Application of rumen microbial genome information to livestock systems in the postgenomic era

2008 ◽  
Vol 48 (7) ◽  
pp. 695 ◽  
Author(s):  
G. T. Attwood ◽  
W. J. Kelly ◽  
E. H. Altermann ◽  
C. D. Moon ◽  
S. Leahy ◽  
...  
Keyword(s):  
Methanogenic Archaea ◽  
Glycosyl Hydrolases ◽  
Rumen Microbes ◽  
Gene And Protein Expression ◽  
Genes Encoding ◽  
Conserved Genes ◽  
Rumen Microbe ◽  
Microbial Dna ◽  
Genome Information ◽  
Livestock Systems

Sequencing the genomes of individual rumen microbes and determining the function of their encoded genes promises to transform our understanding of the microbiology of the rumen. The diversity and density of microbes in the rumen, and our inability to culture the majority of rumen microbes, limit current genome studies to only a small fraction of the microbes present in this environment. Nevertheless, genomes of fibre-degrading organisms are beginning to reveal a previously unexpected abundance of genes encoding glycosyl hydrolases and carbohydrate esterases, which could be used to enhance fibre digestion in the rumen. Additionally, genome sequencing of a rumen methanogen is identifying conserved genes within the methanogenic archaea that may serve as targets for their inhibition and therefore reduction of methane emissions from ruminants. The problem of rumen microbe culturability can be overcome by a new approach called metagenomics, in which microbial DNAs are extracted from rumen samples and sequenced independent of cultivation. In the future, sequencing individual genomes and metagenomic libraries is likely to capture much more of the microbial DNA in the rumen and, coupled with postgenomic studies on gene and protein expression, is likely to enhance our knowledge of the microbial component of ruminant digestion.

scholarly journals Butyrivibrio hungateiMB2003 Competes Effectively for Soluble Sugars Released byButyrivibrio proteoclasticusB316Tduring Growth on Xylan or Pectin

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Nikola Palevich ◽  
William J. Kelly ◽  
Siva Ganesh ◽  
Jasna Rakonjac ◽  
Graeme T. Attwood
Keyword(s):  
Bacterial Species ◽  
Soluble Sugars ◽  
Plant Fiber ◽  
Content Type ◽  
Plant Polysaccharide ◽  
Rumen Microbes ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Enzymatic Machinery

ABSTRACTRumen bacterial species belonging to the genusButyrivibrioare important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four species are recognized; they have very similar substrate utilization profiles, but little is known about how these microorganisms are able to coexist in the rumen. To investigate this question,Butyrivibrio hungateiMB2003 andButyrivibrio proteoclasticusB316Twere grown alone or in coculture on xylan or pectin, and their growth, release of sugars, fermentation end products, and transcriptomes were examined. In monocultures, B316Twas able to grow well on xylan and pectin, while MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Cocultures of B316Tgrown with MB2003 revealed that MB2003 showed growth almost equivalent to that of B316Twhen either xylan or pectin was supplied as the substrate. The effect of coculture on the transcriptomes of B316Tand MB2003 was assessed; B316Ttranscription was largely unaffected by the presence of MB2003, but MB2003 expressed a wide range of genes encoding proteins for carbohydrate degradation, central metabolism, oligosaccharide transport, and substrate assimilation, in order to compete with B316Tfor the released sugars. These results suggest that B316Thas a role as an initiator of primary solubilization of xylan and pectin, while MB2003 competes effectively for the released soluble sugars to enable its growth and maintenance in the rumen.IMPORTANCEFeeding a future global population of 9 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation.Butyrivibriospecies are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings suggest that closely related species ofButyrivibriohave developed unique strategies for the degradation of plant fiber and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes expressed during these competitive interactions gives further insight into the enzymatic machinery used by these bacteria as they degrade the xylan and pectin components of plant fiber.

scholarly journals Evidence that a Linear Megaplasmid Encodes Enzymes of Aliphatic Alkene and Epoxide Metabolism and Coenzyme M (2-Mercaptoethanesulfonate) Biosynthesis in XanthobacterStrain Py2

2001 ◽  
Vol 183 (7) ◽  
pp. 2172-2177 ◽  
Author(s):  
Jonathan G. Krum ◽  
Scott A. Ensign
Keyword(s):  
Ring Opening ◽  
Methanogenic Archaea ◽  
Hypothetical Protein ◽  
Epoxide Ring ◽  
Coenzyme M ◽  
Epoxide Ring Opening ◽  
Propylene Oxidation ◽  
Key Enzymes ◽  
Genes Encoding ◽  
Key Enzyme

ABSTRACT The bacterial metabolism of propylene proceeds by epoxidation to epoxypropane followed by a sequence of three reactions resulting in epoxide ring opening and carboxylation to form acetoacetate. Coenzyme M (2-mercaptoethanesulfonic acid) (CoM) plays a central role in epoxide carboxylation by serving as the nucleophile for epoxide ring opening and the carrier of the C3 unit that is ultimately carboxylated to acetoacetate, releasing CoM. In the present work, a 320-kb linear megaplasmid has been identified in the gram-negative bacterium Xanthobacter strain Py2, which contains the genes encoding the key enzymes of propylene oxidation and epoxide carboxylation. Repeated subculturing of Xanthobacter strain Py2 under nonselective conditions, i.e., with glucose or acetate as the carbon source in the absence of propylene, resulted in the loss of the propylene-positive phenotype. The propylene-negative phenotype correlated with the loss of the 320-kb linear megaplasmid, loss of induction and expression of alkene monooxgenase and epoxide carboxylation enzyme activities, and the loss of CoM biosynthetic capability. Sequence analysis of a hypothetical protein (XecG), encoded by a gene located downstream of the genes for the four enzymes of epoxide carboxylation, revealed a high degree of sequence identity with proteins of as-yet unassigned functions in the methanogenic archaeaMethanobacterium thermoautotrophicum andMethanococcus jannaschii and in Bacillus subtilis. The M. jannaschii homolog of XecG, MJ0255, is located next to a gene, MJ0256, that has been shown to encode a key enzyme of CoM biosynthesis (M. Graupner, H. Xu, and R. H. White, J. Bacteriol. 182: 4862–4867, 2000). We propose that the propylene-positive phenotype of Xanthobacter strain Py2 is dependent on the selective maintenance of a linear megaplasmid containing the genes for the key enzymes of alkene oxidation, epoxide carboxylation, and CoM biosynthesis.

scholarly journals Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Gemma Henderson ◽  
◽  
Faith Cox ◽  
Siva Ganesh ◽  
Arjan Jonker ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Methanogenic Archaea ◽  
Methane Formation ◽  
Core Microbiome ◽  
Rumen Microbes ◽  
Metabolic Interactions ◽  
Occurrence Patterns ◽  
Dominant Bacteria

Abstract Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

scholarly journals Helicobacter pyloriand Its Genome: Lessons from the Treasure Map

1999 ◽  
Vol 13 (3) ◽  
pp. 218-223 ◽  
Author(s):  
Diane E Taylor
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Molecular Mimicry ◽  
Epithelial Tissue ◽  
Functional Studies ◽  
Type Iv ◽  
Genes Encoding ◽  
Conserved Genes ◽  
H Pylori

The availability of the complete genome sequence ofHelicobacter pylori26695 has opened new avenues for research in the molecular biology of this gastric pathogen. The present review gives a general overview ofH pyloriobtained from the complete genome sequence and compares this with data previously obtained from cloning and functional studies ofH pylori. The cagA pathogenicity island of 40 kilobases, which encodes a type IV secretion system, is discussed. The diversity ofH pylorigenomes is well known, yet new data indicate that some aspects of the genome, particularly outer membrane protein genes, are conserved. Genes encoding proteins involved in molecular mimicry between bacterium and gastric epithelial tissue, specifically those encoding Lewis X and Lewis Y antigens, are discussed. The large number of DNA restriction and modification genes and their role inH pyloriinfection are considered. Finally, gene transfer is discussed. The availability of the complete genome sequence ofH pylori26695 and the soon to be available sequence of J99 will speed up and assist in the analysis ofH pylorigenes and their encoded proteins. The genomes of both strains will be useful as references with which otherH pylorigenomes can be compared.

scholarly journals Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

2020 ◽  
Vol 8 (11) ◽  
pp. 1720
Author(s):  
Gabriele Andrea Lugli ◽  
Chiara Tarracchini ◽  
Giulia Alessandri ◽  
Christian Milani ◽  
Leonardo Mancabelli ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Ursus Arctos ◽  
Primate Species ◽  
Comparative Genomic ◽  
Glycosyl Hydrolases ◽  
Genomic Variability ◽  
Fecal Samples ◽  
Genomic Analyses ◽  
Conserved Genes ◽  
Genetic Features

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR–Cas and restriction–modification systems may be responsible for the high genome synteny identified among members of this taxon.

scholarly journals A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Junhua Li ◽  
Huanzi Zhong ◽  
Yuliaxis Ramayo-Caldas ◽  
Nicolas Terrapon ◽  
Vincent Lombard ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Production Systems ◽  
Wall Material ◽  
Rumen Microbes ◽  
Bovine Rumen ◽  
Degrading Enzymes ◽  
Genes Encoding ◽  
Health And Disease ◽  
Metagenome Sequencing ◽  
Available Information

Abstract Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

scholarly journals Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases

1996 ◽  
Vol 318 (1) ◽  
pp. 133-138 ◽  
Author(s):  
Roberto A GEREMIA ◽  
E Alejandro PETRONI ◽  
Luis IELPI ◽  
Bernard HENRISSAT
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Amino Acid Residues ◽  
Glycosyl Hydrolases ◽  
Hydrophobic Cluster Analysis ◽  
Alignment Algorithms ◽  
Automatic Alignment ◽  
Genes Encoding ◽  
Sequence Similarities

A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309–316].

scholarly journals Global Molecular and Morphological Effects of 24-Hour Chromium(VI) Exposure on Shewanella oneidensis MR-1

2006 ◽  
Vol 72 (9) ◽  
pp. 6331-6344 ◽  
Author(s):  
Karuna Chourey ◽  
Melissa R. Thompson ◽  
Jennifer Morrell-Falvey ◽  
Nathan C. VerBerkmoes ◽  
Steven D. Brown ◽  
...  
Keyword(s):  
Untreated Control ◽  
Expression Profiles ◽  
Shewanella Oneidensis ◽  
Transcriptome Profiling ◽  
Molecular Response ◽  
Chromium Vi ◽  
Stress Protection ◽  
Gene And Protein Expression ◽  
Genes Encoding ◽  
Protein Expression Profiles

ABSTRACT The biological impact of 24-h (“chronic”) chromium(VI) [Cr(VI) or chromate] exposure on Shewanella oneidensis MR-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. Cells challenged aerobically with an initial chromate concentration of 0.3 mM in complex growth medium were compared to untreated control cells grown in the absence of chromate. At the 24-h time point at which cells were harvested for transcriptome and proteome analyses, no residual Cr(VI) was detected in the culture supernatant, thus suggesting the complete uptake and/or reduction of this metal by cells. In contrast to the untreated control cells, Cr(VI)-exposed cells formed apparently aseptate, nonmotile filaments that tended to aggregate. Transcriptome profiling and mass spectrometry-based proteomic characterization revealed that the principal molecular response to 24-h Cr(VI) exposure was the induction of prophage-related genes and their encoded products as well as a number of functionally undefined hypothetical genes that were located within the integrated phage regions of the MR-1 genome. In addition, genes with annotated functions in DNA metabolism, cell division, biosynthesis and degradation of the murein (peptidoglycan) sacculus, membrane response, and general environmental stress protection were upregulated, while genes encoding chemotaxis, motility, and transport/binding proteins were largely repressed under conditions of 24-h chromate treatment.

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 Schistosoma mansoni α-N-acetylgalactosaminidase (SmNAGAL) regulates coordinated parasite movement and egg production

2022 ◽  
Vol 18 (1) ◽  
pp. e1009828
Author(s):  
Benjamin J. Hulme ◽  
Kathrin K. Geyer ◽  
Josephine E. Forde-Thomas ◽  
Gilda Padalino ◽  
Dylan W. Phillips ◽  
...  
Keyword(s):  
Schistosoma Mansoni ◽  
Egg Production ◽  
Phylogenetic Analyses ◽  
Significant Inhibition ◽  
Amino Acid Residues ◽  
Glycosyl Hydrolases ◽  
Host Interactions ◽  
Human Genes ◽  
Genes Encoding ◽  
Parenchymal Cells

α-galactosidase (α-GAL) and α-N-acetylgalactosaminidase (α-NAGAL) are two glycosyl hydrolases responsible for maintaining cellular homeostasis by regulating glycan substrates on proteins and lipids. Mutations in the human genes encoding either enzyme lead to neurological and neuromuscular impairments seen in both Fabry- and Schindler/Kanzaki- diseases. Here, we investigate whether the parasitic blood fluke Schistosoma mansoni, responsible for the neglected tropical disease schistosomiasis, also contains functionally important α-GAL and α-NAGAL proteins. As infection, parasite maturation and host interactions are all governed by carefully-regulated glycosylation processes, inhibiting S. mansoni’s α-GAL and α-NAGAL activities could lead to the development of novel chemotherapeutics. Sequence and phylogenetic analyses of putative α-GAL/α-NAGAL protein types showed Smp_089290 to be the only S. mansoni protein to contain the functional amino acid residues necessary for α-GAL/α-NAGAL substrate cleavage. Both α-GAL and α-NAGAL enzymatic activities were higher in females compared to males (p<0.05; α-NAGAL > α-GAL), which was consistent with smp_089290’s female biased expression. Spatial localisation of smp_089290 revealed accumulation in parenchymal cells, neuronal cells, and the vitellaria and mature vitellocytes of the adult schistosome. siRNA-mediated knockdown (>90%) of smp_089290 in adult worms significantly inhibited α-NAGAL activity when compared to control worms (siLuc treated males, p<0.01; siLuc treated females, p<0.05). No significant reductions in α-GAL activities were observed in the same extracts. Despite this, decreases in α-NAGAL activities correlated with a significant inhibition in adult worm motility as well as in egg production. Programmed CRISPR/Cas9 editing of smp_089290 in adult worms confirmed the egg reduction phenotype. Based on these results, Smp_089290 was determined to act predominantly as an α-NAGAL (hereafter termed SmNAGAL) in schistosome parasites where it participates in coordinating movement and oviposition processes. Further characterisation of SmNAGAL and other functionally important glycosyl hydrolases may lead to the development of a novel anthelmintic class of compounds.

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