Use of community genome arrays (CGAs) to assess the effects of Acacia angustissima on rumen ecology

Altered rumen fermentation patterns in lactating dairy cows supplemented with phytochemicals improve milk production and efficiency

Tannins and other phytochemicals are known to improve RUP in the diet by binding protein and then limiting ruminal degradation, which may improve milk yield and milk protein synthesis. The objective of this study was to evaluate the effects of dietary phytochemicals (tannins and Capsicum species) as rumen modifiers on production parameters and milk efficiency in dairy cows. Twenty-four multiparous Holstein cows (96 ± 16 d in milk; mean ± standard deviation) were used in a replicated 3 × 3 Latin square design balanced to measure carryover effects. Cows were blocked according to days in milk, milk production, and body weight and randomly assigned to 1 of 3 groups (n = 8/group). Each group was assigned to a unique treatment sequence across the 3 periods in the Latin square. The experiment consisted of a 14-d covariate period and three 30-d treatment periods. Cows received a basal diet supplemented with soybean meal pellets (SB) as the control diet, phytochemicals (RUM; Rumiviv, CCPA, Janzé, France) pelleted with soybean meal, or expeller soybean meal (ESBM; SoyPlus, West Central Soy, Ralston, IA). Milk production and dry matter intake during the last 4 d of each period were used for statistical analysis. Blood and rumen fluid samples were collected on d 27 of each period. Rumen fluid was analyzed for ammonia N and volatile fatty acids as well as ruminal bacteria via quantitative PCR amplification of 16S ribosomal DNA genes. Greater milk yield (37.9 vs. 36 kg/d), energy-corrected milk (39.7 vs 37.1 kg/d), and protein yield (1.15 vs. 1.08 kg/d) were observed in RUM compared with SB, but these parameters were similar between RUM and ESBM. Concentrations of total volatile fatty acids (118.1 vs. 101.5 mM) were greater in RUM in comparison to SB and ESBM diets. Cows fed RUM had greater β-hydroxybutyrate (0.49 vs. 0.42 mmol/L) than SB and ESBM. Selenomonas ruminantium, Succinimonas amylolytica, and Streptococcus bovis in rumen fluid were lower in RUM fed cows in comparison to SB and ESBM. Increased total volatile fatty acids and lower ruminal abundance of bacteria associated with low feed efficiency in RUM cows can partially explain the improvements observed in milk yield and milk efficiency. Overall, these data suggest that feeding a combination of tannin mixture and Capsicum can significantly affect rumen fermentation characteristics via partial manipulation of rumen microbiota, and these effects were reflected in improved milk production and efficiency.

Effect of tree foliage supplementation of tropical grass diet on in vitro digestibility and fermentation, microbial biomass synthesis and enteric methane production in ruminants

The objective of this study was to evaluate the influence of tree foliage species supplemented in ruminant diets based on Pennisetum purpureum on the in vitro digestibility and fermentation, microbial biomass synthesis and enteric methane production. Seven experimental diets were evaluated, including a control treatment based on P. purpureum (PT) grass, and six additional treatments supplemented with 30.0% foliage from Neomillspaughia emargiata (NE), Tabernaemontana amygdalifolia (TA), Caesalpinia gaumeri (CG), Piscidia piscipula (PP), Leucaena leucocephala (LL) and Havardia albicans (HA). A randomised complete block design repeated in two periods (block) was used. The highest gas production (P < 0.05) was recorded in treatments TA and PT (237 and 228 mL g-1, respectively). The highest in vitro digestibility of dry matter (IVDMD) and organic matter (IVOMD) (P < 0.05) was recorded in the control treatment PT (57.9% and 66.1%, respectively). Treatments LL, NE, TA and PP promoted greater microbial biomass synthesis (290, 223, 220 and 213 mg g-1, respectively) (P < 0.05). The proportion of propionic acid also increased in these latter treatments and in treatments CG and HA (P < 0.05). Additionally, treatments LL, PP, NE and TA decreased methane production (25.8, 29.5, 30.6 and 31.8 L kg-1 of digested dry matter, respectively). In conclusion, supplementation with L. leucocephala, P. piscipula, N. emargiata and T. amygdalifolia in ruminant diets based on P. purpureum is one feed alternative that can promote greater efficiency and synthesis of microbial biomass, increase the proportions of propionic and butyric acid and decrease the production of enteric methane by 15.6 to 31.6%.

A modified method for genomic DNA extraction from the fish intestinal microflora

A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD₂₆₀/OD₂₈₀ ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.

Comparison of feed intake, digestion and rumen function among domestic ruminant species grazing in upland vegetation communities

This study aimed to compare feed intake, digestion, rumen fermentation parameters and bacterial community of 5 beef cows, 12 crossed ewes and 12 goats grazing together in spring-early summer on heather-gorse vegetation communities with an adjacent area of improved pasture. Organic matter intake (OMI) and digestibility (OMD) were estimated using alkane markers. Ruminal fluid samples were collected for measuring fermentation parameters, and studying the bacterial community using terminal restriction fragment length polymorphism (T-RFLP). Spot samples of urine were taken to determine purine derivative (PD) and creatinine concentrations to estimate microbial protein synthesis in the rumen. Herbaceous species were the main dietary component in all animal species. Cattle had higher (p < 0.05) daily OMI (g/kg LW^0.75 ) and OMD, whereas sheep and goats showed similar values. The highest ammonia concentration was observed in sheep. Total VFA, acetate and butyrate concentrations were not influenced by animal species, while propionate concentrations in goats were 1.8 times lower (p < 0.05) than in sheep. Acetate:propionate ratio was greater (p < 0.05) in goats, whereas cattle excreted more allantoin (p < 0.05). Estimated supply of microbial N was higher in cows (p < 0.01), whereas the efficiency of microbial protein synthesis was lower (p < 0.01) in this animal species. Hierarchical clustering analysis indicated a clear effect of animal species on rumen bacterial structure. Differences among animal species were also observed in the relative frequency of several T-RFs. Certain T-RFs compatible with Lachnospiraceae, Proteobacteria and Clostridiales species were not found in goats, while these animals showed high relative frequencies of some fragments compatible with the Ruminococcaceae family that were not detected in sheep and cattle. Results suggest a close relationship between animals' grazing behaviour and rumen bacterial structure and its function. Goats seem to show a greater specialization of their microbial populations to deal with the greater fibrous and tannin content of their diet.

Evaluation of DNA extraction methods of rumen microbial populations

The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extraction protocols (mechanical lysis or chemical lysis with CTAB, ethylxanthogenate or DNAzol(®)) from ruminal fluid. The suitability of two of these protocols (mechanical lysis and DNAzol(®)) was tested on single-strand conformation polymorphism (SSCP) of rDNA of rumen microbial populations. DNAzol(®) was a simple method that rendered good integrity, yield and purity. With this method, subtle changes in protozoan populations were detected in young bulls fed with slightly different formulations of a supplement of multinutritional blocks of molasses and urea. Sequences related to Eudiplodinium maggi and a non-cultured Entodiniomorphid similar to Entodinium caudatum, were related to major fluctuating populations in an SSCP assay.

Is polyethylene glycol innocuous to the rumen bacterial community? A preliminary in vitro study

Polyethylene glycol (PEG) is a polymer that is widely used in nutritional studies examining the effect of tannins on ruminal fermentation. There is no information however on its potential effect on the structure of the rumen bacterial community. Therefore, the aim herein was to investigate its effect on rumen bacterial profile, using an in vitro batch culture experiment with three substrates (alfalfa hay, maize grain, and a combination of both) to simulate three different rumen environments, treated with or without PEG. Rumen fluid was collected from four cannulated sheep and pooled to inoculate the cultures, which were run at 39°C for 22 h. At the end of the incubation, samples were immediately frozen for microbial DNA extraction. Terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that, although there was a high similarity in the fragments detected in the cultures with or without PEG, their relative abundances suggested that PEG might induce some changes in the bacterial community structure when a starch-rich substrate (e.g. maize) is assayed. Furthermore, the relative frequency of some abundant fragments, such as one compatible with bacteria of the phylum Bacteroidetes detected with the enzyme HhaI, and another that may match microorganisms of the genus Ruminococcus obtained with the enzyme MspI, was increased when PEG was added to maize-supplied microbial cultures. These results suggest that the use of PEG in batch cultures may not be as innocuous to rumen bacterial populations as previously described regarding ruminal fermentation, and might be relevant to studies using this polymer to examine the effect of tannins on rumen microbiota.

Bioaugmentation for electricity generation from corn stover biomass using microbial fuel cells

Corn stover is usually treated by an energy-intensive or expensive process to extract sugars for bioenergy production. However, it is possible to directly generate electricity from corn stover in microbial fuel cells (MFCs) through the addition of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to single-chamber, air-cathode MFCs acclimated for power production using glucose. The MFC produced a maximum power of 331 mW/m2 with the bioaugmented mixed culture and corn stover, compared to 510 mW/m2 using glucose. Denaturing gradient gel electrophoresis (DGGE) showed the communities continued to evolve on both the anode and corn stover biomass over 60 days, with several bacteria identified including Rhodopseudomonas palustris. The use of residual solids from the steam exploded corn stover produced 8% more power (406 mW/m2) than the raw corn stover. These results show that it is possible to directly generate electricity from waste corn stover in MFCs through bioaugmentation using naturally occurring bacteria.

Quantification by real-time PCR of cellulolytic bacteria in the rumen of sheep after supplementation of a forage diet with readily fermentable carbohydrates: effect of a yeast additive

AIM

To examine the effect of concentrate and yeast additive on the number of cellulolytic bacteria in the rumen of sheep.

METHODS AND RESULTS

Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens were quantified using real-time PCR (targeting 16S rDNA) in parallel to cellulolytic flora enumeration with cultural techniques. Whatever the conditions tested, R. flavefaciens was slightly more abundant than F. succinogenes, with both species outnumbering R. albus. Before feeding, the shift from hay to hay plus concentrate diet had no effect on rumen pH and on the number of the three specie; while after feeding, the concentrate-supplemented diet induced a decrease (-1 log) of the number of the three species concomitant with the rumen acidification. Overall, the presence of the live yeast resulted in a significant increase (two- to fourfold) of the Ruminococci.

CONCLUSION

The use of real-time PCR allowed us to show changes in the number of cellulolytic bacterial species in vivo in response to diet shift and additives that could not be as easily evidenced by classical microbial methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study contributes to the understanding of the negative impact of readily fermentable carbohydrates on rumen cellulolysis and the beneficial effect of yeast on rumen fermentation.

Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.