Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species

International Journal of Systematic and Evolutionary Microbiology
Morgane Rossi-TamisierPierre-Edouard Fournier

Abstract

Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet b...Continue Reading

References

Jan 11, 1992·International Journal of Systematic Bacteriology·G E FoxP Jurtshuk
Jan 1, 1991·Journal of Endodontics·C T HanksT E Van Dyke
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 4, 1969·Analytical Biochemistry·D J BrennerK E Johnson
Jun 11, 2002·International Journal of Systematic and Evolutionary Microbiology·Erko StackebrandtWilliam B Whitman
Jun 26, 2003·Nucleic Acids Research·Ramu ChennaJulie D Thompson
Oct 8, 2003·Systematic and Applied Microbiology·Ramon Rosselló-Mora
Feb 27, 2004·Nucleic Acids Research·Wolfgang LudwigKarl-Heinz Schleifer
Apr 20, 2004·Journal of Bacteriology·Silvia G AcinasMartin F Polz
Oct 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·G E FoxC R Woese
Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Jul 25, 2006·Journal of Microbiological Methods·S Mignard, J P Flandrois
Jul 13, 2007·Journal of Clinical Microbiology·J Michael Janda, Sharon L Abbott
Jun 24, 2008·Bioinformatics·Aleksandr MorgulisAlejandro A Schäffer
Jun 23, 2009·Annals of the New York Academy of Sciences·Pierre-Edouard Fournier, Didier Raoult
Aug 25, 2009·International Journal of Systematic and Evolutionary Microbiology·B J TindallP Kämpfer
Apr 27, 2010·Applied and Environmental Microbiology·Anna Y PeiZhiheng Pei
May 5, 2010·Nucleic Acids Research·Mickael GoujonRodrigo Lopez
Dec 6, 2011·International Journal of Systematic and Evolutionary Microbiology·Ok-Sun KimJongsik Chun
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Mar 16, 2013·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·E Sentausa, P-E Fournier
Nov 19, 2013·Nucleic Acids Research·Aidan C Parte

❮ Previous
Next ❯

Citations

Oct 21, 2015·Anaerobe·Senthil Alias SankarPierre-Edouard Fournier
Sep 8, 2017·International Journal of Systematic and Evolutionary Microbiology·Jong Woo HyeonChe Ok Jeon
Oct 9, 2019·Microbiology·Natalie Millán-AguiñagaKatherine R Duncan
May 15, 2020·Diseases of Aquatic Organisms·Roy PalmerTobias Eisenberg
Apr 9, 2018·Antonie van Leeuwenhoek·Dhiraj Kumar Chaudhary, Jaisoo Kim
Mar 30, 2018·Frontiers in Microbiology·Mikhail A Moldovan, Mikhail S Gelfand
Sep 27, 2019·Frontiers in Microbiology·Kaisa ThorellAlberto J Martín-Rodríguez
Mar 22, 2020·Applied and Environmental Microbiology·Dewa A P Rasmika DewiTorsten Thomas
Aug 5, 2017·Frontiers in Microbiology·Andre A PulschenFabio Rodrigues
May 21, 2019·Expert Review of Anti-infective Therapy·Grégory DubourgDidier Raoult
Apr 9, 2017·Antonie van Leeuwenhoek·Rita Abou AbdallahPierre-Edouard Fournier
Aug 22, 2017·Frontiers in Microbiology·María V SelmaFrancisco A Tomás-Barberán
Sep 26, 2019·Frontiers in Microbiology·Luisa K Hallmaier-WackerSascha Knauf
Sep 29, 2020·Frontiers in Microbiology·Jing YangJianguo Xu
Sep 16, 2017·Frontiers in Cellular and Infection Microbiology·Samia BenamarBernard La Scola
Aug 21, 2018·Emerging Infectious Diseases·Grégory DubourgDidier Raoult
Feb 9, 2021·Frontiers in Microbiology·Nancy NleyaMulunda Mwanza
Feb 23, 2021·Molecular Ecology·Tyson H Holmes
Feb 28, 2021·Journal of Human Nutrition and Dietetics : the Official Journal of the British Dietetic Association·Erin R ShanahanHeidi M Staudacher
Mar 6, 2021·Biofilm·Joo-Young LeeGemma Reguera
May 26, 2021·Biodegradation·Rangasamy Kavitha, Vembhu Bhuvaneswari

❮ Previous
Next ❯

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.