Related Experiment Video
Updated: Apr 27, 2026
12:08
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
7.3K
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference
H Bjørn Nielsen1, Mathieu Almeida2, Agnieszka Sierakowska Juncker3
11] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark. [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. [3].
Nature Biotechnology
|July 7, 2014
Summary
This study introduces a novel method for analyzing metagenomic data without reference genomes. It enables comprehensive discovery and assembly of microbial genomes and associated genetic entities from complex samples.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Current metagenomic analysis relies heavily on reference genomes, limiting discovery in diverse environments.
- Segregating complex metagenomic data into specific biological entities de novo is a significant challenge.
Purpose of the Study:
- To develop a method for comprehensive metagenomic data analysis without reference sequences.
- To enable the discovery and assembly of novel microbial organisms, viruses, and genetic entities.
Main Methods:
- Binning co-abundant genes across multiple metagenomic samples.
- Application of the method to human gut microbiome data.
Main Results:
- Identification of 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS).
- Assembly of 238 high-quality microbial genomes.
- Discovery of affiliations between MGS and hundreds of viruses or genetic entities.
Conclusions:
- The developed method facilitates comprehensive profiling of microbial diversity in complex metagenomic samples.
- It overcomes limitations of reference-based approaches for discovering novel organisms and genetic elements.
Related Concept Videos
03:36Genome Annotation and Assembly
16.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
16.5K
01:29Modern Molecular Taxonomy
830
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
830
02:02Genomics
35.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.3K
02:54Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
03:21RNA-seq
9.2K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.2K
01:57Sanger Sequencing
800.5K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
800.5K