Factors that alter rumen microbial ecology

Study of rumen metagenome community using qPCR under different diets

The aim of this study was to detect the major bacteria present in rumen microbiota. Here, we performed qPCR based absolute quantitation of selected rumen microbes in rumen fluid of river buffalo adapted to varying proportion of concentrate to roughage diets. Animals were adapted to roughage-to-concentrate ratio in the proportion of 100:00 (T1), 75:25 (T2), 50:50 (T3) and 25:75 (T4) respectively for 30 days. At the end of each treatment, rumen fluid was collected at 0 h and 2 h after feeding. It was found that among fibrolytic bacteria Ruminococcus flavefaciens (2.22 × 10(8) copies/ml) were highest in T2 group and followed by 1.11 × 10(8) copies/ml for Fibrobacter succinogenes (T2), 2.56 × 10(7) copies/ml for Prevotella ruminicola (T1) and 1.25 × 10(7) copies/ml for Ruminococcus albus (T4). In non-fibrolytic bacteria, the Selenomonas ruminantium (2.62 × 10(7) copies/ml) was predominant in group T3 and followed by Treponema bryantii (2.52 × 10(7)copies/ml) in group T1, Ruminobacter amylophilus (1.31 × 10(7)copies/ml) in group T1 and Anaerovibrio lipolytica (2.58 × 10(6) copies/ml) in group T4. It is most notable that R. flavefaciens were the highest in population in the rumen of Surti buffalo fed wheat straw as roughage source.

Effects of wortmannin, sodium nitroprusside, insulin, genistein, and guanosine triphosphate on chemotaxis and cell growth of Entodinium caudatum, Epidinium caudatum, and mixed ruminal protozoa

The mechanisms by which ruminal protozoa sense and migrate toward nutrients are not fully understood. Chemotaxis by many diverse eukaryotic cells is mediated by phosphatidylinositol-3-kinase, which is highly conserved in receptor tyrosine kinase (RTK) signaling pathways and consistently inhibited by wortmannin. In experiment 1a, increasing the concentration of wortmannin inhibited cell growth nonlinearly at 24h of a culture of the rumen protozoan Entodinium caudatum, but high variability prevented growth inhibition of Epidinium caudatum from reaching significance. In experiment 1b, increasing the insulin concentration recovered 24-h cell counts for both cultures, depending on wortmannin concentration. In experiment 2, addition of sodium nitroprusside (Snp; activator of protein kinase G for cilial beat reversal in nonrumen ciliate models) at 500µM or wortmannin at 200µM in beakers containing rumen fluid decreased random swimming by mixed entodiniomorphids into capillary tubes (inserted into beakers) containing saline. Both Snp and wortmannin increased chemotaxis into tubes containing glucose compared with the beaker control. For isotrichids, beaker treatments had no response. Glucose increased chemotaxis, but peptides decreased chemotaxis even when combined with glucose. In experiment 3, we assessed preincubation of genistein (a purported RTK blocker in nonrumen ciliate models) at 40 or 400µM in beakers and guanosine triphosphate (GTP; a universal chemorepellent in nonrumen ciliate models, perhaps mediated through an RTK) at 10 or 100µM combined with glucose in capillary tubes. Neither genistein nor GTP affected chemotaxis toward glucose for entodiniomorphids. However, GTP at 100µM reduced chemotaxis toward glucose for isotrichids. After the animal is fed, isotrichids that are depleted in glycogen migrate to the dorsal area of the rumen, and the rapid uptake of sugars is enhanced through strong chemotaxis but can be reversed by peptides or GTP. In contrast, entodiniomorphids are less intensely chemoattracted to glucose than isotrichids but are chemoattracted to peptides. Entodiniomorphids' chemoattraction appears to be integrated with slower but prolonged availability of energy from digesting starch and fiber.

Effect of fumarate reducing bacteria on in vitro rumen fermentation, methane mitigation and microbial diversity

The metabolic pathways involved in hydrogen (H(2)) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH(4)) emissions by ruminants. H(2) as one of the major substrate for CH(4) production is therefore should be controlled. One of the strategies on reducing CH(4) is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH(4) production, diversity and quantity. M. jalaludinii significantly reduced CH(4) at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH(4) production and quantity, increases succinate and changes the rumen microbial diversity.

Forward modeling of fluctuating dietary 13C signals to validate 13C turnover models of milk and milk components from a diet-switch experiment

Isotopic variation of food stuffs propagates through trophic systems. But, this variation is dampened in each trophic step, due to buffering effects of metabolic and storage pools. Thus, understanding of isotopic variation in trophic systems requires knowledge of isotopic turnover. In animals, turnover is usually quantified in diet-switch experiments in controlled conditions. Such experiments usually involve changes in diet chemical composition, which may affect turnover. Furthermore, it is uncertain if diet-switch based turnover models are applicable under conditions with randomly fluctuating dietary input signals. Here, we investigate if turnover information derived from diet-switch experiments with dairy cows can predict the isotopic composition of metabolic products (milk, milk components and feces) under natural fluctuations of dietary isotope and chemical composition. First, a diet-switch from a C₃-grass/maize diet to a pure C₃-grass diet was used to quantify carbon turnover in whole milk, lactose, casein, milk fat and feces. Data were analyzed with a compartmental mixed effects model, which allowed for multiple pools and intra-population variability, and included a delay between feed ingestion and first tracer appearance in outputs. The delay for milk components and whole milk was ∼12 h, and that of feces ∼20 h. The half-life (t_½) for carbon in the feces was 9 h, while lactose, casein and milk fat had a t_½ of 10, 18 and 19 h. The ¹³C kinetics of whole milk revealed two pools, a fast pool with a t_½ of 10 h (likely representing lactose), and a slower pool with a t_½ of 21 h (likely including casein and milk fat). The diet-switch based turnover information provided a precise prediction (RMSE ∼0.2 ‰) of the natural ¹³C fluctuations in outputs during a 30 days-long period when cows ingested a pure C3 grass with naturally fluctuating isotope composition.

Urea-N recycling in lactating dairy cows fed diets with 2 different levels of dietary crude protein and starch with or without monensin

Rumensin (monensin; Elanco Animal Health, Greenfield, IN) has been shown to reduce ammonia production and microbial populations in vitro; thus, it would be assumed to reduce ruminal ammonia production and subsequent urea production and consequently affect urea recycling. The objective of this experiment was to determine the effects of 2 levels of dietary crude protein (CP) and 2 levels of starch, with and without Rumensin on urea-N recycling in lactating dairy cattle. Twelve lactating Holstein dairy cows (107 ± 21 d in milk, 647 kg ± 37 kg of body weight) were fed diets characterized as having high (16.7%) or low (15.3%) CP with or without Rumensin, while dietary starch levels (23 vs. 29%) were varied between 2 feeding periods with at least 7d of adaptation between measurements. Cows assigned to high or low protein and to Rumensin or no Rumensin remained on those treatments to avoid carryover effects. The diets consisted of approximately 40% corn silage, 20% alfalfa hay, and 40% concentrate mix specific to the treatment diets, with 0.5 kg of wheat straw added to the high starch diets to enhance effective fiber intake. The diets were formulated using Cornell Net Carbohydrate and Protein System (version 6.1), and the low-protein diets were formulated to be deficient for rumen ammonia to create conditions that should enhance the demand for urea recycling. The high-protein diets were formulated to be positive for both rumen ammonia and metabolizable protein. Rumen fluid, urine, feces, and milk samples were collected before and after a 72-h continuous jugular infusion of (15)N(15)N-urea. Total urine and feces were collected during the urea infusions for N balance measurements. Milk yield and dry matter intake were improved in cows fed the higher level of dietary CP and by Rumensin. Ruminal ammonia and milk and plasma urea nitrogen concentrations corresponded to dietary CP concentration. As has been shown in vitro, Rumensin reduced rumen ammonia concentration by approximately 23% but did not affect urea entry rate or gastrointestinal entry rate. Urea entry rate averaged approximately 57% of total N intake for cattle with and without Rumensin, and gastrointestinal rate was similar at 43 and 42% of N intake for cattle fed and not fed Rumensin, respectively. The cattle fed the high-protein diet had a 25% increase in urea entry rate and no effect of starch level was observed for any recycling parameters. Contrary to our hypothesis, Rumensin did not alter urea production and recycling.

Isolation and characterization of a novel endoglucanase from a Bursaphelenchus xylophilus metagenomic library

A novel gene (designated as cen219) encoding endoglucanase was isolated from a Bursaphelenchus xylophilus metagenomic library by functional screening. Sequence analysis revealed that cen219 encoded a protein of 367 amino acids. SDS-PAGE analysis of purified endoglucanase suggested that Cen219 was a monomeric enzyme with a molecular mass of 40 kDa. The optimum temperature and pH for endoglucanase activity of Cen219 was separately 50°C and 6.0. It was stable from 30 to 50°C, and from pH 4.0 to 7.0. The activity was significantly enhanced by Mn²⁺ and dramatically reduced by detergent SDS and metals Fe³⁺, Cu²⁺ or Hg²⁺. The enzyme hydrolyzed a wide range of β-1, 3-, and β-1, 4-linked polysaccharides, with varying activities. Activities towards microcrystalline cellulose and filter paper were relatively high, while the highest activity was towards oat gum. The K_m and V_max of Cen219 towards CMC was 17.37 mg/ml and 333.33 U/mg, respectively. The findings have an insight into understanding the molecular basis of host–parasite interactions in B. xylophilus species. The properties also make Cen219 an interesting enzyme for biotechnological application.

Effects of grain, fructose, and histidine feeding on endotoxin and oxidative stress measures in dairy heifers

Ruminal endotoxin and plasma oxidative stress biomarker concentrations were studied in dairy heifers challenged with grain, fructose, and histidine in a partial factorial study. Holstein-Friesian heifers [n=30; average body weight (BW) of 359.3±47.3 kg] were randomly allocated to 5 treatment groups: (1) control (no grain); (2) grain [crushed triticale at 1.2% of BW dry matter intake (DMI)]; (3) grain (0.8% of BW DMI) + fructose (0.4% of BW DMI); (4) grain (1.2% of BW DMI) + histidine (6g/head); and (5) grain (0.8% of BW DMI) + fructose (0.4% of BW DMI) + histidine (6 g/head). Rumen samples were collected by stomach tube 5, 65, 115, 165, and 215 min after diet consumption and blood samples at 5 and 215 min after consumption. Rumen fluid was analyzed for endotoxin concentrations. Plasma was analyzed for concentrations of the following oxidative stress biomarkers: reactive oxygen metabolites (dROM), biological antioxidant potential (BAP), advanced oxidation protein products, and ceruloplasmin, and activity of glutathione peroxidase. Dietary treatment had no effect on concentrations of endotoxin or oxidative stress biomarkers. We observed no interactions of treatment by time. Ruminal concentrations of endotoxin decreased during the sampling period from 1.12×10(5) ± 0.06 to 0.92×10(5) endotoxin units/mL ± 0.05 (5 and 215 min after diet consumption, respectively). Concentrations of dROM and the oxidative stress index (dROM/BAP × 100) increased over the sampling period, from 108.7 to 123.5 Carratelli units (Carr U), and from 4.1 to 4.8, respectively. Ceruloplasmin concentrations markedly declined 5 min after the consumption of diets, from 190 to 90 mg/L over the 215-min sampling period. Overall, a single feeding challenge for dairy cattle with grain, fructose, and histidine, and combinations thereof, may not be sufficient to induce marked changes in endotoxin or oxidative stress biomarker concentrations.

Agricultural subsidies and the American obesity epidemic

Government-issued agricultural subsidies are worsening obesity trends in America. Current agricultural policy remains largely uninformed by public health discourse. Although findings suggest that eliminating all subsidies would have a mild impact on the prevalence of obesity, a revision of commodity programs could have a measurable public health impact on a population scale, over time. Policy reforms will be important determinants of the future of obesity in America, primarily through indemnity program revisions, and the allocation of increasing amounts of resources to sustainable agriculture. Public health intervention will be required at the policy level to promote healthy behavioral changes in consumers. The 2013 Farm Bill will be the key mechanism to induce such policy change in the near future.

Univariate and multivariate molecular spectral analyses of lipid related molecular structural components in relation to nutrient profile in feed and food mixtures

The objectives of this study were (i) to determine lipid related molecular structures components (functional groups) in feed combination of cereal grain (barley, Hordeum vulgare) and wheat (Triticum aestivum) based dried distillers grain solubles (wheat DDGSs) from bioethanol processing at five different combination ratios using univariate and multivariate molecular spectral analyses with infrared Fourier transform molecular spectroscopy, and (ii) to correlate lipid-related molecular-functional structure spectral profile to nutrient profiles. The spectral intensity of (i) CH(3) asymmetric, CH(2) asymmetric, CH(3) symmetric and CH(2) symmetric groups, (ii) unsaturation (CC) group, and (iii) carbonyl ester (CO) group were determined. Spectral differences of functional groups were detected by hierarchical cluster analysis (HCA) and principal components analysis (PCA). The results showed that the combination treatments significantly inflicted modifications (P<0.05) in nutrient profile and lipid related molecular spectral intensity (CH(2) asymmetric stretching peak height, CH(2) symmetric stretching peak height, ratio of CH(2) to CH(3) symmetric stretching peak intensity, and carbonyl peak area). Ratio of CH(2) to CH(3) symmetric stretching peak intensity, and carbonyl peak significantly correlated with nutrient profiles. Both PCA and HCA differentiated lipid-related spectrum. In conclusion, the changes of lipid molecular structure spectral profiles through feed combination could be detected using molecular spectroscopy. These changes were associated with nutrient profiles and functionality.

Altered protozoan and bacterial communities and survival of Escherichia coli O157:H7 in monensin-treated wastewater from a dairy lagoon

Surviving predation is a fitness trait of Escherichia coli O157:H7 (EcO157) that provides ample time for the pathogen to be transported from reservoirs (e.g. dairies and feedlots) to farm produce grown in proximity. Ionophore dietary supplements that inhibit rumen protozoa may provide such a selective advantage for EcO157 to proliferate in lagoons as the pathogen is released along with the undigested supplement as manure washings. This study evaluated the fate of an outbreak strain of EcO157, protozoan and bacterial communities in wastewater treated with monensin. Although total protozoa and native bacteria were unaffected by monensin, the time for 90% decrease in EcO157 increased from 0.8 to 5.1 days. 18S and 16S rRNA gene sequencing of wastewater samples revealed that monensin eliminated almost all colpodean and oligohymenophorean ciliates, probably facilitating the extended survival of EcO157. Total protozoan numbers remained high in treated wastewater as monensin enriched 94% of protozoan sequences undetected with untreated wastewater. Monensin stimulated 30-fold increases in Cyrtohymena citrina, a spirotrichean ciliate, and also biflagellate bicosoecids and cercozoans. Sequences of gram-negative Proteobacteria increased from 1% to 46% with monensin, but gram-positive Firmicutes decreased from 93% to 46%. It is noteworthy that EcO157 numbers increased significantly (P<0.01) in Sonneborn medium containing monensin, probably due to monensin-inhibited growth of Vorticella microstoma (P<0.05), a ciliate isolated from wastewater. We conclude that dietary monensin inhibits ciliate protozoa that feed on EcO157. Feed supplements or other methods that enrich these protozoa in cattle manure could be a novel strategy to control the environmental dissemination of EcO157 from dairies to produce production environments.

Successional colonization of perennial ryegrass by rumen bacteria

This study investigated successional colonization of perennial ryegrass (PRG) by the rumen microbiota. PRG grown for 6 weeks in a greenhouse was incubated in sacco in the rumens of three Holstein × Freisian cows over a period of 24 h. PRG incubated within the rumen was subsequently harvested at various time intervals postincubation to assess colonization over time. DGGE-based dendograms revealed the presence of distinct primary (0-2 h) and secondary (4 h onwards) attached bacterial communities. Moving window analysis, band number and Shannon-Wiener diversity indices suggest that after 2 h a proportion of primary colonizing bacteria detach, to be replaced with a population of secondary colonizing bacteria between 2 and 4 h after entry of PRG into the rumen. Sequencing and classification of bands lost and gained between 2 and 4 h showed that the genus Prevotella spp. was potentially more prevalent following 4 h of incubation, and Prevotella spp. 16S rDNA-based QPCR supported this finding somewhat, as 2- to 4-h Prevotella QPCR data were greater but not significantly so. Low-temperature scanning electron microscopy showed that attached bacteria were predominantly enveloped in extracellular polymeric substances. In conclusion, colonization of fresh PRG is biphasic with primary colonization completed within 2 h and secondary colonization commencing after 4 h of attachment in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

We investigated, over a 24-h period in sacco, whether attachment of rumen microbiota to perennial ryegrass (PRG) showed successional changes in diversity. Knowledge of the bacterial species that attach to PRG over time may aid our understanding of the temporal function of the attached microbiota and ultimately permit the development of novel strategies for improving animal production to meet the future demands for meat and milk.

Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius)

Rumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool. Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.

Responses of anaerobic rumen fungal diversity (phylum Neocallimastigomycota) to changes in bovine diet

AIMS

Anaerobic rumen fungi (Neocallimastigales) play important roles in the breakdown of complex, cellulose-rich material. Subsequent decomposition products are utilized by other microbes, including methanogens. The aim of this study was to determine the effects of dietary changes on anaerobic rumen fungi diversity.

METHODS AND RESULTS

Altered diets through increasing concentrate/forage (50 : 50 vs 90 : 10) ratios and/or the addition of 6% soya oil were offered to steers and the Neocallimastigales community was assessed by PCR-based fingerprinting with specific primers within the barcode region. Both a decrease in fibre content and the addition of 6% soya oil affected Neocallimastigales diversity within solid and liquid rumen phases. The addition of 6% soya oil decreased species richness. Assemblages were strongly affected by the addition of 6% soya oil, whereas unexpectedly, the fibre decrease had less effect. Differences in volatile fatty acid contents (acetate, propionate and butyrate) were significantly associated with changes in Neocallimastigales assemblages between the treatments.

CONCLUSIONS

Diet clearly influences Neocallimastigales assemblages. The data are interpreted in terms of interactions with other microbial groups involved in fermentation processes within the rumen.

SIGNIFICANCE AND IMPACT OF THE STUDY

Knowledge on the influence of diet on anaerobic fungi is necessary to understand changes in microbial processes occurring within the rumen as this may impact on other rumen processes such as methane production.

The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows

Background

Sub-acute ruminal acidosis (SARA) is a well-recognized digestive disorder found in particular in well-managed dairy herds. SARA can result in increased flow of fermentable substrates to the hindgut, which can increase the production of volatile fatty acids, alter the structure of the microbial community, and have a negative effect on animal health and productivity. However, little is known about changes in the structure of the microbial community and its relationship with fatty acids during SARA. Four cannulated primiparous (60 to 90 day in milk) Holstein dairy cows were assigned to two diets in a 2 × 2 crossover experimental design. The diets contained (on a dry matter basis): 40% (control diet, COD) and 70% (SARA induction diet, SAID) concentrate feeds. Samples of ruminal fluid and feces were collected on day 12, 15, 17 and 21 of the treatment period, and the pH was measured in the ruminal and fecal samples; the fecal microbiota was determined by pyrosequencing analysis of the V1–V3 region of amplified 16S ribosomal RNA (16S rRNA).

Results

SAID decreased ruminal and fecal pH and increased the propionate, butyrate and total volatile fatty acid (TVFA) concentration in feces when compared with the COD. A barcoded DNA pyrosequencing method was used to generate 2116 16S operational taxonomic units (OTUs). A total of 11 phyla were observed, distributed amongst all cattle on both diets; however, only 5 phyla were observed in all animals regardless of dietary treatment, and considerable animal to animal variation was revealed. The average abundance and its range of the 5 phyla were as follows: Firmicutes (63.7%, 29.1–84.1%), Proteobacteria (18.3%, 3.4–46.9%), Actinobacteria (6.8%, 0.4–39.9%), Bacteroidetes (7.6%, 2.2–17.7%) and Tenericutes (1.6%, 0.3–3%). Feeding the SAID resulted in significant shifts in the structure of the fecal microbial community when compared with the traditional COD. Among the 2116 OTUs detected in the present study, 88 OTUs were affected significantly by diet; and the proportion of these OTUs was 20.6% and 17.4% among the total number of sequences, respectively. Among the OTUs affected, the predominant species, including OTU2140 (G: Turicibacter), OTU1695 (G: Stenotrophomonas) and OTU8143 (F: Lachnospiraceae), were increased, while the abundance of OTU1266 (S: Solibacillus silvestris) and OTU2022 (G: Lysinibacillus) was reduced in the SAID group compared with the COD. Further, our results indicated that the fecal volatile fatty acid (VFA) concentrations were significantly related to presence of some certain species of Bacteroidetes and Firmicutes in the feces.

Conclusions

This is, to our knowledge, the first study that has used barcoded DNA pyrosequencing to survey the fecal microbiome of dairy cattle during SARA. Our results suggest that particular bacteria and their metabolites in the feces appear to contribute to differences in host health between those given SAID and traditional COD feeding. A better understanding of these microbial populations will allow for improved nutrient management and increased animal growth performance.

Impacts of human lysozyme transgene on the microflora of pig feces and the surrounding soil

The rapid development of genetic engineering and extensive applications of genetically engineered (GE) animals have provided many research benefits, but concerns have been raised over the potential environmental impact of transgenic animals. We investigated the effects of human lysozyme (hLZ) transgenic pigs which can express hLZ in their mammary glands on the surrounding environment from the angle of the changes of pig feces and the surrounding soil, including the probability of horizontal gene transfer (HGT), the impact on microbial communities in pig gastrointestinal (GI) tracts and soil, and the influence on the total nitrogen (TN) and total phosphorus (TP) content of pig excrement and surrounding soil. Results showed that hLZ gene was not detected by polymerase chain reaction (PCR) or quantitative real-time PCR (Q-PCR) in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis and 16S rDNA sequence analysis showed that hLZ gene had no impact on the microflora structure of pig guts or soil. Finally, TN and TP contents were not significantly different in pig manure or soils taken at different distances from the pig site (P>0.25).

Effects of the oral administration of viable and heat-killed Streptococcus bovis HC5 cells to pre-sensitized BALB/c mice

Antimicrobial peptides have been suggested as an alternative to classical antibiotics in livestock production and bacteriocin-producing bacteria could be added to animal feeds to deliver bacteriocins in the gastrointestinal (GI) tract of ruminant and monogastric animals. In this study, viable (V) and heat-killed (HK) Streptococcus bovis HC5 cells were orally administered to pre-sensitized mice in order to assess the effects of a bacteriocin-producing bacteria on histological parameters and the immune response of the GI tract of monogastric animals. The administration of V and HK S. bovis HC5 cells during 58 days to BALB/c mice did not affect weight gain, but an increase in gut permeability was detected in animals receiving the HK cells. Viable and heat killed cells caused similar morphological alterations in the GI tract of the animals, but the most prominent effects were detected in the small intestine. The oral administration of S. bovis HC5 also influenced cytokine production in the small intestine, and the immune-mediated activity differed between V and HK cells. The relative expression of IL-12 and INF-γ was significantly higher in the small intestine of mice treated with V cells, while an increase in IL-5, IL-13 and TNF-α expression was only detected in mice treated with HK cells. Considering that even under a condition of severe challenge (pre-sensitization followed by daily exposure to the same bacterial immunogen) the general health of the animals was maintained, it appears that oral administration of S. bovis HC5 cells could be a useful route to deliver bacteriocin in the GI tract of livestock animals.

Cloning and identification of novel hydrolase genes from a dairy cow rumen metagenomic library and characterization of a cellulase gene

BACKGROUND

Interest in cellulose degrading enzymes has increased in recent years due to the expansion of the ellulosic biofuel industry. The rumen is a highly adapted environment for the degradation of cellulose and a promising source of enzymes for industrial use. To identify cellulase enzymes that may be of such use we have undertaken a functional metagenomic screen to identify cellulase enzymes from the bacterial community in the rumen of a grass-hay fed dairy cow.

RESULTS

Twenty five clones specifying cellulose activity were identified. Subcloning and sequence analysis of a subset of these hydrolase-positive clones identified 10 endoglucanase genes. Preliminary characterization of the encoded cellulases was carried out using crude extracts of each of the subclones. Zymogram analysis using carboxymethylcellulose as a substrate showed a single positive band for each subclone, confirming that only one functional cellulase gene was present in each. One cellulase gene, designated Cel14b22, was expressed at a high level in Escherichia coli and purified for further characterization. The purified recombinant enzyme showed optimal activity at pH 6.0 and 50°C. It was stable over a broad pH range, from pH 4.0 to 10.0. The activity was significantly enhanced by Mn2+ and dramatically reduced by Fe3+ or Cu2+. The enzyme hydrolyzed a wide range of beta-1,3-, and beta-1,4-linked polysaccharides, with varying activities. Activities toward microcrystalline cellulose and filter paper were relatively high, while the highest activity was toward Oat Gum.

CONCLUSION

The present study shows that a functional metagenomic approach can be used to isolate previously uncharacterized cellulases from the rumen environment.

Rumination and its relationship to feeding and lying behavior in Holstein dairy cows

The objective of this study was to describe the relationship between rumination and feeding and lying behavior in dairy cows. Rumination time was monitored electronically using HR-Tags (SCR Engineers Ltd., Netanya, Israel). Feeding time and dry matter intake (DMI) were monitored using Insentec feed bins (Insentec BV, Marknesse, the Netherlands). All measures were collected in 2-h periods for 42 mature Holstein cows for a minimum of 9 d in the early dry period. Pearson correlation was used to describe associations, among 2-h periods within cow, first examining the relationship within a single period, and then modeling how this relationship changes when a lag of 2, 4, or 6h was imposed. Periods when cows spent more time ruminating were associated with lower feeding times and lower DMI (r = -0.71 and r = -0.72, respectively), likely because cows were unable to feed and ruminate simultaneously. The correlations with rumination time changed from negative to positive when lags of 2, 4, and 6h were modeled (r = -0.09, 0.24, and 0.15, and r = -0.16, 0.23, and 0.17 for feeding time and DMI at lags of 2, 4, and 6h, respectively). These results indicate that following periods of high feeding times and intakes, cows spent more time ruminating. This relationship peaks at approximately 4h after feeding. Periods of rumination were also associated with time spent lying down. Cows that spent more time ruminating per day, spent less time feeding (r = -0.34) and rumination times did not relate to DMI (r = 0.11). These data indicate that rumination time can be used to estimate within-cow variation in feeding behavior and intake, but daily summaries of rumination behavior are a poor indicator of DMI.

Effects of dietary potential Acid production value on productivity in dairy cows

This study was conducted to estimate the potential acid production value (PAPV) of major diets and to determine the relationship between dietary PAPV and dairy production traits. Estimation of PAPV of major cattle feeds was based on an in vitro technique, which determined the degree of Ca dissociation from CaCO₃. Data on feeds and production traits were collected on 744 multiparous lactating Holstein dairy cows from five different farms. Grains had high PAPV with variable protein sources and by-products. High PAPV feedstuffs had a higher total gas production and lower pH compared to those with low PAPV. Dietary PAPV had a positive correlation with intake of dry matter, NDF, ADF, milk yield and milk solid production but a negative correlation with milk protein and milk fat concentration. Current results indicate that dietary PAPV can be utilized in predicting dairy production traits.

Similarity of the ruminal bacteria across individual lactating cows

Dairy cattle hold enormous significance for man as a source of milk and meat. Their remarkable ability to convert indigestible plant mass into these digestible food products resides in the rumen - an anaerobic chambered compartment - in the bovine digestive system. The rumen houses a complex microbiota which is responsible for the degradation of plant material, consequently enabling the conversion of plant fibers into milk and meat and determining their quality and quantity. Hence, an understanding of this complex ecosystem has major economic implications. One important question that is yet to be addressed is the degree of conservation of rumen microbial composition across individual animals. Here we quantified the degree of similarity between rumen bacterial populations of 16 individual cows. We used real-time PCR to determine the variance of specific ruminal bacterial species with different metabolic functions, revealing that while some bacterial strains vary greatly across animals, others show only very low variability. This variance could not be linked to the metabolic traits of these bacteria. We examined the degree of similarity in the dominant bacterial populations across all animals using automated ribosomal intergenic spacer analysis (ARISA), and identified a bacterial community consisting of 32% operational taxonomic units (OTUs) shared by at least 90% of the animals and 19% OTUs shared by 100% of the animals. Looking only at the presence or absence of each OTU gave an average similarity of 75% between each cow pair. When abundance of each OTU was added to the analysis, this similarity decreased to an average of less than 60%. Thus, as suggested in similar recent studies of the human gut, a bovine rumen core microbiome does exist, but taxa abundance may vary greatly across animals.

Gut microbiome of the critically endangered New Zealand parrot, the kakapo (Strigops habroptilus)

The kakapo, a parrot endemic to New Zealand, is currently the focus of intense research and conservation efforts with the aim of boosting its population above the current ‘critically endangered’ status. While virtually nothing is known about the microbiology of the kakapo, given the acknowledged importance of gut-associated microbes in vertebrate nutrition and pathogen defense, it should be of great conservation value to analyze the microbes associated with kakapo. Here we describe the first study of the bacterial communities that reside within the gastrointestinal tract (GIT) of both juvenile and adult kakapo. Samples from along the GIT, taken from the choana (≈throat), crop and faeces, were subjected to 16 S rRNA gene library analysis. Phylogenetic analysis of >1000 16 S rRNA gene clones, derived from six birds, revealed low phylum-level diversity, consisting almost exclusively of Firmicutes (including lactic acid bacteria) and Gammaproteobacteria. The relative proportions of Firmicutes and Gammaproteobacteria were highly consistent among individual juveniles, irrespective of sampling location, but differed markedly among adult birds. Diversity at a finer phylogenetic resolution (i.e. operational taxonomic units (OTUs) of 99% sequence identity) was also low in all samples, with only one or two OTUs dominating each sample. These data represent the first analysis of the bacterial communities associated with the kakapo GIT, providing a baseline for further microbiological study, and facilitating conservation efforts for this unique bird.

Effects of adding food by-products mainly including noodle waste to total mixed ration silage on fermentation quality, feed intake, digestibility, nitrogen utilization and ruminal fermentation in wethers

Four wethers were used in a 4 × 4 Latin square design experiment to evaluate the applicability of two types of total mixed ration (TMR) silage with food by-products. Four food by-products (i.e., potato waste, soy sauce cake, soybean curd residue and noodle waste) were obtained and mixed with commercial concentrate (CC) as TMR silage. The two types of TMR silage, T1 and T2, each contained CC, in addition to all by-products for T1 (TRE1), and soy sauce cake and noodle waste for T2 (TRE2) on a dry matter (DM) basis. The silage was well-fermented with low pH values and high lactic acid concentration. As the experimental treatments, T1, T2 and CC (CTL) were fed with a basal diet. The result showed that the digestibility of DM and organic matter (OM) were higher for T1 than for CC (P < 0.05), while crude protein digestibility was not significantly different among T1, T2 and CC. The retained nitrogen was not affected by inclusion of food by-products. Ruminal pH in TRE1 and TRE2 immediately decreased compared to that in CTL. The study suggested that the two types of TMR silage, including food by-products, might be used as a substitute for commercial concentrate.

Simulação dos efeitos de fatores dietéticos sobre a população de protozoários ruminais

Objetivouse desenvolver modelos estatísticos que possam estimar as variações da população de protozoários ruminais mediante alterações na dieta, por meio de utilização dos parâmetros: teores de fibra em detergente neutro e proteína bruta, consumo de matéria seca e pH, bem como verificar se as variáveis peso vivo e raça exercem influência sobre a população de protozoários do rúmen. Foram construídas planilhas por meio do software Excel e registrados dados referentes aos parâmetros acima mencionados e sobre o perfil da microbiota ruminal. Estas variáveis foram utilizadas e testadas para obtenção das equações para predição do perfil da microbiota. Os modelos estatísticos obtidos foram verificados por análise residual e para a seleção das variáveis foi considerado o nível de significância de 5%, mediante a utlização do software MINITAB Versão 15 (2010). As equações de regressão obtidas a partir dos dados analisados permitem inferir que: ocorreu um aumento no número de protozoários totais proporcional à elevação do pH; as variáveis raça, peso e aditivos exerceram efeito significativo sobre a população de protozoários totais; à medida que elevouse o consumo de matéria seca, diminuiu o número de protozoários ruminais; o aumento do teor de fibra em detergente neutro na dieta promoveu incremento no número de protozoários; quanto maior o teor de proteína bruta, menor o número de protozoários totais. Os modelos obtidos permitem estimar o número de protozoários em função das variáveis raça, peso, pH, consumo de matéria seca, teores fibra em detergente neutro e proteína bruta da dieta e presença ou ausência de aditivos.

Enhancement of starting up anaerobic digestion of lignocellulosic substrate: fique's bagasse as an example

In Colombia there are 20,000 ha of fique fields (Furcraea sp., family Agavaceae), that produce around 93,400 tons of fique's bagasse per year. These residuals are disposed into rivers and soil causing pollution. According to physicochemical characteristics, the lignocellulosic residues from fique crops (fique's bagasse) are appropriate carbon source to biogas production. Anaerobic digestion from fique's Bagasse (FB) requires a specialized microbial consortium capable of degrading its high lignocellulosic concentration. In this study, the capacities of seven microbial consortia for biomethane potential (BMP) from FB were evaluated. Inoculum of ruminal liquid achieved high hydrolytic activity (0.068 g COD/g VSS day), whereas pig waste sludge inoculum showed high methanogenic activity (0.146 g COD/g VSS day). Mixtures of these two inoculums (RL+PWS) showed the best yields for biomethane potential (0.3 m(3) CH4/Kg VS ad).

Interplay between rumen digestive disorders and diet-induced inflammation in dairy cattle

In this review, an overview is provided on the current achievements regarding the interplay between rumen digestive disorders and diet-induced inflammation in dairy cattle. It starts with a review of factors favoring the disturbances in the rumen metabolism, which culminate with development of sub-acute rumen acidosis (SARA). The latter digestive disorder is often linked to greater metabolic stress of gastrointestinal (GI) microbiota and lowered fiber digestion, as well as with disruption of the barrier functions of the GI epithelia, which open the route of deleterious molecules to translocate from the GI lumen into the portal system. A model is suggested to illustrate the mechanisms of the involvement of digestive disorders in the disruption of the host's inner homeostasis leading to activation of acute phase response (APR). The latter is part of multifaceted innate immune and metabolic responses of the host. According to this model, endotoxin, its toxicity, and other metabolic compounds of microbial origin are regarded as important immunogenic components of GI tract, which when favored by disruption of host barriers triggers a systemic APR. Although the activation of an APR is viewed as a protective reaction aiming to reestablish the disturbed homeostasis, the presence of inflammatory state over long periods might be associated with negative consequences for the host. The review concludes that prolonged systemic inflammation can: (1) cause significant changes in the energy and lipid metabolism in different body tissues, (2) lead to the development of refractory states associated with immune suppression and increased susceptibility to various diseases, and (3) artificially increase host's requirements in energy and nutrients, lowering the efficiency of energy and feed use by the animal. The paper emphasizes the critical role that formulation of healthy diets plays for curbing down inflammation and enhancing metabolic health of dairy cows.

Perturbation dynamics of the rumen microbiota in response to exogenous butyrate

The capacity of the rumen microbiota to produce volatile fatty acids (VFAs) has important implications in animal well-being and production. We investigated temporal changes of the rumen microbiota in response to butyrate infusion using pyrosequencing of the 16S rRNA gene. Twenty one phyla were identified in the rumen microbiota of dairy cows. The rumen microbiota harbored 54.5±6.1 genera (mean ± SD) and 127.3±4.4 operational taxonomic units (OTUs), respectively. However, the core microbiome comprised of 26 genera and 82 OTUs. Butyrate infusion altered molar percentages of 3 major VFAs. Butyrate perturbation had a profound impact on the rumen microbial composition. A 72 h-infusion led to a significant change in the numbers of sequence reads derived from 4 phyla, including 2 most abundant phyla, Bacteroidetes and Firmicutes. As many as 19 genera and 43 OTUs were significantly impacted by butyrate infusion. Elevated butyrate levels in the rumen seemingly had a stimulating effect on butyrate-producing bacteria populations. The resilience of the rumen microbial ecosystem was evident as the abundance of the microorganisms returned to their pre-disturbed status after infusion withdrawal. Our findings provide insight into perturbation dynamics of the rumen microbial ecosystem and should guide efforts in formulating optimal uses of probiotic bacteria treating human diseases.

Comparison of nitroethane, 2-nitro-1-propanol, lauric acid, Lauricidin® and the Hawaiian marine algae, Chaetoceros, for potential broad-spectrum control of anaerobically grown lactic acid bacteria

The gastrointestinal tract of bovines often contains bacteria that contribute to disorders of the rumen, and may also contain foodborne or opportunistic human pathogens as well as bacteria capable of causing mastitis in cows. Thus there is a need to develop broad-spectrum therapies that are effective while not leading to unacceptably long antibiotic withdrawal times. The effects of the CH(4)-inhibitors nitroethane (2 mg/mL), 2-nitro-1-propanol (2 mg/mL), lauric acid (5 mg/mL), the commercial product Lauricidin® (5 mg/mL), and a finely ground product of the Hawaiian marine algae, Chaetoceros (10 mg/mL), were compared in pure cultures of Streptococcus agalactia, Enterococcus faecium, Streptococcus bovis, and in a mixed lactic acid rumen bacterial culture. Lauricidin® and lauric acid exhibited the most bactericidal acidity against all bacteria. These results suggest potential animal health benefits from supplementing cattle diets with lauric acid or Lauricidin® to improve the health of the rumen and help prevent shedding of human pathogens.

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.

Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial proteins, short chain fatty acids and gases. In this study, metagenomic approaches were used to study the microbial populations and metabolic potential of the microbial community. DNA was extracted from Surti Buffalo rumen samples (four treatments diet) and sequenced separately using a 454 GS FLX Titanium system. We used comparative metagenomics to examine metabolic potential and phylogenetic composition from pyrosequence data generated in four samples, considering phylogenetic composition and metabolic potentials in the rumen may remarkably be different with respect to nutrient utilization. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of fermentation of carbohydrates in a high roughage diet. The distribution of phylotypes and environmental gene tags (EGTs) detected within each rumen sample were dominated by Bacteroidetes/Chlorobi, Firmicutes and Proteobacteria in all the samples. The results of this study could help to determine the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals.

Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases

The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

Foregut fermentation occurs in mammalian ruminants and in one bird, the South American folivorous hoatzin. This bird has an enlarged crop with a function analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant matter, providing energy to the host from foregut fermentation, in addition to the fermentation that occurs in their hindguts (cecum/colon). As foregut fermentation represents an evolutionary convergence between hoatzins and ruminants, our aim was to compare the community structure of foregut and hindgut bacterial communities in the cow and hoatzin to evaluate the influences of host phylogeny and organ function in shaping the gut microbiome. The approach used was to hybridize amplified bacterial ribosomal RNA genes onto a high-density microarray (PhyloChip). The results show that the microbial communities cluster primarily by functional environment (foreguts cluster separately from hindguts) and then by host. Bacterial community diversity was higher in the cow than in the hoatzin. Overall, compared with hindguts, foreguts have higher proportions of Bacteroidetes and Spirochaetes, and lower proportions of Firmicutes and Proteobacteria. The main host differences in gut bacterial composition include a higher representation of Spirochaetes, Synergistetes and Verrucomicrobia in the cow. Despite the significant differences in host phylogeny, body size, physiology and diet, the function seems to shape the microbial communities involved in fermentation. Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts.

Strategy of controlling the volumetric loading rate to promote hydrogen-production performance in a mesophilic-kitchen-waste fermentor and the microbial ecology analyses

The kitchen waste was chosen as a high solid (42 gL(-1) of volatile suspended solid, VSS) and high organic (107 gL(-1) of chemical oxygen demand) feedstock for operating a 3-L mesophilic fermentor. The greatest specific hydrogen production rate ( r(H2) was observed in Stage 3 as 3.4 L-H2 L(-1) day(-1) with a volumetric loading rate (VLR) of 100 g-CODL(-1) day(-1); the highest hydrogen yield was observed in Stage 2 as 96 mL-H2 g(-1) of influent VSS with a VLR of 46 g-COD L(-1) day(-1). In Stages 1 (with a VLR of 27 g-COD L(-1)) and 2, the sum of Butyrivibrio fibrisolvens and Clostridium proteoclasticum is dominant, but in Stage 3, Olsenella genomosp, became dominant and constituted 44% of the entire population. The dependence of VLR and r(H2)could be regressed as a linear equation of r(H2) = (2.83 VLR + 40.5) x 10(-2) .

Influence of urea-calcium mixtures as rumen slow-release feed on in vitro fermentation using a gas production technique

In this experiment the effects of different urea products (urea [U] and urea-calcium mixtures [UCM]) on rumen fermentation were investigated in dependence of different energy sources by using in vitro techniques. The 7 x 2 factorial arrangement followed a completely randomised design using seven urea products (U100, U40CaCl2, U50CaCl2, U60CaCl2, U40CaSO4, U50CaSO4 and U60CaSO4) in combination with cassava chips (CC) or corn meal (CM). Compared with other treatments, the cumulative gas production (96 h) was significantly increased for U60CaCl2 + CC and U60CaSO4 + CC (p < 0.01), which was combined with a higher in vitro true digestibility (p < 0.01). In addition, the concentration of volatile fatty acids in the fluid of U60CaCl2 + CC and U60CaSO4 + CC was significantly higher than in other treatments. Urea treatments (U100 + CC and U100 + CM) caused the highest concentration of ruminal ammonia nitrogen (p < 0.01), which was significantly decreased by all UCM products in combination with CC, but not with CM. The highest levels of total bacteria, Fibrobacter succinogenes and anaerobic fungi were found for treatment U60CaCl2 + CC and U60CaSO4 + CC (p < 0.05). The findings revealed that the utilisation of U60CaCl2 and U60CaSO4 in combination with cassava chips improved the ruminal fluid fermentation in terms of NH3-N and volatile fatty acid concentration, digestibility of energy and increased the fibrobacter concentrations.