Symposium on 'Nutritional implications of microbial action in the non-ruminal alimentary tract'. Microbes of nutritional importance in the alimentary tract

Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach

Black Bengal goats possess a rich source of rumen microbiota that helps them to adapt for the better utilization of plant biomaterial into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiota. Therefore the study was designed in order to explore the taxonomic profile of rumen microbial communities and potential biomass degradation enzymes present in the rumen of back Bengal goat using Illumina Nextseq-500 platform. A total of 83.18 million high-quality reads were generated and bioinformatics analysis was performed using various tools and subsequently, the predicted ORFs along with the rRNA containing contigs were then uploaded to MG-RAST to analyze taxonomic and functional profiling. The results highlighted that Bacteriodetes (41.38-59.74%) were the most abundant phyla followed by Firmicutes (30.59-39.96%), Proteobacteria (5.07-7.61%), Euryarcheaota (0.71-7.41%), Actinobacteria (2.05-2.75%). Genes that encode glycoside hydrolases (GHs) had the highest number of CAZymes, and accounted for (39.73-37.88%) of all CAZymes in goat rumen. The GT families were the second-most abundant in CAZymes (23.73-23.11%) and followed by Carbohydrate Binding module Domain (17.65-15.61%), Carbohydrate Esterase (12.90-11.95%). This study indicated that goat rumen had complex functional microorganisms produce numerous CAZymes, and that can be further effectively utilised for applied ruminant research and industry based applications.

Comparison of enteric methane yield and diversity of ruminal methanogens in cattle and buffaloes fed on the same diet

An in vivo study was conducted to compare the enteric methane emissions and diversity of ruminal methanogens in cattle and buffaloes kept in the same environment and fed on the same diet. Six cattle and six buffaloes were fed on a similar diet comprising Napier (Pennisetum purpureum) green grass and concentrate in 70:30. After 90 days of feeding, the daily enteric methane emissions were quantified by using the SF6 technique and ruminal fluid samples from animals were collected for the diversity analysis. The daily enteric methane emissions were significantly greater in cattle as compared to buffaloes; however, methane yields were not different between the two species. Methanogens were ranked at different taxonomic levels against the Rumen and Intestinal Methanogen-Database. The archaeal communities in both host species were dominated by the phylum Euryarchaeota; however, Crenarchaeota represented <1% of the total archaea. Methanogens affiliated with Methanobacteriales were most prominent and their proportion did not differ between the two hosts. Methanomicrobiales and Methanomassillicoccales constituted the second largest group of methanogens in cattle and buffaloes, respectively. Methanocellales (Methanocella arvoryza) were exclusively detected in the buffaloes. At the species level, Methanobrevibacter gottschalkii had the highest abundance (55-57%) in both the host species. The relative abundance of Methanobrevibacter wolinii between the two hosts differed significantly. Methanosarcinales, the acetoclastic methanogens were significantly greater in cattle than the buffaloes. It is concluded that the ruminal methane yield in cattle and buffaloes fed on the same diet did not differ. With the diet used in this study, there was a limited influence (<3.5%) of the host on the structure of the ruminal archaea community at the species level. Therefore, the methane mitigation strategies developed in either of the hosts should be effective in the other. Further studies are warranted to reveal the conjunctive effect of diet and geographical locations with the host on ruminal archaea community composition.

Symposium review: Understanding diet-microbe interactions to enhance productivity of dairy cows

Ruminants are dependent on the microbiota (bacteria, protozoa, archaea, and fungi) that inhabit the reticulo-rumen for digestion of feedstuffs. Nearly 70% of energy and 50% of protein requirements for dairy cows are met by microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next-generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements, and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to aid in our understanding of the functional relevance of microbial genomes. In particular, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients so that we can more fully understand the physiology of feed digestion in the rumen. Application of genomics-based approaches offers promise in unraveling microbial niches and respective gene repertoires to potentiate fiber and nonfiber carbohydrate digestion, microbial protein synthesis, and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.

Feed and water deprivation has a negative but transient effect on the rumen kinetics of Bos indicus steers

The effects on rumen kinetics after feed and water had been deprived for 72 hr were studied using four fistulated Bos indicus steers. The animals were assigned in a 2 × 4 crossover design with two treatments: feed and water ad libitum (control) and no feed and water for 72 hr (deprived) with four steers per treatment over two time periods. Feed and water deprivation caused decreases in the numbers of cellulolytic bacteria (1.4 vs. 0.4 cfu × 10⁶ /ml; p = .001), live (23.7 vs. 0.8 × 10⁹ /ml; p = .001), dead (12.7 vs. 0.5 × 10⁹ /ml; p = .001) and total bacterial counts (36.4 vs. 1.4 × 10⁹ /ml; p = .001) at day 0, compared with the control treatment. However, the deprived group had greater numbers of cellulolytic bacteria (2.7 vs. 50.1 cfu × 10⁶ /ml; p = .001), live (18.3 vs. 42.2 × 10⁹ /ml; p = .001), dead (6. 5 vs. 19.1 × 10⁹ /ml; p = .001) and total bacterial counts (24.8 vs. 61.3 × 10⁹ /ml; p = .001) from rumen fluid on day 4, compared with the control treatment. The numbers of protozoa in rumen fluid from the deprived group were less than (551.2 vs. 2.4 × 10³ /ml; p = .001) the control group on day 0. However, the deprived treatment had fewer protozoa in rumen fluid than the control treatment on day 4 (p = .001) and day 9 (p = .001). Volatile fatty acids and in vitro gas production as functional measurements of rumen fluid followed the same trend as the bacterial and protozoa populations. These results indicate that feed and water deprivation would have a negative but transient effect on the rumen kinetics of Bos indicus steers.

Experimental Study and ANN Dual-Time Scale Perturbation Model of Electrokinetic Properties of Microbiota

The electrokinetic properties of the rumen microbiota are involved in cell surface adhesion and microbial metabolism. An in vitro study was carried out in batch culture to determine the effects of three levels of special surface area (SSA) of biomaterials and four levels of surface tension (ST) of culture medium on electrokinetic properties (Zeta potential, ξ; electrokinetic mobility, μe), fermentation parameters (volatile fatty acids, VFAs), and ST over fermentation processes (ST-a, γ). The obtained results were combined with previously published data (digestibility, D; pH; concentration of ammonia nitrogen, c(NH3-N)) to establish a predictive artificial neural network (ANN) model. Concepts of dual-time series analysis, perturbation theory (PT), and Box-Jenkins Operators were applied for the first time to develop an ANN model to predict the variations of the electrokinetic properties of microbiota. The best dual-time series Radial Basis Functions (RBR) model for ξ of rumen microbiota predicted ξ for >30,000 cases with a correlation coefficient >0.8. This model provided insight into the correlations between electrokinetic property (zeta potential) of rumen microbiota and the perturbations of physical factors (specific surface area and surface tension) of media, digestibility of substrate, and their metabolites (NH3-N, VFAs) in relation to environmental factors.

Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies

Cattle with high feed efficiencies (designated "efficient") produce less methane gas than those with low feed efficiencies (designated "inefficient"); however, the role of the methane producers in such difference is unknown. This study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. Two 16S rRNA libraries were constructed using approximately 800-bp amplicons generated from pooled total DNA isolated from efficient (n = 29) and inefficient (n = 29) animals. Sequence analysis of up to 490 randomly selected clones from each library showed that the methanogenic composition was variable: less species variation (22 operational taxonomic units [OTUs]) was detected in the rumens of efficient animals, compared to 27 OTUs in inefficient animals. The methanogenic communities in inefficient animals were more diverse than those in efficient ones, as revealed by the diversity indices of 0.84 and 0.42, respectively. Differences at the strain and genotype levels were also observed and found to be associated with feed efficiency in the host. No difference was detected in the total population of methanogens, but the prevalences of Methanosphaera stadtmanae and Methanobrevibacter sp. strain AbM4 were 1.92 (P < 0.05) and 2.26 (P < 0.05) times higher in inefficient animals, while Methanobrevibacter sp. strain AbM4 was reported for the first time to occur in the bovine rumen. Our data indicate that the methanogenic ecology at the species, strain, and/or genotype level in the rumen may play important roles in contributing to the difference in methane gas production between cattle with different feed efficiencies.

Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics

The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.

Transformation and expression of an anaerobic fungal xylanase in several strains of the rumen bacterium Butyrivibrio fibrisolvens

AIMS

To obtain reliable transformation of a range of Butyrivibrio fibrisolvens strains and to express a Neocallimastix patriciarum xylanase gene in the recipients.

METHODS AND RESULTS

Eight strains (H17c, E14, LP1309, LP1028, AR11a, OB156, LP210B and LP461A) of Bu. fibrisolvens were transformed by the Gram-positive vector pUB110. A xylanase expression/secretion cassette containing Bu. fibrisolvens promoter and signal peptide elements fused to catalytic domain II of the N. patriciarum xylanase A cDNA (xynANp) was inserted into pUB110 to create the plasmid pUBxynA. pUBxynA was used to transform seven of the Bu. fibrisolvens strains transformed by pUB110. In strain H17c pUBxynA, which produced native xylanase, 2.46 U mg-1 total xylanase activity was produced with 45% extracellular xylanase. In strain H17c pUMSX, 0.74 U mg-1 total xylanase activity was produced with 98% extracellular xylanase. H17c pUBxynA exhibited increased (28.7%) degradation of neutral detergent fibre compared with unmodified H17c; however, progressive loss of pUBxynA was observed in long-term cultivation.

CONCLUSIONS

A stable transformation system was developed that was applicable for a range of Bu. fibrisolvens strains and high levels of expression of a recombinant xylanase were obtained in H17c which lead to increased fibre digestion.

SIGNIFICANCE AND IMPACT OF THE STUDY

This stable transformation system with the accompanying recombinant plasmids will be a useful tool for further investigation aimed at improving ruminal fibre digestion.

Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes

Digestibility of fibre in ruminants may be improved by the introduction of highly fibrolytic strains of ruminal bacteria. This approach may be feasible if, for example, strains of Ruminococcus that are significantly more fibrolytic than the normal population of Ruminococcus are used for inoculation purposes. Introduced strains of bacteria, irrespective of ecosystem, often decline after inoculation, and in this study, highly fibrolytic strains of Ruminococcus were continuously dosed to ensure that measurements of fibre digestion were made in the presence of significant numbers of the introduced bacteria. During dosing the total culturable count increased significantly (P<0.05), but declined post-dosing. The level of dosed Ruminococcus, and total Ruminococcus, Fibrobacter succinogenes and eukaryotes measured by 16S rRNA probes increased significantly (P<0.05) during the dosing period, but also declined post-dosing. When in vitro nylon bag digestibility, feed intake or whole-tract digestibility was measured, no improvement could be measured.

The effects of nonautoclaved and autoclaved water-soluble wheat extracts on the growth of Clostridium perfringens

Clostridium perfringens is the causative agent of necrotic enteritis, a commonly diagnosed disease in chickens that is also observed in turkeys and geese. Two trials were conducted to determine the in vitro effect of filter-sterilized, water-soluble wheat extracts on the growth of C. perfringens. The extracts were either nonautoclaved or autoclaved at 121 C for 40 min and were used to reconstitute thioglycolate broth media. Results of this study suggest that growth of C. perfringens is suppressed in vitro by inclusion of either extract. Glycosyl composition analysis revealed no significant differences in arabinose, xylose, or mannose content between the nonautoclaved and autoclaved extracts. Galactose, glucose, and total glycosyl content were significantly higher in the nonautoclaved extract.

Acesulfame K, cyclamate and saccharin inhibit the anaerobic fermentation of glucose by intestinal bacteria

The caecal microflora of Cara rats was incubated in the pH stat with glucose under anaerobic conditions, and the acid production was measured. In the presence of the sweeteners Acesulfame K, Cyclamate and Saccharin, inhibition of the fermentation of glucose was observed with ED50 values of 260, 251, and 140 mM, respectively. The nutritional relevance of these observations is probably slight; an interpretation in terms of bacterial physiology leads to the proposal that the sweeteners may act on glucose transport systems at the bacterial cytomembrane.

Dose dependence of breath hydrogen and methane in healthy volunteers after ingestion of a commercial disaccharide mixture, Palatinit

Breath hydrogen and methane were determined by gas chromatography in eleven normal individuals given a low-fibre, mixed diet (control) and after ingestion of 20-50 g Palatinit/d, an equimolar mixture of D-glucosyl-alpha(1----1)-D-mannitol and D-glucosyl-alpha(1----6)-D-glucitol (Isomalt). A linear relation was found (r 0.85; P less than 0.001) between the amount of Palatinit ingested and breath H2 per 10 h in subjects who did not exhale methane. If methane was formed in addition to H2, the sum of both gases followed a linear dose-effect relation. The mouth-to-caecum time, indicated by the first increase in breath H2 after ingestion, was shortened by about half, yet no sign of diarrhoea was observed. Stool weight and stool frequency did not change significantly. The linear relation between a dose of 20-50 g Palatinit and exhalation of H2 (eventually plus methane) indicated that a relatively constant fraction of the dose given underwent cleavage and absorption in the small intestine, the remainder being transported into the large bowel. Microbial gas formation in the colon as well as the fractional transfer of these gases into the expiratory air occurred at fixed proportions, thus allowing an insight into colonic microbial contributions to carbohydrate utilization in the human large bowel.

Effect of Acarbose on the production of hydrogen and methane and on hormonal parameters in young adults under standardized low-fibre mixed diets

Short and middle term effects of Acarbose were studied in volunteers on a standardized, low-fibre, mixed diet for the development of tolerance phenomena with gas exhalations and some peptide hormone levels as main parameters. Both hydrogen and methane were measured quantitatively as diurnal profiles. Acarbose caused an about 20-fold increase of H2 exhalation and had only moderate effects on methane production, indicating the presence of fermentable carbohydrates in the large bowel. Methanogenic individuals exhaled significantly less H2 than did non-methanogenic subjects. Changes in blood glucose, serum insulin, GIP, gastrin, and plasma glucagon, caused by Acarbose, reflected delayed glucose absorption and were plausible within the regulatory framework of carbohydrate assimilation. When the Acarbose regime was maintained for 5 weeks on a controlled diet, abdominal sensations like e.g. meteorism declined remarkably while carbohydrate fermentation remained high and lowered GIP was sustained. Thus functional responses of the gastro-intestinal tract to altered carbohydrate supplies, elicited by Acarbose, were found by 3 independent parameters: anaerobic gas production, peptide hormone levels, and subjective abdominal sensations. The objective parameters seem to remain constant in the longer run, while subjective parameters show long-term adaptation.