Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids.

Nature Communications
S. Redondo-SalvoFernando de la Cruz

Abstract

Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I-VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.

References

Nov 26, 1971·Nature·N Datta, R W Hedges
Jul 1, 1963·Journal of General Microbiology·E W MEYNELL
Feb 21, 2004·FEMS Microbiology Reviews·M Victoria FranciaFernando de la Cruz
Sep 5, 2006·Current Biology : CB·Hema Prasad Narra, Howard Ochman
Oct 10, 2006·FEMS Microbiology Reviews·Raúl Fernández-LópezFernando de la Cruz
Jan 16, 2007·International Journal of Systematic and Evolutionary Microbiology·Johan GorisJames M Tiedje
May 8, 2008·Nature Reviews. Microbiology·Mark Achtman, Michael Wagner
May 5, 2009·Genome Research·W Ford Doolittle, Olga Zhaxybayeva
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
May 11, 2010·Trends in Microbiology·Xavier Didelot, Martin C J Maiden
Sep 2, 2010·Microbiology and Molecular Biology Reviews : MMBR·Chris SmillieFernando de la Cruz
Sep 21, 2010·Journal of Bacteriology·Haruo SuzukiEva M Top
Oct 5, 2010·Genome Biology and Evolution·Pere PuigbòEugene V Koonin
Oct 12, 2010·The Journal of Antimicrobial Chemotherapy·Laura VillaAlessandra Carattoli
Jun 10, 2011·The Journal of Antimicrobial Chemotherapy·Aurora García-FernándezAlessandra Carattoli
Jun 15, 2011·Nature Reviews. Microbiology·Cheryl P Andam, J Peter Gogarten
Jun 30, 2011·FEMS Microbiology Reviews·Maria Pilar Garcillán-BarciaFernando de la Cruz
Jan 22, 2013·Trends in Genetics : TIG·Martin F PolzWilliam P Hanage
Aug 16, 2013·BMC Bioinformatics·Maria HauserJohannes Söding
Sep 5, 2013·Microbiology·Hirokazu YanoEva M Top
Mar 19, 2014·Trends in Microbiology·B Jesse Shapiro, Martin F Polz
Apr 30, 2014·Antimicrobial Agents and Chemotherapy·Alessandra CarattoliHenrik Hasman
Jul 8, 2015·Nucleic Acids Research·Neha J VargheseAmrita Pati
Jul 18, 2015·Nature Reviews. Genetics·Shannon M SoucyJohann Peter Gogarten
Dec 17, 2015·Molecular Biology and Evolution·Wesley Loftie-EatonEva M Top
Apr 9, 2016·Current Opinion in Microbiology·B Jesse Shapiro
Aug 10, 2016·Molecular Biology and Evolution·Andreas PorseMorten O A Sommer
Aug 10, 2016·Genome Biology and Evolution·Jaime IranzoEugene V Koonin
Nov 29, 2016·Frontiers in Molecular Biosciences·Raul Fernandez-LopezFernando de la Cruz
Jun 7, 2017·Current Opinion in Microbiology·Raul Fernandez-LopezFernando de la Cruz
Jul 9, 2017·Scientific Reports·Thibault StalderEva M Top
Oct 25, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·James P J HallEllie Harrison

❮ Previous
Next ❯

Citations

Jan 7, 2021·International Journal of Systematic and Evolutionary Microbiology·Boas C L van der PuttenC Schultsz
Jan 21, 2021·Nature Reviews. Microbiology·Jerónimo Rodríguez-BeltránÁlvaro San Millán
Nov 8, 2020·Microorganisms·Juan M GonzalezBhagwan Rekadwad
Feb 3, 2021·Proceedings of the National Academy of Sciences of the United States of America·You CheTong Zhang
Jan 30, 2021·Computational and Structural Biotechnology Journal·Martin Zwanzig
Feb 24, 2021·Microbial Genomics·Sergio Mascarenhas Morgado, Ana Carolina Paulo Vicente
Mar 3, 2021·The ISME Journal·William MatlockUNKNOWN REHAB consortium
Apr 13, 2021·Biochemical Society Transactions·Huei-Yi Lai, Tim F Cooper
Apr 16, 2021·Frontiers in Microbiology·Magdalena ZalewskaMagdalena Popowska
Apr 19, 2021·The Science of the Total Environment·Anh Q NguyenLong D Nghiem
May 13, 2021·Proceedings of the National Academy of Sciences of the United States of America·You CheTong Zhang
Jun 8, 2021·Current Opinion in Microbiology·Jenifer MoralezAllison J Lopatkin
Apr 23, 2021·Genome Biology and Evolution·Eric L BrugerChristopher J Marx
Jun 29, 2021·MicrobiologyOpen·Shalini KunhikannanSteve Petrovski
Jun 15, 2021·Genome Biology·Askarbek OrakovPeer Bork
Jul 1, 2021·Clinical Microbiology Reviews·F BaqueroT M Coque
Jul 31, 2021·Journal of Hazardous Materials·Pankaj BhattShaohua Chen
Aug 2, 2021·BMC Bioinformatics·Santiago Redondo-SalvoFernando de la Cruz
Aug 25, 2021·MBio·Carolina Palencia-GándaraFernando de la Cruz
May 26, 2021·Annual Review of Phytopathology·Alexandra J WeisbergJeff H Chang
Aug 15, 2021·Environmental Microbiology·Kyle D BrumfieldRita R Colwell
Aug 28, 2021·International Journal of Molecular Sciences·Federica Dell'AnnunziataGianluigi Franci
Oct 5, 2021·Nucleic Acids Research·Rafael Pinilla-RedondoSøren J Sørensen
Oct 23, 2021·The Science of the Total Environment·Maria Luíza Soares SuhadolnikAndréa Maria Amaral Nascimento
Oct 20, 2021·Genome Biology and Evolution·Gavin M Douglas, B Jesse Shapiro

❮ Previous
Next ❯

Methods Mentioned

BETA
ICEs
gene exchange

Software Mentioned

kClust
ForceAtlas2
AcCNET
Gephi
ForceAtlas
BLAST +
Plasmid Finder
PlasmidFinder
Circos
MOBscan

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.