Final Report Summary - PERMATHREAT (Forecasting the climatic and health consequences <br/>of global warming on permafrost environments)
In our project, we investigated the composition of modern and microbial communities retrieved from metagenomic shotgun sequencing data.
We developed a novel approach that targets the totality of microbes dwelling both in environment (such as permafrost) and in samples preserved under different environmental conditions. The approach, is able to profile and to compare the microbial component of different microbiomes and environments. The microbial profiling algorithm is conservative and relies on a homology-based classification of reads from shotgun DNA data while a fitted statistical-ecological suite is able to analyze and compare microbial profiles from different environments. This approach is fully described in DerSarkissian et al., 2014 (in Molecular Ecology; IF: 6.28; the fellow is first co-author), and Schubert et al 2014 (Nature protocols; IF:8.36; the fellow is second author).
A good opportunity to enhance our metagenomic approach was given by two archeological remains of very ancient horses preserved in permafrost (Siberia, Russia). We profiled the microbial compositions of both specimens and the resulting microbial profiles were compared with various human associated microbiomes and soils. The resulting manuscript is now in press and will be shortly published in Proceedings of the National Academy of Science (Schubert el al, PNAS; IF: 9.8; the fellow is fifth author out of thirty five). This contingency therefore, gave us the opportunity to enlarge the vision of the project towards genomics and also for the fellow to gain solid experience in mapping, assembling and analysing genomes.
We sequenced at deep coverage two ancient horse genomes (about 4000 and 200 years ago) retrieved from archaeological remains preserved in permafrost and also nine modern specimens of horses from the same region (Siberia, Russia). We also profiled the microbial communities in those samples preserved in permafrost. Because of the cold environmental conditions of this geographic area these horses are particularly adapted to extreme environments. Gene variants selected over the time are thus likely to have driven adaptation to cold and more in general to severe environments. We thus reconstructed their phylogeny, inferred their past demographic events and we are identifying those gene variants responsible to adaptation of extreme environment. This work is likely to be receptive to public community and to have an economic impact as genetic markers will most likely show high value in the industry of molecular diagnostics (i.e. regarding racehorses or metabolic performance).
A huge impact on the public community is also expected to be delivered by another genomic work the fellow is involved with. We have undertaken to a large-scale characterization of the genomic diversity of Przewalski's horses, a rare and endangered breed, native of the steppes of central Asia, one time extinct in the wild and reintroduced to its native habitat since the 1990s. We have sequenced and reconstructed complete genomes of thirteen modern-day horses representing the main lineages of the Przewalski's horse pedigree, as well as five ancient horses pre-dating captivity. This work is expected to have a big impact in terms of conservation and biodiversity. In both genomic works the microbial profiling is carried out by the novel approach implemented by the fellow who will be first author in both publications. We aim to submit both works within few weeks in two high impact scientific journals. Proceedings of the National Academy of Science is a candidate.
We developed a novel approach that targets the totality of microbes dwelling both in environment (such as permafrost) and in samples preserved under different environmental conditions. The approach, is able to profile and to compare the microbial component of different microbiomes and environments. The microbial profiling algorithm is conservative and relies on a homology-based classification of reads from shotgun DNA data while a fitted statistical-ecological suite is able to analyze and compare microbial profiles from different environments. This approach is fully described in DerSarkissian et al., 2014 (in Molecular Ecology; IF: 6.28; the fellow is first co-author), and Schubert et al 2014 (Nature protocols; IF:8.36; the fellow is second author).
A good opportunity to enhance our metagenomic approach was given by two archeological remains of very ancient horses preserved in permafrost (Siberia, Russia). We profiled the microbial compositions of both specimens and the resulting microbial profiles were compared with various human associated microbiomes and soils. The resulting manuscript is now in press and will be shortly published in Proceedings of the National Academy of Science (Schubert el al, PNAS; IF: 9.8; the fellow is fifth author out of thirty five). This contingency therefore, gave us the opportunity to enlarge the vision of the project towards genomics and also for the fellow to gain solid experience in mapping, assembling and analysing genomes.
We sequenced at deep coverage two ancient horse genomes (about 4000 and 200 years ago) retrieved from archaeological remains preserved in permafrost and also nine modern specimens of horses from the same region (Siberia, Russia). We also profiled the microbial communities in those samples preserved in permafrost. Because of the cold environmental conditions of this geographic area these horses are particularly adapted to extreme environments. Gene variants selected over the time are thus likely to have driven adaptation to cold and more in general to severe environments. We thus reconstructed their phylogeny, inferred their past demographic events and we are identifying those gene variants responsible to adaptation of extreme environment. This work is likely to be receptive to public community and to have an economic impact as genetic markers will most likely show high value in the industry of molecular diagnostics (i.e. regarding racehorses or metabolic performance).
A huge impact on the public community is also expected to be delivered by another genomic work the fellow is involved with. We have undertaken to a large-scale characterization of the genomic diversity of Przewalski's horses, a rare and endangered breed, native of the steppes of central Asia, one time extinct in the wild and reintroduced to its native habitat since the 1990s. We have sequenced and reconstructed complete genomes of thirteen modern-day horses representing the main lineages of the Przewalski's horse pedigree, as well as five ancient horses pre-dating captivity. This work is expected to have a big impact in terms of conservation and biodiversity. In both genomic works the microbial profiling is carried out by the novel approach implemented by the fellow who will be first author in both publications. We aim to submit both works within few weeks in two high impact scientific journals. Proceedings of the National Academy of Science is a candidate.