In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

Abstract

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third "Golden Age". However, conventional metagenomics strategies necessitate retrograde transfer of samples from extreme or remote environments for later analysis, rendering the powerful insights gained retrospective in nature, striking a contrast with Pasteur's dictum. Here we implement a highly portable USB-based nanopore DNA sequencing platform coupled with field-adapted environmental DNA extraction, rapid sequence library generation and off-line analyses of metagenome profiles to characterize the microbiota of a High Arctic glacier. The profile of the microbial communities produced by this approach are coherent with those from conventional amplicon and shotgun metagenome sequencing of glacier environments, and prompt testable hypotheses regarding microbial community structure and function on the basis of data generated and analysed while in the field. Moreover, we highlight the potential for oligonucleotide mixture model based metagenomic profiling of nanopore reads to deliver off-grid metagenomics analyses. Ultimately, in-field metagenomic sequencing potentiated by nanopore devices raises the prospect of considerably enhanced agility in exploring Earth's microbiomes.not peer-reviewed)

Towards a genomics-informed, real-time, global pathogen surveillance system

“…Importantly, the MinION has been used in field situations, including in diagnostic tent labora tories during the Ebola epidemic 22,23 and in a roving busbased mobile laboratory in Brazil as part of the ZiBRA project 3,24 . Others have taken the MinION to more extreme environments where even the smallest traditional bench-top sequencer could not go, including the Arctic 25 and Antarctic 26 , a deep mine 27 and zero gravity aboard the reduced-gravity aircraft (nicknamed the 'Vomit Comet') 28 and the International Space Station 29 . However, this technology is not yet a panacea; remaining challenges include high DNA or RNA input requirements (currently hundreds of nanograms), which often necessitate PCR-based amplification approaches; a flow cell cost of $500, keeping the cost per sample high despite multiplexing approaches; and high error rates, which require that genomes are sequenced to high coverage for single nucleotide polymorphism-based analysis and analysed at the signal level.…”

Genetic and genomic monitoring with minimally invasive sampling methods

“…A landmark paper in 2011 developed a set of SNPs for investigation of false eco-certification of exploited European fish stocks using population assignment that relies on divergent SNPs under the influence of selection in species in otherwise undifferentiated populations, where standard microsatellitebased population assignment had proved impossible (Nielsen et al, 2012). Furthermore, portable sequencing devices, such as the MinIon (Oxford Nanopore Technologies), are starting to be used to sequence samples in field laboratory conditions (Edwards, Debbonaire, Sattler, Mur, & Hodson, 2016;Quick et al, 2016). This leads to the possibility that in the near future researchers will be able to undertake real-time assessments of the species, and potentially population of origin, of products in markets.…”

Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis

“…Consensus accuracy for an E. coli K12 assembly consequently also increased to 99.96% 15 . A rapid single-stranded sequencing kit was introduced in August 2016, reducing post-extraction sample preparation time to less than 15 minutes (see 16). …”