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ABSTRACT The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle. All publicly available cattle gut microbiota datasets were collected and re-analyzed together to identify shared and differentially abundant archaeal and bacterial groups, as well factors influencing the gut microbiota.

The objective of this experiment was to evaluate the effect of different EOC (0.1425% cobalt lactate + 1.13% oregano essential oil + 98.7275% carrier) levels on in vitro rumen fermentation and microbial changes. Six EOC levels (treatments: 0 mg·L−1, CON; 50 mg·L−1, EOC1; 100 mg·L−1, EOC2; 400 mg·L−1, EOC3; 800 mg·L−1, EOC4 and 1500 mg·L−1, EOC5) were selected to be used to in vitro incubation. The in vitro dry matter digestibility (IVDMD), in vitro neutral detergent fiber digestibility (IVNDFD), in vitro acid detergent fiber digestibility (IVNDFD), pH, ammonia-nitrogen (NH3-N) concentration, total volatile fatty acid (TVFA) concentration and microbial protein (MCP) concentration were measured after 48 h incubation, after which the groups with significant nutrient digestibility and fermentation parameters were subjected to 16S rRNA sequencing. The results showed that the total gas production (GP) of the EOC5 group was higher than that of the other groups after 12 h of in vitro incubation. TVFA, NH3-N and MCP concentrations were also shown to be higher in group EOC5 than those in other groups (p < 0.05), while NH3-N and MCP concentrations in the EOC2 group were lower than those in other groups significantly (p < 0.05). The molar ratio of acetic acid decreased while the molar ratio of propionic acid increased after the addition of EOC. 16S rRNA sequencing revealed that the rumen microbiota was altered in response to adding EOC, especially for the EOC5 treatment, with firmicutes shown to be the most abundant (43.1%). The relative abundance of Rikenellaceae_RC9_gut_group was significantly lower, while the relative abundance of uncultured_bacterium_f_Muribaculaceae and Succiniclasticum was significantly higher in the EOC5 group than those in other groups (p < 0.05). Comprehensive analysis showed that EOC (1500 mg·L−1) could significantly increase gas production, alter sheep rumen fermentation parameters and microbiota composition.

We examined the effects of two direct-fed microbials (DFM) containing multiple microbial species and their fermentation products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers. Nine ruminally cannulated Holstein steers (mean ± SD body weight: 243 ± 12.4 kg) were assigned to three treatments arranged in a triplicated 3 × 3 Latin square design with three 21-d periods. Dietary treatments were 1) control (CON; basal diet), 2) Commence (PROB; basal diet plus 19 g/d of Commence), and 3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both multispecies DFM products. From day 16 to 20 of each period, feed and fecal samples were collected daily to determine the apparent total tract digestibilities of nutrients using indigestible neutral detergent fiber method. On day 21 of each period, blood samples were collected for analysis of plasma glucose and nonesterified fatty acid. Ruminal contents were collected at approximately 1, 3, 6, 9, 12, and 18 h after feeding on day 21 for analysis of volatile fatty acids (VFA), lactate, ammonia-N concentrations, bacterial community, and metabolome profile. Total tract digestibilities of nutrients did not differ (P > 0.05) among treatments. Compared with CON, steers fed either supplemental PROB or SYNB had greater (P = 0.04) plasma glucose concentrations. Compared with CON, total ruminal VFA, propionate, isovalerate, and valerate concentrations increased (P ≤ 0.05) or tended to increase (P ≤ 0.10) with either supplemental PROB or SYNB, but were not different (P > 0.05) between PROB and SYNB. Compared with CON, PROB reduced (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Rikenellaceae RC9, Succinivibrionaceae UCG-001, Succiniclasticum, and Ruminococcaceae UCG-002. Supplemental SYNB decreased (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Prevotella 7, Succinivibrio, Succiniclasticum, and Ruminococcaceae UCG-014. Compared with CON, metabolome analysis revealed that some amino acids were increased (P ≤ 0.05) in steers fed PROB. This study demonstrated that, compared with CON, supplementation of either PROB or SYNB altered the ruminal bacterial community and metabolome differently; however, their effects on the ruminal VFA profile and energy status of the steers were not different from each other.

Dietary energy is crucial for ruminants’ performance and health. To determine optimal dietary energy levels for growing sheep, we evaluated their growth performance, nutrient digestibility, rumen fermentation, barrier function, and microbiota under varying metabolic energy (ME) diets. Forty-five growing Yunnan semi-fine wool sheep, aged 10 months and weighing 30.8 ± 1.9 kg, were randomly allocated to five treatments, each receiving diets with ME levels of 8.0, 8.6, 9.2, 9.8 or 10.4 MJ/kg. The results showed that with increasing dietary energy, the average daily gain (ADG) as well as the digestibility of dry matter (DM) and organic matter (OM) increased (p < 0.05), while the feed conversion ratio (FCR) decreased linearly (p = 0.01). The concentration of total VFA (p = 0.03) and propionate (p = 0.01) in the rumen increased linearly, while rumen pH (p < 0.01) and the acetate–propionate ratio (p = 0.01) decreased linearly. Meanwhile, the protein contents of Claudin-4, Claudin-7, Occludin and ZO-1 as well as the relative mRNA expression of Claudin-4 and Occludin also increased (p < 0.05). In addition, rumen bacterial diversity decreased with the increase of dietary energy, and the relative abundance of some bacteria (like Saccharofermentans, Prevotella and Succiniclasticum) changed. In conclusion, increasing dietary energy levels enhanced growth performance, nutrient digestibility, rumen fermentation, and barrier function, and altered the rumen bacterial community distribution. The optimal dietary ME for these parameters in sheep at this growth stage was between 9.8 and 10.4 MJ/kg.

The yak rumen microflora has more efficient fiber-degrading and energy-harvesting abilities than that of low-altitude cattle; however, few studies have investigated the effects of dietary energy levels on the rumen bacterial populations and the relationship between rumen bacteria and the intramuscular fatty acid profile of fattening yaks. In this study, thirty yaks were randomly assigned to three groups. Each group received one of the three isonitrogenous diets with low (3.72 MJ/kg), medium (4.52 MJ/kg), and high (5.32 MJ/kg) levels of net energy for maintenance and fattening. After 120 days of feeding, results showed that increasing dietary energy significantly increased ruminal propionate fermentation and reduced ammonia concentration. The 16S rDNA sequencing results showed that increasing dietary energy significantly increased the ratio of Firmicutes to Bacteroidetes and stimulated the relative abundance of Succiniclasticum, Saccharofermentans, Ruminococcus, and Blautia populations. The quantitative real-time PCR analysis showed that high dietary energy increased the abundances of Streptococcus bovis, Prevotella ruminicola, and Ruminobacter amylophilus at the species level. Association analysis showed that ruminal acetate was positively related to some intramuscular saturated fatty acid (SFA) contents, and Prevotella was significantly positively related to intramuscular total polyunsaturated fatty acid content and negatively related to intramuscular total SFA content. This study showed that high dietary energy mainly increased ruminal amylolytic and propionate-producing bacteria populations, which gave insights into how the effects of dietary energy on rumen bacteria are related to intramuscular fat fatty acids of fattening yaks.

Background Subacute ruminal acidosis (SARA) is characterized by a ruminal pH depression, and microbiota can also be affected by a higher acidity and/or dietary changes. Previous studies have revealed similar patterns in pH reduction in the rumen and reticulum, whereas changes in reticular pH and bacterial community following a high-grain diet are not fully understood. The aim of this study was to investigate the changes in reticular pH and bacterial community structure following a high-grain diet simultaneously with those in the rumen. Results SARA was diagnosed when ruminal and reticular pH remained under 5.6 for 350 ± 14 and 312 ± 24 min/d, respectively, on the last day of the CON period. During the CON period, lower proportion of acetic acid and higher proportion of butyric acid were observed compared with the HAY period. The proportions of acetic acid and propionic acid were lower and higher, respectively, in the rumen compared with the reticulum. From 454 pyrosequencing analysis, the relative abundance of several genera differed significantly between the two periods and the two locations. During the HAY period, higher relative abundances of Prevotella , Eubacterium , Oscillibacter , and Succiniclasticum and lower relative abundances of Ruminococcus , Clostridium , and Olsenella were identified compared with the CON period. Furthermore, the relative abundance of Eubacterium was lower in the rumen compared with the reticulum. Bacterial diversity indices were significantly different between the HAY and CON periods, being higher in the HAY period. The quantitative real-time PCR showed that the copy numbers of several cellulolytic bacteria ( Fibrobacter succinogenes and Ruminococcus albus ) were higher during the HAY period. Conclusion A high-grain diet showed similar impacts on the pH, fermentation, and bacterial community structure in the rumen and reticulum. During the CON period, ruminal and reticular pH decreased following the high-grain challenge, and lower bacterial diversity and changes in the bacterial composition, similarity, and bacterial copy numbers were observed due to a higher acidity and dietary changes compared with the HAY period. These changes may influence the fermentative ability of the rumen and reticulum.

This study aimed to explore the dynamic variations of rumen fermentation characteristics and bacterial community composition during a 24 h in vitro fermentation. A total of twenty-three samples were collected from original rumen fluid (ORF, n = 3), fermentation at 12 h (R12, n = 10), and fermentation at 24 h (R24, n = 10). Results showed that gas production, concentrations of microbial crude protein, ammonia nitrogen, and individual volatile fatty acids (VFA), as well as total VFA and branched-chain VFA concentrations, were higher in R24 when compared with R12 (p < 0.05). However, no significant differences were observed in acetate to propionate ratio and fermentation efficiency between R12 and R24 (p > 0.05). Bacterial diversity analysis found that Shannon index and Simpson index were higher in R24 (p < 0.05), and obvious clusters were observed in rumen bacterial community between R12 and R24. Taxonomic analysis at the phylum level showed that the abundances of Proteobacteria and Fibrobacteres were higher in R12 than that in R24, and inverse results were observed in Bacteroidetes, Firmicutes, Cyanobacteria, Verrucomicrobia, Lentisphaerae, and Synergistetes abundances. Taxonomic analysis at the genus level revealed that the abundances of Rikenellaceae RC9 gut group, Succiniclasticum, Prevotellaceae UCG-003, Christensenellaceae R-7 group, Ruminococcaceae UCG-002, Veillonellaceae UCG-001, and Ruminococcaceae NK4A214 group were higher in R24, whereas higher abundances of Succinivibrionaceae UCG-002, Ruminobacter, and Fibrobacter, were found in R12. Correlation analysis revealed the negative associations between gas production and abundances of Proteobacteria, Succinivibrionaceae UCG-002, and Ruminobacter. Moreover, the abundances of Firmicutes, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Ruminococcaceae UCG-002 positively correlated with VFA production. These results indicate that both rumen fermentation characteristics and bacterial community composition were dynamic during in vitro fermentation, whereas the fermentation pattern, efficiency, and bacterial richness remained similar. This study provide insight into the dynamics of rumen fermentation characteristics and bacterial composition during in vitro fermentation. This study may also provide a reference for decision-making for the sampling time point when conducting an in vitro fermentation for bacterial community investigation.

Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus , Lachnospira , and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.

Heat stress (HS) causes severe economic losses in sheep industry worldwide. The objective of the present study was to investigate the effects of a herbal formula (HF) supplement on growth, digestibility, antioxidant capacity, and rumen microbes in fattening lambs under HS. The HF composed of four herbs was prepared based on the theory of compatibility of Chinese medicine “Jun-Chen-Zuo-Shi”. Two-hundred forty 3-month weaned lambs (initial weight 36.61 ± 0.73 kg) were randomly allocated into four groups, supplemented 0% (Control), 0.5%, 1.0%, and 1.5% HF in diets. All lambs were exposed to HS conditions with 79.7 of average temperature–humidity index throughout an experimental period of 35 days. Growth performance, apparent digestibility, and antioxidant activities, involving antioxidant enzymes and heat shock proteins (HSPs), were measured at the end of trial, as well as microbial communities in bacteria and archaea. Results showed that 0.5% HF increased ( P  = 0.02) average daily gain by 13.80% and decreased feed-to-gain ratio ( P  = 0.03) by 14.68%, compared to control. With increasing HF doses, the digestibility of ether extract and acid detergent fiber demonstrated a cubical ( P  < 0.01) and quadratic ( P  = 0.03) relation, respectively; moreover, glutathione peroxidase and catalase activities demonstrated a quadratic increase ( P  < 0.01). Serum levels of HSP60, HSP70, and HSP90 for 0.5% HF were lower than that in control ( P  < 0.05). On the other hand, total volatile fatty acid, acetic acid, butyric acid, valeric acid, and isovaleric acid levels exhibited quadratic increases ( P  ≤ 0.01) with HF doses. From rumen microbes, the abundance and diversity of bacterial community were improved by HF supplements. Particularly for 0.5% HF group, the operational taxonomic units were the greatest among all groups. Compared to control, Prevotella abundance for HF supplements from 0.5 to 1.5% increased by 35.57 to 60.15%, and Succiniclasticum abundance demonstrated a quadratic pattern ( P  = 0.02) with doses. Additionally, Methanosphaera abundance in archaeal community raised by 0.2 to 3.3-folds when lambs were fed the HF additions of 0.5 to 1.5%. In summary, dietary HF supplements would contribute to alleviating HS in lambs, and our results suggest the optimal dose of 0.5% HF supplement in diet.

The present study aimed to investigate the effect of hydrogen-consuming compounds on ruminal methane (CH4) production, in vitro fermentation parameters, fatty acids profile, and microbial community in water buffalo. Different sodium nitrate to disodium fumarate ratios [2:1 (F), 1:1 (S), 1:2 (T)] were studied in vitro by batch culture technique in the presence of linoleic acid. Results revealed that the dominant bacterial communities were not affected with sodium nitrate and disodium fumarate, whereas CH4 production and Verrucomicrobia, Succiniclasticum, norank_f__Muribaculaceae, and Prevotellaceae_UCG-003 were reduced (P < 0.05). However, ruminal pH, unsaturated fatty acids/saturated fatty acids (UFA/SFA) and Campilobacterota, Selenomonas, Succinivibrio, Oribacterium, Christensenellaceae_R-7_group, Campylobacter, Shuttleworthia, Schwartzia, and Prevotellaceae_YAB2003_group were increased (P < 0.05). Total volatile fatty acids (TVFA) and Spirochaetae, Fibrobacterota, Verrucomicrobia, Fibrobacter, Treponema, and Prevotellaceae were decreased in F (P < 0.05), but cis-9, trans-11CLA, acetate/propionate and Proteobacteria, Campilobacterota, Selenomonas, Succinivibrio, and Campylobacter were increased in F (P < 0.05). The highly selected bacterial genera in F were Campylobacter and Succinivibrio. The disodium fumarate, enhanced (P < 0.05) the TVFA, propionate, total bacteria, Butyrivibrio proteoclasticus, and Atypical butyrivibrio. The concentrations of C18:3n3, C20:3n6, C21:0, C22:2n6, and C22:1n9, as well as the populations of total fungi, protozoa, methanogens, Butyrivibrio hungatei in T were higher (P < 0.05). The highly selected bacterial genera in T were Fibrobacter and Treponema. Conclusively, the addition of sodium nitrate and disodium fumarate can reduce the CH4 production and optimize ruminal fatty acid composition. Furthermore, disodium fumarate can alleviate the adverse effect of sodium nitrate on the rumen fermentation.