), net energy secreted in milk, and residual feed intake (RFI) records, SNP genotype, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows. We first assessed marginal associations between genotypes and phenotypic and microbial traits through genomic scans, and then, in regions with multiple significant hits, we assessed gene-microbiome-phenotype networks using causal structural learning algorithms. We found significant regions co-localizing the rumen microbiome and feed efficiency traits. Interestingly, we found three types of network relationships: (1) the cow genome directly affects both rumen microbial abundances and feed efficiency traits; (2) the cow genome (Chr3: 116.5 Mb) indirectly affects RFI, mediated by the abundance of Syntrophococcus, Prevotella, and an unknown genus of Class Bacilli; and (3) the cow genome (Chr7: 52.8 Mb and Chr11: 6.1-6.2 Mb) affects the abundance of Rikenellaceae RC9 gut group mediated by DMI. Our findings shed light on how the host genome acts directly and indirectly on the rumen microbiome and feed efficiency traits and the potential benefits of the inclusion of specific microbes in selection indexes or as correlated traits in breeding programs. Overall, the multistep approach described here, combining whole-genome scans and causal network reconstruction, allows us to reveal the relationship between genome and microbiome underlying dairy cow feed efficiency.

Seasonal stability of the rumen microbiome contributes to the adaptation patterns to extreme environmental conditions in grazing yak and cattle

BACKGROUND

The rumen microbiome plays an essential role in maintaining ruminants' growth and performance even under extreme environmental conditions, however, which factors influence rumen microbiome stability when ruminants are reared in such habitats throughout the year is unclear. Hence, the rumen microbiome of yak (less domesticated) and cattle (domesticated) reared on the Qinghai-Tibetan Plateau through the year were assessed to evaluate temporal changes in their composition, function, and stability.

RESULTS

Rumen fermentation characteristics and pH significantly shifted across seasons in both cattle and yak, but the patterns differed between the two ruminant species. Ruminal enzyme activity varied with season, and production of xylanase and cellulase was greater in yak compared to cattle in both fall and winter. The rumen bacterial community varied with season in both yak and cattle, with higher alpha diversity and similarity (beta diversity) in yak than cattle. The diversity indices of eukaryotic community did not change with season in both ruminant species, but higher similarity was observed in yak. In addition, the similarity of rumen microbiome functional community was higher in yak than cattle across seasons. Moreover, yak rumen microbiome encoded more genes (GH2 and GH3) related to cellulose and hemicellulose degradation compared to cattle, and a new enzyme family (GH160) gene involved in oligosaccharides was uniquely detected in yak rumen. The season affected microbiome attenuation and buffering values (stability), with higher buffering value in yak rumen microbiome than cattle. Positive correlations between antimicrobial resistance gene (dfrF) and CAZyme family (GH113) and microbiome stability were identified in yak, but such relationship was negatively correlated in cattle.

CONCLUSIONS

The findings of the potential of cellulose degradation, the relationship between rumen microbial stability and the abundance of functional genes varied differently across seasons and between yak and cattle provide insight into the mechanisms that may underpin their divergent adaptation patterns to the harsh climate of the Qinghai-Tibetan Plateau. These results lay a solid foundation for developing strategies to maintain and improve rumen microbiome stability and dig out the potential candidates for manufacturing lignocellulolytic enzymes in the yak rumen to enhance ruminants' performance under extreme environmental conditions.

Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model

BACKGROUND

The maternal gut microbiome is the direct and important source of early colonization and development of the neonatal gut microbiome. However, differences in unique and shared features between mothers with different physiological phenotypes and their newborns still lack exhaustive investigation. Here, using a cow-to-calf model, a comprehensive investigation was conducted to elucidate the pattern and characterization of microbial transfer from the maternal source to the offspring.

RESULTS

The microbiota in the rumen and feces of dairy cows were divided into two clusters via enterotype analysis. The cows from the enterotype distinguished by Prevotella in the rumen had better production performance, whereas no difference was observed in the cows classified by feces enterotype. Furthermore, through a pairwise combination of fecal and ruminal enterotypes, we screened a group of dairy cows with excellent phenotypes. The gastrointestinal microbiomes of cows with different phenotypes and their offspring differed significantly. The rumen was a more important microbial source for meconium than feces. Transmission of beneficial bacteria from mother to offspring was observed. Additionally, the meconium inherits advantageous metabolic functions of the rumen. The resistome features of the rumen, feces, and meconium were consistent, and resistome abundance from cows to calves showed an expanding trend. The interaction between antibiotic-resistance genes and mobile genetic elements from the rumen to meconium was the most remarkable. The diversity of core metabolites from cows to calves was stable and not affected by differences in phenotypes. However, the abundance of specific metabolites varied greatly.

CONCLUSIONS

Our study demonstrates the microbial taxa, metabolic function, and resistome characteristics of maternal and neonatal microbiomes, and reveals the potential vertical transmission of the microbiome from a cow-to-calf model. These findings provide new insights into the transgenerational transmission pattern of the microbiome. Video Abstract.

Integrating genome- and transcriptome-wide association studies to uncover the host-microbiome interactions in bovine rumen methanogenesis

The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota-mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome- and transcriptome-wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome-wide association study (GWAS). In contrast, the transcriptome-wide association study (TWAS) of rumen microbiota detected 28,260 significant gene-microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host-microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants.

Animal board invited review: The effect of diet on rumen microbial composition in dairy cows

Ruminants play an important part in the food supply chain, and manipulating rumen microbiota is important to maximising ruminants' production. Rumen microbiota through rumen fermentation produces as major end products volatile fatty acids that provide animal's energy requirements, and microbial CP. Diet is a key factor that can manipulate rumen microbiota, and each variation of the physical and chemical composition creates a specific niche that selects specific microbes. Alteration in the chemical composition of forage, the addition of concentrates in the diet, or the inclusion of plant extract and probiotics, can induce a change in rumen microbiota. High-throughput sequencing technologies are the approaches utilised to investigate the microbial system. Also, the application of omics technologies allows us to understand rumen microbiota composition and these approaches are useful to improve selection programmes. The aim of this review was to summarise the knowledge about rumen microbiota, its role in nutrient metabolism, and how diet can influence its composition.

Hybridization promotes growth performance by altering rumen microbiota and metabolites in sheep

Hybridization can substantially improve growth performance. This study used metagenomics and metabolome sequencing to examine whether the rumen microbiota and its metabolites contributed to this phenomenon. We selected 48 approximately 3 month-old male ♂Hu × ♀Hu (HH, n = 16), ♂Poll Dorset × ♀Hu (DH, n = 16), and ♂Southdown × ♀Hu (SH, n = 16) lambs having similar body weight. The sheep were fed individually under the same nutritional and management conditions for 95 days. After completion of the trial, seven sheep close to the average weight per group were slaughtered to collect rumen tissue and content samples to measure rumen epithelial parameters, fermentation patterns, microbiota, and metabolite profiles. The final body weight (FBW), average daily gain (ADG), and dry matter intake (DMI) values in the DH and SH groups were significantly higher and the feed-to-gain ratio (F/G) significantly lower than the value in the HH group; additionally, the papilla height in the DH group was higher than that in the HH group. Acetate, propionate, and total volatile fatty acid (VFA) concentrations in the DH group were higher than those in the HH group, whereas NH3-N concentration decreased in the DH and SH groups. Metagenomic analysis revealed that several Prevotella and Fibrobacter species were significantly more abundant in the DH group, contributing to an increased ability to degrade dietary cellulose and enrich their functions in enzymes involved in carbohydrate breakdown. Bacteroidaceae bacterium was higher in the SH group, indicating a greater ability to digest dietary fiber. Metabolomic analysis revealed that the concentrations of rumen metabolites (mainly lysophosphatidylethanolamines [LPEs]) were higher in the DH group, and microbiome-related metabolite analysis indicated that Treponema bryantii and Fibrobacter succinogenes were positively correlated with the LPEs. Moreover, we found methionine sulfoxide and N-methyl-4-aminobutyric acid were characteristic metabolites in the DH and SH groups, respectively, and are related to oxidative stress, indicating that the environmental adaptability of crossbred sheep needs to be further improved. These findings substantially deepen the general understanding of how hybridization promotes growth performance from the perspective of rumen microbiota, this is vital for the cultivation of new species and the formulation of precision nutrition strategies for sheep.

Comparative Analysis of the Potential Adaptability of Tibetan Dzo and Yellow Cattle Based on Blood Indices, Metabolites, and Fecal Microbiota

This study aimed to investigate the differences in environmental adaptability between dzo and Tibetan yellow cattle by using corresponding assay kits to analyze blood indices, utilizing mass spectrometry for blood metabolite profiling, and performing 16S rDNA sequencing of fecal microbiota. Forty female cattle were randomly divided into a dzomo (female dzo) group (MG, n = 20) and a Tibetan-yellow-cattle group (HG, n = 20). After 150 days of uniform feeding, six cattle from each group were randomly picked for jugular blood sampling and collection of fecal microorganisms. The results showed that the serum albumin, creatinine, total protein, superoxide dismutase, IgG, and IgM concentrations in the MG group were higher (p < 0.05), whereas the serum triglyceride concentration was lower, compared to the HG group (p < 0.05). The higher level of phospholipids containing long-chain polyunsaturated fatty acids (PUFAs) (PC (18:5e/2:0), PC (20:5e/2:0), LPC 18:2, LPC 20:5) observed in the serum of the dzo suggests that they have an advantage in adapting to the challenging conditions of the plateau environment. The fecal microbiota analysis showed that Akkermansia was significantly enriched in the MG group; this might be the key bacterial genus leading to the strong adaptability of dzo. Our findings indicated the dzo's superior adaptation to the Tibetan Plateau's harsh environment.