Populations of select cultured and uncultured bacteria in the rumen of sheep and the effect of diets and ruminal fractions

Changes in Rumen Microbiology and Metabolism of Tibetan Sheep with Different Lys/Met Ratios in Low-Protein Diets

In ruminants, supplementing appropriate amounts of amino acids improves growth, feed utilization efficiency, and productivity. This study aimed to assess the effects of different Lys/Met ratios on the ruminal microbial community and the metabolic profiling in Tibetan sheep using 16S rDNA sequencing and non-target metabolomics. Ninety-two-month-old Tibetan rams (initial weight = 15.37 ± 0.92 kg) were divided into three groups and fed lysine/methionine (Lys/Met) of 1:1 (LP-L), 2:1 (LP-M), and 3:1 (LP-H) in low-protein diet, respectively. Results: The T-AOC, GSH-Px, and SOD were significantly higher in the LP-L group than in LP-H and LP-M groups (p < 0.05). Cellulase activity was significantly higher in the LP-L group than in the LP-H group (p < 0.05). In the fermentation parameters, acetic acid concentration was significantly higher in the LP-L group than in the LP-H group (p < 0.05). Microbial sequencing analysis showed that Ace and Chao1 indicators were significantly higher in LP-L than in LP-H and LP-M (p < 0.05). At the genus level, the abundance of Rikenellaceae RC9 gut group flora and Succiniclasticum were significantly higher in LP-L than in LP-M group (p < 0.05). Non-target metabolomics analyses revealed that the levels of phosphoric acid, pyrocatechol, hydrocinnamic acid, banzamide, l-gulono-1,4-lactone, cis-jasmone, Val-Asp-Arg, and tropinone content were higher in LP-L. However, l-citrulline and purine levels were lower in the LP-L group than in the LP-M and LP-H groups. Banzamide, cis-jasmone, and Val-Asp-Arg contents were positively correlated with the phenotypic contents, including T-AOC, SOD, and cellulase. Phosphoric acid content was positively correlated with cellulase and lipase activities. In conclusion, the Met/Lys ratio of 1:1 in low-protein diets showed superior antioxidant status and cellulase activity in the rumen by modulating the microbiota and metabolism of Tibetan sheep.

Rumen-Protected Lysine and Methionine Supplementation Reduced Protein Requirement of Holstein Bulls by Altering Nitrogen Metabolism in Liver

The aim of this study was to investigate the effect of low-protein diets supplemented with rumen-protected lysine (RPLys) and methionine (RPMet) on growth performance, rumen fermentation, blood biochemical parameters, nitrogen metabolism, and gene expression related to N metabolism in the liver of Holstein bulls. Thirty-six healthy and disease-free Holstein bulls with a similar body weight (BW) (424 ± 15 kg, 13 months old) were selected. According to their BW, they were randomly divided into three groups with 12 bulls in each group in a completely randomized design. The control group (D1) was fed with a high-protein basal diet (CP13%), while bulls in two low-protein groups were supplied a diet with 11% crude protein and RPLys 34 g/d·head + RPMet 2 g/d·head (low protein with low RPAA, T2) or RPLys 55 g/d·head + RPMet 9 g/d·head (low protein with high RPAA, T3). At the end of the experiment, the feces and urine of dairy bulls were collected for three consecutive days. Blood and rumen fluid were collected before morning feeding, and liver samples were collected after slaughtering. The results showed that the average daily gain (ADG) of bulls in the T3 group was higher than those in D1 (p < 0.05). Compared with D1, a significantly higher nitrogen utilization rate (p < 0.05) and serum IGF-1 content (p < 0.05) were observed in both T2 and T3 groups; however, blood urea nitrogen (BUN) content was significantly lower in the T2 and T3 groups (p < 0.05). The content of acetic acid in the rumen of the T3 group was significantly higher than that of the D1 group. No significant differences were observed among the different groups (p > 0.05) in relation to the alpha diversity. Compared with D1, the relative abundance of Christensenellaceae_R-7_group in T3 was higher (p < 0.05), while that of Prevotellaceae _YAB2003_group and Succinivibrio were lower (p < 0.05). Compared with D1 and T2 group, the T3 group showed an expression of messenger ribonucleic acid (mRNA) that is associated with (CPS-1, ASS1, OTC, ARG) and (N-AGS, S6K1, eIF4B, mTORC1) in liver; moreover, the T3 group was significantly enhanced (p < 0.05). Overall, our results indicated that low dietary protein (11%) levels added with RPAA (RPLys 55 g/d +RPMet 9 g/d) can benefit the growth performance of Holstein bulls by reducing nitrogen excretion and enhancing nitrogen efficiency in the liver.

Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes

Antimicrobial growth promoters (AGPs) are commonly used in broiler production. There is a huge societal concern around their use and their contribution to the proliferation of antimicrobial resistance (AMR) in food-producing animals and dissemination to humans or the environment. However, there is a paucity of comprehensive experimental data on their impact on poultry production and the AMR resistome. Here, we investigated the effect of five antimicrobial growth promoters (virginiamycin, chlortetracycline, bacitracin methyl disalicylate, lincomycin, and tylosin) used in the commercial broiler production in the Indian subcontinent and in the different parts of the world for three consecutive production cycles on performance variables and also the impact on gut bacteria, bacteriophage, and resistome profile using culture-independent approaches. There was no significant effect of AGPs on the cumulative growth or feed efficiency parameters at the end of the production cycles and cumulative mortality rates were also similar across groups. Many antibiotic resistance genes (ARGs) were ubiquitous in the chicken gut irrespective of AGP supplementation. In total, 62 ARGs from 15 antimicrobial classes were detected. Supplementation of AGPs influenced the selection of several classes of ARGs; however, this was not correlated necessarily with genes relevant to the AGP drug class; some AGPs favored the selection of ARGs related to antimicrobials not structurally related to the AGP. AGPs did not impact the gut bacterial community structure, including alpha or beta diversity significantly, with only 16-20 operational taxonomic units (OTUs) of bacteria being altered significantly. However, several AGPs significantly reduced the population density of some of the potential pathogenic genera of bacteria, such as Escherichia coli. Chlortetracycline increased the abundance of Escherichia phage, whereas other AGPs did not influence the abundance of bacteriophage significantly. Considering the evidence that AGPs used in poultry production can select for resistance to more than one class of antimicrobial resistance, and the fact that their effect on performance is not significant, their use needs to be reduced and there is a need to monitor the spread of ARGs in broiler chicken farms.

Ruminal bacterial community is associated with the variations of total milk solid content in Holstein lactating cows

Total milk solid (TMS) content directly reflects the quality of milk. Rumen bacteria ferment dietary components, the process of which generates the precursors for the synthesis of milk solid, therefore, the variation in rumen bacterial community could be associated with milk solid in dairy cows. In this study, 45 healthy mid-lactation Holstein dairy cows with the similar body weight, lactation stage, and milk yield were initially used for the selection of 10 cows with high TMS (HS) and 10 cows with low TMS (LS). All those animals were under the same feeding management, and the individual milk yield was recorded for 14 consecutive days before milk and rumen fluid were sampled. Rumen fluid was used to determine bacterial community by 16S rRNA gene sequencing technique. The HS cows had significantly greater feed intake and milk TMS, fat, protein content than LS cows (P < 0.05). Among the volatile fatty acids (VFA), propionic acid and valeric acid concentrations were significantly greater in HS cows than those in LS cows (P < 0.05). There was no significant difference in the concentrations of acetate, butyrate, isobutyrate, valerate, and the total VFA (P > 0.05), nor was the acetate-to-propionate ratio, pH value, ammonia nitrogen and microbial crude protein concentrations (P > 0.05). Significant differences in the relative abundances of some bacterial genera were found between HS and LS cows. Spearman’s rank correlation analysis revealed that TMS content was correlated positively with the abundances of Ruminococcaceae UCG-014, Ruminococcaceae NK4A214 group, Prevotellaceae UCG-001, Butyrivibrio 2, Prevotellaceae UCG-003, Candidatus Saccharimonas, Ruminococcus 2, Lachnospiraceae XPB1014 group, probable genus 10, Eubacterium ventriosum group, but negatively correlated with Pyramidobacte. In addition, Ruminococcaceae UCG-014, Ruminococcus 2, Ruminococcaceae UCG001, probable genus 10 and Eubacterium ventriosum group might boost the total VFA production in the rumen. In conclusion, the dry matter intake of dairy cows and some special bacteria in rumen were significantly associated with TMS content, which suggests the potential function of rumen bacteria contributing to TMS content in dairy cows.

Fertilizer stabilizers reduce nitrous oxide emissions from agricultural soil by targeting microbial nitrogen transformations

Nitrous oxide (N₂O) is a pollutant released from agriculture soils following N fertilizer application. N stabilizers, such as N-(n-butyl) thiophosphoric triamide (NBPT) and 3,4-dimethylpyrazole phosphate (DMPP) could mitigate these N₂O emissions when applied with fertilizer. Here, field experiments were conducted to investigate the microbial mechanisms by which NBPT and DMPP mitigate N₂O emissions following urea application. We determined dynamic N₂O emissions and inorganic N concentrations for two wheat seasons and combined this with metagenomic sequencing. Application of NBPT, DMPP, and both NBPT and DMPP together with urea decreased mean N₂O accumulative emissions by 77.8, 91.4 and 90.7%, respectively, compared with urea application alone, mainly via repressing the increase in NO₂^- concentration after N fertilization. Sequencing results indicated that urea application enriched microorganisms that were positively correlated with N₂O production, whereas N stabilizers enriched microorganisms that were negatively correlated with N₂O production. Furthermore, compared to urea application alone, NBPT with urea reduced the abundances of genes related to denitrification, including napA/nasA, nirS/nirK, and norBC, resulting in a higher soil NO₃^- pool. Conversely, DMPP application, either alone or together with NBPT, decreased the abundance of genes involved in ammonia oxidation and denitrification, including amoCAB, hao, napA/nasA, nirS/nirK, and norBC, and maintained a greater soil NH₄⁺ pool. Both N stabilizers resulted in similar abundances of nirABD-which is related to NO₂^- reducers-as when no N fertilizer was applied, which could prevent NO₂^- accumulation, consequently mitigating N₂O emissions. These findings suggest that the high effectiveness of N stabilizers on mitigating N₂O emissions could be attributed to changes to soil microbial communities and N-cycling functional genes to control the by-product or intermediate products of microbial N-cycling processes in agricultural soils.

Effect of barley straw and Egyptian clover hay on the rumen fermentation and structure and fibrolytic activities of rumen bacteria in dromedary camel

Background and Aim

Understanding the regulations of rumen microbiota and their fibrolytic capabilities under different forages are essential to improve rumen fermentation and animal feed efficiency. This study aimed to evaluate the changes in the rumen fermentation and the structure and fibrolytic activities of rumen bacteria in camels fed barley straw and Egyptian clover hay.

Materials and Methods

Three fistulated camels were fed a diet containing barley straw for 30 days; then transitioned to a diet containing Egyptian clover hay for 30 days. In addition, bacterial media enriched with xylan and different cellulose sources, namely, filter paper, wheat straw, and alfalfa hay, were used to evaluate the ability of camel rumen bacteria to produce xylanase and cellulase enzymes.

Results

The camel group fed Egyptian clover hay showed higher crude protein intake, rumen ammonia, total volatile fatty acids, and acetic acid. Moreover, the camel group fed barley straw showed higher neutral detergent fiber intake, rumen pH, and propionic and butyric acids. Principal component analysis showed that bacterial communities were separated based on the forage type. Forage type affected the composition of rumen bacteria and most of the bacterial community was assigned to phylum Bacteroidetes and Firmicutes. Egyptian clover hay diet increased the proportions of genus Prevotella and Ruminococcus; while fed barley straw diet increased the Butyrivibrio, RC9_gut_group, and Fibrobacteres. The bacterial culture of the Egyptian clover hay fed group produced the greatest xylanase and the bacterial culture of the barley straw fed group produced the maximum cellulase.

Conclusion

Egyptian clover hay is recommended to feed camels in intensive production. Moreover, the bacterial community in the camel rumen is a promising source of lignocellulolytic enzymes.

Inhibition of methanogenesis by nitrate, with or without defaunation, in continuous culture

Within the rumen, nitrate can serve as an alternative sink for aqueous hydrogen [H₂(aq)] accumulating during fermentation, producing nitrite, which ideally is further reduced to ammonium but can accumulate under conditions not yet explained. Defaunation has also been associated with decreased methanogenesis in meta-analyses because protozoa contribute significantly to H₂ production. In the present study, we applied a 2 × 2 factorial treatment arrangement in a 4 × 4 Latin square design to dual-flow continuous culture fermentors (n = 4). Treatments were control without nitrate (-NO₃^-) versus with nitrate (+NO₃^-; 1.5% of diet dry matter), factorialized with normal protozoa (faunated, FAUN) versus defaunation (DEF) by decreasing the temperature moderately and changing filters over the first 4 d of incubation. We detected no main effects of DEF or interaction of faunation status with +NO₃^-. The main effect of +NO₃^- increased H₂(aq) by 11.0 µM (+117%) compared with -NO₃^-. The main effect of +NO₃^- also decreased daily CH₄ production by 8.17 mmol CH₄/d (31%) compared with -NO₃^-. Because there were no treatment effects on neutral detergent fiber digestibility, the main effect of +NO₃^- also decreased CH₄ production by 1.43 mmol of CH₄/g of neutral detergent fiber degraded compared with -NO₃^-. There were no effects of treatment on other nutrient digestibilities, N flow, or microbial N flow per gram of nutrient digested. The spike in H₂(aq) after feeding NO₃^- provides evidence that methanogenesis is inhibited by substrate access rather than concentration, regardless of defaunation, or by direct inhibition of NO₂^-. Methanogens were not decreased by defaunation, suggesting a compensatory increase in non-protozoa-associated methanogens or an insignificant contribution of protozoa-associated methanogens. Despite adaptive reduction of NO₃^- to NH₄⁺ and methane inhibition in continuous culture, practical considerations such as potential to depress dry matter intake and on-farm ration variability should be addressed before considering NO₃^- as an avenue for greater sustainability of greenhouse gas emissions in US dairy production.

Inhibition of Rumen Protozoa by Specific Inhibitors of Lysozyme and Peptidases in vitro

Defaunation studies have shown that rumen protozoa are one of the main causes of low nitrogen utilization efficiency due to their bacterivory and subsequent intraruminal cycling of microbial protein in ruminants. In genomic and transcriptomic studies, we found that rumen protozoa expressed lysozymes and peptidases at high levels. We hypothesized that specific inhibition of lysozyme and peptidases could reduce the activity and growth of rumen protozoa, which can decrease their predation of microbes and proteolysis and subsequent ammoniagenesis by rumen microbiota. To test the above hypothesis, we evaluated three specific inhibitors: imidazole (IMI), a lysozyme inhibitor; phenylmethylsulphonyl fluoride (PMSF), a serine protease inhibitor; and iodoacetamide (IOD), a cysteine protease inhibitor; both individually and in combinations, with sodium dodecyl sulfate (SDS) as a positive control. Rumen fluid was collected from two Jersey dairy cows fed either a concentrate-based dairy ration or only alfalfa hay. Each protozoa-enriched rumen fluid was incubated for 24 h with or without the aforementioned inhibitors and fed a mixture of ground wheat grain, alfalfa, and grass hays to support microbial growth. Live protozoa cells were morphologically identified and counted simultaneously at 3, 6, 12, and 24 h of incubation. Fermentation characteristics and prokaryotic composition were determined and compared at the end of the incubation. Except for IOD, all the inhibitors reduced all the nine protozoal genera identified, but to different extents, in a time-dependent manner. IOD was the least inhibitory to protozoa, but it lowered ammoniagenesis the most while not decreasing feed digestibility or concentration of volatile fatty acids (VFA). ANCOM analysis identified loss of Fibrobacter and overgrowth of Treponema, Streptococcus, and Succinivibrio in several inhibitor treatments. Functional prediction (from 16S rRNA gene amplicon sequences) using the CowPI database showed that the inhibitors decreased the relative abundance of the genes encoding amino acid metabolism, especially peptidases, and lysosome in the rumen microbiota. Overall, inhibition of protozoa resulted in alteration of prokaryotic microbiota and in vitro fermentation, and peptidases, especially cysteine-peptidase, may be targeted to improve nitrogen utilization in ruminants.

Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach

Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.

Modifications and optimization of manual methods for polymerase chain reaction and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta

Background and Aim:

A critical prerequisite for studying rumen microbial community by high throughput molecular biology methods is good quality community DNA. Current methods of extraction use kits designed for samples from the different origin for rumen. This puts stress on the development of a relevant manual method for DNA extraction. The objective of this study was to modify the existing methods of community DNA extraction and thereby systematic comparison of their efficiency based on DNA yield, purity, 16S rRNA gene sequencing, and identification to determine the optimal DNA extraction methods whose DNA products reflect targeted bacterial communities special to rumen.

Materials and Methods:

Enzymatic method, Chemical method, Enzymatic + Chemical method, and Enzymatic + Chemical + Physical method were modified toward evaluation of community DNA extraction from solid, squeezed, and liquid fractions of goat rumen digesta. Each method was assessed critically for nucleic acid yield and its quality. The methods resulting in high nucleic acid yield, optimal purity ratios with intact band on agarose gel electrophoresis were optimized further. Optimized methods were studied using standard polymerase chain reaction (PCR) with universal bacterial primers and 16S rRNA primers of targeted rumen bacteria. Methods denoting the presence of targeted rumen bacteria were assessed further with 16S rRNA gene sequencing and identification studies. It led toward methods efficacy estimation for molecular biology applications. Effect of rumen sample preservation on community DNA extraction was also studied. Their mean standard deviation values were calculated to understand sampling criticality.

Results:

Modified Chemical method (Cetrimonium bromide) and Enzymatic+Chemical+Physical (ECP) method (Lysozyme-Cetrimonium bromide-Sodium Dodecyl Sulfate-freeze-thaw) could extract 835 ng/µl and 161 ng/µl community DNA from 1.5 g solid and 2 ml squeezed rumen digesta with purity ratios of 1.8 (A_260nm/A_{280 nm}) and 2.3 (A_260nm/A_{230 nm}) respectively. Comparative analysis showed the better efficiency of ECP method and chemical method toward freshly squeezed rumen digesta and solid rumen digesta. However, sample preservation at −80°C for 1.5 months drastically affected the yield and purity ratios of community DNA. New protocol revealed targeted microbial community having Gram-positive as well as Gram-negative bacteria such as Prevotella ruminicola, Streptococcus lutetiensis, Ruminococcus flavefaciens, Fibrobacter succinogenes, and Selenomonas ruminantium.

Conclusion:

To date, this is the first report of modified methods wherein least chemicals and steps lead toward PCR and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta. Detection of targeted rumen bacteria in solid and squeezed rumen digesta proves their strongest association with rumen fiber mat. It also marks the presence of distinct microbial communities in solid and squeezed rumen fractions that in turn differs the performance of each different method employed and yield of nucleic acid obtained. It also leaves a possibility of the presence of complex microbial consortia in squeezed rumen digesta whose DNA extraction methods need more attention. Finally, manual protocols of community DNA extraction may vary in different ruminant which suggests undertaking rigorous research in their establishment.

Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation

Nitrogenous emissions from ruminant livestock production are of increasing public concern and, together with methane, contribute to environmental pollution. The main cause of nitrogen-(N)-containing emissions is the inadequate provision of N to ruminants, leading to an excess of ammonia in the rumen, which is subsequently excreted. Depending on the size and molecular structure, various bacterial, protozoal and fungal species are involved in the ruminal breakdown of nitrogenous compounds (NC). Decelerating ruminal NC degradation by controlling the abundance and activity of proteolytic and deaminating microorganisms, but without reducing cellulolytic processes, is a promising strategy to decrease N emissions along with increasing N utilization by ruminants. Different dietary options, including among others the treatment of feedstuffs with heat or the application of diverse feed additives, as well as vaccination against rumen microorganisms or their enzymes have been evaluated. Thereby, reduced productions of microbial metabolites, e.g. ammonia, and increased microbial N flows give evidence for an improved N retention. However, linkage between these findings and alterations in the rumen microbiota composition, particularly NC-degrading microbes, remains sparse and contradictory findings confound the exact evaluation of these manipulating strategies, thus emphasizing the need for comprehensive research. The demand for increased sustainability in ruminant livestock production requests to apply attention to microbial N utilization efficiency and this will require a better understanding of underlying metabolic processes as well as composition and interactions of ruminal NC-degrading microorganisms.

Isolation and identification of a cellulolytic Enterobacter from rumen of Aceh cattle

Aims:

The aim of this study was to isolate and identify a cellulolytic bacterium from the rumen fluid of Aceh’s cattle. Biodegradation by cellulolytic rumen bacteria can be used as a source of cellulolytic bacteria that act to degrade feed fibrous material so as to improve the quality of nutrients and digestibility of feed ingredients at a cheaper price than the use of commercial cellulase enzymes.

Materials and Methods:

Samples were collected from rumen fluid of Aceh’s cattle in Abattoirs (RPH) of Banda Aceh city, Indonesia, isolation, and screening of cellulolytic bacteria were done in Microbiology Laboratory, Faculty of Veterinary Medicine, Syiah Kuala University, Banda Aceh, Indonesia.

Results:

The S1 isolates showed ±2.5 cm of clear zone diameter. Microscopically, this strain was found to be a Gram-negative, Bacillus. Homology and phylogenetic tree analysis of 16S rRNA showed that S1 isolate has 91% of sequence similarity with that of Enterobacter cloacae. 91% sequence homology shown in this study proved that the S1 isolate is probably either a new species or another genus of Enterobacteriaceae.

Conclusion:

Current study suggests that cellulose hydrolytic bacteria isolated from rumen fluid of Aceh cattle on Bushnell Haas medium-carboxymethylcellulose agar, and some potent cellulose degrading bacteria have been identified.

Metagenomic investigation of gastrointestinal microbiome in cattle

The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980’s to the late early 2000’s greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy

Biochemical pathways of methanogenesis and methanotrophy coupled with carbon (C)-nitrogen (N) metabolism were studied in long term (13years) manured systems in lowland rice paddy through metagenomics approach. Manured systems included in this study were, control (exclusion of application of any manure), farm yard manure (FYM, @5Mgha^-1yr^-1) and green manuring (GM with Sesbania aculeata). Metagenomic sequence data revealed the dominance of C decomposing bacterial communities' like Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Acidobacteria, in manure amended soils as compared to control. Diversities for assimilatory and dissimilatory N-fixing microorganisms at phylum level were found higher under GM as compared to rest. Two genera responsible for methanogenesis, viz. Methanolobus and Methanotorris were absent in manured systems as compared to control. The acetoclastic and serine pathway was found as the predominant pathway for methanogenesis and methanotrophy, respectively, in tropical lowland rice paddy. Abundance reads of enzymes were in the range of 254-445 in the acetoclastic methanogenesis pathway. On the other hand, these were varied from 165 to 216 in serine pathway of methanotrophy. Lowland paddy soil exhibited higher functional and structural diversities in manured systems as compared to unamended control in respect to labile C pools and CH₄ production. Methane (CH₄) emission was 31% higher in FYM system than GM. However, nitrous oxide (N₂O) emission was found 25% higher in GM as compared to FYM. As a whole, bacterial diversities were higher under FYM system in tropical lowland rice paddy as compared to GM and unamended systems.

Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder

Moringa oleifera (M. oleifera) is a remarkable species with high nutritional value and good biomass production, which can be used as livestock fodder. In this study, we examined changes in the faecal microbiota of thirty dairy cows in response to alternative M. oleifera diets and their effects on nutrient digestion, milk traits and the faecal concentrations of short-chain fatty acids. No differences in milk yield and constituents were found between the control and the M. oleifera alternative groups. Cows fed M. oleifera silage had lower dry matter digestibility, as well as the propionate and isovalerate concentrations in M. oleifera treated group. Using 16S rDNA gene sequencing, 1,299,556 paired-end reads were obtained. Clustering analysis revealed 13 phyla and 93 genera across all samples. Firmicutes and Bacteroidetes were the co-dominant phyla. Ten taxa displayed a significant difference in response to the high M. oleifera diet. In addition, strong correlations between Akkermansia and Prevotella with milk yield and protein indicated that some bacterial groups could be used to improve milk traits. Our results provided an insight into the microbiome-associated responses to M. oleifera in livestock diets, and could aid the development of novel applications of M. oleifera.

Use of Lysozyme as a Feed Additive on In vitro Rumen Fermentation and Methane Emission

This study was conducted to determine the effect of lysozyme addition on in vitro rumen fermentation and to identify the lysozyme inclusion rate for abating methane (CH₄) production. An in vitro ruminal fermentation technique was done using a commercial concentrate to rice straw ratio of 8:2 as substrate. The following treatments were applied wherein lysozyme was added into 1 mg dry matter substrate at different levels of inclusion: Without lysozyme, 2,000, 4,000, and 8,000 U lysozyme. Results revealed that, lysozyme addition had a significant effect on pH after 24 h of incubation, with the highest pH (p<0.01) observed in 8,000 U lysozyme, followed by the 4,000 U, 2,000 U, and without lysozyme. The highest amounts of acetic acid, propionic acid (p<0.01) and total volatile fatty acid (TVFA) (p<0.05) were found in 8,000 U after 24 h of incubation. The CH₄ concentration was the lowest in the 8,000 U and the highest in the without lysozyme addition after 24 h of incubation. There was no significant differences in general bacteria, methanogen, or protozoan DNA copy number. So far, addition of lysozyme increased the acetate, propionate, TVFA, and decreased CH₄ concentration. These results suggest that lysozyme supplementation may improve in vitro rumen fermentation and reduce CH₄ emission.

Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations

BACKGROUND

Rumen microbiome has a great influence on ruminant health and productivity. Different plant extracts have been tested for their ability to modulate the rumen microbiome to improve feed digestion and fermentation. Among the evaluated plant extracts, essential oils, tannins, and saponins appeared to have positive effects on rumen protein metabolism, volatile fatty acids production, and methane and ammonia production.

METHODS

The objective of this study was to evaluate the effect of rosemary (Rosmarinus officinalis L.) leaves and essential oils on rumen microbial populations. Four ruminally cannulated sheep were used in a 4×4 Latin square design fed (21 d/period): 1) a control diet composed of alfalfa hay and concentrate pellet (CTR), 2) CTR supplemented with 7 g/d/sheep of rosemary essential oil adsorbed on an inert support (EO), 3) CTR with 10 g/d/sheep of dried and ground rosemary leaves (RL), and 4) CTR with 10 g/d of dried and ground rosemary leaves pelleted into concentrate (RL pellet). Abundance of total bacteria, archaea, protozoa, and some select bacterial species or groups was quantified using qPCR, while the community of bacteria and archaea was profiled using denaturing gradient gel electrophoresis.

RESULTS

No difference in abundance was noted for total bacteria, protozoa, or Ruminococcus flavefaciens between the control and the treatments, but the rosemary leaves, either in loose form or in pellet, decreased the abundance of archaea and the genus Prevotella (P < 0.001). The rosemary leaves in loose form also decreased (P < 0.001) the abundance of Ruminococcus albus and Clostridium aminophilum, while the EO increased (P < 0.001) the abundance of Fibrobacter succinogenes. The community of bacteria and archaea was not affected by any of the supplements.

CONCLUSIONS

Being able to affect the abundance of several groups of rumen microbes that are known to be involved in degradation of protein and fiber and production of methane and ammonia, rosemary leaves may be used to modulate rumen microbiome and its function.

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO2T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management.

Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation

Research is being conducted with the objective of decreasing methane (CH4) production in the rumen, as methane emissions from ruminants are environmentally damaging and a loss of digestible energy to ruminants. Inhibiting ruminal methanogenesis generally results in accumulation of dihydrogen (H2), which is energetically inefficient and can inhibit fermentation. It would be nutritionally beneficial to incorporate accumulated H2 into propionate or butyrate production, or reductive acetogenesis. The objective of this analysis was to examine three possible physicochemical limitations to the incorporation of accumulated H2 into propionate and butyrate production, and reductive acetogenesis, in methanogenesis-inhibited ruminal batch and continuous cultures: (i) Thermodynamics; (ii) Enzyme kinetics; (iii) Substrate kinetics. Batch (N = 109) and continuous (N = 43) culture databases of experiments with at least 50% inhibition in CH4 production were used in this meta-analysis. Incorporation of accumulated H2 into propionate production and reductive acetogenesis seemed to be thermodynamically feasible but quite close to equilibrium, whereas this was less clear for butyrate. With regard to enzyme kinetics, it was speculated that hydrogenases of ruminal microorganisms may have evolved toward high-affinity and low maximal velocity to compete for traces of H2, rather than for high pressure accumulated H2. Responses so far obtained to the addition of propionate production intermediates do not allow distinguishing between thermodynamic and substrate kinetics control.

Effects of different sources of physically effective fiber on rumen microbial populations

Physically effective fiber is needed by dairy cattle to prevent ruminal acidosis. This study aimed to examine the effects of different sources of physically effective fiber on the populations of fibrolytic bacteria and methanogens. Five ruminally cannulated Holstein cows were each fed five diets differing in physically effective fiber sources over 15 weeks (21 days/period) in a Latin Square design: (1) 44.1% corn silage, (2) 34.0% corn silage plus 11.5% alfalfa hay, (3) 34.0% corn silage plus 5.1% wheat straw, (4) 36.1% corn silage plus 10.1% wheat straw, and (5) 34.0% corn silage plus 5.5% corn stover. The impact of the physically effective fiber sources on total bacteria and archaea were examined using denaturing gradient gel electrophoresis. Specific real-time PCR assays were used to quantify total bacteria, total archaea, the genus Butyrivibrio, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens and three uncultured rumen bacteria that were identified from adhering ruminal fractions in a previous study. No significant differences were observed among the different sources of physical effective fiber with respect to the microbial populations quantified. Any of the physically effective fiber sources may be fed to dairy cattle without negative impact on the ruminal microbial community.

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing

The digestive systems of mammals harbor a complex gut microbiome, comprising bacteria and other microorganisms that confer metabolic and immunological benefits to the host. Ruminants that digest plant-based foods have a four-compartment stomach consisting of the rumen, reticulum, omasum, and abomasum. The microorganisms in the stomach are essential for providing the host with critical nutrients. However, the majority of these microorganisms are unknown species. The microbiome of the stomach is diverse, and the majority of these organisms cannot be cultured. Next-generation sequencing (NGS) combined with bioinformatic analysis tools have allowed the dissection of the composition of the microbiome in samples collected from a specific environment. In this study, for the first time, the bacterial composition in two compartments, the reticulum and the omasum, of bovine were analyzed using a metagenomic approach and compared to the bacterial composition of the rumen. These data will assist in understanding the biology of ruminants and benefit the agricultural industry. The diversity and composition of the bacterial community in samples collected from the rumen, reticulum, and omasum of bovines in the Changchun Region of Northeast China were analyzed by sequencing the V3 region of the 16S rRNA gene using a barcoded Illumina paired-end sequencing technique, and the primary composition of the microbiome in the rumen, reticulum, and omasum of the bovines was determined. These microbiomes contained 17 phyla and 107 genera in all three samples. Five phyla, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, and Lentisphaerae, were the most abundant taxonomic groups. Additionally, the different stomach compartments harbored different compositions of the microorganisms.

Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis

BACKGROUND

Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a glycocalyx, and cellulosomes. Here, we used a combination of comparative genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7.

RESULTS

A comparison of the R. albus 7 genome sequence against the genome sequences of related bacteria that either encode or do not encode cellulosomes revealed that R. albus 7 does not encode for most canonical cellulosomal components. Fermentation analysis of R. albus 7 revealed the ability to produce ethanol and acetate on a wide range of fibrous substrates in vitro. Global transcriptomic analysis of R. albus 7 grown at identical dilution rates on cellulose and cellobiose in a chemostat showed that this bacterium, when growing on cellulose, utilizes a carbohydrate-degrading strategy that involves increased transcription of the rare carbohydrate-binding module (CBM) family 37 domain and the tryptophan biosynthetic operon.

CONCLUSIONS

Our data suggest that R. albus 7 does not use canonical cellulosomal components to degrade cellulose, but rather up-regulates the expression of CBM37-containing enzymes and tryptophan biosynthesis. This study contributes to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.

High potential source for biomass degradation enzyme discovery and environmental aspects revealed through metagenomics of Indian buffalo rumen

The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs). We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs), carbohydrate binding module (CBM: 23 contigs), glycosyl transferase (GT: 373 contigs), carbohydrate esterases (CE: 259 contigs), and polysaccharide lyases (PE: 16 contigs). The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.

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.

Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet

Rumen microbiome represents rich source of enzymes degrading complex plant polysaccharides. We describe here analysis of Carbohydrate Active Enzymes (CAZymes) from 3.5 gigabase sequences of metagenomic data from rumen samples of Mehsani buffaloes fed on different proportions of green or dry roughages to concentrate ration. A total of 2597 contigs encoding putative CAZymes were identified by CAZyme Analysis Toolkit (CAT). The phylogenetic analysis of these contigs by MG-RAST revealed predominance of Bacteroidetes, followed by Firmicutes, Proteobacteria, and Actinobacteria phyla. Moreover, a higher abundance of oligosaccharide degrading and debranching enzymes in buffalo rumen metagenome and that of cellulases and hemicellulases in termite hindgut was observed when we compared glycoside hydrolase (GH) profile of buffalo rumen metagenome with cow rumen, termite hindgut and chicken caecum metagenome. Further, comparison of microbial profile of green or dry roughage fed animals showed significantly higher abundance (p-value<0.05) of various polysaccharide degrading bacterial genera like Fibrobacter, Prevotella, Bacteroides, Clostridium and Ruminococcus in green roughage fed animals. In addition, we found a significantly higher abundance (p-value<0.05) of enzymes associated with pectin digestion such as pectin lyase (PL) 1, PL10 and GH28 in green roughage fed animals. Our study outlines CAZyme profile of buffalo rumen metagenome and provides a scope to study the role of abundant enzyme families (oligosaccharide degrading and debranching enzymes) in digestion of coarse feed.

Variations in 16S rRNA-based microbiome profiling between pyrosequencing runs and between pyrosequencing facilities

Pyrosequencing of 16S rRNA gene amplicons on the 454 FLX Titanium platform has been widely used to analyze microbiomes in various environments. However, different results may stem from variations among sequencing runs or among sequencing facilities. This study aimed to evaluate these variations between different pyrosequencing runs by sequencing 16S rRNA gene amplicon libraries generated from three sets of rumen samples twice each on the 454 FLX Titanium system at two independent sequencing facilities. Similar relative abundances were found for predominant taxa represented by large numbers of sequence reads but not for minor taxa represented by small numbers of sequence reads. The two sequencing facilities revealed different bacterial profiles with respect to both predominant taxa and minor taxa, including the most predominant genus Prevotella, the family Lachnospiraceae, and the phylum Proteobacteria. Differences in primers used to generate amplicon libraries may be a major source of variations in microbiome profiling. Because different primers and regions of 16S rRNA genes are often used by different researchers, significant variations likely exist among studies. Quantitative interpretation for relative abundance of taxa, especially minor taxa, from prevalence of sequence reads and comparisons of results from different studies should be done with caution.

An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass- and tree-based diets

AIMS

To measure the impact of supplementing a forage diet with tree-based browse on the ruminal bacterial communities of Nigerian West African Dwarf (WAD) sheep.

METHODS AND RESULTS

Fifteen WAD sheep were fed a control diet of forage (Panicum maximum), with 12 animals shifted in groups of three to one of four browse-supplemented diets (Albizia saman, Bridelia micrantha, Ficus sur, or Gmelina arborea). These browse plants were shown in a concurrent but separate study to be reasonably nutritious (based on chemical composition and fibre constituents) and nontoxic (based on tannin, phytate, saponin, alkaloid and oxalate levels). Rumen liquids and solids for DNA extraction were collected via intubation from two animals in each group before and after dietary shift. Bacterial 16S rRNA gene regions V6-V8 were sequenced by 454 pyrosequencing. All communities were highly diverse and dominated by the phyla Firmicutes, Bacteroidetes, Tenericutes, Actinobacteria and Proteobacteria. All communities shared members of the genera Butryivibrio, Prevotella and Ruminococcus. Our analysis defined a core sets of bacteria shared by all animals, forage-fed animals and browse-fed animals. Community structure shifted dramatically in animals fed A. saman or G. arborea.

CONCLUSIONS

The impact of tree-based browse on the ruminal bacterial community of Nigerian WAD sheep varies by browse species, likely due to differences in browse composition.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study describes the first neotropical small ruminant bacterial microbiome and supports diet supplementation with specific tree-based browse for WAD sheep.

Investigation of bacterial diversity in the feces of cattle fed different diets

The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.

Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product

The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant prefeeding. Seven of the target taxa were more abundant in either the liquid or solid fractions of ruminal digesta. By accounting for the total mass of liquid and solid fractions in the rumen and the relative abundance of total bacteria in each fraction, it was estimated that 92% of total bacteria were found in the solid digesta fraction.

Effects of quillaja and yucca saponins on communities and select populations of rumen bacteria and archaea, and fermentation in vitro

AIMS

The objective of this study was to comprehensively evaluate quillaja (QSP) and yucca saponin (YSP) products with respect to their effects on diversity of rumen bacteria and archaea, abundance of selected microbes, and feed degradability and fermentation.

METHODS AND RESULTS

Both QSP and YSP at doses 0-0.6 g l(-1) tended to increase degradability of feed substrate in in vitro rumen cultures, but to different extents. Neither one of the saponins affected the concentrations of ammonia, total volatile fatty acids, or molar proportion of acetate. However, QSP increased molar proportion of propionate and decreased that of butyrate, whereas YSP tended to decrease that of butyrate. As determined by qPCR, QSP and YSP did not affect the abundance of total bacteria or Ruminococcus albus. The QSP did not affect the abundances of Fibrobacter succinogenes or genus Prevotella, but tended to decrease that of Ruminococcus flavefaciens, whereas YSP significantly increased the abundance of R. flavefaciens and Prevotella, and numerically increased that of F. succinogenes. Both saponins increased archaeal abundance, although to small magnitudes (0.3-0.4 log). The protozoal populations were decreased significantly by QSP, but not by YSP. Based on DGGE and T-RFLP analysis, both saponins altered the bacterial community and species organization, but less so the archaeal community.

CONCLUSIONS

This study demonstrated that saponins, although not effective in mitigating methane emission, may improve feed utilization at low doses, and modulate ruminal microbial communities in a dose-dependent manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study suggest that saponins at low doses may directly stimulate the growth of some rumen bacteria including cellulolytic bacteria, thus improving digestibility of feeds, independent of their defaunation activity. In contrast, saponins at high doses modulate rumen fermentation characteristically similar to defaunation.

Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets

Background

The number and diversity of uncultured ruminal bacterial and archaeal species revealed by 16S rRNA gene (rrs) sequences greatly exceeds that of cultured bacteria and archaea. However, the significance of uncultured microbes remains undetermined. The objective of this study was to assess the numeric importance of select uncultured bacteria and cultured bacteria and the impact of diets and microenvironments within cow rumen in a comparative manner.

Results

Liquid and adherent fractions were obtained from the rumen of Jersey cattle fed hay alone and Holstein cattle fed hay plus grain. The populations of cultured and uncultured bacteria present in each fraction were quantified using specific real-time PCR assays. The population of total bacteria was similar between fractions or diets, while total archaea was numerically higher in the hay-fed Jersey cattle than in the hay-grain-fed Holstein cattle. The population of the genus Prevotella was about one log smaller than that of total bacteria. The populations of Fibrobacter succinogenes, Ruminococcus flavefaciens, the genus Butyrivibrio, and R. albus was at least one log smaller than that of genus Prevotella. Four of the six uncultured bacteria quantified were as abundant as F. succinogenes, R. flavefaciens and the genus Butyrivibrio. In addition, the populations of several uncultured bacteria were significantly higher in the adherent fractions than in the liquid fractions. These uncultured bacteria may be associated with fiber degradation.

Conclusions

Some uncultured bacteria are as abundant as those of major cultured bacteria in the rumen. Uncultured bacteria may have important contribution to ruminal fermentation. Population dynamic studies of uncultured bacteria in a comparative manner can help reveal their ecological features and importance to rumen functions.

Effects of essential oils on methane production and fermentation by, and abundance and diversity of, rumen microbial populations

Five essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were tested in vitro at 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, cellulolytic bacteria, archaea, and protozoa. All the EOs significantly reduced methane production with increasing doses, with reductions by 34.4%, 17.6%, 42.3%, 87%, and 25.7% for CLO, EUO, GAO, ORO, and PEO, respectively, at 1.0 g/liter compared with the control. However, apparent degradability of dry matter and neutral detergent fiber also decreased linearly with increasing doses by all EOs except GAO. The concentrations of total volatile fatty acids were not affected by GAO, EUO, or PEO but altered linearly and quadratically by CLO and ORO, respectively. All the EOs also differed in altering the molar proportions of acetate, propionate, and butyrate. As determined by quantitative real-time PCR, all the EOs decreased the abundance of archaea, protozoa, and major cellulolytic bacteria (i.e., Fibrobacter succinogenes, Ruminococcus flavefaciens, and R. albus) linearly with increasing EO doses. On the basis of denaturing gradient gel electrophoresis analysis, different EOs changed the composition of both archaeal and bacterial communities to different extents. The Shannon-Wiener diversity index (H') was reduced for archaea by all EOs in a dose-dependent manner but increased for bacteria at low and medium doses (0.25 and 0.50 g/liter) for all EOs except ORO. Due to the adverse effects on feed digestion and fermentation at high doses, a single EO may not effectively and practically mitigate methane emission from ruminants unless used at low doses in combinations with other antimethanogenic compounds.