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

2009 ◽  
Vol 106 (6) ◽  
pp. 1948-1953 ◽  
Author(s):  
Jennifer M. Brulc ◽  
Dionysios A. Antonopoulos ◽  
Margret E. Berg Miller ◽  
Melissa K. Wilson ◽  
Anthony C. Yannarell ◽  
...  
Keyword(s):  
Glycoside Hydrolases ◽  
Bovine Rumen ◽  
Rumen Microbiome

scholarly journals Complete Genome Sequences of Three Clostridiales R-7 Group Strains Isolated from the Bovine Rumen in New Zealand

2021 ◽  
Vol 10 (26) ◽  
Author(s):  
Sam C. Mahoney-Kurpe ◽  
Nikola Palevich ◽  
Samantha J. Noel ◽  
Sandeep Kumar ◽  
Dragana Gagic ◽  
...  
Keyword(s):  
New Zealand ◽  
Dairy Cows ◽  
Complete Genome ◽  
Genome Sequences ◽  
Bovine Rumen ◽  
Rumen Microbiome

Members of the Clostridiales R-7 group are abundant bacterial residents of the rumen microbiome; however, they are poorly characterized. We report the complete genome sequences of three members of the R-7 group, FE2010, FE2011, and XBB3002, isolated from the ruminal contents of pasture-grazed dairy cows in New Zealand.

scholarly journals The rumen microbiome of yak co-evolves with its host probably adding the adaptation to its harsh environments

2021 ◽  
Author(s):  
Congcong Zhao ◽  
Lamei Wang ◽  
Shanlin Ke ◽  
Xinhua Chen ◽  
Ákos Kenéz ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Bos Taurus ◽  
Glycoside Hydrolases ◽  
Rumen Microbiota ◽  
Rumen Microbes ◽  
Bos Grunniens ◽  
Molar Proportion ◽  
Rumen Microbiome ◽  
Sufficient Energy ◽  
Genes Encoding

Abstract Background Rumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that yak (Bos grunniens) rumen microbiome and fermentation differ from other ruminants. However, little is understood on the features of the rumen microbiome that make yak adapted to its unique environmental and dietary conditions. Here we investigated the rumen microbiome and metabolome to understand how yak adapts to the coarse forage and harsh environment in the high Qinghai-Tibetan plateau. Result Metataxonomic analysis of the rumen microbiota revealed that yak (Bos grunniens), domesticated cattle (Bos taurus), and dzo (a hybrid between the yak and domestic cattle) have distinct rumen microbiota. Metagenomic analysis displayed a larger gene pool encoding a richer repertoire of carbohydrate-active enzymes (CAZymes) in the rumen microbiome of yak and dzo than cattle. Some of the genes encoding glycoside hydrolases (GH) that mediate the digestion of cellulose and hemicellulose were significantly enriched in the rumen of yak than cattle, but the cattle rumen microbiome had more genes assigned to GH57 that primarily includes amylases. The rumen fermentation profile differed also, with cattle having a higher molar proportion of acetate but a lower molar proportion of propionate than dzo and yak. Metabolomic analysis showed differences in both rumen microbial metabolic pathways and metabolites, mainly amino acids, carboxylic acids, sugars, and bile acids. Notably, styrene degradation, primary bile acid biosynthesis, glyoxylate, and dicarboxylate metabolism significantly differed between cattle and dzo; streptomycin biosynthesis was significantly different between cattle and yak; and the pathways for biotin metabolism and styrene degradation significantly differed between dzo and yak. Correlation analysis revealed certain microbial species correlated with differential rumen metabolites. Nine differential metabolites showed a positive correlation with seven species belonging to Bacteroides and Alistipes but a negative correlation with ten species belonging to Prevotella and Ruminococcus. Conclusion The present study showed that the rumen microbiome of yak and its host had probably co-evolved aiding in the adaptation of yak to the harsh dietary environment of the Qinghai-Tibetan plateau. In particular, the yak rumen microbiome has more enzymes involved in the degradation of rough forage than that of cattle, providing sufficient energy for its host.

scholarly journals Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ankit T. Hinsu ◽  
Nilam J. Tulsani ◽  
Ketankumar J. Panchal ◽  
Ramesh J. Pandit ◽  
Basanti Jyotsana ◽  
...  
Keyword(s):  
Glycoside Hydrolases ◽  
Rumen Content ◽  
Dromedary Camel ◽  
Carbohydrate Active Enzymes ◽  
Shotgun Metagenomics ◽  
Rumen Microbiota ◽  
Microbial Profile ◽  
Rumen Microbiome ◽  
Main Compartment ◽  
Metagenomics Data

AbstractIn dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.

scholarly journals Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

2021 ◽  
Vol 10 (1) ◽  
pp. 71
Author(s):  
Xiaofeng Wu ◽  
Chijioke O. Elekwachi ◽  
Shiping Bai ◽  
Yuheng Luo ◽  
Keying Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Plant Biomass ◽  
High Arctic ◽  
Glycoside Hydrolases ◽  
Microbial Consortia ◽  
Biomass Hydrolysis ◽  
Host Animal ◽  
Ovibos Moschatus ◽  
Plant Polysaccharide ◽  
Rumen Microbiome

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

scholarly journals High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
K. M. Singh ◽  
Bhaskar Reddy ◽  
Dishita Patel ◽  
A. K. Patel ◽  
Nidhi Parmar ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Metagenomic Sequencing ◽  
Environmental Aspects ◽  
Rumen Microbiome ◽  
Polysaccharide Lyases ◽  
Effective System ◽  
Plant Cell Wall Degradation ◽  
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.

scholarly journals Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

2016 ◽  
Vol 19 (1) ◽  
pp. 185-197 ◽  
Author(s):  
Lizi Bensoussan ◽  
Sarah Moraïs ◽  
Bareket Dassa ◽  
Nir Friedman ◽  
Bernard Henrissat ◽  
...  
Keyword(s):  
Bovine Rumen ◽  
Rumen Microbiome

scholarly journals A Polysaccharide Utilization Locus from an Uncultured Bacteroidetes Phylotype Suggests Ecological Adaptation and Substrate Versatility

2014 ◽  
Vol 81 (1) ◽  
pp. 187-195 ◽  
Author(s):  
A. K. Mackenzie ◽  
A. E. Naas ◽  
S. K. Kracun ◽  
J. Schückel ◽  
J. U. Fangel ◽  
...  
Keyword(s):  
Anion Exchange Chromatography ◽  
Gene Organization ◽  
Exchange Chromatography ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Content Type ◽  
Svalbard Reindeer ◽  
Uncultured Bacteria ◽  
Rumen Microbiome ◽  
Polysaccharide Utilization Locus

ABSTRACTRecent metagenomic analyses have identified uncultured bacteria that are abundant in the rumen of herbivores and that possess putative biomass-converting enzyme systems. Here we investigate the saccharolytic capabilities of a polysaccharide utilization locus (PUL) that has been reconstructed from an unculturedBacteroidetesphylotype (SRM-1) that dominates the rumen microbiome of Arctic reindeer. Characterization of the three PUL-encoded outer membrane glycoside hydrolases was performed using chromogenic substrates for initial screening, followed by detailed analyses of products generated from selected substrates, using high-pressure anion-exchange chromatography with electrochemical detection. Two glycoside hydrolase family 5 (GH5) endoglucanases (GH5_g and GH5_h) demonstrated activity against β-glucans, xylans, and xyloglucan, whereas GH5_h and the third enzyme, GH26_i, were active on several mannan substrates. Synergy experiments examining different combinations of the three enzymes demonstrated limited activity enhancement on individual substrates. Binding analysis of a SusE-positioned lipoprotein revealed an affinity toward β-glucans and, to a lesser extent, mannan, but unlike the two SusD-like lipoproteins previously characterized from the same PUL, binding to cellulose was not observed. Overall, these activities and binding specificities correlated well with the glycan content of the reindeer rumen, which was determined using comprehensive microarray polymer profiling and showed an abundance of various hemicellulose glycans. The substrate versatility of this single PUL putatively expands our perceptions regarding PUL machineries, which so far have demonstrated gene organization that suggests one cognate PUL for each substrate type. The presence of a PUL that possesses saccharolytic activity against a mixture of abundantly available polysaccharides supports the dominance of SRM-1 in the Svalbard reindeer rumen microbiome.

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