Progress 09/15/01 to 03/14/06
Outputs
The sequencing work for this project has been completed for some time. The genome of Prevotella ruminicola strain 23 was sequenced to closure and the genome of Prevotella bryantii strain B14 was sequenced and assembled following draft coverage. In the latter instance, approximately 35 gaps remains in the pseudomolecule, representing almost complete coverage. The genome of P. ruminicola has also been fully annotated by TIGR bioinformatics personnel, and a preliminary comparison of the P. ruminicola and P. bryantii genomes has been made with the oral bacterium, Prevotella intermedia. Similar to phylogenetic analysis, the P. bryantii genome shares features in common with both P. ruminicola and P. intermedia, moreso than features in common between P. intermedia and P. ruminicola. A particular case in point are the types and kinds of antibiotic resistance genes present in P. bryantii. Many are quite similar to those found in P. intermedia, whereas P. ruminicola has much
fewer antiobiotic resistance genes compared to the other two species, and the types present are most similar to those from human colonic Bacteroides species. With respect to glycoside hydrolases, both P. ruminicola and P. bryantii possess a large number of family 43 genes, indicating the recrutiment of genes supporting the breakdown of arabinoxylans. Functional cahracterization of one of the beta-xylosidases from P. ruminicola is now underway, and grant applications have been prepared and submitted to USDA NRICGP concerning nitrogen regulation and ammonia utilization by P. ruminicola. Manuscript(s) describing the key features of these genomes will be prepared during 2007.
Impacts
The availability of these genome sequences will empower investigators to better understand the breakdown of plant hemicelluloses, which is key to improving the efficiency of plant biomass conversion. Similarly, the genome data empowers our ability to better understand factors affecting nitrogen utilization by this numerically dominant group of rumen bacteria. This should provide new opportunities to productively manipulate nitrogen metabolism and retention in ruminant livestock production systems.
Publications
- No publications reported this period
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Progress 01/01/05 to 12/31/05
Outputs
During 2005, we were able to complete the sequencing of the Prevotella ruminicola strain 23 genome, and also complete sequencing the Prevotella bryantii B14 genome to 8x coverage. We are now proceeding with the annotation of both genomes.
Impacts
By the end of the project we will be well positioned to characterize how these bacteria coordinate the hydroylsis of plant structural polysachharides, especially the "hemicellulose" component of plant cell walls. This information will be especially useful for ongoing and new efforts which strive to improve feed digestibility, as well as increased the yield of soluble sugars from plant-based feedstocks to be use for bioethanol production.
Publications
- No publications reported this period
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Progress 01/01/04 to 12/31/04
Outputs
The P. ruminicola (strain 23) genome project has proceeded smoothly and is now closed and assembled, with cost savings used to produce 8x genome coverage for a second strain (Prevotella bryantii strain B14). Manual annotation of the strain 23 genome is about to start. Compared to R. albus and F. succinogenes, the P. ruminicola 23 genome is characterized by containing a relatively large number of family 43 and 51 glycosyl hydrolases, which are typically xylosidases and (or) arabinofuranosidases.
Impacts
This strain is a member of the Prevotella spp. resident in vertebrate gastrointestinal tracts. Knowledge of this genome should be particularly helpful to the scientific community with interests in ruminal and gastrointestinal microbiology, as well as comparative genomics of the Cytophage-Flexibacter-Bacteroides phylum. We expect the study of this bacterium to improve our understanding of plant fiber digestion in all herbivores, which may result in more efficient production of animal products with reduced environmental impact.
Publications
- Morrison, M., K. E. Nelson, D. Antonopoulos, B. Cheng, E. Devillard, D. E. Goodheart, H-S Jun, V. A. Parisi, J-S Park, S. M. Qi, C. Reveneau, I. K. O. Cann, S. Daugherty, C. W. Forsberg, I. Hance, R. I. Mackie, W. C. Nelson, J. B. Russell, B. A. White, and D. B. Wilson. (2003) New and Emerging Approaches to Improve Herbivore Nutrition: Rumen Microbiology in the Genomics Era. pp. 309-320 In: (L. t'Mannetje and J. K. Vera, Eds.) Proceedings of the Sixth International Symposium on the Nutrition of Herbivores. Universidad Autonoma de Yucatan, Mexico.
- Morrison, M., K. E. Nelson, D. Antonopoulos, B. Cheng, E. Devillard, D. E. Goodheart, H-S. Jun, V. A. Parisi, J-S. Park, S. M. Qi, C. Reveneau, I. K. O. Cann, S. Daugherty, C. W. Forsberg, I. Hance, R. I. Mackie, W. C. Nelson, J. B. Russell, B. A. White, and D. B. Wilson (2004) Genomics of Ruminal Cellulose-Degrading Bacteria. Pp. 265-273. In: (K. Ohmiya et al.) Biotechnology of Lignocellulose Degradation and Biomass Utilization. Proceedings of Mie Bioforum 2003. Uni Publishers Co. Ltd. Tokyo, Japan
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Progress 01/01/03 to 12/31/03
Outputs
Relative to original objectives, the sequencing phase of this project is virtually complete. The genome has been sequenced in its entirety, and reached the final stages of polishing and assembly. The latest version of the unfinished genome is available via the TIGR website. We need additional time to complete the assembly and annotation of the genome, as well as manuscript development.
Impacts
This strain is a member of the Prevotella spp. resident in vertebrate gastrointestinal tracts. Knowledge of this genome should be particularly helpful to the scientific community with interests in ruminal and gastrointestinal microbiology, as well as comparative genomics of the Cytophage-Flexibacter-Bacteroides phylum. We expect the study of this bacterium to improve our understanding of plant fiber digestion in all herbivores, which may result in more efficient production of animal products with reduced environmental impact.
Publications
- No publications reported this period
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Progress 01/01/02 to 12/31/02
Outputs
This sequencing project is proceeding smoothly, with little or no difficulties in library construction or their randomness. This project is close to entering the closure stages of the project and it appears that the genome size is much smaller than initially predicted (3.5 Megabase pairs, as opposed to 6.4 Megabase pairs). A preliminary gene list and data release should occur within weeks.
Impacts
Knowing the complete genome sequence of Prevotella ruminicola should enhance our understanding of rumen microbiology and also enhance our potential to productively alter rumen function.
Publications
- No publications reported this period
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Progress 01/01/01 to 12/31/01
Outputs
Genomic DNA is being prepared from Prevotella ruminicola strain 23, and shall be provided to The Institute for Genomic Research in the near future, to initiate the random phase of this genome sequencing project.
Impacts
Knowing the entire genetic code for Prevotella ruminicola strain 23 will allow us to better understand how this bacterium survives in livestock, and how it contributes to the digestion of feeds.
Publications
- No publications reported this period
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