Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

ELife
Tali Raveh-SadkaJillian F Banfield

Abstract

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

References

Jun 26, 2001·European Journal of Pediatrics·D BocciaM L Moro
May 30, 2002·Nucleic Acids Research·Arthur L DelcherSteven L Salzberg
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Mar 27, 2004·Bioinformatics·Rasko LeinonenRolf Apweiler
Sep 1, 2004·Trends in Microbiology·Abigail A SalyersYanping Wang
Jun 3, 2006·Science·Steven R GillKaren E Nelson
Dec 13, 2006·Archives of Internal Medicine·Sophia V KazakovaL Clifford McDonald
Apr 27, 2007·Journal of Pediatric Gastroenterology and Nutrition·Marie-José ButelChristophe Dupont
Sep 27, 2007·Environmental Microbiology·Gene W Tyson, Jillian F Banfield
Apr 15, 2008·World Journal of Gastroenterology : WJG·Kareena-L SchnablMichael-T Clandinin
Jun 7, 2008·The Journal of Pediatrics·Reina M Turcios-RuizHelena E Friss
Aug 16, 2008·The Journal of Antimicrobial Chemotherapy·Susanne SchjørringKaren A Krogfelt
Dec 30, 2008·The Journal of Pediatrics·Jareen Meinzen-DerrPaul A Succop
Aug 25, 2009·Genome Biology·Gregory J DickJillian F Banfield
Sep 29, 2009·The Journal of Pediatrics·Maka MshvildadzeVolker Mai
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
Aug 17, 2010·Bioinformatics·Robert C Edgar
Nov 10, 2010·MBio·Kelli L Palmer, Michael S Gilmore
Dec 15, 2010·The New England Journal of Medicine·Chen-Shan ChinMatthew K Waldor
Jan 21, 2011·The New England Journal of Medicine·Josef Neu, W Allan Walker
Feb 15, 2011·International Journal of Food Microbiology·Carmen Nueno-Palop, Arjan Narbad
Jul 8, 2011·Journal of Pediatric Gastroenterology and Nutrition·Ju Y ChangJeong-Kee Seo
Jul 29, 2011·The New England Journal of Medicine·David A Relman
Sep 2, 2011·Genome Research·Samuel MinotFrederic D Bushman
Dec 20, 2011·Nature Reviews. Genetics·Justin KuczynskiRob Knight
Apr 25, 2012·PloS One·Denina HospodskyJordan Peccia
Jun 15, 2012·The New England Journal of Medicine·Claudio U KöserSharon J Peacock
Aug 8, 2012·Nature Reviews. Genetics·Xavier DidelotDerrick W Crook
Aug 24, 2012·Science Translational Medicine·Evan S SnitkinJulia A Segre
Apr 11, 2013·JAMA : the Journal of the American Medical Association·Nicholas J LomanMark J Pallen
May 10, 2013·Current Opinion in Pediatrics·Erica M Carlisle, Michael J Morowitz
May 25, 2013·Journal of Perinatology : Official Journal of the California Perinatal Association·P Wan-HuenE Parravicini
Sep 7, 2013·Bioinformatics·Eric P Nawrocki, Sean R Eddy
Oct 31, 2013·MBio·Elizabeth K CostelloDavid A Relman

❮ Previous
Next ❯

Citations

Oct 24, 2015·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·Nadim CassirBernard La Scola
Jan 21, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Fardou H HeidaMarcus C de Goffau
Feb 9, 2016·Future Microbiology·Nadim CassirBernard La Scola
Feb 8, 2016·Clinical Therapeutics·Timothy G ElginSteven J McElroy
Jan 17, 2016·Current Opinion in Biotechnology·Nicholas A BokulichDavid A Mills
May 6, 2015·Trends in Microbiology·Christopher James Stewart, Stephen Paul Cummings
May 15, 2015·Genome Biology·Jack A Gilbert
Jun 1, 2016·Frontiers in Microbiology·Ilana L Brito, Eric J Alm
Jun 28, 2016·Seminars in Fetal & Neonatal Medicine·Barbara B Warner, Phillip I Tarr
Oct 22, 2016·Annals of the New York Academy of Sciences·Boahemaa Adu-OppongGautam Dantas
Oct 22, 2016·Critical Reviews in Food Science and Nutrition·Eric Banan-Mwine DaliriByong H Lee
Nov 8, 2016·Nature Biotechnology·Christopher T BrownJillian F Banfield
Feb 1, 2017·Environmental Science & Technology·Rose S KantorJillian F Banfield
Feb 9, 2017·Genome Research·Duy Tin TruongNicola Segata
Mar 3, 2018·Genome Research·Patrick T WestJillian F Banfield
Apr 11, 2018·Nature Medicine·Jack A GilbertRob Knight
Mar 20, 2020·Genome Research·Lin-Xing ChenJillian F Banfield
Sep 14, 2018·Microbiome·Thao T B HoAkhil Maheshwari
Mar 1, 2018·Expert Review of Gastroenterology & Hepatology·Daniel Johannes Cornelis BerkhoutTimotheüs Gualtherus Jacob de Meij
Sep 25, 2020·The Journal of International Medical Research·Miao DuanNanqu Huang
Jan 9, 2019·Frontiers in Microbiology·Lorena CorettiFrancesca Lembo
Sep 4, 2019·Genome Biology·Elijah BogartGeorg K Gerber
Feb 14, 2020·Nature·Basem Al-ShayebJillian F Banfield

❮ Previous
Next ❯

Datasets Mentioned

BETA
KTE32
SRP052967

Methods Mentioned

BETA
PCR
phylogenetic profile

Software Mentioned

bowtie2
SE
QuantaSoft
ud
Infernal
Mauve genome
idba
nucmer
MAFFT
tRNAscan

Related Concepts

Related Feeds

CRISPR & Staphylococcus

CRISPR-Cas system enables the editing of genes to create or correct mutations. Staphylococci are associated with life-threatening infections in hospitals, as well as the community. Here is the latest research on how CRISPR-Cas system can be used for treatment of Staphylococcal infections.

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

CRISPRi Screens for Antibiotics

The CRISPR-Cas system is a gene editing technique that can be used for high-throughput genome-wide screens to identify modes of actions of novel antibiotics. Here is the latest research.

BioHub - Researcher Network

The Chan-Zuckerberg Biohub aims to support the fundamental research and develop the technologies that will enable physicians to cure, prevent, or manage all diseases in our childrens' lifetimes. The CZ Biohub brings together researchers from UC Berkeley, Stanford, and UCSF. Find the latest research from the CZ Biohub researcher network here.

Aminoglycosides

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

Actinomycosis

Actinomycosis is a rare, chronic, and slowly progressive granulomatous disease caused by filamentous Gram positive anaerobic bacteria from the Actinomycetaceae family (genus Actinomyces). The disease is characterised by the formation of painful abscesses in the mouth, lungs,breast or gastrointestinal tract. Discover the latest research on actinomycosis here.

Aminoglycosides (ASM)

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.

Related Papers

Beiträge zur pathologischen Anatomie und zur allgemeinen Pathologie
R RABL
The Journal of Pediatrics
A MIZRAHIW A SILVERMAN
Acta Paediatrica Academiae Scientiarum Hungaricae
J DénesA Mohácsi
© 2022 Meta ULC. All rights reserved