Microbiome network traits in the rumen predict average daily gain in beef cattle under different backgrounding systems

Effects of Steviol Glycosides on Growth Performance, Ruminal Fermentation and Microbial Diversity of Hu Sheep

The experiment was conducted to investigate the potential effects of steviol glycosides on growth performance, rumen fermentation processes, and microbial diversity in Hu sheep. A single-factor design was used for the trial. Twenty healthy weaned Hu lambs, possessing comparable body weights averaging 18.31 ± 1.24 kg, were randomly allocated into two distinct groups: the control group (CON) and the experimental group (STE), with each comprising 10 lambs. The CON was fed the basal diet, and the STE was supplemented with 0.07% steviol glycosides based on the basal diet. During the experimental period, variations in body weight and feed intake were closely monitored and recorded. After feeding for 90 d, blood was collected to determine blood biochemical indices, and rumen fluid samples were gathered for an in-depth analysis of rumen fermentation parameters and microbial diversity. The outcomes revealed no statistically significant differences in growth performance or serum biochemical indices between the two groups (p > 0.05). Rumen pH in STE and CON was within the normal range. The rumen ammonia nitrogen (NH3-N) and acetic acid (AA) content of STE decreased significantly compared with CON (p < 0.05). No significant variations were observed in the levels of other volatile fatty acids (VFAs) between the two groups (p > 0.05). The rumen microbial OTUs count, as well as the Shannon, Simpson, Chao1, and Ace indices, were notably lower in the STE group compared to the CON group (p < 0.05). Additionally, at the phylum level, the relative abundance of Firmicutes, Bacteroidetes, and Proteobacteria collectively accounted for over 97% of the total phylum composition. In comparison to the CON group, the STE group exhibited an increase in the relative abundance of Proteobacteria (p < 0.05), accompanied by a significant reduction in the relative abundance of Patescibacteria and Desulfobacteria (p < 0.05). At the genus level, there was a notable increase in the relative abundance of Prevotella_7 and Succinivibrionaceae_UCG_001 in the STE group, whereas the relative abundance of Rikenellaceae_RC9_gut_group significantly decreased (p < 0.05). According to the correlation analysis between rumen microflora and VFAs, the relative abundance of Succinivibrionaceae_UCG_001 displayed a significant negative correlation with AA (p < 0.05), whereas Lactobacillus exhibited a notable positive correlation with isobutyric acid (IBA) (p < 0.05). In summary, steviol glycosides had no significant effect on the production performance and blood biochemical indexes of Hu sheep. Steviol glycosides can improve rumen fermentation parameters and rumen microflora structure of Hu sheep and have a certain effect on rumen microbial diversity and composition.

Effect of Milk-Feeding Frequency and Calcium Gluconate Supplementation on Growth, Health, and Reproductive and Metabolic Features of Holstein Heifers at a Rearing Farm

We compared the effects of milk-feeding in 288 Holstein calves (72 per group) which were fed twice (2F) or thrice (3F) daily, with or without the addition of hydrogenated fat-embedded calcium gluconate (G) supplemented in the starter food and in the daily diet up to the age of 9 months, on the calves' metabolism, growth, health, and reproductive efficiency up to first pregnancy. The calves received 6 L of milk replacer (130 g/L) and had ad libitum access to water and textured calf starter with or without gluconate. Gluconate supplementation promoted a "catch-up" in growth in supplemented calves compared to their counterparts that did not receive gluconate. Gluconate appeared to reduce animal metabolic stress during key events, such as weaning and transfer into open-door pens, reducing fructosamine (352.61 vs. 303.06 in 3FG and 3F, respectively; p = 0.028) and urea (3F revealed the highest values compared with the other three groups: 19.06 for 3F vs. 13.9 (2F), 13.7 (2FG), and 14.3 (3FG), respectively, p = 0.002) from weaning onwards. The feeding of dairy calves with milk replacer three rather than two times per day tended to be associated with better health from weaning to 4 months old; parameters such as ultrasound lung score and calf health score improved over time (p < 0.001). Thrice-daily feeding with milk replacer tended to reduce the number of artificial inseminations per pregnancy in heifers by 0.2 points (p = 0.092). We confirmed significant correlations between early health and growth parameters and reproductive efficiency and a positive correlation between body weight and average daily weight gain and the thickness of the back fat layer in young heifers (r = 0.245; p < 0.0001; r = 0.214; p < 0.0001 respectively). Our study was conducted on a commercial farm with reasonably effective animal management, so baseline welfare was likely satisfactory.

Effects of non-pelleted or pelleted low-native grass and pelleted high-native grass diets on meat quality by regulating the rumen microbiota in lambs

Diet modulates the rumen microbiota, which in turn can impact the animal performance. The rumen microbiota is increasingly recognized for its crucial role in regulating the growth and meat quality of the host. Nevertheless, the mechanism by which the rumen microbiome influences the fatty acid and amino acid profiles of lambs in the grass feeding system remains unclear. This study aimed to evaluate the effects of different native grass-based diets on animal performance, meat quality, fatty acid compositions, amino acid profiles, and rumen microbiota of lamb. Seventy-two Ujumqin lambs were randomly assigned into three treatments according to the initial body weight (27.39 ± 0.51 kg) and age (6 months ± 6 days). The lambs received three diets: (i) non-pelleted native grass hay with 40% concentrate diet; the native grass and concentrate were fed individually; (ii) pelleted native grass hay with 40% concentrate diet (PHLC); (iii) pelleted native grass hay with 60% concentrate diet (PHHC). The results showed that among the three groups, the PHHC and PHLC diets had markedly (P < 0.05) higher average daily gain and pH45 min, respectively. All amino acid levels were significantly (P < 0.05) decreased in the PHHC diet than in the PHLC diet. The principal coordinate analysis of the ruminal microbiota indicated the markedly distinct separation (P = 0.001) among the three groups. In addition, the correlation analysis showed that the Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Succinivibrio, and Succiniclasticum were significantly (P < 0.05) associated with most of the fatty acid and amino acid profiles. The correlation analysis of the association of microbiome with the meat quality provides us with a comprehensive understanding of the composition and function of the rumen microbial community, and these findings will contribute to the direction of future research in lamb.

IMPORTANCE

Diet modulates the gut microbiome, which in turn impact the meat quality, yet few studies investigate the correlation between the rumen microbiome and the fatty acid profile of meat. Here, the current study develops an experiment to investigate the correlation of the rumen microbiome and fatty acid profile of meat: rumen microbiome responses to feed type and meat quality. The results indicated a unique microbiota in the rumen of lamb in response to diets and meat quality. Associations between utilization and production were widely identified among the affected microbiome and meat quality, and these findings will contribute to the direction of future research in lamb.

Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle

BACKGROUND

Stocker cattle diet and management influence beef cattle performance during the finishing stage, but knowledge of the dynamics of the rumen microbiome associated with the host are lacking. A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota. During the stocker phase, either dry hay or wheat pasture were provided, and three levels of monensin were administrated. All calves were then transported to a feedlot and received similar finishing diets with or without monensin. Rumen microbial samples were collected on d 0, 28, 85 during the stocker stage (S0, S28 and S85) and d 0, 14, 28, 56, 30 d before slaughter and the end of the trial during the finishing stage (F0, F14, F28, F56, Pre-Ba, and Final). The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced.

RESULTS

Higher alpha diversity, including the number of observed bacterial features and the Shannon index, was observed in the stocker phase compared to the finishing phase. The bacterial amplicon sequence variants (ASVs) differentiating different sampling time points were identified. Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota. For example, shared bacteria, including Bacteroidales (ASV19) and Streptococcus infantarius (ASV94), were significantly higher in hay rumen on S28, S85, and F0, while Bacteroidaceae (ASV11) and Limivicinus (ASV15) were more abundant in wheat. Monensin affected rumen microbial composition at a specific time. Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves. Bacterial taxa associated with body weight were classified, and core microbiotas interacted with each other during the trial.

CONCLUSIONS

In summary, the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy. Diet at the stocker phase may temporarily affect the microbial composition during this stage. Modulating the rumen microbiome in the steers at the stocker stage affects the microbial interactions and performance in the finishing stage.

Effect of Dietary and Age Changes on Ruminal Microbial Diversity in Holstein Calves

Ruminal microorganisms play a crucial role in the energy supply of ruminants and animal performance. We analyzed the variations in rumen bacteria and fungi at 45 d, 75 d, and 105 d by using 16SrRNA and ITS sequencing data and investigated their correlation with rumen fermentation. According to the results, rumen microflora tended to gradually mature with age, and bacterial and fungal establishment gradually stabilized. Upon comparing the three periods, the concentration of propionic acid increased significantly (p < 0.05) after weaning, and weaning accompanied by a transition in diet remarkably decreased (p < 0.05) rumen diversity in the short term and induced a corresponding change in the rumen microbiota composition. Bacteroidota, Actinobacteriota, and Firmicutes were the core bacterial phyla for all age periods. Ruminococcus, NK4A214_group, Sharpea, Rikenellaceae_RC9_gut_group, and norank_f__Butyricicoccaceae were the markedly abundant bacterial genera in pre-weaning. After weaning, the relative abundance of Erysipelotrichaceae_ UCG-002, Eubacterium_ruminantium_group, and Solobacterium significantly increased (p < 0.05). The relative abundance of Acetitomaculum increased with age with the greatest abundance noted at 105 d (37%). The dominant fungal phyla were Ascomycota and Basidiomycota, and Aspergillus and Xeromyces were the most abundant fungal genera after weaning. Trichomonascus, Phialosimplex, and Talaromyces were enriched at 105 d. However, the low abundance of Neocallimastigomycota was not detected throughout the study, which is worthy of further investigation. In addition, correlations were observed between age-related abundances of specific genera and microbiota functions and rumen fermentation-related parameters. This study revealed that rumen microbiota and rumen fermentation capacity are correlated, which contributed to a better understanding of the effects of age and diet on rumen microbiology and fermentation in calves.

Integrated rumen microbiome and serum metabolome analysis responses to feed type that contribution to meat quality in lambs

BACKGROUND

Lifestyle factors, such as diet, are known to be a driver on the meat quality, rumen microbiome and serum metabolites. Rumen microbiome metabolites may be important for host health, the correlation between rumen microbiome and production of rumen metabolites are reported, while the impact of rumen microbiome on the serum metabolome and fatty acid of meat are still unclear. This study was designed to explore the rumen microbiome, serum metabolome and fatty acid of meat in response to the grass diet and concentrate diet to lambs, and the relationship of which also investigated.

METHODS

In the present study, 12 lambs were randomly divided into two groups: a grass diet (G) and a concentrate diet (C). Here, multiple physicochemical analyses combined with 16S rRNA gene sequences and metabolome analysis was performed to reveal the changes that in response to feed types.

RESULTS

The concentrate diet could improve the growth performance of lambs compared to that fed with the grass diet. The microbiome composition was highly individual, compared to the concentrate group, the abundance of Rikenellaceae_RC9_gut_group, F082_unclassified, Muribaculaceae_unclassified, Ruminococcaceae_NK4A214_group, Bacteroidetes_unclassified, and Bacteroidales_UCG-001_unclassified were significantly (P < 0.05) lower in the grass group, while, the abundance of Succinivibrio, Succinivibrionaceae_UCG-002, Fibrobacter and Christensenellaceae_R-7_group were significantly (P < 0.05) higher in the grass group. Serum metabolomics analysis combined with enrichment analysis revealed that serum metabolites were influenced by feed type as well as the metabolic pathway, and significantly affected serum metabolites involved in amino acids, peptides, and analogues, bile acids, alcohols and derivatives, linoleic acids derivatives, fatty acids and conjugates. Most of the amino acids, peptides, and analogues metabolites were positively associated with the fatty acid contents. Among the bile acids, alcohols and derivatives metabolites, glycocholic was positively associated with all fatty acid contents, except C18:0, while 25-Hydroxycholesterol and lithocholic acid metabolites were negatively associated with most of the fatty acid contents.

CONCLUSION

Correlation analysis of the association of microbiome with metabolite features, metabolite features with fatty acid provides us with comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified among affected microbiome, metabolites and fatty acid, and these findings will contribute to the direction of future research in lamb.

Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves

BACKGROUND

Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.

RESULTS

Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.

CONCLUSIONS

Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.

Preweaning period is a critical window for rumen microbial regulation of average daily gain in Holstein heifer calves

BACKGROUND

Rumen bacterial groups can affect growth performance, such as average daily gain (ADG), feed intake, and efficiency. The study aimed to investigate the inter-relationship of rumen bacterial composition, rumen fermentation indicators, serum indicators, and growth performance of Holstein heifer calves with different ADG. Twelve calves were chosen from a trail with 60 calves and divided into higher ADG (HADG, high pre- and post-weaning ADG, n = 6) and lower ADG (LADG, low pre- and post-weaning ADG, n = 6) groups to investigate differences in bacterial composition and functions and host phenotype.

RESULTS

During the preweaning period, the relative abundances of propionate producers, including g_norank_f_Butyricicoccaceae, g_Pyramidobacter, and g_norank_f_norank_o_Clostridia_vadinBB60_group, were higher in HADG calves (LDA > 2, P < 0.05). Enrichment of these bacteria resulted in increased levels of propionate, a gluconeogenic precursor, in preweaning HADG calves (adjusted P < 0.05), which consequently raised serum glucose concentrations (adjusted P < 0.05). In contrast, the relative abundances of rumen bacteria in post-weaning HADG calves did not exert this effect. Moreover, no significant differences were observed in rumen fermentation parameters and serum indices between the two groups.

CONCLUSIONS

The findings of this study revealed that the preweaning period is the window of opportunity for rumen bacteria to regulate the ADG of calves.

Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition

This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p < 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p < 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p < 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p < 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.

Diversity of growth performance and rumen microbiota vary with feed types

Diet is a major factor in influencing the growth performance and the microbial community of lambs. This study aimed to investigate how diverse diets influence their growth performance and rumen microbiota. Ninety male lambs were randomly allocated into three groups in a completely randomized design with equal lambs: non-pelleted native grass hay (HA) as the control diet and pelleted native grass hay (GP) and pelleted native grass hay with concentrate (GPC) as experimental diets. The rumen fluid samples of the lambs in the HA, GP, and GPC groups were used to study rumen microbiota diversity through 16S rDNA high-throughput sequencing. In the present study, the final body weight, dry matter intake, and average daily gain differed significantly (p &lt; 0.05) among the HA, GP, and GPC groups. Compared to the HA group, higher final body weight, dry matter intake, and average daily gain were found in the GP group. Similarly, better animal performance was observed in the GPC group than in the GP group. The principal coordinates analysis displayed that the composition of the rumen microbiota in the three groups was distinctly separated from each other. Bacteroidetes and Firmicutes were the dominant members of the community in the HA and GP groups, while Bacteroidetes, Firmicutes, and Proteobacteria became the predominant members in the GPC group. The comparison among these groups showed significant (p &lt; 0.05) differences in Rikenellaceae_RC9_gut_group, Prevotella_1, Ruminococcaceae_NK4A214_group, and Succiniclasticum. These results suggest that the GP and GPC diets are more beneficial for growth performance than the HA diet and also indicate that the rumen microbiota varied in response to different feed types. In conclusion, these results could provide strategies to influence rumen microbiota for better growth and a healthier ecosystem on the Mongolian Plateau and lay the theoretical groundwork for feeding the pelleted native grass diet.

Evaluating the fermentation characteristics, bacterial community, and predicted functional profiles of native grass ensiled with different additives

Bioaugmentation of native grass ensiling with Lactobacillus plantarum or Lactobacillus buchneri or Pediococcus pentosaceus on the ensiling performance and bacterial community was investigated after 30 days of the fermentation process. The native grass was inoculated with distilled water, Lactobacillus plantarum, Lactobacillus plantarum, and Lactobacillus buchneri, and Lactobacillus plantarum, Lactobacillus buchneri, and Pediococcus pentosaceus as the CON treatment, T1 treatment, T2 treatment, and T3 treatment, respectively. The addition of lactic acid bacteria was added at a total of 1 × 10⁶ colony-forming unit/g of fresh weight. As expected, the markedly (p < 0.05) lower water-soluble carbohydrate content was tested in the T2 and T3 treatments compared to the CON and T1 treatments. Compared to the CON and T1 treatment, significantly (p < 0.05) higher crude protein content, and lower acid detergent fiber and neutral detergent fiber contents were found in the T2 and T3 treatments. Compared to the CON treatment, the pH significantly (p < 0.05) decreased in the lactic acid bacteria (LAB) inoculated silage, and the lowest pH was measured in the T3 treatment. Similarly, significantly higher lactic acid and acetic acid contents were also found in the T3 treatment compared to those in other treatments. After 30 days of ensiling, the Shannon and Chao1 indexes in silages decreased compared to that in the fresh materials (FMs). The principal coordinate analysis indicated that both FM and silage were distinctly separated in each treatment with no interactions on the confidence ellipse (R = 0.8933, p = 0.001). At the phylum level, the dominant phylum was shifted from Proteobacteria to Firmicutes after the fermentation process. Interestingly, Weissella dominated the fermentation in the CON treatment and Lactobacillus dominated the fermentation in all inoculated LAB silages at the genus level. Results of functional prediction analyses showed that the metabolism of amino acid, cofactors, and vitamins, and membrane transport was reduced, while the metabolism of nucleotide and majority carbohydrates was increased after ensiling. The complex LAB (Lactobacillus plantarum, Lactobacillus buchneri, and Pediococcus pentosaceus) exhibited the potential possibility to decrease pH and enhance the relative abundance of LAB in response to obtaining high-quality silage by the synergistic effects. These results suggested that the complex LAB could improve the ensiling performance of native grass silage, and lay a theoretical basis for inoculant application in native grass.