A comprehensive survey of integron-associated genes present in metagenomes

BMC Genomics
Mariana Buongermino PereiraErik Kristiansson

Abstract

Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging. Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,3...Continue Reading

References

Jul 23, 1999·Annals of the New York Academy of Sciences·R M HallH W Stokes
Feb 15, 2000·Research in Microbiology·D A Rowe-MagnusD Mazel
Oct 27, 2001·Applied and Environmental Microbiology·H W StokesM R Gillings
Nov 28, 2001·Molecular Microbiology·R VaisvilaE A Raleigh
Mar 6, 2002·Applied Microbiology and Biotechnology·S Vuilleumier, M Pagni
Jan 10, 2003·Nucleic Acids Research·Daniel H HaftOwen White
Apr 26, 2003·Environmental Microbiology·Andrew J HolmesH W Stokes
Aug 26, 2004·FEBS Letters·Héctor MustoGiorgio Bernardi
Dec 1, 2004·Annual Review of Genetics·Stephen D Bentley, Julian Parkhill
Aug 27, 2005·Current Opinion in Microbiology·Jeffrey G Lawrence, Heather Hendrickson
Oct 4, 2005·EMBO Reports·Konrad U FoerstnerPeer Bork
Apr 28, 2006·Nature·Douglas MacDonaldDeshmukh N Gopaul
Jul 18, 2006·Nature Reviews. Microbiology·Didier Mazel
Oct 6, 2006·Molecular Microbiology·Mikkel Christensen-Dalsgaard, Kenn Gerdes
Jan 17, 2007·Genome Biology·Jeroen RaesPeer Bork
Mar 16, 2007·PLoS Biology·Rekha SeshadriMarvin Frazier
Mar 21, 2007·Molecular Microbiology·Silvia SzekeresDean A Rowe-Magnus
Jun 15, 2007·Trends in Microbiology·Yan BoucherH W Stokes
Oct 23, 2008·Nucleic Acids Research·Dennis A BensonEric W Sayers
Feb 21, 2009·Bioinformatics·Alexandra MouraAntónio Correia
Mar 28, 2009·PLoS Genetics·Laurence Van Melderen, Manuel Saavedra De Bast
May 7, 2009·FEMS Microbiology Reviews·Sally R PartridgeJonathan R Iredell
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Feb 16, 2010·Journal of Biomedical Informatics·Christopher J MungallJane Lomax
Aug 17, 2010·Annual Review of Genetics·Guillaume CambrayDidier Mazel
Feb 22, 2011·Mobile DNA·André Larouche, Paul H Roy
Jun 13, 2012·Bioinformatics·Steffen HeyneRolf Backofen
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
Jul 17, 2012·Bioinformatics·Doug HyattEdward C Uberbacher
Oct 5, 2012·Genome Biology and Evolution·Guoqin Yu, Arlin Stoltzfus
Sep 7, 2013·Bioinformatics·Eric P Nawrocki, Sean R Eddy
Oct 15, 2013·FEMS Microbiology Ecology·Hosam ElsaiedAkihiko Maruyama

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
amplicon sequencing

Software Mentioned

EBI Metagenomics
LocaRNA
BacMet
- finder (
PFAM
NTenv
BLAST
INTEGRALL
Metagenomic Integron - associated Gene finder )
HMMER

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2021 Meta ULC. All rights reserved