Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

Frontiers in Cellular and Infection Microbiology
Federica GigliucciStefano Morabito

Abstract

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients...Continue Reading

References

Jul 1, 1995·Journal of Dairy Science·G PerdigonN Gobbato
May 23, 2003·Infection and Immunity·Shantini D GamageAlison A Weiss
Mar 26, 2005·Science·Fredrik BäckhedJeffrey I Gordon
Apr 23, 2005·Veterinary Research·Alfredo CaprioliEric Oswald
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Oct 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Harry SokolPhilippe Langella
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 16, 2009·Environmental Microbiology·Julien TapMarion Leclerc
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Sep 18, 2010·Inflammatory Bowel Diseases·Seungha KangChris S McSweeney
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Aug 17, 2012·Nutrition Reviews·Willem M de Vos, Elisabeth A J de Vos
Sep 28, 2012·Genome Biology·Xochitl C MorganCurtis Huttenhower
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
Feb 28, 2014·Journal of Clinical Microbiology·Katrine Grimstrup JoensenFrank M Aarestrup
Mar 19, 2014·Cell Host & Microbe·Dirk GeversRamnik J Xavier
Nov 14, 2014·Current Opinion in Gastroenterology·Andrew B ShreinerVincent B Young
Nov 18, 2014·Nature Methods·Benjamin BuchfinkDaniel H Huson
Aug 10, 2015·Cellular and Molecular Life Sciences : CMLS·Daniel R Garza, Bas E Dutilh
Jun 19, 2016·Microbial Pathogenesis·Perrine HugonDidier Raoult
Jul 6, 2016·Frontiers in Microbiology·Amy O'Callaghan, Douwe van Sinderen
Jul 28, 2016·Frontiers in Microbiology·Jessica D ForbesCharles N Bernstein
Mar 17, 2017·Genome Research·Sergey NurkPavel A Pevzner

❮ Previous
Next ❯

Citations

Sep 30, 2018·The Journal of Microbiology·Eun-Ji SongYoung-Do Nam
May 15, 2019·International Journal of Environmental Research and Public Health·Mario GiordanoNicola Laforgia
May 13, 2019·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Xiaoyu HuNaisheng Zhang
Jul 3, 2021·Toxins·Kyung-Soo LeeMoo-Seung Lee

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJEB23207

Methods Mentioned

BETA
PCR
electrophoresis
chip

Software Mentioned

MetaBAT2
QUAST
Burrows Aligner ( BWA )
MEM
samtools flagstat
samtools idxstats
SAMtools
CheckM
MetaBAT
CAT ( The Contig Annotation Tool )

Related Concepts

Related Feeds

Biodiversity Data

Biodiversity refers to the variety and variability of life on Earth. Biodiversity is typically a measure of variation at the genetic, species, and ecosystem level.Discover the latest research on biodiversity data here.