Phenome-Genome Profiling of Single Bacterial Cell by Raman-Activated Gravity-Driven Encapsulation and Sequencing.

Small
Teng XuBo Ma

Abstract

The small size and low DNA amount of bacterial cells have hindered establishing phenome-genome links in a precisely indexed, one-cell-per-reaction manner. Here, Raman-Activated Gravity-driven single-cell Encapsulation and Sequencing (RAGE-Seq) is presented, where individual cells are phenotypically screened via single-cell Raman spectra (SCRS) in an aquatic, vitality-preserving environment, then the cell with targeted SCRS is precisely packaged in a picoliter microdroplet and readily exported in a precisely indexed, "one-cell-one-tube" manner. Such integration of microdroplet encapsulation to Raman-activated sorting ensures high-coverage one-cell genome sequencing or cultivation that is directly linked to metabolic phenotype. For clinical Escherichia coli isolates, genome assemblies derived from precisely one cell via RAGE-Seq consistently reach >95% coverage. Moreover, directly from a urine sample of urogenital tract infection, metabolic-activity-based antimicrobial susceptibility phenotypes and genome sequence of 99.5% coverage are obtained simultaneously from precisely one cell. This single-cell global mutation map corroborates resistance phenotype and genotype, and unveils epidemiological features with high specificity and ...Continue Reading

References

Jan 1, 1991·Journal of Bacteriology·W G WeisburgD J Lane
Jun 13, 1998·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·J H Jorgensen, M J Ferraro
Sep 25, 2003·Antimicrobial Agents and Chemotherapy·Patricia Komp LindgrenDiarmaid Hughes
Jan 31, 2008·Lab on a Chip·Shia-Yen TehAbraham P Lee
Apr 17, 2008·Nature Reviews. Microbiology·Rudolf Amann, Bernhard M Fuchs
Jun 25, 2010·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·James R JohnsonMariana Castanheira
Apr 6, 2011·Nature Methods·Stanislav S RubakhinJonathan V Sweedler
May 12, 2011·The Journal of Antimicrobial Chemotherapy·Pedro Eduardo Almeida Almeida Da Silva, Juan Carlos Palomino
Sep 20, 2011·Nature Biotechnology·Hamidreza ChitsazRoger S Lasken
Dec 6, 2011·Current Opinion in Biotechnology·Mengqiu LiWei E Huang
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 14, 2012·Methods : a Companion to Methods in Enzymology·John P NolanSamuel A Stoner
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jul 7, 2012·Lab on a Chip·Benjamin LandenbergerAlexander Rohrbach
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
Oct 2, 2012·Applied and Environmental Microbiology·Ian P G MarshallStephen R Quake
Jan 10, 2013·FEMS Microbiology Reviews·Paul C Blainey
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
May 31, 2013·Langmuir : the ACS Journal of Surfaces and Colloids·Hongcheng GuZhongze Gu
Feb 1, 2009·Environmental Microbiology Reports·Wei E HuangAndrew S Whiteley
Oct 3, 2013·Analytical Chemistry·Yun WangWei E Huang
Feb 14, 2014·Nature Methods·James EberwineJunhyong Kim
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Mar 20, 2014·Bioinformatics·Torsten Seemann
Jul 2, 2014·Clinical Microbiology Reviews·Marie-Hélène Nicolas-ChanoineJean-Yves Madec
Aug 6, 2014·Nature Reviews. Genetics·Roger S Lasken, Jeffrey S McLean
Aug 12, 2014·Bioinformatics·Timothy Daley, Andrew D Smith
Jan 1, 2015·Proceedings of the National Academy of Sciences of the United States of America·David BerryMichael Wagner
Jan 7, 2015·Saudi Journal of Biological Sciences·Sibhghatulla ShaikhMohammad Amjad Kamal
Apr 17, 2015·Nature Communications·Cheng-Zhong ZhangJ Christopher Love
Dec 26, 2015·Nucleic Acids Research·Angus M SidoreAdam R Abate
Jun 25, 2016·Neurology. Neuroimmunology and Neuroinflammation·Steven L SalzbergCarlos A Pardo
Jul 15, 2016·Proceedings of the National Academy of Sciences of the United States of America·Kaston LeungCarl L Hansen

❮ 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.