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  • 1
    Electronic Resource
    Electronic Resource
    Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology reviews 27 (2003), S. 0 
    Details
    ISSN: 1574-6976
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0168-6445(03)00072-X
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    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    The use of PCR for the identification and characterisation of bacteriocin genes from bacterial strains isolated from rumen or caecal contents of cattle and sheep (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 48 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: PCR primers were designed to amplify the gene that encodes bovicin 255 from Streptococcus gallolyticus LRC0255 and the bacteriocin genes from Butyrivibrio fibrisolvens strains AR10 and OR79A (bviD and bvi79A) in order to screen for their incidence in rumen and caecal B. fibrisolvens and Streptococcus bovis-like isolates from New Zealand and North American ruminants. None of the B. fibrisolvens-like strains (n=34) isolated from New Zealand or North America had the genes encoding for butyrivibriocins AR10 (bviD) or OR79 (bvi79A). However, seven S. bovis isolates from New Zealand ruminants and three from North American animals had the bovicin 255 gene. Sequence comparison of cloned bovicin 255 PCR products indicated a 92.9–95.7% similarity to that of the corresponding bovicin 255 gene sequence of S. gallolyticus. Four of the New Zealand bovicin 255 positive S. bovis isolates were from the caecal contents of the same sheep and had identical PFGE profiles. Two other S. bovis isolates sharing the same PFGE profile were isolated from a separate animal from the same flock. PFGE analysis of the North American strains indicated that all three were closely related as two of three had identical PFGE profiles with the remaining isolate differing only by a single band position. The 16S rRNA gene sequences of the 10 isolates were at least 99.8% identical to S. bovis. All 10 S. bovis isolates having the gene for bovicin 255 produced bacteriocin activity that inhibited the growth of Peptostreptococcus anaerobius D1 in a deferred antagonism plating (DAP) assay. Certain S. bovis isolates obtained from ruminants have bacteriocin activity associated with a distinct bovicin 255 gene sequence but it appears that bacteriocin production by the rumen anaerobe B. fibrisolvens may be uncommon in strains isolated from cattle and sheep in New Zealand.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.01.003
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Transcriptional analysis of the Clostridium cellulovorans endoglucanase gene, engB (1994)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 124 (1994), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract An endoglucanase gene, which was shown to be identical to the previously sequenced engB gene [Attwood et al. (1993) Abstr. Ann. Meet. Am. Soc. Microbiol.], was isolated from a Clostridium cellulovorans genomic library. Because of the lack of transcriptional information concerning engB we examined its expression in C. cellulovorans and in the geterologous hosts Escherichia coli and C. acetobutylicum following transformation of engB. Northern analysis suggested that both E. coli and C. acetobutylicum produced several transcripts of various sizes. C. cellulovorans produced a single transcript of 1600 bp with the relative amount of engB mRNA from cellulose-grown cells being much greater than that from cellobiose-grown cells. Primer extensions showed that engB was transcribed from a single transcription initiation site in C. cellulovorans preceded by sequences similar to promoter sequences found in Gram-positive bacteria. Primer extensions from both E. coli and C. acetobutylicum strains containing the engB gene showed multiple transcription initiation sites, none of which corresponded to the site determined in C. cellulovorans. We conclude that transcriptional control of the engB gene is less stringent in heterologous backgrounds and postulate that expression of the engB gene in C. cellulovorans is increased in the presence of cellulose.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1994.tb07297.x
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Genetic diversity in ruminal isolates ofSelenomonas ruminantium (1991)
    Springer
    Current microbiology 22 (1991), S. 279-284 
    Details
    ISSN: 1432-0991
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Diversity in the ruminal bacterial speciesSelenomonas ruminantium has been investigated by DNA fingerprinting, DNA-DNA hybridization, plasmid analysis, bacteriophage sensitivity, and monoclonal antibody-based immunoassay. Twenty different isolates from the sheep rumen were initially classified morphologically and by carbon source utilization. DNA fingerprint analyses and quantitative genomic DNA hybridizations showed that limited grouping of these isolates was possible, with the largest group comprising four isolates, and two other groups comprising two isolates each. The remaining isolates were unique. Plasmids in four different size classes, 2.5, 3.7, 6.5 and 12.0 kbp, were identified, but these did not appear in all isolates. There was no apparent relationship between DNA fingerprint pattern and plasmid content. Only three isolates were sensitive to theS. ruminantium-specific temperate bacteriophage S-1. These data indicate that substantial genetic diversity exists within the ruminal speciesS. ruminantium, but that at least one strain may represent up to 20% of isolates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02091955
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    Paper (German National Licenses)
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  • 5
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    Unraveling the functional dark matter through global metagenomics (2023)
    Nature Research
    Details
    Publication Date: 2024-02-07
    Description: Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
    Type: Article , PeerReviewed
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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