Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.

Authors:
Krithika Arumugam
Krithika Arumugam
Bishop Heber College
Irina Bessarab
Irina Bessarab
National Taiwan University
Taiwan
Sina Beier
Sina Beier
ZBIT Center for Bioinformatics
Benjamin Buchfink
Benjamin Buchfink
University of Tübingen
Anna Gorska
Anna Gorska
Harvard University
United States
Guanglei Qiu
Guanglei Qiu
National University of Singapore
Singapore
Daniel H Huson
Daniel H Huson
Tübingen University
Germany

Microbiome 2019 04 16;7(1):61. Epub 2019 Apr 16.

Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

Background: Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.

Results: We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts.

Conclusions: Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.

Download full-text PDF

Source
https://microbiomejournal.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/s40168-019-0665-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469205PMC
April 2019
5 Reads

Article Mentions


Provided by Crossref Event Data
twitter
Twitter:
April 17, 2019, 12:51 am EST
datacite
Datacite: Datacite
April 17, 2019, 12:00 am EST
twitter
Twitter:
April 16, 2019, 3:35 pm EST

Publication Analysis

Top Keywords

bacterial chromosomes
12
long-read sequencing
8
multiple closed
4
assembles multiple
4
sequence assembles
4
closed bacterial
4
provide simple
4
processing data
4
pipeline processing
4
simple pipeline
4
producing sequence
4
chromosomes provide
4
ebpr bioreactor
4
enriched community
4
chromosomes enriched
4
demonstrate bacterial
4
feasibleresults demonstrate
4
community application
4
application minion
4
data includes
4

Altmetric Statistics

References

(Supplied by CrossRef)
Article in Nature
The Human Microbiome Project Consortium et al.
Nature 2012
Article in Antimicrob Agents Chemother
M Willmann et al.
Antimicrob Agents Chemother 2015
Article in PLoS Comput Biol
DH Huson et al.
PLoS Comput Biol 2016
Article in Nat Biotechnol
C Quince et al.
Nat Biotechnol 2017
Article in Genome Biol
M Jain et al.
Genome Biol 2016
Article in PLoS Comput Biol
RR Wick et al.
PLoS Comput Biol 2017
Article in Bioinformatics
H Li et al.
Bioinformatics 2018
Article in Genome Res
R Vaser et al.
Genome Res 2017
Article in Genome Res
DH Parks et al.
Genome Res 2014
Article in Bioinformatics
T Seemann et al.
Bioinformatics 2014
Article in Nat Methods
B Buchfink et al.
Nat Methods 2015

Similar Publications