Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes

Loss of Myostatin leads to low production of CH4 by altering rumen microbiota and metabolome in cattle

Myostatin (MSTN) is a protein that plays a crucial role in regulating skeletal muscle development. Despite the known benefits of MSTN mutant cattle for increasing beef production, their potential impact on CH4 emissions has not been quantified. The study comparing wild-type (WT) cattle to MSTN-knockout (MSTN-KO) cattle revealed that CH4 production was lower. Macrogenomic analysis revealed a significant decrease in rumen archaea, with reduced Richness indices (P = 0.036). The MSTN-KO cattle also showed altered archaea distribution and composition at different taxonomic levels. LEfSe results showed changes in 21 methanogenic archaea clades, with obligately hydrogen (H2)-dependent methylotrophs Candidatus Methanoplasma termitum species belonging to Methanomassiliicoccales order demonstrating the most significant decrease. Rumen metabolites revealed a decrease in the ratio of acetate to propionate, indicating a shift in rumen fermentation pattern towards propionate fermentation. Additionally, the changing trend of methanogenic archaea is consistent with the evolution of methanogens, and this is correlated with the higher levels of linoleic acid in the rumen of MSTN-KO cattle. Linoleic acid affects the utilization of H2 by methanogenic archaea, leading to a reduction in obligately H2-dependent methylotrophs. Our study suggests that MSTN-KO cattle have potential as an economically and ecologically benign breed for reducing methane emissions.

Partial replacement of soybean meal with microalgae biomass on in vitro ruminal fermentation may reduce ruminal protein degradation

The objective of this study was to evaluate the effects of partially replacing soybean meal (SBM) with algal sources on in vitro ruminal fermentation. Using 6 fermenters in a 3 × 3 replicated Latin square with 3 periods of 10 d each, we tested 3 treatments: a control diet (CRT) with SBM at 17.8% of the diet dry matter (DM); and 50% SBM biomass replacement with either Chlorella pyrenoidosa (CHL); or Spirulina platensis (SPI). The basal diet was formulated to meet the requirements of a 680-kg Holstein dairy cow producing 45 kg/d of milk with 3.5% fat and 3% protein. All diets had a similar nutritional composition (16.0% CP; 34.9% NDF; 31.0% starch, DM basis) and fermenters were provided with 106 g DM/d split into 2 portions. After 7 d of adaptation, samples were collected for 3 d of each period for analyses of ruminal fermentation at 0, 1, 2, 4, 6, and 8 h after morning feeding for evaluation of the ruminal fermentation kinetics. For the evaluation of the daily production of total metabolites and for the evaluation of nutrient degradability, samples from the effluent containers were collected daily. Statistical analysis was performed with the MIXED procedure of SAS with treatment, time, and their interactions considered as fixed effects; day, square, and fermenter were considered as random effects. Orthogonal contrasts (CRT vs. algae; and CHL vs. SPI) were used to depict the treatment effect, and significance was declared when P ≤ 0.05. Fermenters that received algae-based diets had a greater propionate molar concentration and molar proportion when compared with the fermenters fed CRT diets. In addition, those algae-fed fermenters had lower branched short-chain fatty acids (BSCFA) and isoacids (IA), which are biomarkers of ruminal protein degradation, along with lower ammonia (NH3-N) concentration and greater nonammonia nitrogen (NAN). When contrasting with fermenters fed SPI-diets, fermenters fed based CHL-diets had a lower molar concentration of BSCFA and IA, along with lower NH3-N concentration and flow, and greater NAN, bacterial nitrogen flow, and efficiency of nitrogen utilization. Those results indicate that CHL protein may be more resistant to ruminal degradation, which would increase efficiency of nitrogen utilization. In summary, partially replacing SBM with algae biomass, especially with CHL, is a promising strategy to improve the efficiency of nitrogen utilization, due to the fact that fermenters fed CHL-based diets resulted in a reduction in BSCFA and IA, which are markers of protein degradation, and it would improve the efficiency of nitrogen utilization. However, further validation using in vivo models are required.

Simulating Rumen Conditions Using an Anaerobic Dynamic Membrane Bioreactor to Enhance Hydrolysis of Lignocellulosic Biomass

An anaerobic dynamic membrane bioreactor (AnDMBR) mimicking rumen conditions was developed to enhance the hydrolysis of lignocellulosic materials and the production of volatile fatty acids (VFAs) when treating food waste. The AnDMBR was inoculated with cow rumen content and operated at a 0.5 day hydraulic retention time, 2-4 day solids retention time, a temperature of 39 °C, and a pH of 6.3, characteristics similar to those of a rumen. Removal rates of neutral detergent fiber and acid detergent fiber of 58.9 ± 8.4 and 69.0 ± 8.6%, respectively, and a VFA yield of 0.55 ± 0.12 g VFA as chemical oxygen demand g volatile solids (VS)fed-1 were observed at an organic loading rate of 18 ± 2 kg VS m-3 day-1. The composition and activity of the microbial community remained consistent after biofilm disruption, bioreactor upset, and reinoculation. Up to 66.7 ± 5.7% of the active microbial populations and 51.0 ± 7.0% of the total microbial populations present in the rumen-mimicking AnDMBR originated from the inoculum. This study offers a strategy to leverage the features of a rumen; the AnDMBR achieved high hydrolysis and fermentation rates even when treating substrates different from those fed to ruminants.

Methane mitigation in ruminants with structural analogues and other chemical compounds targeting archaeal methanogenesis pathways

Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.

In vitro evaluation of microencapsulated organic acids and pure botanicals as a supplement in lactating dairy cows diet on in vitro ruminal fermentation

The utilization of microencapsulated organic acids and pure botanicals (mOAPB) is widely used in the monogastric livestock industry as an alternative to antibiotics; in addition, it can have gut immunomodulatory functions. More recently, an interest in applying those compounds in the ruminant industry has increased; thus, we evaluated the effects of mOAPB on ruminal fermentation kinetics and metabolite production in an in vitro dual-flow continuous-culture system. For this study, two ruminal cannulated lactating dairy Holstein cows were used as ruminal content donors, and the inoculum was incubated in eight fermenters arranged in a 4 × 4 Latin square design. The basal diet was formulated to meet the nutritional requirements of a 680-kg Holstein dairy cow producing 45 kg/d of milk and supplemented with increasing levels of mOAPB (0; 0.12; 0.24; or 0.36% of dry matter [DM]), which contained 55.6% hydrogenated and refined palm oil, 25% citric acid, 16.7% sorbic acid, 1.7% thymol, and 1% vanillin. Diet had 16.1 CP, 30.9 neutral detergent fiber (NDF), and 32.0 starch, % of DM basis, and fermenters were fed 106 g/d split into two feedings. After a 7 d adaptation, samples were collected for 3 d in each period. Samples of the ruminal content from the fermenters were collected at 0, 1, 2, 4, 6, and 8 h postmorning feeding for evaluation of the ruminal fermentation kinetics. For the evaluation of the daily production of total metabolites and for the evaluation of nutrient degradability, samples from the effluent containers were collected daily at days 8 to 10. The statistical analysis was conducted using MIXED procedure of SAS and treatment, time, and its interactions were considered as fixed effects and day, Latin square, and fermenter as random effects. To depict the treatment effects, orthogonal contrasts were used (linear and quadratic). The supplementation of mOAPB had no major effects on the ruminal fermentation, metabolite production, and degradability of nutrients. The lack of statistical differences between control and supplemented fermenters indicates effective ruminal protection and minor ruminal effects of the active compounds. This could be attributed to the range of daily variation of pH, which ranged from 5.98 to 6.45. The pH can play a major role in the solubilization of lipid coat. It can be concluded that mOAPB did not affect the ruminal fermentation, metabolite production, and degradability of dietary nutrients using an in vitro rumen simulator.

Methane Reduction Potential of Brown Seaweeds and Their Influence on Nutrient Degradation and Microbiota Composition in a Rumen Simulation Technique

This study aimed to investigate the effects of two brown Icelandic seaweed samples (Ascophyllum nodosum and Fucus vesiculosus) on in vitro methane production, nutrient degradation, and microbiota composition. A total mixed ration (TMR) was incubated alone as control or together with each seaweed at two inclusion levels (2.5 and 5.0% on a dry matter basis) in a long-term rumen simulation technique (Rusitec) experiment. The incubation period lasted 14 days, with 7 days of adaptation and sampling. The methane concentration of total gas produced was decreased at the 5% inclusion level of A. nodosum and F. vesiculosus by 8.9 and 3.6%, respectively (P < 0.001). The total gas production was reduced by all seaweeds, with a greater reduction for the 5% seaweed inclusion level (P < 0.001). Feed nutrient degradation and the production of volatile fatty acids and ammonia in the effluent were also reduced, mostly with a bigger effect for the 5% inclusion level of both seaweeds, indicating a reduced overall fermentation (all P ≤ 0.001). Microbiota composition was analyzed by sequencing 16S rRNA amplicons from the rumen content of the donor cows, fermenter liquid and effluent at days 7 and 13, and feed residues at day 13. Relative abundances of the most abundant methanogens varied between the rumen fluid used for the start of incubation and the samples taken at day 7, as well as between days 7 and 13 in both fermenter liquid and effluent (P < 0.05). According to the differential abundance analysis with q2-ALDEx2, in effluent and fermenter liquid samples, archaeal and bacterial amplicon sequence variants were separated into two groups (P < 0.05). One was more abundant in samples taken from the treatment without seaweed supplementation, while the other one prevailed in seaweed supplemented treatments. This group also showed a dose-dependent response to seaweed inclusion, with a greater number of differentially abundant members between a 5% inclusion level and unsupplemented samples than between a 2.5% inclusion level and TMR. Although supplementation of both seaweeds at a 5% inclusion level decreased methane concentration in the total gas due to the high iodine content in the seaweeds tested, the application of practical feeding should be done with caution.

Effect of Methane Inhibitors on Ruminal Microbiota During Early Life and Its Relationship With Ruminal Metabolism and Growth in Calves

The present study aimed to determine whether dietary supplementation with methanogen inhibitors during early life may lead to an imprint on the rumen microbial community and change the rumen function and performance of calves to 49-weeks of rearing. Twenty-four 4-day-old Friesian x Jersey cross calves were randomly assigned into a control and a treatment group. Treated calves were fed a combination of chloroform (CF) and 9,10-anthraquinone (AQ) in the solid diets during the first 12 weeks of rearing. Afterward, calves were grouped by treatments until week 14, and then managed as a single group on pasture. Solid diets and water were offered ad libitum. Methane measurements, and sample collections for rumen metabolite and microbial community composition were carried out at the end of weeks 2, 4, 6, 8, 10, 14, 24 and 49. Animal growth and dry matter intake (DMI) were regularly monitored over the duration of the experiment. Methane emissions decreased up to 90% whilst hydrogen emissions increased in treated compared to control calves, but only for up to 2 weeks after treatment cessation. The near complete methane inhibition did not affect calves’ DMI and growth. The acetate:propionate ratio decreased in treated compared to control calves during the first 14 weeks but was similar at weeks 24 and 49. The proportions of Methanobrevibacter and Methanosphaera decreased in treated compared to control calves during the first 14 weeks; however, at week 24 and 49 the archaea community was similar between groups. Bacterial proportions at the phylum level and the abundant bacterial genera were similar between treatment groups. In summary, methane inhibition increased hydrogen emissions, altered the methanogen community and changed the rumen metabolite profile without major effects on the bacterial community composition. This indicated that the main response of the bacterial community was not a change in composition but rather a change in metabolic pathways. Furthermore, once methane inhibition ceased the methanogen community, rumen metabolites and hydrogen emissions became similar between treatment groups, indicating that perhaps using the treatments tested in this study, it is not possible to imprint a low methane microbiota into the rumen in the solid feed of pre-weaned calves.

PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System

The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.

Comparisons of bacterial and archaeal communities in the rumen and a dual-flow continuous culture fermentation system using amplicon sequencing

Dual-flow continuous culture (CC) fermenters are commonly used to study rumen fermentation in vitro. Research using culture-based and oligonucleotide techniques has shown that certain microbial populations within fermenters may be maintained at abundances similar to those observed in vivo. In this study, bacterial and archaeal communities in the rumen of dairy cattle and in a dual-flow CC fermentation system were compared using high-throughput amplicon sequencing targeting the V4 hypervariable region of 16S rRNA. We hypothesized that the in vitro system harbored a comparable bacterial and archaeal community to that observed in the rumen. Members of the Bacteroidetes and Firmicutes made up the 2 most abundant phyla in the rumen, inoculum, and fermenters and did not differ among sample types (P > 0.10). Similarly, Prevotellaceae, the most abundant family in all 3 sample types, did not differ based on source (P = 0.80). However, beta diversity analyses revealed that bacterial and archaeal communities differed between fermenters and rumen samples (P ≤ 0.001), but fermenter bacterial and archaeal communities stabilized by day 4 of each period. While the overall bacterial and archaeal community differs between natural rumens and those detected in in vitro fermenter systems, several prominent taxa were maintained at similar relative abundances suggesting that fermenters may provide a suitable environment in which to study shifts among the predominant members of the microbial community.

Isolation and characterization of a new Methanoculleus bourgensis strain KOR-2 from the rumen of Holstein steers

Objective

To isolate and identify new methanogens from the rumen of Holstein steers in Korea.

Methods

Representative rumen contents were obtained from three ruminally cannulated Holstein steers (793±8 kg). Pre-reduced media were used for the growth and isolation of methanogens. Optimum growth temperature, pH, and sodium chloride (NaCl) concentration as well as substrate utilization and antibiotic tolerance were investigated to determine the physiological characteristics of the isolated strain. Furthermore, the isolate was microscopically studied for its morphology. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification.

Results

One strain designated as KOR-2 was isolated and found to be a non-motile irregular coccus with a diameter of 0.2 to 0.5 μm. KOR-2 utilized H₂+CO₂ and formate but was unable to metabolize acetate, methanol, trimethylamine, 2-propanol, and isobutanol for growth and methane production. The optimum temperature and pH for the growth of KOR-2 were 38°C and 6.8 to 7.0, respectively, while the optimum NaCl concentration essential for KOR-2 growth was 1.0% (w/v). KOR-2 tolerated ampicillin, penicillin G, kanamycin, spectromycin, and tetracycline. In contrast, the cell growth was inhibited by chloramphenicol. Phylogenetic analysis of 16S rRNA and mcrA genes revealed the relatedness between KOR-2 and Methanoculleus bourgensis.

Conclusion

Based on the physiological and phylogenetic characteristics, KOR-2 was thought to be a new strain within the genus Methanoculleus and named Methanoculleus bourgensis KOR-2.

Quantitative qPCR Analysis of Ruminal Microorganisms in Beef Cattle Grazing in Pastures in the Rainy Season and Supplemented with Different Protein Levels

We tested the hypothesis that supplementation with three protein levels improves fermentation parameters without changing the rumen microbial population of grazing beef cattle in the rainy season. Four rumen-cannulated Nellore bulls (432 ± 21 kg of body weight) were used in a 4 × 4 Latin square design with four supplements and four experimental periods of 21 days each. The treatments were mineral supplement (ad libitum) and supplements with low, medium (MPS), and high protein supplement (HPS), supplying 106, 408, and 601 g/day of CP, respectively. The abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific and domain bacteria primers. Supplemented animals showed lower (P < 0.05) proportions of Ruminococcus flavefaciens and greater (P < 0.05) proportions of Ruminococcus albus and Butyrivibrio fibrisolvens than animals that received only the mineral supplement. The HPS supplement resulted in higher (P < 0.05) proportions of Fibrobacter succinogenes, R. flavefaciens, and B. fibrisolvens and lower (P < 0.05) proportions of R. albus than the MPS supplement. Based on our results, high protein supplementation improves the ruminal conditions and facilitates the growth of cellulolytic bacteria in the rumen of bulls on pastures during the rainy season.

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens

The rumen simulation technique (RUSITEC) is a well-established semicontinuous in vitro model for investigating ruminal fermentation; however, information on the stability of the ruminal bacterial microbiota and metabolome in the RUSITEC system is rarely available. The availability of high resolution methods, such as high-throughput sequencing and metabolomics improve our knowledge about the rumen microbial ecosystem and its fermentation processes. Thus, we used Illumina MiSeq 16S rRNA amplicon sequencing and a combination of direct injection mass spectrometry with a reverse-phase LC-MS/MS to evaluate the dynamics of the bacterial community and the concentration of several metabolites in a RUSITEC experiment as a function of time and in response to a challenge with a pathogenic Clostridium perfringens (C. perfringens) strain. After four days of equilibration, samples were collected on days 5, 6, 7, 10, 12 and 15 of the steady-state and experimental period. From a total of six fermenters, three non-infected fermenters were used for investigating time-dependent alterations; three fermenters were incubated with C. perfringens and compared with the non-infected vessels at days 10, 12 and 15. Along the time-line, there was no statistically significant change of the overall bacterial community, however, some phylotypes were enriched at certain time points. A decrease in Fibrobacter and Elusimicrobia over time was followed by an increase in Firmicutes and Actinobacteria. In contrast, classical fermentation measurements such as pH, redox potential, NH3-N, short chain fatty acids and the concentrations of metabolites determined by metabolomics (biogenic amines, hexoses and amino acids) remained stable throughout the experiment. In response to C. perfringens addition the concentrations of several amino acids increased. Although the overall bacterial community was not altered here either, some minor changes such as an enrichment of Synergistetes and Bacteroidetes were detectable over time. In conclusion, both, the bacterial community composition and the metabolome in the RUSITEC system were relatively stable during the experiment.

Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives

Lignocellulosic biomass is the most abundant renewable bioresource on earth. In lignocellulosic biomass, the cellulose and hemicellulose are bound with lignin and other molecules to form a complex structure not easily accessible to microbial degradation. Anaerobic digestion (AD) of lignocellulosic biomass with a focus on improving hydrolysis, the rate limiting step in AD of lignocellulosic feedstocks, has received considerable attention. This review highlights challenges with AD of lignocellulosic biomass, factors contributing to its recalcitrance, and natural microbial ecosystems, such as the gastrointestinal tracts of herbivorous animals, capable of performing hydrolysis efficiently. Biological strategies that have been evaluated to enhance hydrolysis of lignocellulosic biomass include biological pretreatment, co-digestion, and inoculum selection. Strategies to further improve these approaches along with future research directions are outlined with a focus on linking studies of microbial communities involved in hydrolysis of lignocellulosics to process engineering.

Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats

This study was performed to investigate the initial colonization of metabolically active methanogens and subsequent changes in four fractions: the rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) from 1 to 60 d after birth, and manipulate methanogen community by early weaning on 40 d and supplementing rhubarb from 40 to 60 d in black goats. The RNA-based real-time quantitative PCR and 16S rRNA amplicon sequencing were employed to indicate the metabolically active methanogens. Results showed that active methanogens colonized in RL and RE on 1 d after birth. RP and RE contained the highest and lowest density of methanogens, respectively. Methanobrevibacter, Candidatus Methanomethylophilus, and Methanosphaera were the top three genera. The methanogen communities before weaning differed from those post weaning and the structure of the methanogen community in RE was distinct from those in the other three fractions. The discrepancies in the distribution of methanogens across four fractions, and various fluctuations in abundances among four fractions according to age were observed. The addition of rhubarb significantly (P < 0.05) reduced the abundances of Methanimicrococcus spp. in four fractions on 50 d, but did not change the methanogen community composition on 60 d.

The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot

Background

The nasopharyngeal (NP) microbiota plays an important role in bovine health, comprising a rich and diverse microbial community. The nasopharynx is also the niche for potentially pathogenic agents which are associated with bovine respiratory disease (BRD), a serious and costly illness in feedlot cattle. We used 14 beef heifers from a closed and disease-free herd to assess the dynamics of the NP microbiota of cattle that are transported to a feedlot. Cattle were sampled prior to transport to the feedlot (day 0) and at days 2, 7, and 14.

Results

The structure of the NP microbiota changed significantly over the course of the study, with the largest shift occurring between day 0 (prior to transport) and day 2 (P < 0.001). Phylogenetic diversity and richness increased following feedlot placement (day 2; P < 0.05). The genera Pasteurella, Bacillus, and Proteus were enriched at day 0, Streptococcus and Acinetobacter at day 2, Bifidobacterium at day 7, and Mycoplasma at day 14. The functional potential of the NP microbiota was assessed using PICRUSt, revealing that replication and repair, as well as translation pathways, were more relatively abundant in day 14 samples. These differences were driven mostly by Mycoplasma. Although eight cattle were culture-positive for the BRD-associated bacterium Pasteurella multocida at one or more sampling times, none were culture-positive for Mannheimia haemolytica or Histophilus somni.

Conclusions

This study investigated the effect that feedlot placement has on the NP microbiota of beef cattle over a 14-d period. Within two days of transport to the feedlot, the NP microbiota changed significantly, increasing in both phylogenetic diversity and richness. These results demonstrate that there is an abrupt shift in the NP microbiota of cattle after transportation to a feedlot. This may have importance for understanding why cattle are most susceptible to BRD after feedlot placement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0978-6) contains supplementary material, which is available to authorized users.

Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances

Methanogenic archaea reside primarily in the rumen and the lower segments of the intestines of ruminants, where they utilize the reducing equivalents derived from rumen fermentation to reduce carbon dioxide, formic acid, or methylamines to methane (CH₄). Research on methanogens in the rumen has attracted great interest in the last decade because CH₄ emission from ruminants contributes to global greenhouse gas emission and represents a loss of feed energy. Some DNA-based phylogenetic studies have depicted a diverse and dynamic community of methanogens in the rumen. In the past decade, researchers have focused on elucidating the underpinning that determines and affects the diversity, composition, structure, and dynamics of methanogen community of the rumen. Concurrently, many researchers have attempted to develop and evaluate interventions to mitigate enteric CH₄ emission. Although much work has been done using plant secondary metabolites, other approaches such as using nitrate and 3-nitrooxy propanol have also yielded promising results. Most of these antimethanogenic compounds or substances often show inconsistent results among studies and also lead to adverse effects on feed intake and digestion and other aspects of rumen fermentation when fed at doses high enough to achieve effective mitigation. This review provides a brief overview of the rumen methanogens and then an appraisal of most of the antimethanogenic compounds and substances that have been evaluated both in vitro and in vivo. Knowledge gaps and future research needs are also discussed with a focus on methanogens and methane mitigation.

Microbial Community and Chemical Characteristics of Swine Manure during Maturation

Swine diet formulations have the potential to lower animal emissions, including odor and ammonia (NH). The purpose of this study was to determine the impact of manure storage duration on manure chemical and microbial properties in swine feeding trials. Three groups of 12 pigs were fed a standard corn-soybean meal diet over a 13-wk period. Urine and feces were collected at each feeding and transferred to 12 manure storage tanks. Manure chemical characteristics and headspace gas concentrations were monitored for NH, hydrogen sulfide (HS), volatile fatty acids, phenols, and indoles. Microbial analysis of the stored manure included plate counts, community structure (denaturing gradient gel electrophoresis), and metabolic function (Biolog). All odorants in manure and headspace gas concentrations were significantly ( < 0.01) correlated for length of storage using quadratic equations, peaking after Week 5 for all headspace gases and most manure chemical characteristics. Microbial community structure and metabolic utilization patterns showed continued change throughout the 13-wk trial. Denaturing gradient gel electrophoresis species diversity patterns declined significantly ( < 0.01) with time as substrate utilization declined for sugars and certain amino acids, but functionality increased in the utilization of short chain fatty acids as levels of these compounds increased in manure. Studies to assess the effect of swine diet formulations on manure emissions for odor need to be conducted for a minimum of 5 wk. Efforts to determine the impact of diets on greenhouse gas emissions will require longer periods of study (>13 wk).

Changes in Rumen Microbial Community Composition during Adaption to an In Vitro System and the Impact of Different Forages

This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum) decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2–4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species.

Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise

Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.

Biodiversity and composition of methanogenic populations in the rumen of cows fed alfalfa hay or triticale straw

It is clear that methanogens are responsible for ruminal methane emissions, but quantitative information about the composition of the methanogenic community in the bovine rumen is still limited. The diversity and composition of rumen methanogens in cows fed either alfalfa hay or triticale straw were examined using a full-cycle rRNA approach. Quantitative fluorescence in situ hybridization undertaken applying oligonucleotide probes designed here identified five major methanogenic populations or groups in these animals: the Methanobrevibacter TMS group (consisting of Methanobrevibacter thaueri, Methanobrevibacter millerae and Methanobrevibacter smithii), Methanbrevibacter ruminantium-, Methanosphaera stadtmanae-, Methanomicrobium mobile-, and Methanimicrococcus-related methanogens. The TMS- and M. ruminantium-related methanogens accounted for on average 46% and 41% of the total methanogenic cells in liquid (Liq) and solid (Sol) phases of the rumen contents, respectively. Other prominent methanogens in the Liq and Sol phases included members of M. stadtmanae (15% and 33%), M. mobile (17% and 12%), and Methanimicrococcus (23% and 9%). The relative abundances of these methanogens in the community varied among individual animals and across diets. No clear differences in community composition could be observed with dietary change using cloning techniques. This study extends the known biodiversity levels of the methanogenic communities in the rumen of cows.

Fermentation in the large intestine of single-stomached animals and its relationship to animal health

The phasing out of antibiotic compounds as growth promoters from the animal industry means that alternative practices will need to be investigated and the promising ones implemented in the very near future. Fermentation in the gastrointestinal tract (GIT) is being recognized as having important implications for health of the gut and thus of the host animal. Fermentation in single-stomached animals occurs to the largest extent in the large intestine, mainly because of the longer transit time there. The present review examines the micro-ecology of the GIT, with most emphasis on the large intestine as the most important site of fermentative activity, and an attempt is made to clarify the importance of the microfloral activity (i.e. fermentation) in relation to the health of the host. The differences between carbohydrate and protein fermentation are described, particularly in relation to their endproducts. The roles of volatile fatty acids (VFA) and NH3 in terms of their relationship to gut health are then examined. The large intestine has an important function in relation to the development of diarrhoea, particularly in terms of VFA production by fermentation and its role in water absorption. Suggestions are made as to feeds and additives (particularly those which are carbohydrate-based) which could be, or are, added to diets and which could steer the natural microbial population of the GIT. Various methods are described which are used to investigate changes in microbial populations and reasons are given for the importance of measuring the kinetics of fermentation activity as an indicator of microbial activity.

Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem

Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.

Changes in ruminal microbiota due to rumen content processing and incubation in single-flow continuous-culture fermenters

The aim of this study was to investigate the impact of rumen content manipulation and its incubation in an in vitro system on the abundance of some microbial groups and the bacterial diversity of goat rumens. Animals and single-flow continuous-culture fermenters were fed diets differing in forage to concentrate ratio (70 : 30; LC and 30 : 70; HC). Rumen contents were sampled after animals’ adaptation to the experimental diets, processed for inoculum preparation and inoculated into fermenters. Fermenter contents were sampled 1 and 7 days after inoculation. Total bacteria, Fibrobacter succinogenes, fungi and methanogen abundances were lower in the fermenter than in goat rumens, but no differences were found for Ruminococcus flavefaciens. The abundances of all these microorganisms were similar at 1 and 7 days of rumen content incubation in fermenters. Bacterial species richness did not change due to rumen content processing or the in vitro incubation. Shannon–Wiener index and Pielou evenness were lower in the fermenter than in rumen only when the enzyme HaeIII was used in terminal-restriction fragment length polymorphism analysis. Non-metric multidimensional scaling analysis, both in denaturing gradient gel electrophoresis and terminal-restriction fragment length polymorphism, showed a segregation of in vivo and in vitro samples, but no trends of grouping for fermenter samples was observed. The HC diet promoted higher abundance of total bacteria than LC in rumen but not in fermenters. Diet only had an effect on bacterial diversity when the enzyme HaeIII was considered. Rumen content processing and incubation in fermenters caused an important decline of the studied ruminal microbial groups although bacterial community structure and diversity did not significantly change.

Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities

Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis electropherograms of bacterial pellets across the full set of 64 samples, from which 160 were detected in at least 1 individual from each system (sheep or fermenter). Diversity of liquid-associated bacterial pellets was greater with G diets in fermenters but seemed to be unaffected by diet in sheep. Bacterial diversity in solid-associated bacteria pellets was greater for G diets compared with A diets in sheep and fermenters. Different conditions in the fermenters compared with sheep rumen might have caused a selection of some bacterial strains.

Changes in bacterial communities from swine feces during continuous culture with starch

Bacteria from swine feces were grown in continuous culture with starch as the sole carbohydrate in order to monitor changes during fermentation and to determine how similar fermenter communities were to each other. DNA extracted from fermenter samples was analyzed by denaturing gradient gel electrophoresis (DGGE). A significant decrease in diversity was observed, the Shannon-Weaver index dropped from 1.92 to 1.13 after 14 days of fermentation. Likewise, similarity of fermenter communities to those in the fecal inoculum also decreased over time. Both diversity and similarity to the inoculum decreased most rapidly in the first few days of fermentation, reflecting a period of adaptation. Sequencing of DGGE bands indicated that the same species were present in replicate fermenters. Most of these bacteria were placed in the Clostridium coccoides/Eubacterium rectale group (likely saccharolytic butyrate producers), a dominant bacterial group in the intestinal tract of pigs. DGGE proved useful to monitor swine fecal communities in vitro and indicated the selection and maintenance of native swine intestinal bacteria during continuous culture.

Microbial fuel cells and microbial ecology: applications in ruminant health and production research

Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.

Effects of antibiotics and oil on microbial profiles and fermentation in mixed cultures of ruminal microorganisms

Ionophores and supplemental fat are fed to lactating cows to improve feed efficiency. Their effect on rumen fermentation is similar, but less is known about their impact on rumen microbes. The objective of this study was to determine the effects of monensin (M), bacitracin (B), and soybean oil (O) on microbial populations. Mixed cultures of rumen microbes were incubated in 5 dual-flow continuous fermentors and fed 13.8 g of alfalfa hay pellets daily (DM basis) for 16 d. All fermentors were allowed to stabilize for 4 d. From d 5 to 10, two fermentors received O (5% of diet DM), one fermentor received M (22 mg/kg), and one received B (22 mg/kg). From d 11 to 16, the 2 fermentors receiving O also received either M (OM) or B (OB) and O was included in the fermentors receiving M (MO) and B (BO). One fermentor served as the control and received 100% alfalfa pellets throughout the experiment. Each run was replicated 3 times. Samples were taken at 2 h after the morning feeding on d 4, 10, and 16 and were analyzed for bacterial populations using terminal restriction fragment length polymorphism. Volatile fatty acid concentration, methane production, and pH in the control cultures were not affected by time and remained similar during the entire experiment. The M and O treatments reduced molar concentration of acetate, increased concentration of propionate, and decreased methane production. Bacitracin did not alter acetate or propionate concentration, but reduced methane production. All 3 treatments (M, B, and O) altered the fragment patterns of microbial profiles. In contrast, treatments MO, OM, BO, and OB had little effect on culture fermentation despite differences in the patterns of microbial fragments. The terminal restriction fragment length polymorphism data suggest that microbial adaptation to the in vitro system in the control fermentor occurred within 4 d.

Investigating unsaturated fat, monensin, or bromoethanesulfonate in continuous cultures retaining ruminal protozoa. I. Fermentation, biohydrogenation, and microbial protein synthesis

Methane is an end product of ruminal fermentation that is energetically wasteful and contributes to global climate change. Bromoethanesulfonate, animal-vegetable fat, and monensin were compared with a control treatment to suppress different functional groups of ruminal prokaryotes in the presence or absence of protozoa to evaluate changes in fermentation, digestibility, and microbial N outflow. Four dual-flow continuous culture fermenter systems were used in 4 periods in a 4 x 4 Latin square design split into 2 subperiods. In subperiod 1, a multistage filter system (50-microm smallest pore size) retained most protozoa. At the start of subperiod 2, conventional filters (300-microm pore size) were substituted to efflux protozoa via filtrate pumps over 3 d; after a further 7 d of adaptation, the fermenters were sampled for 3 d. Treatments were retained during both subperiods. Flow of total N and digestibilities of NDF and OM were 18, 16, and 9% higher, respectively, for the defaunated subperiod but were not different among treatments. Ammonia concentration was 33% higher in the faunated fermenters but was not affected by treatment. Defaunation increased the flow of nonammonia N and bacterial N from the fermenters. Protozoal counts were not different among treatments, but bromoethanesulfonate increased the generation time from 43.2 to 55.6 h. Methanogenesis was unaffected by defaunation but tended to be increased by unsaturated fat. Defaunation did not affect total volatile fatty acid production but decreased the acetate:propionate ratio; monensin increased production of isovalerate and valerate. Biohydrogenation of unsaturated fatty acids was impaired in the defaunated fermenters because effluent flows of oleic, linoleic, and linolenic acids were 60, 77, and 69% higher, and the ratio of vaccenic acid:unsaturated FA ratio was decreased by 34% in the effluent. This ratio was increased in both subperiods with the added fat diet, indicating an accumulation of intermediates of biohydrogenation. However, the flow of 18:2 conjugated linoleic acid was unaffected by defaunation or by treatments other than added fat. The flows of trans-10, trans-11, and total trans-18:1 fatty acids were not affected by monensin or faunation status.

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).

Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestion - review

Fibrobacter succinogenes is a major cellulolytic species in the rumen. On the basis of molecular data, this species can be classified into four phylogenetic groups. Recently gathered ecological and physiological data have revealed the importance of this species, particularly phylogenetic group 1, in rumen fiber digestion. These data indicate that group 1 should be the focus of future efforts to maximize the fibrolytic function of the rumen.

Evaluation of group-specific, 16S rRNA-targeted scissor probes for quantitative detection of predominant bacterial populations in dairy cattle rumen

AIMS

To develop a suite of group-specific, rRNA-targeted oligonucleotide scissor probes for the quantitative detection of the predominant bacterial groups within the ruminal microbial community with the rRNA cleavage reaction-mediated microbial quantification method.

METHODS AND RESULTS

Oligonucleotides that complement the conserved sites of the 16S rRNA of phylogenetically defined groups of bacteria that significantly contribute to the anaerobic fermentation of carbohydrates in ruminal ecosystems were selected from among published probes or were newly designed. For each probe, target-specific rRNA cleavage was achieved by optimizing the formamide concentration in the reaction mixture. The set of scissor probes was then used to analyse the bacterial community in the rumen fluids of four healthy dairy cows. In the rumen fluid samples, the genera Bacteroides/Prevotella and Fibrobacter and the Clostridium coccoides-Eubacterium rectale group were detected in abundance, accounting for 44-48%, 2.9-10%, and 9.1-10% of the total 16S rRNA, respectively. The coverage with the probe set was 71-78% of the total bacterial 16S rRNA.

CONCLUSIONS

The probe set coupled with the sequence-specific small-subunit rRNA cleavage method can be used to analyse the structure of a ruminal bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

The probe set developed in this study provides a tool for comprehensive rRNA-based monitoring of the community members that dominate ruminal ecosystems. As the ruminal microbial community can be perturbed, it is important to track its dynamics by analysing microbiological profiles under specific conditions. The method described here will provide a convenient approach for such tracking.

Characterization and synergistic interactions of Fibrobacter succinogenes glycoside hydrolases

The objectives of this study were to characterize Fibrobacter succinogenes glycoside hydrolases from different glycoside hydrolase families and to study their synergistic interactions. The gene encoding a major endoglucanase (endoglucanase 1) of F. succinogenes S85 was identified as cel9B from the genome sequence by reference to internal amino acid sequences of the purified native enzyme. Cel9B and two other glucanases from different families, Cel5H and Cel8B, were cloned and overexpressed, and the proteins were purified and characterized. These proteins in conjunction with two predominant cellulases, Cel10A, a chloride-stimulated cellobiosidase, and Cel51A, formerly known as endoglucanase 2 (or CelF), were assayed in various combinations to assess their synergistic interactions using ball-milled cellulose. The degree of synergism ranged from 0.6 to 3.7. The two predominant endoglucanases produced by F. succinogenes, Cel9B and Cel51A, were shown to have a synergistic effect of up to 1.67. Cel10A showed little synergy in combination with Cel9B and Cel51A. Mixtures containing all the enzymes gave a higher degree of synergism than those containing two or three enzymes, which reflected the complementarity in their modes of action as well as substrate specificities.

The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review

This paper analyses the research progress in the use of molecular techniques based on ribosomal RNA and DNA (rRNA/rDNA) for rumen microbial ecosystem since first literature by Stahl et al. (1988). Because rumen microbial populations could be under-estimated by adopting the traditional techniques such as roll-tube technique or most-probable-number estimates, modern molecular techniques based on 16S/18S rRNA/rDNA can be used to more accurately provide molecular characterization, microbe populations and classification scheme than traditional methods. Phylogenetic-group-specific probes can be used to hybridize samples for detecting and quantifying of rumen microbes. But, competitive-PCR and real-time PCR can more sensitively quantify rumen microbes than hybridization. Molecular fingerprinting techniques including both denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and restriction fragment length polymorphisms (RFLP) can used to explore diversity of bacteria, protozoa and fungi in the rumen ecosystem. By constructing clone libraries of 16S/18S rRNA/rDNA of rumen microbes, more new microbes can be discovered and identified. For fungi, internal transcribed spacers (ITS) of fungi are better than 18S rRNA/rDNA for discriminating operational taxonomic units. In conclusion, 16S/18S rRNA/rDNA procedures have been used with success in rumen microbes and are quickly gaining acceptance for studying rumen microbial ecosystem, and will become useful methods for rumen ecology research. However, molecular techniques based on 16S/18S rRNA/rDNA don't preclude classical and traditional microbiological techniques. It should used together to acquire accurate and satisfactory results.