Dasytricha dominance in Surti buffalo rumen revealed by 18S rRNA sequences and real-time PCR assay

Reducing Ruminal Ammonia Production With Improvement in Feed Utilization Efficiency and Performance of Murrah Buffalo (Bubalus bubalis) Through Dietary Supplementation of Plant-Based Feed Additive Blend

The study evaluated the potential of blends of eucalyptus oil and aqueous extract of mulethi (root of Glycyrrhiza glabra) to reduce rate of ruminal ammonia production without affecting feed digestion to improve nitrogen utilization efficiency and performance of Murrah buffalo (Bubalus bubalis). Based on preliminary independent studies with graded doses of eucalyptus oil and mulethi root aqueous extract in modulating in vitro rumen fermentation, four blends of feed additive comprising graded doses (5, 10, 15, and 25 μL) of eucalyptus oil and a fixed quantity (15 μL) of aqueous extract of mulethi roots were prepared and examined for their effects on in vitro rumen fermentation and on methane and gas production in 100-mL calibrated glass syringes by standard IVGP protocol. Rumen liquor was collected from four rumen fistulated Murrah buffaloes fed a total mixed ration. Out of four blends, blend-1 comprising 5 μL of eucalyptus oil and 15 μL of aqueous extract (233.6 g/L DW) of mulethi per 40 mL of in vitro medium was found to reduce ammonia production significantly (p < 0.001) without affecting feed digestibility. An equivalent dose of blend-1 (10.5 mL of eucalyptus oil and 7.35 g of mulethi root powder/h/day) fed to four rumen fistulated buffaloes for 24 days resulted in 50% reduction (p < 0.05) in rumen ammonia level with no inhibition in feed fermentation or short-chain fatty acid production. The total bacterial population including Ruminococcus albus, Fibrobacter succinogenes, Butyrivibrio fibrisolvens, and Megasphaera elsdenii as well as anaerobic fungi and methanogenic archaea remained unaffected (p > 0.05). Twelve buffalo calves (avg. BW 137.5 ± 9.2 kg, 8–12 months old) divided into two groups of six each and fed a total mixed ration (concentrate: roughage; 60:40) with or without supplementation of blend-1 for about 3 months demonstrated 14% increase (p < 0.05) in average daily gain in BW with a trend (p < 0.10) in improvement of feed or protein utilization efficiency (1.4 vs. 1.1 g crude protein/g average daily gain; 21.4% increase). Thus, supplementation of eucalyptus oil–mulethi root blend could reduce ruminal ammonia production and improve feed utilization efficiency in ruminants.

Diversity and fluctuation in ciliate protozoan population in the rumen of cattle

The purpose of this study was to investigate the diversity and fluctuation in the ciliate protozoan population in the rumen of cattle. DNA was extracted from the rumen of three ruminally cannulated, crossbred cattle and a polymerase chain reaction (PCR)-derived clone library was constructed, using a specific primer set targeting 18S ribosomal RNA genes of ciliate protozoa. DNA fragments of seven selected clones were validated for standard DNA of the protozoa-specific real-time PCR assay. Furthermore, population fluctuation of ciliate protozoa and methanogens in the cattle rumen was determined by real-time PCR. A total of 60 clones were sequenced, phylogenetically analyzed, and classified into 24 operational taxonomic units (OTUs) based on a 99% similarity criterion. More than 80% sequences were phylogenetically placed in the genus Entodinium. The rest of the sequences were placed in the genus Diploplastron (5%), Dasytricha (8.3%) and Isotricha (3.3%). The results suggest that Entodinium was the dominant group in the rumen of cattle used in this study. The ciliate protozoan population showed no significant change in numbers during the monitoring period and reached a peak at 3 h after feeding. Changes in the protozoa population were lower than those of the methanogens.

New Primers Targeting Full-Length Ciliate 18S rRNA Genes and Evaluation of Dietary Effect on Rumen Ciliate Diversity in Dairy Cows

Analysis of the full-length 18S rRNA gene sequences of rumen ciliates is more reliable for taxonomical classification and diversity assessment than the analysis of partial hypervariable regions only. The objective of this study was to develop new oligonucleotide primers targeting the full-length 18S rRNA genes of rumen ciliates, and to evaluate the effect of different sources of dietary fiber (corn stover or a mixture of alfalfa hay and corn silage) and protein (mixed rapeseed, cottonseed, and/or soybean meals) on rumen ciliate diversity in dairy cows. Primers were designed based on a total of 137 previously reported ciliate 18S rRNA gene sequences. The 3'-terminal sequences of the newly designed primers, P.1747r_2, P.324f, and P.1651r, demonstrated >99% base coverage. Primer pair D (P.324f and P.1747r_2) was selected for the cloning and sequencing of ciliate 18S rRNA genes because it produced a 1423-bp amplicon, and did not amply the sequences of other eukaryotic species, such as yeast. The optimal species-level cutoff value for distinguishing between the operational taxonomic units of different ciliate species was 0.015. The phylogenetic analysis of full-length ciliate 18S rRNA gene sequences showed that distinct ciliate profiles were induced by the different sources of dietary fiber and protein. Dasytricha and Entodinium were the predominant genera in the ruminal fluid of dairy cattle, and Dasytricha was significantly more abundant in cows fed with corn stover than in cows fed with alfalfa hay and corn silage.

Molecular Phylogeny of the Family Ophryscolecidae (Ciliophora, Litostomatea) Inferred from 18S rDNA Sequences

The 18S rDNA was used to infer oral ciliature patterns of evolution within the family Ophryoscolecidae, with the addition of five new sequences of ciliates from the genus Ostracodinium. Our data confirmed the monophyly of the subfamilies Entodiniinae and Ophryoscolecinae, but more analysis would be required for the definition of the status of the subfamily Diplodiniinae. The oral infraciliature patterns reflect evolutionary divergence in the family Ophryscolecidae, observing monophyly on Entodinium-type, Diplodinium-type, Ostracodinium-type, Epidinium-type, and Ophryoscolex-type. The ancestral infraciliature of Entodinium-type cannot be proven, however, the position of Entodinium-type showed closer of Diplodinium-type than Ophryoscolex-type, corroborating previous studies using morphological characters. The observed inconsistencies reflect the need to increase the number of 18S rDNA sequences to family Ophryoscolecidae and investigate the evolution of this group using other molecular markers.

Molecular Genetic Diversity and Quantitation of Methanogen in Ruminal Fluid of Buffalo (Bubalus bubalis) Fed Ration (Wheat Straw and Concentrate Mixture Diet)

High roughage diet causes more methane emissions; however, the total methanogen abundance is not influenced by roughage proportion. Technologies to reduce methane emissions are lacking, and development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on present knowledge of the methanogens. In this work, we have investigated molecular diversity of rumen methanogens of Surti buffalo. DNA from rumen fluid was extracted, and 16S rRNA encoding genes were amplified using methanogen specific primer to generate 16S rDNA clone libraries. Seventy-six clones were randomly selected and analysed by RFLP resulting in 21 operational taxonomic units (OTUs). BLAST analysis with available sequences in database revealed sequences of 13 OTUs (55 clones) showing similarity with Methanomicrobium sp, 3 OTUs (15 clones) with Methanobrevibacter sp. The remaining 5 OTUs (6 clones) belonged to uncultured archaea. The phylogenetic analysis indicated that methanogenic communities found in the library were clustered in the order of Methanomicrobiales (18 OTUs) and Methanobacteriales (3 OTUs). The population of Methanomicrobiales, Methanobacteriales, and Methanococcales were also observed, accounting for 1.94%, 0.72%, and 0.47% of total archaea, respectively.

Effect of condensed tannins on bovine rumen protist diversity based on 18S rRNA gene sequences

Molecular diversity of protists from bovine rumen fluid incubated with condensed tannins of Leucaena leucocephala hybrid-Rendang at 20 mg/500 mg dry matter (treatment) or without condensed tannins (control) was investigated using 18S rRNA gene library. Clones from the control library were distributed within nine genera, but clones from the condensed tannin treatment clone library were related to only six genera. Diversity estimators such as abundance-based coverage estimation and Chao1 showed significant differences between the two libraries, although no differences were found based on Shannon-Weaver index and Libshuff.

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.