Meta-OMIC reconstruction in the gut microbiome of wild primates: Impactions for human origins
J. Craig Venter Institute, United States of America
The concept of the holobiont considers both host and symbiotic microbes a single unit for selection in evolution. This idea suggest that the evolution process may not be fully understood without considering the role that residing microbes play in the physiological landscape of the host. Here, I show that an extensive molecular analysis of the primate gut microbiome offers a complementary view of the extrinsic and intrinsic forces that triggered human evolution. To that end, I used integrated Meta-OMICS; merging metagenomic, metabolomic and metatranscriptomics data from stool samples to reconstruct the organizational and functional complexity of the gut microecosystem of wild gorillas, chimpanzees and humans. This comparative framework is implemented to assess the potential impact that the gut microbiome has exerted in the genomic landscape of the host. In synthesis, these data sheds light on how, over evolutionary timescales, diet and gut microbes intersected to influence energy harvest and immunity, impacting the emergence of the lineage leading to humans.
Gut Microbiota Sequencing: From Single Studies To Large-Scale Analysis
1University Hospital RWTH Aachen, Germany; 2ZIEL Institute, TU Munich, Freising, Germany
Since the discovery of Polymerase Chain Reaction and pioneering work on 16S ribosomal RNA genes in the 1980’s, the use of molecular techniques to study microbial ecosystems and pathogenic microorganisms has been increasing exponentially. Because microbial communities inhabiting various body sites such as the skin or the intestine can influence our physiology, there has been a massive interest in studying their diversity, functions, and role in the development of acute and chronic diseases. In my presentation, I will talk about sequencing approaches to study microbial communities, especially human body microbiota, and give opinions on their potential and limitations. Moreover, I will present a new bioinformatic tool, the Integrated Microbial Next Generation Sequencing (IMNGS) platform, for user-friendly, large-scale studies of 16S rRNA gene amplicon datasets. IMNGS uniformly and systematically screens for, retrieves, processes, and analyses all prokaryotic 16S rRNA amplicon data available in the Sequence Read Archive (SRA) and uses them to build sample-specific sequence databases. Using a web interface, this massively integrated sequence resource can be queried and used to address a broad range of questions of relevance in microbial ecology and applied microbiology. The platform also offers a complete workflow for de novo analysis of users’ own raw 16S rRNA amplicon data. This new resource can be accessed at www.imngs.org.
Clavel, Lagkouvardos, Hiergeist (2016) Microbiome sequencing: challenges and opportunities for molecular medicine. Expert Rev Mol Diagn 16:795.
Lagkouvardos, Joseph, Kapfhammer, Giritli, Horn, Haller, Clavel (2016) IMNGS: A massive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep 6:33721.
Lagkouvardos, Kumar, Fischer, Clavel (2017) Rhea: A transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 5:e2836.
From qualitative to quantitative data in microbiome analysis: Using metagenomics for qPCR validation.
1Helmholtz Zentrum München, Germany; 2Technical University of Munich, Germany
Microbial diversity in nature is enormous and even today we are unable to predict the correct number of species which are harboured by most ecosystems including our human body. This situation becomes even worse when not one marker gene is studied, like in the case of the analysis of species richness, but complete metagemones and the related functional traits should be described. Here also most next generation sequencing approaches fail as sequencing efforts are needed to cover functional diversity which go far beyond 5 Tbases. Furthermore as still most of the functional traits are not well described and an annotation of reads towards predicted functions is hard to do or even impossible. In this presentation we describe an approach linking sequencing of metagenomes with a relative low coverage (10 Gbases or less), with the aim to identify key genes of interest which drive certain processes and to use this information to develop highly targeted primer pairs, which might be useful for in depth analysis of the diversity of those genes as well as a quantitative assessment. We consider this approach as “2nd generation full cycle” in microbial ecology.
Unravelling The Evolution Of Prostate Cancer Through Whole Genome Sequence Data.
1Norwich Medical School, University of East Anglia, United Kingdom; 2Cancer Genome Project, Wellcome Trust Sanger Institute, United Kingdom; 3Oxford Big Data Institute & Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, United Kingdom; 4HCA Pathology Laboratories, London, United Kingdom; 5Cancer Research UK Cambridge Institute, Cambridge, United Kingdom; 6University of Tampere and Tampere University Hospital, Finland; 7Institute of Cancer Research, United Kingdom
As part of the CRUK-ICGC Prostate UK project we have been gathering whole genome sequencing data from tissue from prostate cancer patients and applying sophisticated data analysis techniques to unravel how prostate cancer evolves. In this talk we will describe two projects:
Project 1 - Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of on-going abnormal mutational processes, consistent with field-effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harbouring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissue or between different ERG-lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.
Project 2 - Cancers emerge from an on-going Darwinian evolutionary process, often leading to multiple competing subclones within a single primary tumour. This evolutionary process culminates in the formation of metastases, which is the cause of 90% of cancer-related deaths. However, despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. Although the hypothesis that each metastasis originates from a single tumour cell is generally supported, recent studies using mouse models of cancer demonstrated the existence of polyclonal seeding from and inter-clonal cooperation between multiple subclones. Using whole genome sequencing, we characterised multiple metastases arising from prostate tumours in ten patients. Integrated analyses of subclonal architecture revealed the patterns of metastatic spread in unprecedented detail. Metastasis-to-metastasis spread was found to be common, either through de novo monoclonal seeding of daughter metastases or, in five cases, through the transfer of multiple tumour clones between metastatic sites. Lesions affecting tumour suppressor genes usually occur as single events, whereas mutations in genes involved in androgen receptor signalling commonly involve multiple, convergent events in different metastases. Our results elucidate in detail the complex patterns of metastatic spread and further our understanding of the development of resistance to androgen deprivation therapy in prostate cancer.
Nanopore Sequencing - Entering New Next
Advances in sequencing technologies have provided the scientific community with ample opportunities for almost unrestricted exploration of organisms of their choice. However, complete de novo assembly of ‘larger’ genomes continues to be technically challenging. Among other things, this barrier hinders genomics core facilities from offering this application to their user base.
Ultimately, a straightforward system able to deliver comprehensive information also on the primary code of organisms with uncharacterized genomes would ideally complement core facilities’ otherwise wide range of methods, which they utilize for description of other nucleic-acid cellular components.
EMBL GeneCore has applied nanopore sequencing for finishing several de novo genome sequencing projects. With simplified DNA isolation protocol enabling ‘reads’ over 100 kb long we have been able to considerably improve assembly of several 0.5-1 Gb genomes. Positive results from our first attempts with new R9 flowcells indicate that to achieve worthwhile genomes’ assemblies, we will be able to reduce amount of data generated by short-read sequencing technology soon.
Overcoming NGS analysis bottlenecks with a systematic, scalable system
Basepair, United States of America
Next generation DNA sequencing (NGS) has led to a paradigm shift in biomedical research. The ability to study the genome, transcriptome, epigenome, etc. has present many opportunities to accelerate innovation in life sciences. While the cost and accessibility of NGS technology have improved exponentially, the biggest bottleneck is now data analysis and interpretation. NGS generates several gigabytes of raw data for each sample, leading to huge cost for setting up storage and computation infrastructure. The analysis is complex, and requires installing and running several different software. Finally, communicating the research to physicians and scientists is cumbersome. Basepair has been developed as a response to these challenges. We designed our system from scratch, to solve each of these problems in the best possible way.
Evaluation of Regulatory Small Variants in Human Genetics
Genomatix GmbH, Germany
Next Generation Sequencing has become a basis for the detection of small sequence variants in whole exomes and whole genomes. The correct interpretation of the relevance of identified variants is a major challenge in clinical diagnostics. For coding single nucleotide variants, published standards and guidelines have been widely adopted by clinical laboratories. The majority of disease-associated variants, however, are found in non-coding regions, suggesting that they affect the regulation of gene expression. Their analysis and reliable evaluation is methodically challenging and so far not standardized. This talk will provide an overview of recent developments in the assessment of potential regulatory variants.