Metagenomic and bioinformatic approaches have been used to characterize microbial metabolism and plant biomass degrading capacity within the foregut microbiome of the Tammar wallaby (Macropus eugenii) and Svalbard Reindeer (Rangifer tarandus platyrhynchus). Key findings include:
• Similar to the termite hindgut and bovine rumen, key enzymes and modular structures characteristic of the “free enzyme” and “cellulosome” paradigms of cellulose solubilisation remain either poorly represented or elusive to capture by shotgun sequencing methods.
• Instead, multi-gene polysaccharide utilization loci (PULs)-like systems coupled with genes encoding β-1,4-endoglucanases and β-1,4-endoxylanases - which have not been previously encountered in metagenomic datasets were identified.
• Comparative metagenomic analysis and expression screening reveals the Svalbard reindeer rumen harbours a numerically greater glycoside hydrolase (GH) profile specialized in cellulose and hemicellulose degradation that what has been previously reported in other herbivores.
• Nucleotide composition-based sequence binning methods have facilitated the assemblage of more than 2 Megabase pairs of metagenomic sequence for several dominant and uncultured novel clades found in the Tammar wallaby foregut.
• The reconstruction of metabolic pathways encoded within these metagenomic assemblages has led to new insights and hypothesis into their functional capabilities thus enabling a successful selective isolation strategy to specifically isolate organisms of interest.
• Whole genome sequence analysis and phenotypic studies on an abundant host-specific isolate, confirmed its ability to provide the host with essential nutrients and potentially contribute towards the adaptation of the host to its environment.
Background
PUBLICATIONS:
1. C.P. Rosewarne, P.B. Pope, S.E. Denman, C.S. McSweeney, P. O'Cuiv, M. Morrison (2010). High-Yield and Phylogenetically Robust Methods of DNA Recovery for Analysis of Microbial Biofilms Adherent to Plant Biomass in the Herbivore Gut. Microb Ecol. PMID: 20838785.
2. P.B. Pope, M. Totsika, D. Aguirre de Carcer, M. A. Schembri and M. Morrison (2010). Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell-aggregation and biofilm formation ISME J. PMID: 20668486.
3. P.B. Pope, S.E. Denman, M. Jones, S.G. Tringe, K. Barry, S.A. Malfatti, A.C. McHardy, J-F. Cheng, P. Hugenholtz, C.S. McSweeney, and M. Morrison (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different to other herbivores. Proc. Natl Acad. Sci. USA. 107(33):14793-8.
4. M. Morrison, P.B. Pope, S. Denman, C. McSweeney (2009). Plant biomass degradation by gut microbiomes: More of the same or something new? Curr Opin Biotechnol. 20 (3); p358-363
5. P.B. Pope and BKC Patel (2008). Metagenomics of Cyanobacterial Blooms. FEMS Microbiol Ecol. 64; p9-27.
PUBLICATIONS IN REVIEW:
1. P.B. Pope, W. Smith, S.E. Denman, S.G. Tringe, A.C. McHardy, K. Barry, P. Hugenholtz, C.S. McSweeney, and M. Morrison (2010). Reverse metagenomic approaches results in the isolation a previously uncultured bacterial lineage which might contribute to the low methane phenotype of Australian macropods (Submitted to PNAS, Oct 2010).
2. K.Patil, P. Haider, P.B. Pope, P.J. Turnbaugh, M. Morrison, T. Scheffer, and A.C. McHardy (2010). PhyloPythiaS: Fast and accurate binning of metagenome sequence samples (Submitted Oct 2010).
3. P.B. Pope, S. Denman, C. McSweeney and M. Morrison (2010). Metagenomic procedures for complex gut microbiome samples (In preparation).
INVITED SPEAKER:
1. P.B. Pope (2009). The plant cell wall degrading capacity of the microbial community in marsupials. GRC conference for Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes. July 26-31, Andover, NH, USA.
GRANTS
1. P. B. Pope and V. Eijsink (2010). Bilateralt forskningssamarbeid - prosjektetablering (BILAT) program, The Research Council of Norway. Project title: Bioprospecting in the svalbard reindeer microbiome - establishing a Norwegian-Australian joint research effort. Funding: $445 000 NOK
2. P. B. Pope and S. Denman (2009). Acorn Grant, Transformational Biology Capability Platform, CSIRO. Project title: Large scale sequence processing and annotation of metagenomic datasets. Funding: $25 000 AUD.