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Assembly of microbial genomes from metagenomic sequencing of the cow rumen. One strategy includes minimizing abrupt changes in the diet, which can make things to go awry quickly. Another strategy is to encourage cattle to snack eat to optimize rumen microbe populations. The science of nutrition is having a balanced diet and providing nutrients to the cow to keep rumen microbes from going bad. Does your nutrition program stack up?
Find out with a Proof Pays feeding trial. Bryant and R. Applied and Environmental Microbiology. New Zealand Journal of Agricultural Research. Vol 8, No. Bregendahl, J.
Coverdale and S. Animal Feeding and Nutrition. It was previously thought that — different species of bacteria existed in the rumen, but now using modern techniques based on 16S rRNA gene sequence analysis, over species are thought to exist in the rumen and over species in the human gastrointestinal tract [ 3 ]. Real-time polymerase chain reaction PCR has been successfully used to quantify the microbial population in the rumen [ 4 , 5 ].
The methanogenic archaea have aroused interest among ruminal microbiologists, who are trying to improve efficiency of the fermentation process and reduce the environmental impacts caused by enteric methane emissions. Methanobrevibacter species have been found in high densities in the rumen of buffalo fed three different diets [ 7 ], while buffalo fed wheat straw had more Methanomicrobium spp. Knowledge of the microbial community is critical to development of specific strategies to increase the efficiency of production of ruminant meat and milk with energy saving and reduction of methane production [ 9 ].
The objective of this study was to evaluate the concentration of bacteria, methanogenic archaea, and ciliated protozoa i. Seventeen buffalo Bubalus bubalis , 11 castrated males and six females, all Mediterranean breed, aged 23—26 months with live weight — kg, were fed two different diets.
Twelve animals six males and six females were maintained on Brachiaria brizantha for 12 months. All 12 animals were slaughtered approximately 12 h after fasting.
The concentrate ration was composed of the following ingredients: Samples, consisting of liquid and fine particles, from five different regions within the rumen and five different regions within the reticulum were collected from each animal immediately after slaughter and the samples were pooled by animal to form a single sample approximately mL from each of the two compartments of the stomach.
Samples were mixed and a 1 mL aliquot was placed in a test tube, using a wide-bore pipet. The samples were stained with two drops of Brilliant Green overnight. Counts were made using a counting grid, measuring 0. The ciliates were counted inside grids along the total chamber 50 grids in the front side and 50 grids in the reverse side. Ciliates belonging to the subfamily Diplodiniinae family Ophryoscolecidae e. Diplodinium , Eudiplodinium , Ostracodinium , Metadinium , Enoploplastron and Polyplastron were counted together.
For each microbial group bacteria, methanogenic archaea, and ciliate protozoa , extracted DNA from the rumen contents of water buffalo were analyzed in triplicate a using the real time PCR protocol [ 11 ]. The external standards for rumen protozoa real-time PCR were as described and validated by Sylvester et al.
The external standards for bacteria were described, validated and used a 6 log dilution series with the bacterial 16S rRNA gene primers F and R [ 13 ]. The external standards for methanogens were prepared using a mixture of pure cultures of Methanobrevibacter ruminantium M1 T and Methanobrevibacter smithii PS T , and ranged from 1. Real-time PCR for methanogens was achieved using the primer pairs, qmcrA-F and qmcrA-R, to specifically target the methyl-coenzyme M reductase subunit [ 14 ].
Fluorescence was acquired during extension using an excitation wavelength of nm, and emission detection at nm. Threshold cycles were calculated automatically by the Icycler software version 3. PCR efficiency for each extract was calculated from the logarithmic portion of the sigmoid shaped curve in real-time PCR reactions according to the methods described by Liu and Saint [ 15 ].
No significant differences were observed between males and females. There were significant differences in the ciliate community between two feeding systems within the same gastric chamber, except for Isotricha rumen or reticulum and Entodinium in the reticulum Table 1. The average values of different groups and of the total ciliates were higher in grazing buffalo than those in the feedlot on a concentrated diet.
There were significant interactions between location in the gastrointestinal tract rumen vs reticulum and types of diets grazing vs feedlot in the composition of ciliates Table 2. Grazing buffalo showed a higher proportion of ciliates belonging to the subfamily Diplodiniinae, both in the rumen and reticulum as compared to feedlot diet, except for the Isotricha.
Species of Isotricha and Dasytricha order Vestibuliferida; i. However, our findings confirmed the existence of high concentration and composition of protozoa ciliates belonging to subfamily Diplodiniinae compared to protozoa of the genus Entodinium in grazing buffalo [ 17 — 19 ].
However, this did not occur in the feedlot animals, indicating that feeding with soluble carbohydrate favors the growth of Entodinium.
Our current findings also showed that there is an indicative ecological niche of the vestibuliferids, Isotricha and Dasytricha , with a predominance in reticulum [ 20 ]. There is an important symbiotic association between methanogenic archaea and protozoa in the rumen [ 4 ]. Rumen protozoa are associated with high H 2 production which is utilized by the methanogens associated either on the outside of or inside the protozoa [ 21 , 22 ].
In the present study, methanogens appear to be associated with the vestibuliferid ciliates, Isotricha and Dasytricha , in the reticulum in grazing animals. The methanogenic community in the rumen is small in proportion to the total density of bacteria ranging from 0.
In the case of concentrate diet used in feedlot, there were no vestibuliferid ciliates, and no differences between the rumen and reticulum, but the percentage of methanogens in relation to total bacteria was much higher in the reticulum 4. The energy concentration and the dietary protein, as well as the carbohydrate and nitrogen sources have key roles in the concentration and composition of the microbiota in the rumen-reticulum [ 23 ].
Carbohydrate source cassava chip and rice bran did not affect rumen bacterial concentration in swamp buffalo, whereas cottonseed meal had a negative influence [ 24 ]. Also, replacing a rich diet of concentrate for an exclusive roughage diet increased cellulolytic bacteria in the swamp buffalo in diet with urea-treated rice straw with the highest concentration observed for Fibrobacter succinogenes [ 5 ].
Considering the great diversity of microorganisms in the rumen with wide variation between ruminant animals distributed in different geographical regions in the world, our data showed differences in the microbial community of the rumen and reticulum between grazing and feedlot feeding systems demonstrating relevant changes in the microorganism:host relationship existing on rumen-reticulum ecosystem. Van Soest P. Nutritional ecology of ruminant. Ithaca: Cornell University Press;
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