(Q37735516)

22 August 2017

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates (English)

1 reference

22 August 2017

0 references

0 references

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Jillian Banfield

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

author name string

Matthew R Olm

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Christopher T Brown

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Brandon Brooks

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Brian Firek

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Robyn Baker

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Karina Soenjoyo

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Brian C Thomas

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Michael Morowitz

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

publication date

10 January 2017

1 reference

22 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

volume

27

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

page(s)

601-612

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

9 June 2020

Jupyter notebook file

1 reference

Measurement of bacterial replication rates in microbial communities.

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Rapid evolution of microbe-mediated protection against pathogens in a worm host

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The first microbial environment of infants born by C-section: the operating room microbes

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Gut biogeography of the bacterial microbiota

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Early infancy microbial and metabolic alterations affect risk of childhood asthma

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

ConStrains identifies microbial strains in metagenomic datasets

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The infant microbiome development: mom matters

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Identifying strains that contribute to complex diseases through the study of microbial inheritance

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Dynamics and associations of microbial community types across the human body

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Strain/species identification in metagenomes using genome-specific markers

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Intestinal microbial diversity during early-life colonization shapes long-term IgE levels

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Data, information, knowledge and principle: back to metabolism in KEGG

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Microbiome assembly across multiple body sites in low-birthweight infants

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Infernal 1.1: 100-fold faster RNA homology searches

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Multifactorial diversity sustains microbial community stability

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Deep sequencing of the oral microbiome reveals signatures of periodontal disease

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The application of ecological theory toward an understanding of the human microbiome

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Fast gapped-read alignment with Bowtie 2

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Multidrug-resistant enterococci lack CRISPR-cas

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Search and clustering orders of magnitude faster than BLAST

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Prodigal: prokaryotic gene recognition and translation initiation site identification

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The population genetics of commensal Escherichia coli

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Viral and microbial community dynamics in four aquatic environments.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

CRISPR/Cas, the immune system of bacteria and archaea

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Shifting the genomic gold standard for the prokaryotic species definition

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Reordering contigs of draft genomes using the Mauve aligner

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The Sequence Alignment/Map format and SAMtools

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Microbial diversity and the genetic nature of microbial species

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The role of ecological theory in microbial ecology.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

UniRef: comprehensive and non-redundant UniProt reference clusters

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Measurement of microbial activity and growth in the ocean by rates of stable ribonucleic Acid synthesis

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

YadA, the multifaceted Yersinia adhesin

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Analyzing genomes with cumulative skew diagrams

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

22 August 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

22 August 2017

https://api.crossref.org/works/10.1101%2FGR.213256.116

Basic local alignment search tool

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

The neonatal gastrointestinal microbiota: the foundation of future health?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Bacterial colonization and gut development in preterm neonates

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Use of a fluorescent redox probe for direct visualization of actively respiring bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Microbial diversity. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Prediction of effective genome size in metagenomic samples

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Beware of mis-assembled genomes

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5378178

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

1 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1101%2FGR.213256.116

21 January 2018

Identifiers

DOI

10.1101/GR.213256.116

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

release_xg2ekuy4ufd5nedaak7oplgn5i

9 June 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/xg2ekuy4ufd5nedaak7oplgn5i

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28073918%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

PubMed publication ID

28073918

1 reference