Factors that alter rumen microbial ecology

Effects of supplementing an active dry yeast product on rumen microbial community composition and on subsequent rumen fermentation of lactating cows in the mid-to-late lactation period

The effects of supplementing feed of cows in mid-to-late lactation with an active yeast product (Actisaf Sc 47) were evaluated using 15 Holstein cows in a replicated 3 × 3 Latin square design. The animals were fed a mixed ration with 33% neutral detergent fiber, consisting of timothy hay (29.8%), a commercial concentrate (70.0%) and commercial calcium triphosphate (0.2%), twice daily to meet 105% of their energy requirement. Yeast supplement was set at 0, 5 and 10 g per day over 21-day periods, each of which consisted of 14 days for adaptation followed by 7 days of data collection. Milking performance, plasma metabolite parameters, rumen volatile fatty acids, lipopolysaccharide and microbial properties were measured. Although there were no significant differences in feeding and milking performance or blood parameters associated with supplementation, the acetate to propionate ratio in the rumen fluid tended to decrease (P = 0.08). The population of Bacteroidetes tended to be less prominent (P = 0.07) and the fibrolytic bacterium Fibrobacter significantly increased (P < 0.05) in the rumen fluid of the yeast 10 g group compared with that of the control. These data suggest that effects of supplementing live yeast to cows in mid-to-late lactation may be limited to microbial composition and fermentation characteristics in the rumen.

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides

BACKGROUND

Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cattle are the major reservoir hosts of these organisms, and while there have been advancements in food safety practices and industry standards, STEC still remains prevalent within beef cattle operations with cattle hides implicated as major sources of carcass contamination. To investigate whether the composition of hide-specific microbial communities are associated with STEC prevalence, 16S ribosomal RNA (rRNA) bacterial community profiles were obtained from hide and fecal samples collected from a large commercial feedlot over a 3-month period. These community data were examined amidst an extensive collection of prevalence data on a subgroup of STEC that cause illness in humans, referred to as enterohemorrhagic E. coli (EHEC). Fecal 16S rRNA gene OTUs (operational taxonomic units) were subtracted from the OTUs found within each hide 16S rRNA amplicon library to identify hide-specific bacterial populations.

RESULTS

Comparative analysis of alpha diversity revealed a significant correlation between low bacterial diversity and samples positive for the presence of E. coli O157:H7 and/or the non-O157 groups: O26, O111, O103, O121, O45, and O145. This trend occurred regardless of diversity metric or fecal OTU presence. The number of EHEC serogroups present in the samples had a compounding effect on the inverse relationship between pathogen presence and bacterial diversity. Beta diversity data showed differences in bacterial community composition between samples containing O157 and non-O157 populations, with certain OTUs demonstrating significant changes in relative abundance.

CONCLUSIONS

The cumulative prevalence of the targeted EHEC serogroups was correlated with low bacterial community diversity on pre-harvest cattle hides. Understanding the relationship between indigenous hide bacterial communities and populations may provide strategies to limit EHEC in cattle and provide biomarkers for EHEC risk assessment.

Stress as a Normal Cue in the Symbiotic Environment

All multicellular hosts form associations with groups of microorganisms. These microbial communities can be taxonomically diverse and dynamic, and their persistence is due to robust, and sometimes coevolved, host-microbe and microbe-microbe interactions. Chemical and physical sources of stress are prominently situated in this molecular exchange, as cues for cellular responses in symbiotic microbes. Stress in the symbiotic environment may arise from three sources: host tissues, microbe-induced immune responses, or other microbes in the host environment. The responses of microbes to these stresses can be general or highly specialized, and collectively may contribute to the stability of the symbiotic system. In this review, we highlight recent work that emphasizes the role of stress as a cue in the symbiotic environment of plants and animals.

Insights on Alterations to the Rumen Ecosystem by Nitrate and Nitrocompounds

Nitrate and certain short chain nitrocompounds and nitro-oxy compounds are being investigated as dietary supplements to reduce economic and environmental costs associated with ruminal methane emissions. Thermodynamically, nitrate is a preferred electron acceptor in the rumen that consumes electrons at the expense of methanogenesis during dissimilatory reduction to an intermediate, nitrite, which is primarily reduced to ammonia although small quantities of nitrous oxide may also be produced. Short chain nitrocompounds act as direct inhibitors of methanogenic bacteria although certain of these compounds may also consume electrons at the expense of methanogenesis and are effective inhibitors of important foodborne pathogens. Microbial and nutritional consequences of incorporating nitrate into ruminant diets typically results in increased acetate production. Unlike most other methane-inhibiting supplements, nitrate decreases or has no effect on propionate production. The type of nitrate salt added influences rates of nitrate reduction, rates of nitrite accumulation and efficacy of methane reduction, with sodium and potassium salts being more potent than calcium nitrate salts. Digestive consequences of adding nitrocompounds to ruminant diets are more variable and may in some cases increase propionate production. Concerns about the toxicity of nitrate's intermediate product, nitrite, to ruminants necessitate management, as animal poisoning may occur via methemoglobinemia. Certain of the naturally occurring nitrocompounds, such as 3-nitro-1-propionate or 3-nitro-1-propanol also cause poisoning but via inhibition of succinate dehydrogenase. Typical risk management procedures to avoid nitrite toxicity involve gradually adapting the animals to higher concentrations of nitrate and nitrite, which could possibly be used with the nitrocompounds as well. A number of organisms responsible for nitrate metabolism in the rumen have been characterized. To date a single rumen bacterium is identified as contributing appreciably to nitrocompound metabolism. Appropriate doses of the nitrocompounds and nitrate, singly or in combination with probiotic bacteria selected for nitrite and nitrocompound detoxification activity promise to alleviate risks of toxicity. Further studies are needed to more clearly define benefits and risk of these technologies to make them saleable for livestock producers.

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps

Gut microbiome shapes various aspects of a host’s physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host’s growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

New Insights into the Microbiota of the Svalbard Reindeer Rangifer tarandus platyrhynchus

Svalbard reindeer (Rangifer tarandus platyrhynchus) is a non-migratory subspecies of reindeer inhabiting the high-arctic archipelago of Svalbard. In contrast to other Rangifer tarandus subspecies, Svalbard reindeer graze exclusively on natural sources of food and have no chance of ingestion of any crops. We report the use of a non-invasive method for analysis of fecal microbiome by means of sequencing the 16S rDNA extracted from the fecal microbiota of R. tarandus platyrhynchus from a small, isolated population in Hornsund, South Spitsbergen National Park. Analyses of all samples showed that 99% of the total reads were represented by Bacteria. Taxonomy-based analysis showed that fecal bacterial communities consisted of 14 phyla. The most abundant phyla across the population were Firmicutes and Bacteroidetes, and those phyla jointly accounted for more than 95% of total bacterial sequences (ranging between 90.14 and 98.19%). Specifically, Firmicutes comprised 56.53% (42.98–63.64%) and Bacteroidetes comprised 39.17% (34.56–47.16%) of the total reads. The remaining 5% of the population reads comprised of Tenericutes, Cyanobacteria, TM7, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia, Planctomycetes, Fibrobacteres, Spirochaetes, Chloroflexi, and Deferribacteres. Differences in the fecal bacteria composition between particular reindeer were not statistically significant which may reflect the restricted location and similar diet of all members of the local population.

The effects of a ration change from a total mixed ration to pasture on rumen fermentation, volatile fatty acid absorption characteristics, and morphology of dairy cows

To investigate the effect of the change from a concentrate and silage-based ration (total mixed ration, TMR) to a pasture-based ration, a 10-wk trial (wk 1-10) was performed, including 10 rumen- and duodenum-fistulated German Holstein dairy cows (182±24 d in milk, 23.5±3.5kg of milk/d; mean ± standard deviation). The cows were divided in either a pasture group (PG, n=5) or a confinement group (CG, n=5). The CG stayed on a TMR-based ration (35% corn silage, 35% grass silage, 30% concentrate; dry matter basis), whereas the PG was gradually transitioned from a TMR to a pasture-based ration (wk 1: TMR only; wk 2: 3 h/d on pasture wk 3 and 4: 12 h/d on pasture wk 5-10: pasture only). Ruminal pH, volatile fatty acids (VFA), NH3-N, and lipopolysaccharide (LPS) concentrations were measured in rumen fluid samples collected medially and ventrally on a weekly basis. Ruminal pH was continuously recorded during 1 to 4 consecutive days each week using ruminal pH measuring devices. In wk 1, 5, and 10, rumen contents were evacuated and weighed, papillae were collected from 3 locations in the rumen, and subsequently a VFA absorption test was performed. In the PG, mean rumen pH and molar acetate proportions decreased, and molar butyrate proportions increased continuously over the course of the trial, which can most likely be ascribed to an increased intake of rapidly fermentable carbohydrates. During the first weeks on a full grazing ration (wk 5-7), variation of rumen pH decreased, and in wk 5 a lower rumen content, papillae surface area, and potential for VFA absorption were observed. In wk 8 to 10, variation of rumen pH and total VFA concentrations increased again, and acetate/propionate ratio decreased. In wk-10 rumen content, papillae area and VFA absorption characteristics similar to initial levels were observed. Although continuous rumen pH assessments and LPS concentrations did not reveal an increased risk for subacute rumen acidosis (SARA) during the adaption period, histopathology of rumen papillae and potential for VFA absorption indicated a possible risk for rumen health. An increased risk for SARA was observed in wk 9 and 10 in the PG, but rumen LPS concentrations and histopathology were not adversely affected. Results of the present study suggest that after behavioral and metabolic adaptation to the transition from a TMR to a pasture-based ration, no adverse effects on rumen morphology and absorption capacity occurred, although rumen pH after adaptation to pasture indicated increased risk of SARA.

A biologically inspired variable-pH strategy for enhancing short-chain fatty acids (SCFAs) accumulation in maize straw fermentation

This study investigates the feasibility of varying the pH to enhance the accumulation of short-chain fatty acids (SCFAs) in the in vitro fermentation of maize straw. The corresponding hydrolysis rate and the net SCFA yield increased as inoculum ratio (VSinoculum/VSsubstrate) increased from 0.09 to 0.79. The pH were maintained at 5.3, 5.8, 6.3, 6.8, 7.3, and 7.8, respectively. A neutral pH of approximately 6.8 was optimal for hydrolysis. The net SCFA yield decreased by 34.9% for a pH of less than 5.8, but remained constant at approximately 721±5mg/gvs for a pH between 5.8 and 7.8. In addition, results were obtained for variable and constant pH levels at initial substrate concentrations of 10, 30 and 50g/L. A variable pH increased the net SCFA yield by 23.6%, 29.0%, and 36.6% for concentrations of 10, 30 and 50g/L. Therefore, a variable pH enhanced SCFA accumulation in maize straw fermentation.

An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms

Symbiotic associations are ubiquitous in the microbial world and have a major role in shaping the evolution of both partners. One of the most interesting mutualistic relationships exists between protozoa and methanogenic archaea in the fermentative forestomach (rumen) of ruminant animals. Methanogens reside within and on the surface of protozoa as symbionts, and interspecies hydrogen transfer is speculated to be the main driver for physical associations observed between the two groups. In silico analyses of several rumen methanogen genomes have previously shown that up to 5% of genes encode adhesin-like proteins, which may be central to rumen interspecies attachment. We hypothesized that adhesin-like proteins on methanogen cell surfaces facilitate attachment to protozoal hosts. Using phage display technology, we have identified a protein (Mru_1499) from Methanobrevibacter ruminantium M1 as an adhesin that binds to a broad range of rumen protozoa (including the genera Epidinium and Entodinium). This unique adhesin also binds the cell surface of the bacterium Butyrivibrio proteoclasticus, suggesting a broad adhesion spectrum for this protein.

Triclocarban Influences Antibiotic Resistance and Alters Anaerobic Digester Microbial Community Structure

Triclocarban (TCC) is one of the most abundant organic micropollutants detected in biosolids. Lab-scale anaerobic digesters were amended with TCC at concentrations ranging from the background concentration of seed biosolids (30 mg/kg) to toxic concentrations of 850 mg/kg to determine the effect on methane production, relative abundance of antibiotic resistance genes, and microbial community structure. Additionally, the TCC addition rate was varied to determine the impacts of acclimation time. At environmentally relevant TCC concentrations (max detect = 440 mg/kg), digesters maintained function. Digesters receiving 450 mg/kg of TCC maintained function under gradual TCC addition, but volatile fatty acid concentrations increased, pH decreased, and methane production ceased when immediately fed this concentration. The concentrations of the mexB gene (encoding for a multidrug efflux pump) were higher with all concentrations of TCC compared to a control, but higher TCC concentrations did not correlate with increased mexB abundance. The relative abundance of the gene tet(L) was greater in the digesters that no longer produced methane, and no effect on the relative abundance of the class 1 integron integrase encoding gene (intI1) was observed. Illumina sequencing revealed substantial community shifts in digesters that functionally failed from increased levels of TCC. More subtle, yet significant, community shifts were observed in digesters amended with TCC levels that did not inhibit function. This research demonstrates that TCC can select for a multidrug resistance encoding gene in mixed community anaerobic environments, and this selection occurs at concentrations (30 mg/kg) that can be found in full-scale anaerobic digesters (U.S. median concentration = 22 mg/kg, mean = 39 mg/kg).

Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen

The bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for 1% and 0.1% of the total non-rRNAs, respectively. The majority (98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.

Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass

This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG.

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

The Effects of GH Transgenic Goats on the Microflora of the Intestine, Feces and Surrounding Soil

The development of genetically engineered animals has brought with it increasing concerns about biosafety issues. We therefore evaluated the risks of growth hormone from transgenic goats, including the probability of horizontal gene transfer and the impact on the microbial community of the goats’ gastrointestinal tracts, feces and the surrounding soil. The results showed that neither the GH nor the neoR gene could be detected in the samples. Moreover, there was no significant change in the microbial community of the gastrointestinal tracts, feces and soil, as tested with PCR-denaturing gradient gel electrophoresis and 16S rDNA sequencing. Finally, phylogenetic analysis showed that the intestinal content, feces and soil samples all contained the same dominant group of bacteria. These results demonstrated that expression of goat growth hormone in the mammary of GH transgenic goat does not influence the microflora of the intestine, feces and surrounding soil.

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.

Treatment of grain with organic acids at 2 different dietary phosphorus levels modulates ruminal microbial community structure and fermentation patterns in vitro

Recent data indicate positive effects of treating grain with citric (CAc) or lactic acid (LAc) on the hydrolysis of phytate phosphorus (P) and fermentation products of the grain. This study used a semicontinuous rumen simulation technique to evaluate the effects of processing of barley with 50.25 g/L (wt/vol) CAc or 76.25 g/L LAc on microbial composition, metabolic fermentation profile, and nutrient degradation at low or high dietary P supply. The low P diet [3.1g of P per kg of dry matter (DM) of dietary P sources only] was not supplemented with inorganic P, whereas the high P diet was supplemented with 0.5 g of inorganic P per kg of DM through mineral premix and 870 mg of inorganic P/d per incubation fermenter via artificial saliva. Target microbes were determined using quantitative PCR. Data showed depression of total bacteria but not of total protozoa or short-chain fatty acid (SCFA) concentration with the low P diet. In addition, the low P diet lowered the relative abundance of Ruminococcus albus and decreased neutral detergent fiber (NDF) degradation and acetate proportion, but increased the abundance of several predominantly noncellulolytic bacterial species and anaerobic fungi. Treatment of grain with LAc increased the abundance of total bacteria in the low P diet only, and this effect was associated with a greater concentration of SCFA in the ruminal fluid. Interestingly, in the low P diet, CAc treatment of barley increased the most prevalent bacterial group, the genus Prevotella, in ruminal fluid and increased NDF degradation to the same extent as did inorganic P supplementation in the high P diet. Treatment with either CAc or LAc lowered the abundance of Megasphaera elsdenii but only in the low P diet. On the other hand, CAc treatment increased the proportion of acetate in the low P diet, whereas LAc treatment decreased this variable at both dietary P levels. The propionate proportion was significantly increased by LAc at both P levels, whereas butyrate increased only with the low P diet. Treatments with CAc or LAc reduced the degradation of CP and ammonia concentration compared with the control diet at both P levels. In conclusion, the beneficial effects of CAc and LAc treatment on specific ruminal microbes, fermentation profile, and fiber degradation in the low P diet suggest the potential for the treatment to compensate for the lack of inorganic P supplementation in vitro. Further research is warranted to determine the extent to which the treatment can alleviate the shortage of inorganic P supplementation under in vivo conditions.

Structural and genetic diversity in antibody repertoires from diverse species

The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes.

Effect of Probiotics/Prebiotics on Cattle Health and Productivity

Probiotics/prebiotics have the ability to modulate the balance and activities of the gastrointestinal (GI) microbiota, and are, thus, considered beneficial to the host animal and have been used as functional foods. Numerous factors, such as dietary and management constraints, have been shown to markedly affect the structure and activities of gut microbial communities in livestock animals. Previous studies reported the potential of probiotics and prebiotics in animal nutrition; however, their efficacies often vary and are inconsistent, possibly, in part, because the dynamics of the GI community have not been taken into consideration. Under stressed conditions, direct-fed microbials may be used to reduce the risk or severity of scours caused by disruption of the normal intestinal environment. The observable benefits of prebiotics may also be minimal in generally healthy calves, in which the microbial community is relatively stable. However, probiotic yeast strains have been administered with the aim of improving rumen fermentation efficiency by modulating microbial fermentation pathways. This review mainly focused on the benefits of probiotics/prebiotics on the GI microbial ecosystem in ruminants, which is deeply involved in nutrition and health for the animal.

Substitution of common concentrates with by-products modulated ruminal fermentation, nutrient degradation, and microbial community composition in vitro

A rumen simulation technique was used to evaluate the effects of the complete substitution of a common concentrate mixture (CON) with a mixture consisting solely of by-products from the food industry (BP) at 2 different forage-to-concentrate ratios on ruminal fermentation profile, nutrient degradation, and abundance of rumen microbiota. The experiment was a 2×2 factorial arrangement with 2 concentrate types (CON and BP) and 2 concentrate levels (25 and 50% of diet dry matter). The experiment consisted of 2 experimental runs with 12 fermentation vessels each (n=6 per treatment). Each run lasted for 10d, with data collection on the last 5d. The BP diets had lower starch, but higher neutral detergent fiber (NDF) and fat contents compared with CON. Degradation of crude protein was decreased, but NDF and nonfiber carbohydrate degradation were higher for the BP diets. At the 50% concentrate level, organic matter degradation tended to be lower for BP and CH4 formation per unit of NDF degraded was also lower for BP. The BP mixture led to a higher concentration of propionate and a lower acetate-to-propionate ratio, whereas concentrations of butyrate and caproate decreased. Concentrate type did not affect microbial community composition, except that the abundance of bacteria of the genus Prevotella was higher for BP. Increasing the concentrate level resulted in higher degradation of organic matter and crude protein. At the higher concentrate level, total short-chain fatty acid formation increased and concentrations of isobutyrate and valerate decreased. In addition, at the 50% concentrate level, numbers of protozoa increased, whereas numbers of methanogens, anaerobic fungi, and fibrolytic bacteria decreased. No interaction was noted between the 2 dietary factors on most variables, except that at the higher concentrate level the effects of BP on CH4 and CO2 formation per unit of NDF degraded, crude protein degradation, and the abundance of Prevotella were more prominent. In conclusion, the results of this study suggest that BP in the diet can adequately substitute CON with regard to ruminal fermentation profile and microbiota, showing even favorable fermentation patterns when fed at 50% inclusion rate.

Response of the Rumen Microbiota of Sika Deer (Cervus nippon) Fed Different Concentrations of Tannin Rich Plants

High throughput sequencing was used to examine the rumen microbiota of sika deer fed high (OLH) and low concentration (OLL) of tannin rich oak leaves. The results showed that Prevotella spp. were the most dominant bacteria. The most predominant methanogens were the members of the order Methanoplasmatales. The dominant rumen protozoa were Entodinium longinucleatum, Eudiplodinium maggii, and Epidinium caudatum, and the fungal communities were mostly represented by Piromyces spp. Moreover, the relative abundance of Pseudobutyrivibrio spp. (P=0.026), unidentified bacteria (P=0.028), and Prevotella spp. (P=0.022) was lower in the OLH group than in the OLL group. The concentration of propionate in the OLH group was greater than in the OLL group (P=0.006). Patterns of relationships showed that methanogens belonging to the order Methanoplasmatales were negatively correlated with Treponema spp., Ent. Longinucleatum, and acetate. Methanosphaera stadtmanae was positively correlated to propionate, while Methanobrevibacter ruminantium was negatively associated with Methanobrevibacter thaueri and Methanobrevibacter millerae. Tannins altered the rumen microbes and fermentation patterns. However, the response of the entire rumen microbiota and the relationship between rumen microorganisms and the fermentation parameters were not fully understood.

Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis

A balanced gastrointestinal microbial ecosystem is crucial for the health and growth of animals. In the gastrointestinal tract (GIT) of ruminants, cellulolytic bacteria aid in the digestion and absorption of nutrients. Rumen contents and feces in ruminants are often used to assess gastrointestinal microbial communities; however, these sites do not guarantee to represent the diversity of microbes found in the entire GIT. In this study, we investigated the microbiota along the GIT of five Chinese Mongolian sheep using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbiota were more abundant in the stomach and large intestine than in the small intestine. DGGE and real-time PCR revealed the predominance of Firmicutes and Bacteroidetes in the GIT. Meanwhile, Ruminococcus flavefaciens and Clostridium cluster IV showed significant difference in their abundance along the GIT (P < 0.05). Fibrobacter succinogenes was the most dominant species, followed by Ruminococcus albus and R. flavefaciens. The ileum harbored a larger number of cellulolytic bacteria, particularly-Clostridium cluster IV, than reported previously. In addition, comparisons between microbiota in the rumen and rectum indicated similar number of total bacteria, Firmicutes, Bacteroidetes, F. succinogenes, Butyrivibrio fibrisolvens, Clostridium cluster IV, and Clostridium cluster XIVa, whereas the number of R. albus and R. flavefaciens was higher in the rumen. This study investigated the composition and quantification of GIT microbial community in Chinese Mongolian sheep, and revealed for the first time the cellulolytic bacterial community in these sheep.

Exploring the sheep rumen microbiome for carbohydrate-active enzymes

The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animal's digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.

High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats

High-grain (HG) feeding used in intensive goat production can affect the physiology of the rumen wall, but the changes induced in the epimural bacterial community and host Toll-like receptors (TLRs) are not well understood. In this study, 10 male goats were randomly allocated to two groups and fed either a hay diet (0% grain; n = 5) or an HG diet (65% grain; n = 5). The changes in the ruminal epithelial bacterial community and expression of TLRs during long-term (7 weeks) HG feeding were determined using pyrosequencing and quantitative real-time polymerase chain reaction. Principal coordinate analysis and analysis of molecular variance (AMOVA) results showed that HG feeding caused a strong shift in bacterial composition and structure. At the genus level, our data revealed that it increased the relative abundance of taxa Butyrivibrio, unclassified Clostridiales, Mogibacterium, unclassified Anaerolineaceae, and Succiniclasticum, and decreased the proportion of unclassified Ruminococcaceae, unclassified Rikenellaceae, unclassified Erysipelotrichaceae, Howardella, and unclassified Neisseriaceae. The HG-fed goats also exhibited upregulation of the relative mRNA expression of TLR2, TLR3, and TLR5 in the rumen epithelium (P < 0.05). Correlation analysis revealed that the increase in TLR expression was associated with changes in the relative abundance of ruminal epithelial bacteria. This study provides a first insight into the adaptive response of ruminal epithelial bacterial populations to HG feeding in goats and shows that these changes were associated with alterations in TLR expression. These findings provide new insight into understanding of host–microbial relationships in ruminants.

Development of the honey bee gut microbiome throughout the queen-rearing process

The European honey bee (Apis mellifera) is used extensively to produce hive products and for crop pollination, but pervasive concerns about colony health and population decline have sparked an interest in the microbial communities that are associated with these important insects. Currently, only the microbiome of workers has been characterized, while little to nothing is known about the bacterial communities that are associated with queens, even though their health and proper function are central to colony productivity. Here, we provide a large-scale analysis of the gut microbiome of honey bee queens during their developmental trajectory and through the multiple colonies that host them as part of modern queen-rearing practices. We found that queen microbiomes underwent a dramatic shift in size and composition as they aged and encountered different worker populations and colony environments. Queen microbiomes were dominated by enteric bacteria in early life but were comprised primarily of alphaproteobacteria at maturity. Furthermore, queen gut microbiomes did not reflect those of the workers who tended them and, indeed, they lacked many of the bacteria that are considered vital to workers. While worker gut microbiotas were consistent across the unrelated colony populations sampled, the microbiotas of the related queens were highly variable. Bacterial communities in mature queen guts were similar in size to those of mature workers and were characterized by dominant and specific alphaproteobacterial strains known to be associated with worker hypopharyngeal glands. Our results suggest a model in which queen guts are colonized by bacteria from workers' glands, in contrast to routes of maternal inoculation for other animal microbiomes.

Use of salivary cortisol to evaluate the influence of rides in dromedary camels

Animals in captivity and in the wild face numerous challenges, including the risk of enduring acute or chronic stress. In captivity, facilities attempt to alleviate the risk of chronic stress by providing environmental enrichment, shown to minimize behavioral disorders and stress in several species. One potential form of enrichment in zoos is training animals to provide rides for guests, however, the effect of this activity on the welfare of individual animals has never been examined. We validated the use of saliva for assessing stress in dromedary camels (Camelus dromedarius), an animal commonly used for rides. We then measured variation in salivary cortisol in four male camels while providing rides of differing frequency for guests at the Toronto Zoo. The camels were sampled during the ride season (June to September) using four treatments: (1) in their pasture, (2) at the ride area when not performing rides, (3) while providing a low number of rides (n=50/day) and (4) while providing a high number of rides (n=150/day). Furthermore, samples were taken before and after the ride season for comparison. There was a significant difference between the post-ride season treatment and the three treatments involving guest presence during the ride season (ride area, low rides, high rides). In general, cortisol concentrations were lower during the ride season and higher during the non-ride season. Based on the metrics we used, performing rides is not a stressful experience for these dromedary camels and suggests that rides may be a form of enrichment.

Naked-eye and fluorescence detection of basic pH and F−with a 1,8-naphthalimide-based multifunctional probe

A novel multifunctional colorimetric and fluorescent 1,8-naphthalimide-based probe toward basic pH and F⁻has been developed.

Bacteria and methanogens differ along the gastrointestinal tract of Chinese roe deer (Capreolus pygargus)

The current study provides the insight into the bacteria in the gastrointestinal tract (GIT) and methanogens presented in the rumen and cecum of the Chinese roe deer (Capreolus pygargus). The ruminal, ileal, cecal, and colonic contents, as well as feces, were obtained from each of the three, free-range, roe deer ingesting natural pasture after euthanasia. For the bacterial community, a total of 697,031 high-quality 16S rRNA gene sequences were generated using high-throughput sequencing, and assigned to 2,223 core operational taxonomic units (OTUs) (12 bacterial phyla and 87 genera). The phyla Firmicutes (51.2%) and Bacteroidetes (39.4%) were the dominant bacteria in the GIT of roe deer. However, the bacterial community in the rumen was significantly (P<0.01) different from the other sampled regions along the GIT. Secondly, Prevotella spp., Anaerovibrio spp., and unidentified bacteria within the families Veillonellaceae and Paraprevotellaceae were more abundant in the rumen than in the other regions. Unidentified bacteria within the family Enterobacteriaceae, Succinivibrio spp., and Desulfovibrio spp. were more predominant in the colon than in other regions. Unidentified bacteria within the family Ruminococcaceae, and Bacteroides spp. were more prevalent in the ileum, cecum and fecal pellets. For methanogens in the rumen and cecum, a total of 375,647 high quality 16S rRNA gene sequences were obtained and assigned to 113 core OTUs. Methanobrevibacter millerae was the dominant species accounting for 77.3±7.4 (S.E) % and 68.9±4.4 (S.E) % of total sequences in the rumen and cecum of roe deer, respectively. However, the abundance of Methanobrevibacter smithii was higher in the rumen than in the cecum (P = 0.004). These results revealed that there was intra variation in the bacterial community composition across the GIT of roe deer, and also showed that the methanogen community in the rumen differed from that in the cecum.

Fermentable fibres condition colon microbiota and promote diabetogenesis in NOD mice

AIMS/HYPOTHESIS

Gut microbiota (GM) and diet both appear to be important in the pathogenesis of type 1 diabetes. Fermentable fibres (FFs), of which there is an ample supply in natural, diabetes-promoting diets, are used by GM as a source of energy. Our aim was to determine whether FFs modify GM and diabetes incidence in the NOD mouse.

METHODS

Female NOD mice were weaned to a semisynthetic diet and the effects of FF supplementation on diabetes incidence and insulitis were evaluated. Real-time quantitative PCR was employed to determine the effects imposed to gene transcripts in the colon and lymph nodes. Changes to GM were analysed by next-generation sequencing.

RESULTS

NOD mice fed semisynthetic diets free from FFs were largely protected from diabetes while semisynthetic diets supplemented with the FFs pectin and xylan (PX) resulted in higher diabetes incidence. Semisynthetic diet free from FFs altered GM composition significantly; addition of PX changed the composition of the GM towards that found in natural-diet-fed mice and increased production of FF-derived short-chain fatty acid metabolites in the colon. The highly diabetogenic natural diet was associated with expression of proinflammatory and stress-related genes in the colon, while the semisynthetic diet free from FFs promoted Il4, Il22, Tgfβ and Foxp3 transcripts in the colon and/or pancreatic lymph node. PX in the same diet counteracted these effects and promoted stress-related IL-18 activation in gut epithelial cells. 16S RNA sequencing revealed each diet to give rise to its particular GM composition, with different Firmicutes to Bacteroidetes ratios, and enrichment of mucin-degrading Ruminococcaceae following diabetes-protective FF-free diet.

CONCLUSIONS/INTERPRETATION

FFs condition microbiota, affect colon homeostasis and are important components of natural, diabetes-promoting diets in NOD mice.

Characterization of butyrate transport across the luminal membranes of equine large intestine

The diet of the horse, pasture forage (grass), is fermented by the equine colonic microbiota to short-chain fatty acids, notably acetate, propionate and butyrate. Short-chain fatty acids provide a major source of energy for the horse and contribute to many vital physiological processes. We aimed to determine both the mechanism of butyrate uptake across the luminal membrane of equine colon and the nature of the protein involved. To this end, we isolated equine colonic luminal membrane vesicles. The abundance and activity of cysteine-sensitive alkaline phosphatase and villin, intestinal luminal membrane markers, were significantly enriched in membrane vesicles compared with the original homogenates. In contrast, the abundance of GLUT2 protein and the activity of Na(+)-K(+)-ATPase, known markers of the intestinal basolateral membrane, were hardly detectable. We demonstrated, by immunohistochemistry, that monocarboxylate transporter 1 (MCT1) protein is expressed on the luminal membrane of equine colonocytes. We showed that butyrate transport into luminal membrane vesicles is energized by a pH gradient (out < in) and is not Na(+) dependent. Moreover, butyrate uptake is time and concentration dependent, with a Michaelis-Menten constant of 5.6 ± 0.45 mm and maximal velocity of 614 ± 55 pmol s(-1) (mg protein)(-1). Butyrate transport is significantly inhibited by p-chloromercuribenzoate, phloretin and α-cyano-4-hydroxycinnamic acid, all potent inhibitors of MCT1. Moreover, acetate and propionate, as well as the monocarboxylates pyruvate and lactate, also inhibit butyrate uptake. Data presented here support the conclusion that transport of butyrate across the equine colonic luminal membrane is predominantly accomplished by MCT1.

High-grain diets suppress ruminal tissue abundance of angiopoietin-like protein 4 in cattle

Angiopoietin-like protein 4 (ANGPTL4) is expressed in bovine ruminal epithelium, making it possible that dietary components or commensal microbes may influence gastrointestinal ANGPTL4 production via interactions at the mucosal surface. Therefore, we conducted 3 experiments to evaluate the effects of dietary concentrate level and VFA infusions on ANGPTL4 abundance in ruminal tissue. In Exp. 1, we assigned 12 nonlactating Holstein cows to either 8% or 64% concentrate diets; diets were fed 28 d before euthanasia and ruminal tissue collection. Ruminal tissue and plasma ANGPTL4 protein abundance were unaltered by treatment. In Exp. 2, we assigned 8 continental crossbred heifers to either a 45% or 90% concentrate diet; diets were fed for 75 d before euthanasia and ruminal tissue collection. Compared with the 45% concentrate diet, the 90% concentrate diet decreased (P < 0.01) ruminal tissue ANGPTL4 protein abundance. In Exp. 3, we assigned 6 ruminally cannulated lactating Holstein cows to a treatment sequence in replicated 3 × 3 Latin squares and fed a standard lactation diet. Cows were infused with 5 mol/d sodium acetate, sodium propionate, or sodium butyrate for 2 d. Infusions of VFA did not affect (P > 0.10) mRNA or protein abundance of ANGPTL4 in ruminal papillae. Ruminal papillae ANGPTL4 abundance was, however, negatively correlated with (P = 0.01) ruminal VFA concentrations. ANGPTL4 abundance in ruminal tissue decreases in response to very high dietary concentrate and is inversely correlated with ruminal total VFA concentrations.

Using Plant Source as a Buffering Agent to Manipulating Rumen Fermentation in an In vitro Gas Production System

The objective of this study was to investigate the effect of banana flower powder (BAFLOP) supplementation on gas production kinetics and rumen fermentation efficiency in in vitro incubation with different ratios of roughage to concentrate in swamp buffalo and cattle rumen fluid. Two male, rumen fistulated dairy steers and swamp buffaloes were used as rumen fluid donors. The treatments were arranged according to a 2×2×3 factorial arrangement in a Completely randomized design by using two ratios of roughage to concentrate (R:C; 75:25 and 25:75) and 3 levels of BAFLOP supplementation (0, 2 and 4% of dietary substrate) into two different kinds of rumen fluid (beef cattle and swamp buffalo). Under this investigation, the results revealed that the rumen ecology was affected by R:C ratio. The pH declined as a result of using high concentrate ratio; however, supplementation of BAFLOP could buffer the pH which led to an improvement of ruminal efficiency. BAFLOP supplementation affected acetic acid (C2) when the proportion of concentrate was increased. However, there were no effect on total volatile fatty acid (TVFA) and butyric acid (C4) by BAFLOP supplementation. The microbial community was affected by BAFLOP supplementation, especially the bacterial population. As revealed by real-time PCR, the populations of F. succinogenes and R. albus were reduced by the high concentrate treatments while that of R. flavafaciens were increased. The populations of three dominant cellulolytic bacteria were enhanced by BAFLOP supplementation, especially on high concentrate diet. BAFLOP supplementation did not influence the ammonia nitrogen (NH₃-N) concentration, while R:C did. In addition, the in vitro digestibility was improved by either R:C or BAFLOP supplementation. The BAFLOP supplementation showed an effect on gas production kinetics, except for the gas production rate constant for the insoluble fraction (c), while treatments with high concentrate ratio resulted in the highest values. In addition, BAFLOP tended to increase gas production. Based on this study, it could be concluded that R:C had an effect on rumen ecology both in buffalo and cattle rumen fluid and hence, BAFLOP could be used as a rumen buffering agent for enhancing rumen ecology fed on high concentrate diet. It is recommended that level of BAFLOP supplementation should be at 2 to 4% of total dry matter of substrate. However, in vivo trials should be subsequently conducted to investigate the effect of BAFLOP in high concentrate diets on rumen ecology as well as ruminant production.

Effect of carbohydrate sources and levels of cotton seed meal in concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in young dairy bulls

The objective of this study was to investigate the effect of levels of cottonseed meal with various carbohydrate sources in concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in dairy bulls. Four, 6 months old dairy bulls were randomly assigned to receive four dietary treatments according to a 2×2 factorial arrangement in a 4×4 Latin square design. Factor A was carbohydrate source; cassava chip (CC) and cassava chip+rice bran in the ratio of 3:1 (CR3:1), and factor B was cotton seed meal levels in the concentrate; 109 g CP/kg (LCM) and 328 g CP/kg (HCM) at similar overall CP levels (490 g CP/kg). Bulls received urea-lime treated rice straw ad libitum and were supplemented with 10 g of concentrate/kg BW. It was found that carbohydrate source and level of cotton seed meal did not have significant effects on ruminal pH, ammonia nitrogen concentration, microbial protein synthesis or feed intake. Animals which received CC showed significantly higher BUN concentration, ruminal propionic acid and butyric acid proportions, while dry matter, organic matter digestibility, populations of total viable bacteria and proteolytic bacteria were lower than those in the CR3:1 treatment. The concentration of total volatile fatty acids was higher in HCM than LCM treatments, while the concentration of butyric acid was higher in LCM than HCM treatments. The population of proteolytic bacteria with the LCM treatments was higher than the HCM treatments; however other bacteria groups were similar among the different levels of cotton seed meal. Bulls which received LCM had higher protein digestibility than those receiving HCM. Therefore, using high levels of cassava chip and cotton seed meal might positively impact on energy and nitrogen balance for the microbial population in the rumen of the young dairy bull.

Effect of Saccharomyces cerevisiae Fermentation Product on Lactation Performance and Lipopolysaccharide Concentration of Dairy Cows

To evaluate lactation performance and changes in plasma and fecal lipopolysaccharide (LPS) concentrations in response to the supplementation of Saccharomyces cerevisiae fermentation product (SC), two dairy farms were selected. On each farm, 32 cows in early to mid lactation (21 to 140 DIM) were blocked by parity and days in milk (DIM), and randomly assigned to one of the two treatments within block (Control or 56 g SC/cow/d). Effect of SC on lactation performance (daily) and changes in blood and fecal LPS level were examined on d 0 and 28 of supplementation. The results showed that SC supplementation increased lactation performance of dairy cows on both farms. On Farm 1, milk production, 3.5% fat corrected milk (FCM), and yield of milk fat and protein were greater (p<0.01) for cows supplemented with SC. Supplementation of SC increased percentage milk fat (p = 0.029) from 81 to 110 DIM. There was no significant effect (p>0.05) of SC supplementation on percentage of milk protein, dry matter intake and feed efficiency. On Farm 2, cows supplemented with SC had a greater (p<0.05) milk yield, percentage of milk fat and milk protein, yield of milk fat and protein, 3.5% FCM and feed efficiency. Supplemental SC had no effect on LPS concentrations in feces (p>0.05) while it trended to reduce (p = 0.07 or 0.207) the concentration in plasma. The results indicate that supplemental SC can increase lactation performance of dairy cattle and has potential for reducing plasma LPS concentration.

Influence of Rain Tree Pod Meal Supplementation on Rice Straw Based Diets Using In vitro Gas Fermentation Technique

The objective of this study was to determine the roughage to concentrate (R:C) ratio with rain tree pod meal (RPM) supplementation on in vitro fermentation using gas production technique. The experiment design was a 6×4 factorial arrangement in a CRD. Factor A was 6 levels of R:C ratio (100:0, 80:20, 60:40, 40:60, 20:80 and 0:100) and factor B was 4 levels of RPM (0, 4, 8 and 12 mg). It was found that gas kinetic, extent rate (c) was linearly increased (p<0.01) with an increasing level of concentrate while cumulative gas production (96 h) was higher in R:C of 40:60. In addition, interaction of R:C ratio and RPM level affected NH3-N and IVDMD and were highest in R:C of 0:100 with 0, 4 mg of RPM and 40:60 with 8 mg of RPM, respectively. Moreover, interaction of R:C ratio and RPM level significantly increased total volatile fatty acids and propionate concentration whereas lower acetate, acetate to propionate ratios and CH4 production in R:C of 20:80 with 8 mg of RPM. Moreover, the two factors, R:C ratio and RPM level influenced the protozoal population and the percentage of methanogens in the total bacteria population. In addition, the use of real-time PCR found that a high level of concentrate in the diet remarkably decreased three cellulolytic bacteria numbers (F. succinogenes, R. flavefaciens and R. albus). Based on this study, it is suggested that the ratio of R:C at 40:60 and RPM level at 12 mg could improve ruminal fluid fermentation in terms of reducing fermentation losses, thus improving VFA profiles and ruminal ecology.

Effect of carbohydrate source and cottonseed meal level in the concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in swamp buffaloes

The objective of this study was to investigate the effect of carbohydrate source and cottonseed meal level in the concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in swamp buffaloes. Four, 4-yr old rumen fistulated swamp buffaloes were randomly assigned to receive four dietary treatments according to a 2×2 factorial arrangement in a 4×4 Latin square design. Factor A was carbohydrate source; cassava chip (CC) and CC+rice bran at a ratio 3:1 (CR3:1), and factor B was level of cottonseed meal (CM); 109 g CP/kg (LCM) and 328 g CP/kg (HCM) in isonitrogenous diets (490 g CP/kg). Buffaloes received urea-treated rice straw ad libitum and supplemented with 5 g concentrate/kg BW. It was found that carbohydrate source did not affect feed intake, nutrient intake, digested nutrients, nutrient digestibility, ammonia nitrogen concentration, fungi and bacterial populations, or microbial protein synthesis (p>0.05). Ruminal pH at 6 h after feeding and the population of protozoa at 4 h after feeding were higher when buffalo were fed with CC than in the CR3:1 treatment (p<0.05). Buffalo fed with HCM had a lower roughage intake, nutrient intake, population of total viable and cellulolytic bacteria and microbial nitrogen supply than the LCM fed group (p<0.05). However, nutrient digestibility, ruminal pH, ammonia concentration, population of protozoa and fungi, and efficiency of microbial protein synthesis were not affected by cottonseed meal levels (p>0.05). Based on this experiment, concentrate with a low level of cottonseed meal could be fed with cassava chips as an energy source in swamp buffalo receiving rice straw.

Effect of ground corn cob replacement for cassava chip on feed intake, rumen fermentation and urinary derivatives in swamp buffaloes

Four Thai - rumen fistulated male swamp buffaloes (Bubalus bubalis), about four years old with 400±20 kg liveweight, were randomly assigned according to a 4×4 Latin square design to receive dietary treatments. The treatments were: ground corn cob (GCC) replacement for cassava chip (CC) in concentrate at 0% (T1); GCC replacement at 33% (T2); GCC replacement at 67% (T3); and GCC replacement at 100% (T4), respectively. During the experiment, concentrate was offered at 0.5% BW while 5% urea-treated rice straw was given at ad libitum. The result revealed that there was no effect of GCC replacement on DMI among treatments. In addition, digestibilities of DM, OM and CP were not different while aNDF linearly increased with an increasing level of GCC replacement. However, GCC replacement did not affect rumen fermentation such as ruminal pH, NH₃-N and VFA concentration; except C3 proportion which was the highest at 33% replacement while the lowest was at 100% replacement. All replacements of GCC resulted in similar protozoal and bacterial populations and microbial protein synthesis (MPS). Purine derivatives (PD) concentration in urine and PD to creatinine (PDC) index were varied with time of urination and among treatments at 0 to 8 and 8 to 16 h post feeding and higher values were shown among the GCC replacement groups. However at 16 to 24 h-post feeding, it was untraceable. In addition, creatinine concentration was similar among all treatments at every sampling time. Based on the above results, GCC can be used as an energy source for swamp buffalo fed with rice straw. Spot sampling of urine can be used for purine derivatives determination.

Effect of dietary forage sources on rumen microbiota, rumen fermentation and biogenic amines in dairy cows

BACKGROUND

Fifteen lactating Holstein dairy cows were assigned to three diets in a 3 × 3 Latin square design to evaluate the effects of dietary forage sources on rumen microbiota, rumen fermentation and biogenic amines. Diets were isonitrogenous and isocaloric, with a forage/concentrate ratio of 45:55 (dry matter basis) but different main forage sources, namely cornstalk (CS), Leymus chinensis (LC) or alfalfa hay (AH).

RESULTS

Pyrosequencing of the V3-V6 hypervariable coding region of 16S rRNA revealed that the rumen microbiota was significantly affected by forage sources. AH feeding increased the proportion of genera Prevotella and Selenomonas compared with the CS diet, while CS feeding increased the proportion of genera Anaerotruncus, Papillibacter, Thermoactimoyces, Bacillus and Streptomyces compared with the LC or AH diet. AH and LC feeding both increased the propionate concentration compared with the CS diet. AH feeding decreased the concentrations of tyramine, putrescine and histamine compared with the LC diet.

CONCLUSION

These results indicate that a high proportion of alfalfa hay in the ration is beneficial for milk yield and a healthy and balanced rumen microbiota in lactating cattle. This can be attributed to the higher degradation of rumen organic matter and the more balanced carbohydrates and proteins for optimal rumen microbial growth.

High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism

Diversity in the forestomach microbiome is one of the key features of ruminant animals. The diverse microbial community adapts to a wide array of dietary feedstuffs and management strategies. Understanding rumen microbiome composition, adaptation, and function has global implications ranging from climatology to applied animal production. Classical knowledge of rumen microbiology was based on anaerobic, culture-dependent methods. Next-generation sequencing and other molecular techniques have uncovered novel features of the rumen microbiome. For instance, pyrosequencing of the 16S ribosomal RNA gene has revealed the taxonomic identity of bacteria and archaea to the genus level, and when complemented with barcoding adds multiple samples to a single run. Whole genome shotgun sequencing generates true metagenomic sequences to predict the functional capability of a microbiome, and can also be used to construct genomes of isolated organisms. Integration of high-throughput data describing the rumen microbiome with classic fermentation and animal performance parameters has produced meaningful advances and opened additional areas for study. In this review, we highlight recent studies of the rumen microbiome in the context of cattle production focusing on nutrition, rumen development, animal efficiency, and microbial function.

Effect of dried distillers’ grains and solubles when replacing corn or soybean meal on rumen microbial growth in vitro as measured using DNA as a microbial marker

Castillo-Lopez, E., Klopfenstein, T. J., Fernando, S. C. and Kononoff, P. J. 2014. Effect of dried distillers’ grains and solubles when replacing corn or soybean meal on rumen microbial growth in vitro as measured using DNA as a microbial marker. Can. J. Anim. Sci. 94: 349–356. The objectives were to evaluate the use of rDNA markers to measure the effects of dried distillers’ grains with solubles (DDGS) and the potential treatment×time interaction on microbial crude protein (MCP) synthesis in vitro and secondly to measure the contribution of yeast based protein originating from DDGS. Treatments were: (1) CONT, control with no DDGS, but with alfalfa hay, corn silage, ground corn (GC) and soybean meal (SBM) included at 25% (DM basis); (2) LOWCORN, 20% DDGS (DM basis) replacing GC; (3) LOWSBM, 20% DDGS (DM basis) replacing SBM; and (4) LOWCORNSBM, 20% DDGS (DM basis) replacing 10% GC and 10% SBM. Treatments (0.5 g) were incubated in 50 mL of inoculum in duplicate. At 0, 4, 16, 32, 48 and 96 h of fermentation total DNA was extracted from each treatment and MCP was measured using rDNA markers. The sum of bacterial crude protein (BCP) and protozoal crude protein (PCP) was considered as MCP. Data were analyzed as a completely randomized design. The treatment×time interaction was tested and the SLICE option was included to evaluate the effect of treatment at each fermentation time point. There was a tendency to a treatment×time interaction (P=0.07) for MCP. Specifically, at 16 h, LOWCORNSBM yielded greater (P<0.05) MCP compared to either CONT or LOWCORN with estimates of 68.5, 33.8 and 23.3±8.9 mg g–1DM, for LOWCORNSBM, CONT and LOWCORN, respectively. At 48 h, however, LOWCORN yielded greater MCP (P<0.05) compared with LOWSBM with estimates of 72.2 and 32.5±8.9 mg g–1DM, for LOWCORN and LOWSBM, respectively. Yeast crude protein (YCP) was not affected (P=0.21) and averaged 0.04±0.02 mg g–1of substrate (DM basis). Overall, rDNA markers were effective for quantifying MCP, but further research on the methodology is needed. With DDGS inclusion, MCP was maintained; however, yeast cells were extensively degraded during fermentation.

A Na+-coupled C4-dicarboxylate transporter (Asuc_0304) and aerobic growth of Actinobacillus succinogenes on C4-dicarboxylates

Actinobacillus succinogenes, which is known to produce large amounts of succinate during fermentation of hexoses, was able to grow on C4-dicarboxylates such as fumarate under aerobic and anaerobic conditions. Anaerobic growth on fumarate was stimulated by glycerol and the major product was succinate, indicating the involvement of fumarate respiration similar to succinate production from glucose. The aerobic growth on C4-dicarboxylates and the transport proteins involved were studied. Fumarate was oxidized to acetate. The genome of A. succinogenes encodes six proteins with similarity to secondary C4-dicarboxylate transporters, including transporters of the Dcu (C4-dicarboxylate uptake), DcuC (C4-dicarboxylate uptake C), DASS (divalent anion : sodium symporter) and TDT (tellurite resistance dicarboxylate transporter) family. From the cloned genes, Asuc_0304 of the DASS family protein was able to restore aerobic growth on C4-dicarboxylates in a C4-dicarboxylate-transport-negative Escherichia coli strain. The strain regained succinate or fumarate uptake, which was dependent on the electrochemical proton potential and the presence of Na(+). The transport had an optimum pH ~7, indicating transport of the dianionic C4-dicarboxylates. Transport competition experiments suggested substrate specificity for fumarate and succinate. The transport characteristics for C4-dicarboxylate uptake by cells of aerobically grown A. succinogenes were similar to those of Asuc_0304 expressed in E. coli, suggesting that Asuc_0304 has an important role in aerobic fumarate uptake in A. succinogenes. Asuc_0304 has sequence similarity to bacterial Na(+)-dicarboxylate cotransporters and contains the carboxylate-binding signature. Asuc_0304 was named SdcA (sodium-coupled C4-dicarboxylate transporter from A. succinogenes).

Diversity of rumen bacteria in canadian cervids

Interest in the bacteria responsible for the breakdown of lignocellulosic feedstuffs within the rumen has increased due to their potential utility in industrial applications. To date, most studies have focused on bacteria from domesticated ruminants. We have expanded the knowledge of the microbial ecology of ruminants by examining the bacterial populations found in the rumen of non-domesticated ruminants found in Canada. Next-generation sequencing of 16S rDNA was employed to characterize the liquid and solid-associated bacterial communities in the rumen of elk (Cervus canadensis), and white tailed deer (Odocoileus virginianus). Despite variability in the microbial populations between animals, principle component and weighted UniFrac analysis indicated that bacterial communities in the rumen of elk and white tail deer are distinct. Populations clustered according to individual host animal and not the association with liquid or solid phase of the rumen contents. In all instances, Bacteroidetes and Firmicutes were the dominant bacterial phyla, although the relative abundance of these differed among ruminant species and between phases of rumen digesta, respectively. In the elk samples Bacteroidetes were more predominant in the liquid phase whereas Firmicutes was the most prevalent phyla in the solid digesta (P = 1×10⁻⁵). There were also statistically significant differences in the abundance of OTUs classified as Fibrobacteres (P = 5×10⁻³) and Spirochaetes (P = 3×10⁻⁴) in the solid digesta of the elk samples. We identified a number of OTUs that were classified as phylotypes not previously observed in the rumen environment. Our results suggest that although the bacterial diversity in wild North American ruminants shows overall similarities to domesticated ruminants, we observed a number of OTUs not previously described. Previous studies primarily focusing on domesticated ruminants do not fully represent the microbial diversity of the rumen and studies focusing on non-domesticated ruminants should be expanded.