16s rrna sequence analysis portable#
16s rrna sequence analysis Offline#

This delay prevents the collection of meaningful information about field samples until much later, when field trips have ended and opportunities to adjust sampling strategies are gone. In most of these previous cases of in situ sequencing, researchers have had to wait to analyze data until there was an internet connection or sufficient computing power available. To exemplify its portability, the MinION sequencer has been used to sequence DNA in space, in remote field locations like the high Arctic and during a ski touring expedition in Iceland. While several Nanopore platforms have been developed and are in use, the MinION sequencer has gained recognition as relatively inexpensive and exceptionally portable. Nanopore sequencing allows for the continuous sequencing of long sequences of nucleotides, e.g., the full-length, 1500 bp 16S rRNA gene, enabling better taxonomic resolution than much shorter Illumina sequences. Sequencing with Oxford Nanopore technology, or “third generation” sequencing, is quickly gaining favor in the microbiological research community. Rapid analysis of 16S rRNA gene diversity in a microbial community could be used to quickly characterize a sample in circumstances when time or access to resources are limited. Sequencing of microbial genes (e.g., the 16S rRNA gene) is often used for environmental monitoring and medical diagnostics, as well as to identify indicators of environmental conditions, disturbances, and diseases. Despite this, it is not always certain that the samples will address the research question, sometimes leaving researchers in situations where they are uninformed during sampling campaigns. In these situations, every sample taken is valuable in terms of the resources required for collection. Fieldwork is also logistically challenging as it can be complex to move people, equipment, and samples long distances, across borders, and through difficult terrain. Collecting samples from these remote locations requires fieldwork that can be expensive and time consuming.

16s rrna sequence analysis portable#

SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.Įxamining the microbiome of extreme and remote environments has increased our collective understanding of microbial physiology and diversity. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson’s r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA.

16s rrna sequence analysis Offline#

Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem.