Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages.

ABSTRACT: Seven Italian Simmental cows were monitored during three different physiological stages, namely late lactation (LL), dry period (DP), and postpartum (PP), to evaluate modifications in their metabolically-active rumen bacterial and protozoal communities using the RNA-based amplicon sequencing method. The bacterial community was dominated by seven phyla: Proteobacteria, Bacteroidetes, Firmicutes, Spirochaetes, Fibrobacteres, Verrucomicrobia, and Tenericutes. The relative abundance of the phylum Proteobacteria decreased from 47.60 to 28.15% from LL to DP and then increased to 33.24% in PP. An opposite pattern in LL, DP, and PP stages was observed for phyla Verrucomicrobia (from 0.96 to 4.30 to 1.69%), Elusimicrobia (from 0.32 to 2.84 to 0.25%), and SR1 (from 0.50 to 2.08 to 0.79%). The relative abundance of families Succinivibrionaceae and Prevotellaceae decreased in the DP, while Ruminococcaceae increased. Bacterial genera Prevotella and Treponema were least abundant in the DP as compared to LL and PP, while Ruminobacter and Succinimonas were most abundant in the DP. The rumen eukaryotic community was dominated by protozoal phylum Ciliophora, which showed a significant decrease in relative abundance from 97.6 to 93.9 to 92.6 in LL, DP, and PP, respectively. In conclusion, the physiological stage-dependent dietary changes resulted in a clear shift in metabolically-active rumen microbial communities.

SUBMITTER: Bailoni L

PROVIDER: S-EPMC8066057 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder.

Project description:Moringa oleifera (M. oleifera) is a remarkable species with high nutritional value and good biomass production, which can be used as livestock fodder. In this study, we examined changes in the faecal microbiota of thirty dairy cows in response to alternative M. oleifera diets and their effects on nutrient digestion, milk traits and the faecal concentrations of short-chain fatty acids. No differences in milk yield and constituents were found between the control and the M. oleifera alternative groups. Cows fed M. oleifera silage had lower dry matter digestibility, as well as the propionate and isovalerate concentrations in M. oleifera treated group. Using 16S rDNA gene sequencing, 1,299,556 paired-end reads were obtained. Clustering analysis revealed 13 phyla and 93 genera across all samples. Firmicutes and Bacteroidetes were the co-dominant phyla. Ten taxa displayed a significant difference in response to the high M. oleifera diet. In addition, strong correlations between Akkermansia and Prevotella with milk yield and protein indicated that some bacterial groups could be used to improve milk traits. Our results provided an insight into the microbiome-associated responses to M. oleifera in livestock diets, and could aid the development of novel applications of M. oleifera.

| S-EPMC5278366 | biostudies-literature

Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows.

Project description:BackgroundEnteric methane from rumen methanogens is responsible for 25.9 % of total methane emissions in the United States. Rumen methanogens also contribute to decreased animal feed efficiency. For methane mitigation strategies to be successful, it is important to establish which factors influence the rumen methanogen community and rumen volatile fatty acids (VFA). In the present study, we used next-generation sequencing to determine if dairy breed and/or days in milk (DIM) (high-fiber periparturient versus high-starch postpartum diets) affect the rumen environment and methanogen community of primiparous Holstein, Jersey, and Holstein-Jersey crossbreeds.ResultsWhen the 16S rRNA gene sequences were processed and assigned to operational taxonomic units (OTU), a core methanogen community was identified, consisting of Methanobrevibacter (Mbr.) smithii, Mbr. thaueri, Mbr. ruminantium, and Mbr. millerae. The 16S rRNA gene sequence reads clustered at 3 DIM, but not by breed. At 3 DIM, the mean % abundance of Mbr. thaueri was lower in Jerseys (26.9 %) and higher in Holsteins (30.7 %) and Holstein-Jersey crossbreeds (30.3 %) (P < 0.001). The molar concentrations of total VFA were higher at 3 DIM than at 93, 183, and 273 DIM, whereas the molar proportions of propionate were increased at 3 and 93 DIM, relative to 183 and 273 DIM. Rumen methanogen densities, distributions of the Mbr. species, and VFA molar proportions did not differ by breed.ConclusionsThe data from the present study suggest that a core methanogen community is present among dairy breeds, through out a lactation. Furthermore, the methanogen communities were more influenced by DIM and the breed by DIM interactions than breed differences.

| S-EPMC4855434 | biostudies-literature

Modulation of Plasma and Milk Sphingolipids in Dairy Cows Fed High-Starch Diets.

Project description:Bovine milk is a significant source of sphingolipids, dietary compounds that can exert anti-inflammatory actions, and which can modulate the host's microbiome. Because sphingolipid synthesis can be modified by diet, we hypothesized that dietary conditions which reduced FFA availability may result in reduced sphingolipid synthesis. Twelve ruminally cannulated cows (120 ± 52 DIM; 35.5 ± 8.9 kg of milk/d; mean ± SD) were randomly assigned to treatment in a crossover design with 21-d periods. Treatments were (1) High starch (HS), (2) Control. The HS diet contained 29% starch, 24% NDF, and 2.8% fatty acids (FA), whereas the Control diet contained 20% starch, 31% NDF, and 2.3% FA. Plasma and milk samples were obtained on d 21 of each period and sphingolipids were quantified using targeted metabolomics. Univariate and multivariate analyses of generalized log-transformed and Pareto-scaled data included ANOVA (fixed effects of treatment) and discriminant analysis. The lipidomics analysis detected 71 sphingolipids across plasma and milk fat, including sphinganines (n = 3), dihydro-ceramides (n = 8), ceramides (Cer; n = 15), sphingomyelins (SM; n = 17), and glycosylated ceramides (n = 28). Followed by Cer, SM were the most abundant sphingolipids detected in milk and plasma, with a preponderance of 16:0-, 23:0-, and 24:0-carbon sidechains. Although no effects of HS diets were observed on plasma sphingolipids, we detected consistent reductions in the concentrations of several milk Cer (e.g., 22:0- and 24:0-Cer) and SM (17:0- and 23:0-SM) in response to HS. Discriminant analysis revealed distinct metabolite separation of HS and Control groups, with several Cer and SM being distinctively predictive of dietary treatment. We conclude that HS diets can reduce the secretion of milk Cer and SM, even in the absence of changes in circulating sphingolipids.

| S-EPMC8540507 | biostudies-literature

Rumen-derived lipopolysaccharide provoked inflammatory injury in the liver of dairy cows fed a high-concentrate diet.

Project description:Rumen-derived lipopolysaccharide (LPS) is translocated from the rumen into the bloodstream when subacute ruminal acidosis (SARA) occurs following long-term feeding with a high-concentrate (HC) diet in dairy cows. The objective of this study was to investigate the mechanism of inflammatory responses in the liver caused by HC diet feeding. We found that SARA was induced in dairy cows when rumen pH below 5.6 lasted for at least 3 h/d with HC diet feeding. Also, the LPS levels in the portal and hepatic veins were increased significantly and hepatocytes were impaired as well as the liver function was inhibited during SARA condition. Meanwhile, the mRNA expression of immune genes including TNF receptor associated factor 6 (TRAF6), nuclear factor-kappa B (NF-κB), p38 mitogen-activated protein kinase (MAPK), extracellular regulated protein kinases (ERK) MAPK, Interleukin-1 (IL-1) and serum amyloid A (SAA) in the liver were significantly increased in SARA cows. Moreover, the phosphorylation level of NF-κB p65 and p38 MAPK proteins in the liver and the concentration of Tumor Necrosis Factor (TNF-α), Interleukin-1β (IL-1β) and Interleukin-6 (IL-6) in peripheral blood were obviously increased under SARA condition. In conclusion, the inflammatory injury in the liver caused by LPS that traveled from the digestive tract to the liver through the portal vein after feeding with a HC diet.

| S-EPMC5564522 | biostudies-other

Effects of Different Growth Stages of Amaranth Silage on the Rumen Degradation of Dairy Cows.

Project description:The purpose of this study was to investigate the rumen degradation characteristic of amaranth silage (Amaranthus hypochondriacus) including four kinds of growing stages (budding stage (BS), 50 d after planting (DAP); early flowering stage (ES), 58 DAP; peak flowering stage (PS), 70 DAP; heading stage (HS), 90 DAP). Four Holstein dairy cows with permanent ruminal cannulas were used as experimental animals. Nylon-bag method was used to assess the ruminal degradability of dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF). The results showed that the concentration of DM in HS was significantly higher than other stages (p < 0.05), whereas the contents of CP, were lower than in other stages (p < 0.05). With the extension of the growing period, the DM effective degradability of amaranth silage decreased gradually, and the difference was significant (p < 0.05). The ruminal CP degradation of 72 h was more than 80%, and compared with ES and HS, the degradation rate of BS and PS was significantly increased (p < 0.05). Compared to BS, the effective degradability of CP was increased (p < 0.05) in ES and HS. For ruminal NDF degradability, the effective degradability of HS was minimum, and it had a noticeable difference with BS and ES (p < 0.05). Thus, the different quality of amaranth growth stage including chemical contents and rumen degradation should be taken into consideration when making amaranth silage. In the present study, the optimal growth stage of amaranth was from the peak flowering stage to heading stage for ensiling.

| S-EPMC6826743 | biostudies-literature

Estimation of between-Cow Variability in Nutrient Digestion of Lactating Dairy Cows Fed Corn-Based Diets.

Project description:The objective of this study was to estimate cow variability that can be used to determine the optimal sample size for digestibility trials using lactating dairy cows. Experimental design was randomized complete block design having three blocks and three dietary treatments. Three similarly managed nearby intensive farms were considered as blocks, and three diets were formulated to have 0.7, 1.0, and 1.3 neutral detergent fiber (NDF): starch ratio. In each farm, 18 cows were assigned for each dietary treatment and five sample sizes per each treatment group were simulated by simple random sampling of data from 18, 15, 12, 9 and 6 cows respectively. Intake was not affected by diet or sample size (p > 0.05). Estimated cow variability (as standard deviation) for digestibility of dry matter, NDF and starch were 3.8 g/kg, 5.1 g/kg and 3.3 g/kg, respectively. A major implication of this study is that cow variability is greatest for NDF digestibility and the use of a minimum of 12 cows per dietary treatment is adequate to reliably detect treatment effects on the digestibility of NDF, starch and dry matter using cows fed in groups with randomized block design under these experimental conditions.

| S-EPMC7460325 | biostudies-literature

Altered rumen microbiome and correlations of the metabolome in heat-stressed dairy cows at different growth stages.

Project description:ImportanceHeat stress is one of the main causes of economic losses in the dairy industry worldwide; however, the mechanisms associated with the metabolic and microbial changes in heat stress remain unclear. Here, we characterized both the changes in metabolites, rumen microbial communities, and their functional potential indices derived from rumen fluid and serum samples from cows at different growth stages and under different climates. This study highlights that the rumen microbe may be involved in the regulation of lipid metabolism by modulating the fatty acyl metabolites. Under heat stress, the changes in the metabolic status of growing heifers, heifers, and lactating cows were closely related to arachidonic acid metabolism, fatty acid biosynthesis, and energy metabolism. Moreover, this study provides new markers for further research to understand the effects of heat stress on the physiological metabolism of Holstein cows and the time-dependent changes associated with growth stages.

| S-EPMC10714726 | biostudies-literature

CowNflow: A dataset on nitrogen flows and balances in dairy cows fed maize forage or herbage-based diets.

Project description:Diet and animal characteristics have a significant impact on the nitrogen (N)-use efficiency of dairy cows. A dataset (CowNflow) was built that compiles 28 N-balance experiments with Holstein dairy cows from 1983 to 2019, corresponding to 414 individual N flows, for a wide range of diets and animal characteristics. The dataset is composed of six Microsoft® Excel files that correspond to six levels of information. The main file, "CowNflow_6_Cow_measurements" reports individual weekly measurements of dry matter intake, daily faeces and urine excretion, milk production and composition, cow characteristics, and chemical composition of diets, faeces, urine, and milk. These raw data were used to calculate the N-balance, N-use efficiency, and nutrients' in vivo total-tract digestibility. The experiments, conducted under standardised conditions, had multiple aims and offered a wide range of diets. Consequently, each diet is classified according to the main forage offered, resulting in six diet types: (1) maize forage (maize silage or dehydrated maize) alone, (2) maize forage and dehydrated lucerne, (3) maize forage and grass hay, (4) maize forage and freshly cut herbage, (5) freshly cut herbage alone, and (6) dehydrated herbage. The other five Excel files provide supplementary information at larger scales and describe experiment characteristics, experimental treatments, offered feeds along with their chemical composition, ingredient composition of compound feeds, and cow characteristics. This dataset can be used to better understand animal and dietary determinants of N-use efficiency and the origin of N losses to the environment, to identify feeding strategies that reduce protein-rich concentrate use, and to decrease environmental impacts of dairy farming with a variety of foraging systems.

| S-EPMC8479390 | biostudies-literature

Enteric and Fecal Methane Emissions from Dairy Cows Fed Grass or Corn Silage Diets Supplemented with Rapeseed Oil.

Project description:This study evaluated potential trade-offs between enteric methane (CH4) emissions and CH4 emissions from feces of dairy cows fed grass silage or partial replacement of grass silage with corn silage, both with and without supplementation of rapeseed oil. Measured data for eight dairy cows (two blocks) included in a production trial were analyzed. Dietary treatments were grass silage (GS), GS supplemented with rapeseed oil (GS-RSO), GS plus corn silage (GSCS), and GSCS supplemented with rapeseed oil (GSCS-RSO). Feces samples were collected after each period and incubated for nine weeks to estimate fecal CH4 emissions. Including RSO (0.5 kg/d) in the diet decreased dry matter intake (DMI) by 1.75 kg/d. Enteric CH4 emissions were reduced by inclusion of RSO in the diet (on average 473 vs. 607 L/d). In 9-week incubations, there was a trend for lower CH4 emissions from feces of cows fed diets supplemented with RSO (on average 3.45 L/kg DM) than cows with diets not supplemented with RSO (3.84 L/kg DM). Total CH4 emissions (enteric + feces, L/d) were significantly lower for the cows fed diets supplemented with RSO. Total fecal CH4 emissions were similar between treatments, indicating no trade-offs between enteric and fecal CH4 emissions.

| S-EPMC8148109 | biostudies-literature

RNA sequencing reveals differential expression of genes associated with an altered morphology of rumen papillae in lactating dairy cows fed diets with various forage sources

Project description:Total RNA from rumen epithelial tissues of cows fed alfalfa hay (AL),Rice straw (RS) or Corn stover (CS)diet were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR.

2017-06-09 | GSE78197 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data