Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases
Jennifer M. BrulcDionysios A. AntonopoulosMargret E. Berg MillerMelissa K. WilsonAnthony C. YannarellElizabeth A. DinsdaleRobert A. EdwardsE.D. FrankJoanne EmersonPirjo WacklinPedro M. CoutinhoBernard HenrissatWilliam NelsonBryan A. White
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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).Keywords:
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In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)–energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH–ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.
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Spirochetes are observed in the hindguts of termites and the wood-eating cockroach. Hindgut spirochetes occur free in the gut fluid as well as attached to the surfaces of hindgut protozoa. The two species of spirochetes from termite hindguts were determined to be Treponema azotonutricium and Treponema primitia. Some hindgut spirochetes attach by one end to the surface of certain flagellate protozoa found only in the lower termites and Cryptocercus punctulatus. Motile spirochetes have been observed within the cytoplasm of hindgut protozoa. The hindgut spirochetes and Cryptocercus punctulatus will be included in the family Spirochaetaceae and placed among the spirochetal genera. Spirochaetes / Spirochaetia / Spirochaetales / Hindgut spirochetes of termites and Cryptocercus punctulatus
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Environmental microorganisms have vast diversity, but as many as 99% of microorganisms can not be cultured by standard techniques. Culture-independent genomic analysis has been rapidly developed being fitting to analyze complex microbial genomics in ecology. Principle and method of metagenomics as well as application in microbial diversity were also reviewed.
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Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.
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This case study shows the application of nontraditional diagnostic methods to investigate the microbial consortia inhabiting an ancient manuscript. The manuscript was suspected to be biologically deteriorated and SEM observations showed the presence of fungal spores attached to fibers, but classic culturing methods did not succeed in isolating microbial contaminants. Therefore, molecular methods, including PCR, denaturing gradient gel electrophoresis (DGGE), and clone libraries, were used as a sensitive alternative to conventional cultivation techniques. DGGE fingerprints revealed a high biodiversity of both bacteria and fungi inhabiting the manuscript. DNA sequence analysis confirmed the existence of fungi and bacteria in manuscript samples. A number of fungal clones identified on the manuscript showed similarity to fungal species inhabiting dry or saline environments, suggesting that the manuscript environment selects for osmophilic or xerophilic fungal species. Most of the bacterial sequences retrieved from the manuscript belong to phylotypes with cellulolytic activities.
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Specialized junctional complexes and the ultrastructural morphology of the hindgut epithelial cells indicate that the terrestrial isopod hindgut epithelium functions in transport. The hindgut is divided into an anterior hindgut (typhlosole region), a posterior hindgut (papillate region) and a rectum. Using mitochondrial morphometry as an indicator of cell transport activity, Coruzzi et al. demonstrated that the posterior hindgut of Arniadillidium vulgare is active in osmoregulation to a greater degree than O. asellus . A study was undertaken to determine if this difference is reflected in the CA ++ -ATPase activity of the hindgut epithelial cells of O. asellus .
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