Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice (Q46274162)

2 July 2018

title

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice (English)

1 reference

2 July 2018

4

Jeffrey I Gordon

1 reference

2 July 2018

Jessica L Mark Welch

1

object named as

Jessica L Mark Welch

1 reference

2 July 2018

author name string

Yuko Hasegawa

2

1 reference

2 July 2018

Nathan P McNulty

3

1 reference

2 July 2018

Gary G Borisy

5

1 reference

2 July 2018

language of work or name

English

0 references

publication date

9 October 2017

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2 July 2018

Proceedings of the National Academy of Sciences of the United States of America

published in

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2 July 2018

volume

114

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2 July 2018

issue

43

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2 July 2018

page(s)

E9105-E9114

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2 July 2018

describes a project that uses

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5664539/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Best practices for germ-free derivation and gnotobiotic zebrafish husbandry

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Decoding molecular interactions in microbial communities

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Multiplexed Spectral Imaging of 120 Different Fluorescent Labels

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Host Selection of Microbiota via Differential Adhesion.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Lypd8 promotes the segregation of flagellated microbiota and colonic epithelia

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Ordering structured populations in multiplayer cooperation games

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Biogeography of a human oral microbiome at the micron scale

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The biogeography of polymicrobial infection

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The ecology of the microbiome: Networks, competition, and stability.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Gut biogeography of the bacterial microbiota

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Quantitative Imaging of Gut Microbiota Spatial Organization

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The outer mucus layer hosts a distinct intestinal microbial niche.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

In vivo imaging and tracking of host-microbiota interactions via metabolic labeling of gut anaerobic bacteria

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Structural insights into bacterial recognition of intestinal mucins.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tracts of preweaned calves

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Spatial self-organization favors heterotypic cooperation over cheating

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Bacterial colonization factors control specificity and stability of the gut microbiota

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Gastrointestinal transit measurements in mice with 99mTc-DTPA-labeled activated charcoal using NanoSPECT-CT.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Divergent mechanisms of interaction of Helicobacter pylori and Campylobacter jejuni with mucus and mucins

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Mining the "glycocode"--exploring the spatial distribution of glycans in gastrointestinal mucin using force spectroscopy.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The gut microbiota--masters of host development and physiology

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The evolution of mutualism in gut microbiota via host epithelial selection

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

NIH Image to ImageJ: 25 years of image analysis

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Fast renewal of the distal colonic mucus layers by the surface goblet cells as measured by in vivo labeling of mucin glycoproteins

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Fiji: an open-source platform for biological-image analysis

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

A crypt-specific core microbiota resides in the mouse colon

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

CLASI-FISH: principles of combinatorial labeling and spectral imaging

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Bacterial biogeography of the human digestive tract

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Eating for two: how metabolism establishes interspecies interactions in the gut

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Social evolution in multispecies biofilms

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Mucin-bacterial interactions in the human oral cavity and digestive tract

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Spatial organization of intestinal microbiota in the mouse ascending colon

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Oral multispecies biofilm development and the key role of cell-cell distance.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The sociobiology of biofilms.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

daime, a novel image analysis program for microbial ecology and biofilm research

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Visualization of Helicobacter species within the murine cecal mucosa using specific fluorescence in situ hybridization.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Glycan foraging in vivo by an intestine-adapted bacterial symbiont

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Spatial distribution and stability of the eight microbial species of the altered schaedler flora in the mouse gastrointestinal tract

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

An abundance of Escherichia coli is harbored by the mucosa-associated bacterial flora of interleukin-2-deficient mice

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

ARB: a software environment for sequence data

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Variability of gastrointestinal transit in healthy women and men.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. V. Unitarian Theory of the origin of the four epithelial cell types

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. I. Columnar cell.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Preservation of three-dimensional spatial structure in the gut microbiome.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Impact of spatial distribution on the development of mutualism in microbes.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. III. Entero-endocrine cells.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5664539

Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. II. Mucous cells

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29073107

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. IV. Paneth cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29073107

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1711596114

1 reference

2 July 2018

PMC publication ID

5664539

1 reference

2 July 2018

PubMed publication ID

29073107

1 reference

2 July 2018