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Kim, Guan, Lee, Lee, Lee, Lee, Lee, and Lee: Effects of Flavonoid-rich Plant Extracts on In vitro Ruminal Methanogenesis, Microbial Populations and Fermentation Characteristics


The objective of this study was to evaluate the in vitro effects of flavonoid-rich plant extracts (PE) on ruminal fermentation characteristics and methane emission by studying their effectiveness for methanogenesis in the rumen. A fistulated Holstein cow was used as a donor of rumen fluid. The PE (Punica granatum, Betula schmidtii, Ginkgo biloba, Camellia japonica, and Cudrania tricuspidata) known to have high concentrations of flavonoid were added to an in vitro fermentation incubated with rumen fluid. Total gas production and microbial growth with all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05) than that of the control. The decrease in methane accumulation relative to the control was 47.6%, 39.6%, 46.7%, 47.9%, and 48.8% for Punica, Betula, Ginkgo, Camellia, and Cudrania treatments, respectively. Ciliate populations were reduced by more than 60% in flavonoid-rich PE treatments. The Fibrobacter succinogenes diversity in all added flavonoid-rich PE was shown to increase, while the Ruminoccocus albus and R. flavefaciens populations in all PE decreased as compared with the control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others. In conclusion, the results of this study showed that flavonoid-rich PE decreased ruminal methane emission without adversely affecting ruminal fermentation characteristics in vitro in 24 h incubation time, suggesting that the flavonoid-rich PE have potential possibility as bio-active regulator for ruminants.


Agricultural greenhouse gas emission, mainly methane from ruminants, has currently been recognized as an important issue worldwide as it is a driver for global warming and climate change. Methane eructated from ruminants is considered to be one of the most important contributors to global warming, imposing an environmental burden that cannot be ignored. Meanwhile, it represents a loss of 2% to 15% of the gross energy intake (Johnson and Johnson, 1995; Ellis et al., 2007). Animal nutritionists have been studying manipulation of the rumen microbial ecosystem to reduce methane emission without the adverse effects on rumen function. There is a need to identify feed additives to modify ruminal fermentation characteristics and increase the efficiency of feed utilization, thereby inhibiting the ruminal methanogenesis. In recent years, essential oils (Benchaar, 2007), plant secondary metabolites such as condensed tannins and saponins (Pen et al., 2006; Bhatta et al., 2009) and dietary lipids (Dohme et al., 2001) have arisen as attractive rumen modifiers to improve rumen microbial metabolism as well as inhibit methane production in ruminants. The positive effects of flavonoid-rich plant extracts (PE) on methane emission and methanogens population in vitro as well as in vivo have been examined (Patra et al., 2006; Bodas et al., 2008; Patra and Saxena, 2010; Oskoueian et al., 2013; Becker et al., 2014). In addition, flavonoid supplementation could improve ruminal fermentation of dairy cows with increasing milk yield (Theodorou et al., 1994), protecting ruminal acidosis (Balcells et al., 2012), reducing methane emission and changing microbial populations such as protozoa and methanogen (Baker, 1999).
The objective of this study was to evaluate the effect of flavonoid-rich PE on the growth of rumen microorganisms using quantitative real-time polymerase chain reaction (PCR) assay and in vitro rumen fermentation with respect to methane emissions.


Preparation of plant extracts

Plant extracts were obtained from Plant Extract Bank at the Korea Research Institute of Bioscience and Biotechnology (Daejeon, Korea). Plants were collected from fields in Korea (Table 1). Each plant was cut into small pieces and dried naturally under shade. The dried plant (100 g) were extracted with 99.9% methyl alcohol (1 L) using ultrasonic cleaner (Branson Ultrasonics corporation, Danbury, CT, USA) at room temperature for 3 days. After extraction, the solutions were filtered and the solvents were evaporated under vacuum. Stock solutions (20 mg/mL) of the extract were dissolved in dimethyl sulfoxide (Sigma-Aldrich Chemical Co., St. Louis, Mo, USA) and diluted using culture media immediately before experiments.

Ruminal inoculum and in vitro incubation

A fistulated Holstein cow was used as a donor of rumen fluid. Timothy and commercial concentrate in the ratio of 60:40 were fed at 2% of body weight twice a day (09:00 and 17:00). Water and mineral-vitamin block were allowed ad libitum. The rumen fluid was collected from the fistulated Holstein cow before morning feeding. Rumen liquor was filtered through four layers of cheesecloth before mixing with buffer and was maintained at 39°C. Fifteen mililiters of rumen fluid-buffer mixture, comprising McDougall buffer (McDougall, 1948) and rumen liquor in the ratio of 2 to 1, was dispensed anaerobically into 50 mL serum bottles containing 0.3 g of timothy substrate and PE (5% of substrate). The serum bottles were filled with O2-free N2 gas capped with a rubber stopper and held in a shaking incubator (Jeio Tech, SI-900R, Daejeon, Korea; 120× rpm) at 39°C for 72 h. The in vitro experiment was evaluated in triplicate run for data analysis using 90 serum bottles (6 treatments×5 incubation times×3 replication) with a completely randomized design.

Gas production measurement and analysis of gas profiles and ruminal fermentation

At the end of incubation, total gas production was measured according to the assay outlined by Theodorou et al. (1994). A detachable pressure transducer and a digital readout voltmeter (Laurel Electronics, Inc., Costa Mesa, CA, USA) were used to measure the headspace gas pressure of fermenting cultures. For the total gas production measurement, the transducer was modified in a way that it could be linked to the inlet of a disposable Luer-lock three-way stopcock (Theodorou et al., 1994). Gas pressure in the headspace was read from the display unit after insertion of the hypodermic syringe needle through the butyl rubber stopper above the culture medium. The headspace gas in the serum bottle was collected for analyzing methane and hydrogen by gas chromatography (Agilent Technologies HP 5890, Santa Clara, CA, USA) conducted using a TCD detector with a Column Carboxen 1006PLOT capillary column 30 m×0.53 mm (Supelco). The culture was subsampled for the analysis of pH (Mettler-Toledo, MP230, Greifensee, Switzerland), volatile fatty acid (VFA) concentration and genomic DNA extraction. The VFA analysis was performed with a HPLC (High Performance Liquid Chromatography, Agilent-1200, Waldbronn, Germany) equipped with column (300 mm×7.8 mm I.d. MetaCarb 87H, Varian, Palo Alto, CA, USA). In vitro DM disappearance rate was estimated by the modified method of nylon bag digestion process. Briefly, after incubation, the nylon bag with substrate was washed twice in a water-bath equipped with Heidolphs Rotamax 120 (Heidolph Instrument, Nuremberg, Germany) at 100×rpm for 30 min. Washed nylon bags were then dried to a constant weight at 60°C. Dry matter disappearance was determined by weight difference before and after incubation in the serum bottle.

Microbial growth rate

Incubated samples taken from each fermentation period were centrifuged at 3,000×rpm for 3 min to remove feed particles, and the supernatants were re-centrifuged at 14,000×rpm for 3 min to settle the pellets down. After that, sodium phosphate buffer (pH 6.5) was added to these precipitates and vortexed. Growth rates of total microbes were estimated as optical density (OD) values using spectrophotometer (Model 680, Bio-Rad Laboratories, Hercules, CA, USA) at 550 nm.

Quantitative polymerase chain reaction assays

DNA extraction

A high-speed reciprocal shaker which retains samples in screw-capped tubes containing silica beads was used for DNA extraction. Total nucleic acid was extracted from the incubated rumen samples by using the modified bead-beating protocol with the Soil kit (Macherey-nagel, Düren, Germany). Briefly 1.0 mL aliquot was taken from the incubated culture solution and was centrifuged at 3,000×rpm. Nucleic acid concentrations were measured by using a NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

PCR primers

The PCR primer sets (Table 2) used in this study for amplification of total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, methanogenic archaea, and ciliate protozoa were from the published reports (Koike and Kobayashi, 2001; Denman and McSweeney, 2005; Skillman et al., 2006; and Denman et al., 2007). All microbial data were analyzed for calculating relative expressions to total bacteria (Denman and McSweeney, 2006).

Quantitative Real-time PCR

Quantitative PCR assays for enumeration of microbes were performed according to the methods described by Denman and McSweeney (2006) and Denman et al. (2007) on a real-time PCR Machine (CFX96 Real-Time system, BIO RAD, Hercules, CA, USA) using the SYBR Green Supermix (QPK-201, Toyobo Co., LTD., Tokyo, Japan). The values of cycle threshold (Ct) after real-time PCR were used to determine fold change (number of fold difference) of different microbial population relative to control without additives. Abundance of these microbes was expressed by the equation: relative quantification = 2−ΔCt(Target)−ΔCt(Control), where Ct represents threshold cycle. All quantitative (q) PCR reaction mixtures (final volume of 20 μL) contained forward and reverse primers, the SYBR Green Supermix and DNA template. A negative control without the template DNA was used in every qPCR assay for each primer. The PCR amplification of the target DNA, included the annealing and the extension temperature, was conducted following the references in Table 2.

Total polyphenol and total flavonoid concentration

Total polyphenol concentration

Total polyphenol content in the PE was determined with Folin-Ciocalteu reagent using modified method by Velioglu et al. (1998) in a 96 well plate. Reaction mixture consisted of 10 μL of PE, 180 μL of Na2CO3 (2%), 10 μL of Folin-Ciocalteu reagent (1:1 with water) and 10 μL distilled water. Total polyphenolic content in PE was estimated as OD values using enzyme-linked immunosorbent assay (ELISA) reader (Spectra Max reader M5, Molecular Devices, Sunnyvale, CA, USA) at 750 nm after 30 min incubation (37°C). The standard calibration plot was generated at 750 nm using known concentration of gallic acid.

Total flavonoid concentration

The aluminum chloride method modified by Jia et al. (1999) was used for the determination of total flavonoid content of PE. Aliquots of PE solutions were taken and made up the volume 100 μL with methanol. Then, 7.5 μL of NaNO (5%), 15 μL of AlCl3 (10%), 100 μL of NaOH (1 M) and 25 μL of distilled water were added sequentially. Total flavonoid content in PE was estimated as OD values using ELISA reader (Spectra Max reader M5, Molecular Devices, Sunnyvale, CA, USA) at 510 nm after 30 min incubation. The standard calibration plot was generated at 510 nm using known concentration of catechin.

Statistical analysis

Data were analyzed using the general linear model procedure of the Statistical Analysis System Institute, Inc. (SAS Institute, 2002). The effects of PE on total gas production, gas profiles, pH, VFA, and microbial growth were compared to the controls and significant differences between treatment means were examined using Duncan’s multiple comparison tests. A p<0.05 was considered to indicate statistical significance.


In vitro ruminal fermentation characteristics

The concentration of total polyphenol and total flavonoid in PE used in this experiment is shown in Figure 1. In particular, the concentration of total flavonoid was higher in Pomegranate and Birch extracts compared with others. The in vitro ruminal fermentation profiles are shown in Table 3. pH did not significantly show a difference (p< 0.05) with the addition of all PE except at 72 h incubation time. Our study supports the previous studies that pH was not significant different in in vitro ruminal incubation with flavonoids such as flavone, myricetin, naringin, catechin, rutin, quercetin and kaempferol (Oskoueian et al., 2013) as well as flavonoid, tannin and essential oil (Bodas et al., 2008). The tVFA concentrations were decreased or increased by flavonoid-rich PE according to incubation times (6 h, 12 h, 24 h, 48 h, and 72 h) but were not affected significantly as compared to control. Although dry matter (DM) disappearance was not significantly different except with the addition of Cudrania tricuspidata at 24 h incubation and pomegranate at 72 h incubation (p<0.05), DM disappearance in added flavonoid-rich PE was lower than that of the control at 6 h, 12 h, and 24 h incubation. The effect of flavonoid-rich PE on gas production and gas profiles is shown in Table 4. In particular, total gas production in added all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05) than that of the control. This finding supports the finding that flavonoid-rich PE reduced methane emission by 4.7% to 14% after 24 h incubation (Bodas et al., 2008). The decreased methane emission may be due to the changes in ciliate protozoan community (Figure 3B).

The in vitro change in microbial diversity in the rumen

Rumen bacterial growth with the addition of flavonoid-rich PE is shown in Figure 3. Although flavonoids are widely known to possess antifungal, antiviral and antibacterial activities (Cushnie and Lamb, 2005), the result of microbial growth under supplement of all PE was higher than that in control for 72 h incubation (Figure 2), which may be the cause of total gas production increase. The ciliate protozoa community with the addition flavonoid-rich PE was decreased more than that of the control (Figure 3A). Patra et al. (2006) reported that extracts containing phenolics decreased the ruminal methane emission and protozoa count although they appeared not effective against ruminal methanogenesis. This study also showed that ciliate protozoan populations were reduced by more than 60% in flavonoid-rich PE treatments. Ciliate protozoa are an important key in methanogenesis in the rumen as methanogens attach to their surface. Flavonoid-rich PE reduced the ciliated-associated methanogens population and hence decreased the methane emission. Patra and Saxena (2010) reported that flavonoids gave direct effects against methanogens, and reduced protozoa related with ruminal methanogenesis. The Fibrobacter succinogenes diversity under all flavonoid-rich PE was shown to increase, while the Ruminococcus albus and Ruminococcus flavefaciens populations under all PE decreased as compared with control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others (Figure 3C, 3D, and 3E). R. albus, one of ruminal fibrolytic bacteria, is a very promising bacteria to produce hydrogen (H2) from energy forage, with the potential of utilizing the cellulosic and hemicellulosic biomass (Ntaikou et al., 2008). Latham and Wollin (1977) reported that succinic acid is produced by R. flavefaciens culture as a major fermentation product with acetic and formic acids, H2, and CO2. H2 is the critical concern to the microbial ecosystem in ruminants. H2 produced during enteric fermentation is the precursor of methane emission from ruminants and the regulation of H2 rather than methane is the key to control ruminant methane emission. The formation of propionate from succinate would result in a lower availability of H2 for the methanogenesis. The ruminal microbe population may show that PE with flavonoid influences ruminal methanogenesis in this study.
In conclusion, the results of this study indicate that flavonoid-rich PE appears to have a potential possibility as bio-active regulator for ruminants with decreasing ruminal methane emission. Future studies need to be aimed at finding a suitable effective dose of PE for inhibiting ruminal methanogenesis.


This research was supported by Bio-industry Technology Development Program, Ministry of Agriculture, Food and Rural Affairs, and Cooperative Research Program for Agriculture Science & Technology Development, Rural Development Administration, Republic of Korea. E. T. Kim was supported by Postdoctoral Fellowship Program of National Institute of Animal Science, Rural Development Administration, Republic of Korea.

Figure 1
Concentration of total polyphenol (A) and total flavonoid (B) in flavonoid-rich plant extracts used in the experiment (T1, Pomegranate; T2, Birch; T3, Ginkgo; T4, Camellia; T5, Cudrania tricuspidata).
Figure 2
Effects of flavonoid-rich included plant extracts on growth rate of ruminal microbes in fermentation after time-scheduled batch incubation (■: control ◆: Pomegranate, ▲: Birch, □: Ginkgo, ⋄: Camellia, Δ: Cudrania tricuspidata).
Figure 3
Relative quantification analysis of rumen microorganism populations in vitro ruminal fermentation by the addition of different plant extracts after 24 h incubation (T0, Control; T1, Pomegranate; T2, Birch; T3, Ginkgo; T4, Camellia; T5, Cudrania tricuspidata).
Table 1
Technical information regarding flavonoid-rich plant extracts used in the experimenta
Stock No. Botanical name Scientific name Family name Partb
034–052 Pomegranate Punica granatum Punicaceae L+S+F
015–042 Brich Betula schmidtii Betulaceae S
019–076 Ginkgo Ginkgo biloba Ginkgoaceae L
001–053 Camellia Camellia japonica Theaceae L
026–020 Tricuspid cudrania Cudrania tricuspidata Moraceae L

a Plant extracts were obtained from Plant Extract Bank (PEB) at Korea Research Institute of Bioscience and Biotechnology (Daejeon, Korea).

b L: Leaf, S: Stem, F: Flower.

Table 2
PCR primer sets for real-time PCR assay
Target species Primer sequence (5′→3′) References
Total bacteria F: CGG CAA CGA GCG CAA CCC
Denman and McSweeney (2006)
Fibrobacter succinogenes F: GTT CGG AAT TAC TGG GCG TAA A
Denman and McSweeney (2006)
Ruminococcus albus F: CCC TAA AAG CAG TCT TAG TTC G
Koike and Kobayashi (2001)
Ruminocuccus flavefaciens F: CGA ACG GAG ATA ATT TGA GTT TAC TTA GG
Denman and McSweeney (2006)
Methanogenic archaea F: TTC GGT GGA TCD CAR AGR GC
Denman et al. (2007)
Ciliate protozoa F: GAG CTA ATA CAT GCT AAG GC
Skillman et al. (2006)

PCR, polymerase chain reaction.

Table 3
Effects of flavonoid-rich plant extracts on ruminal fermentation characteristics during 72 h incubation
Treatments SEM p-value

Control Pomegranate Birch Ginkgo Camellia Cudrania tricuspidata
----------------------------------------------------------- pH ------------------------------------------------------
6 h 7.43a 7.31a 7.39a 7.45a 7.47a 7.52a 0.07 0.061
12 h 7.07a 7.06a 7.04a 7.08a 7.15a 7.15a 0.04 0.143
24 h 6.67 a 6.71 a 6.71 a 6.69 a 6.69 a 6.71 a 0.04 0.637
48 h 6.45 a 6.46 a 6.47 a 6.47 a 6.52 a 6.49 a 0.05 0.523
72 h 6.48b 6.47b 6.68a 6.65a 6.74a 6.66a 0.07 0.002
---------------------------------------------------- tVFA (mM) ---------------------------------------------------
6 h 30.96 a 37.02 a 30.66 a 32.46 a 30.90 a 28.74 a 4.73 0.424
12 h 37.99b 39.66ab 39.09b 40.05ab 38.27b 42.28a 1.45 0.037
24 h 64.08a 60.46a 59.93a 61.72a 62.49a 62.16a 1.87 0.168
48 h 78.21a 73.37abc 74.79ab 69.03bc 67.43c 70.87bc 3.77 0.041
72 h 75.80a 76.05a 64.92ab 66.36ab 57.51b 70.21a 6.49 0.033
--------------------------------------------------- DM degradability (%) ----------------------------------------
6 h 22.61a 22.17a 21.91a 22.10a 21.90a 20.58b 0.57 0.018
12 h 25.94 a 25.59 a 24.18 a 24.65 a 23.90 a 27.67 a 2.83 0.617
24 h 31.19a 30.67a 30.90a 29.85a 29.72a 28.50a 1.10 0.096
48 h 40.69 a 41.88 a 41.78 a 39.65 a 41.03 a 40.80 a 1.29 0.362
72 h 41.59b 46.17a 32.82c 41.78b 34.72c 43.04b 1.57 0.000

SEM: standard error of the mean; tVFA, total volatile fatty acids; DM, dry matter.

a–c Means in the same row with different superscripts differ significantly (p<0.05).

Table 4
Effects of flavonoid-rich included plant extracts on gas production and gas profiles during 72 h incubation
Treatments SEM p-value

Control Pomegranate Birch Ginkgo Camellia Cudrania tricuspidata
---------------------------------------------- Total gas (mL/g DM) ---------------------------------------
6 h 142.9ab 143.0ab 143.7a 144.0a 144.0a 142.0b 0.46 0.061
12 h 170.3b 179.1a 181.1a 179.2a 177.1a 175.5ab 2.02 0.033
24 h 218.9 a 221.0 a 220.3 a 220.4 a 220.4 a 219.5 a 2.33 0.989
48 h 258.5 b 272.2 a 237.8 c 277.9 a 245.1 c 275.5 a 3.97 <.0001
72 h 274.3b 294.9a 237.8c 278.1b 245.1c 276.8b 3.18 0.006
---------------------------------------------------- CH4 (mL/g DM) ------------------------------------------
6 h 1.70 a 1.63 a 2.09 a 1.57 a 1.60 a 1.47 a 0.26 0.610
12 h 6.24a 6.25a 5.46a 5.59a 5.63a 5.47a 0.45 0.632
24 h 15.87a 8.31b 9.59b 8.46b 8.27b 8.12b 1.35 0.010
48 h 29.90ab 22.81ab 16.99b 32.91a 22.61ab 35.70a 5.20 0.170
72 h 39.64ab 44.96a 30.16c 40.27ab 35.82bc 37.69abc 2.36 0.017
---------------------------------------------------- CO2 (mL/g DM) -----------------------------------------
6 h 19.73a 16.55ab 18.90ab 15.42ab 16.04ab 14.81b 1.72 0.384
12 h 44.08a 52.74a 48.39a 49.05a 49.75a 48.43a 3.37 0.643
24 h 77.47a 59.12a 74.65a 64.28a 67.89a 62.48a 9.23 0.705
48 h 102.1ab 109.0ab 74.99d 93.65bc 78.14cd 116.6a 5.41 0.001
72 h 104.4a 115.6a 103.9a 110.5a 107.81a 100.5a 6.30 0.613

SEM, standard error of the mean; DM, dry matter.

a–d Means in the same row with different superscripts differ significantly (p<0.05).


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