Human long-read whole genome sequencing: applications and results
Dante Labs moved long-read whole genome sequencing into wellness and social care leveraging Oxford Nanopore PromethION technology. Results will be presented on large scale long-read sequencing, data results and actual impact on people's lives.
Andrea Riposati is the CEO & co-founder of Dante Labs, the global whole genome data company. Prior to Dante Labs, Andrea was a Senior Product Manager at Amazon in Seattle, where he launched 3D Printing and the Marketplace for Professional Medical Supplies. Andrea holds an MS summa cum laude in Business from Bocconi University and an MBA from Harvard Business School.
MinION sequencing from the extreme to the everyday
The portability and agility of the MinION platform means it can reach places other sequencers can’t. In our hands, this means we are able to deploy MinION DNA sequencing to provide real-time insights into microbial communities using metagenomics and 16S microbiome analyses in extreme environments. It also means that DNA data can be used to enrich public discourse about genomics and microbiomes by sequencing for the media. Here, I will share some of the insights and lessons learned from using MinION for research in off-grid environments and for public outreach. Case studies will include the use of MinION in an off-grid ice camp enduring subzero temperatures and hurricane force blizzards, which showed for the first time the potential for anoxygenic photosynthesis as novel metabolic process on the Greenland Ice Sheet, the live sequencing of soil metagenomes for national radio and the blending of extreme and everyday by sequencing deep subsurface microbiomes and metagenomes in a carbon sequestration experiment in the US directly followed by microbiome analysis for the Royal Institution Christmas Lectures. From these experiences, we are able to offer guidance on ensuring robust outcomes for sequencing in unlikely locations which may help others develop genomics data and discourse in the extreme and the everyday.
Dr. Arwyn Edwards is Senior Lecturer in Biology and Director of the Interdisciplinary Centre for Environmental Microbiology at Aberystwyth University. Portable DNA sequencing using the MinION is enabling Arwyn and other Arctic microbiologists respond to rapid changes in the Arctic, and access unprecedented insights into the diversity and function of extreme microbial ecosystems. This area of research is supported by NERC, Leverhulme, the Welsh Government and the European Union.
‘O nā Hōkū nō nā Kiu o ka Lani: Bridging genomics research and culture-based science education through astrobiology in Hawaiʻi
Culture-based science education provides a framework to develop the potential of every student (haumāna), through the mutual exchange of cultural and academic knowledge (a`o). Using this framework and nanopore technology, we are developing teacher training programs and classroom exercises (ʻĀina-Informatics) that bridge research in bacterial quorum sensing and Hawaiian cultural traditions. Quorum sensing is a type of intercellular signaling found in Bacteria and Archaea that coordinates activities among microbes through gene expression. Students and teachers have sequenced complete genomes of bacterial strains of interest in our research. We are also using nanopore reads to assist with de-convolution of genomes from microbial mats found in a variety of extreme environments. These data will address the importance of cooperative behavior in extreme environments. Our educational programs focus on increasing interest in groups underrepresented in STEM, help provide a cultural identity, and provide teachers training in genomics and bioinformatics.
Rebecca (Becks) received her B.A. degree in Ecology and Evolutionary Biology from the University of Arizona in USA. She then went on to continue her studies in Natural Resources at University of Arizona, where she worked on marine benthic ecology and community-based resource management to obtain a Masters degree. During this work, she began studying biofilms, which is the focus of her research. Her Ph.D work at the University of Hawai‘i at Mānoa investigated interactions between coral larvae and biofilms on the Great Barrier Reef in Australia. She is currently a National Science Foundation Postdoctoral Fellow in Biology working on “Survival in extreme environments through cooperation: biofilms and looking for life on Mars.”
Nanopore sequencing in space: one small step for a MinION, one giant leap for spaceflight research
As NASA sets sights beyond low-Earth orbit, real-time monitoring and diagnostics of crew health and the environment are required. The majority of previous research on the International Space Station (ISS) has relied on ground-based analyses following sample return to Earth. As a result, biological insights could be lost due to sample fixation and time to receipt in the laboratory. Moreover, sample return will become impractical as missions move beyond the ISS. Oxford Nanopore Technologies’ MinION has made in situ sequencing a reality in any field setting. Since our 2016 demonstration of the MinION’s high-performance off-Earth, four astronauts across the last ten ISS expeditions have successfully completed 18 sequencing experiments. Here, we will describe our end-to-end, sample-to-sequencer process that can be conducted entirely aboard the ISS, and which resulted in the first identification of microbes collected and cultured entirely off-Earth. Expanding beyond the need to first culture the microbes, our culture-independent, swab-to-sequencer investigation is currently underway to characterize further the microbiome of the ISS. One of our long-term goals is to enable crew health monitoring using functional genomics. As a start, we sequenced native poly-A RNA (and cDNA) from a human cell line (GM12878) aboard the ISS and will present findings from these experiments. Nanopore sequencing technology and our sample preparation procedures have expanded the reach of molecular biology to the final frontier. These proven capabilities hold the potential to revolutionize space-based research and in-flight medical operations.
Dr. Sarah Wallace serves as technical lead in the Microbiology Laboratory at the NASA Johnson Space Center, which is responsible for mitigating infectious disease risk during human spaceflight. Her responsibilities include the assessment of microbial risk based on vehicle and mission architectures as well as crewmember, food, and environmental monitoring. These assessments are used to develop requirements for NASA and commercial spaceflight vehicles, including the International Space Station. In addition to her operational support of human spaceflight, Dr. Wallace leads new technology initiatives for her discipline with the goal of reducing Earth dependence for complex sample analysis. She has served as PI for numerous spaceflight investigations, including those to increase off-planet molecular biology capabilities and also to understand how the spaceflight environment impacts cellular behavior.
Mobile antibiotic resistome in wastewater treatment plants revealed by nanopore metagenomic sequencing
In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge and effluent of three wastewater treatment plants (WWTPs) and simultaneously track the hosts of antibiotic resistance genes (ARG). The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Oxford Nanopore and Illumina sequencing platforms demonstrated the feasibility of nanopore sequencing for resistome quantification. Overall, these findings substantially expand our current knowledge of the resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.
Dr Tong Zhang is a Professor in the Environmental Biotechnology Laboratory in Department of Civil Engineering, and an Honorary Professor in the School of Public Health, at The University of Hong Kong. He received his Bachelor and Master’s degrees in Environmental Science and Engineering from Nanjing University, and his PhD from The University of Hong Kong. His research interests include environmental bioinformatics, omics technologies, anaerobic digestion and bioenergy from wastes/wastewater, biological wastewater treatment (N removal and P recovery), biodegradation of emerging pollutants (antibiotics, PPCP and EDCs) and antibiotic and antibiotic resistance genes. He has published over 200 peer-reviewed papers, and has more than 14, 000 citations and an H index of 68 on Google Scholar. He is an associate editor of Microbiome and Applied Microbiology and Biotechnology and had served as an advisor for Beijing Genomics Institute on Environmental Microbiology and Biotechnology from 2011 to 2014. He was Yi Xing Chair Professor of Nanjing University from 2013 to 2016, and currently is a distinguished visiting professor of Southern University of Science and Technology in China. He got First-Class Award in Natural Science of China Ministry of Education in 2015, Second-Class Award State Natural Science Award of China State Council in 2016, and Outstanding Research Student Supervisor Award of HKU in 2017. He is listed as one of the Highly Cited Researchers by Clarivate in 2018.
The fever tree: extracting and preparing the DNA of Cinchona pubescens