Full-length Metagenomic Sequencing (Nanopore)_Microbial diversity_Services

TECHNOLOGY SERVICES

Product introduction
Common problem
Classic case
Result display

Product introduction

Full-length metagenomic sequencing is to extract the total DNA of microbial colonies in a specific environment (soil, water, gut, etc.), use Nanopore sequencing technology to obtain the complete sequence of these DNA, and study the species distribution of environmental microorganisms through bioinformatics analysis , community structure and techniques of gene function and metabolic networks. More drug resistance genes and multi-drug resistance genes can be identified, and some bacterial completed maps can be assembled.

Advantages of full-length metagenomic

long read length:N50 can reach 3-10Kb, and the longest read can reach more than 100Kb, which can span long and complex regions. ^[1]
Functional mining is accurate:differential gene analysis is more accurate, and virulence factor analysis is more comprehensive.
Accurately mining resistance genes:mining more antibiotic resistance genes and multi-drug resistance genes. ^[1]
Completed genome acquisition diagram:Species, strain genomes and plasmid genomes are assembled after binning.
Retention of modification information:6mA, 5mC and other base modification information can be detected at the same time.

Figure a: Illumina Contig column height represents the length of Contig after data assembly by Illumina platform sequencing, Nanopore Min and Nanopore Max represent the minimum and maximum length of reads obtained by Nanopore platform sequencing respectively; Figure b: Nanopore and Illumina two The number of antibiotic resistance genes obtained by analyzing the sequencing data of each platform.

[1] Che Y , Xia Y , Liu L , et al. Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing[J]. Microbiome, 2019, 7(1).

Classic Case

Case Analysis 1 Using Nanopore high-throughput sequencing technology to analyze the mobile resistance genome

results of sewage treatment system:

Nanopore sequencing reads N50 reaches 5.8-10.7Kb, and Illumina assembled contigs N50 is only 1.7Kb.
Nanopore identified 1791 antibiotic resistance genes (ARGs) based on reads, while Illumina contigs identified only 316 ARGs.
A large number of sulfonamide resistance genes were observed in the cultures of the water inlet and outlet, which proved that persistent drug resistance was related to plasmids.
Multiple types of ARGs are often located on the same plasmid, and Nanopore can detect multidrug resistance genes that Illumina cannot detect.
References: Che Y , Xia Y , Liu L , et al. Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing[J]. Microbiome, 2019, 7(1).

Case analysis 2 Using Nanopore sequencing from the microbiome Obtain the bacterial completion map

results:
Fecal samples from 13 individuals assembled 20 circular genomes, including Prevotella copri and Cibiobacter sp.
The integrity of the assembled genome of Nanopore is better than that of PacBio, and 7630 gaps of more than 2 bp are obtained by comparing the assembly results of PB to the assembly results of ONT.
The species diversity obtained by Nanopore based on reads is higher, and the Shannon index is higher.
Reference: Eli LM, Dylan GM & Ami SB. Complete, closed bacterial genomes from microbiomes using nanopore sequencing[J]. Nature Biotechnology, 2020.

results:

Fecal samples from 13 individuals assembled 20 circular genomes, including Prevotella copri and Cibiobacter sp.
The integrity of the assembled genome of Nanopore is better than that of PacBio, and 7630 gaps of more than 2 bp are obtained by comparing the assembly results of PB to the assembly results of ONT.

The species diversity obtained by Nanopore based on reads is higher, and the Shannon index is higher.
Reference: Eli LM, Dylan GM & Ami SB. Complete, closed bacterial genomes from microbiomes using nanopore sequencing[J]. Nature Biotechnology, 2020.