Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules (Q33779279)

29 July 2017

Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules (English)

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ecological community assembly

29 July 2017

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1 reference

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2

Elhanan Borenstein

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29 July 2017

1

Roie Levy

1 reference

PubMed ID

24637600

29 July 2017

language of work or name

English

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publication date

20 February 2014

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29 July 2017

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29 July 2017

5

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29 July 2017

2

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29 July 2017

265-270

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Diet rapidly and reproducibly alters the human gut microbiome

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Gut microbiota from twins discordant for obesity modulate metabolism in mice

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Understanding the interactions between bacteria in the human gut through metabolic modeling

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Bacterial colonization factors control specificity and stability of the gut microbiota

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Insights into the phylogeny and coding potential of microbial dark matter

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Phylogenetic diversity theory sheds light on the structure of microbial communities

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Genomic variation landscape of the human gut microbiome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

The evolution of mutualism in gut microbiota via host epithelial selection

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

A systems biology approach to studying the role of microbes in human health.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Reverse Ecology: from systems to environments and back

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Microbial co-occurrence relationships in the human microbiome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

A framework for human microbiome research

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Structure, function and diversity of the healthy human microbiome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Computational systems biology and in silico modeling of the human microbiome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Predicting a human gut microbiota's response to diet in gnotobiotic mice

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Enterotypes of the human gut microbiome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Spatial organization of intestinal microbiota in the mouse ascending colon

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Stochastic community assembly causes higher biodiversity in more productive environments

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Bacterial diversity in the oral cavity of 10 healthy individuals

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

A human gut microbial gene catalogue established by metagenomic sequencing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

The large-scale organization of the bacterial network of ecological co-occurrence interactions.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

A core gut microbiome in obese and lean twins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Network-based approaches for linking metabolism with environment

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Phylogenetic analysis of community assembly and structure over space and time

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Large-scale reconstruction and phylogenetic analysis of metabolic environments

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

An obesity-associated gut microbiome with increased capacity for energy harvest

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

A trait-based test for habitat filtering: convex hull volume

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Diversity of the human intestinal microbial flora

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Host-bacterial mutualism in the human intestine

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Mechanisms That Control Bacterial Populations in Continuous-Flow Culture Models of Mouse Large Intestinal Flora

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4063856

Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-gamma and RelA.

4 July 2018

1 reference

https://api.crossref.org/works/10.4161%2FGMIC.28261

The checkerboard score and species distributions

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FGMIC.28261

Competition and Biodiversity in Spatially Structured Habitats

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FGMIC.28261

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FGMIC.28261

Advantageous indirect interactions in systems of competition

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24637600

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.4161/GMIC.28261

1 reference

29 July 2017

1 reference

29 July 2017

1 reference

PubMed ID

24637600