Application of metagenomics in the human gut microbiome (Q26851464)

Xu SY

2

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Ren ZG

3

1 reference

Tao L

4

1 reference

Jiang JW

5

1 reference

Zheng SS

6

1 reference

language of work or name

1 reference

21 January 2015

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World Journal of Gastroenterology

published in

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volume

21

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issue

3

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page(s)

803-14

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Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes

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Human gut microbiome viewed across age and geography

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A framework for human microbiome research

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Structure, function and diversity of the healthy human microbiome

7 April 2017

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Metagenomics - a guide from sampling to data analysis

7 April 2017

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Linking long-term dietary patterns with gut microbial enterotypes

7 April 2017

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Enterotypes of the human gut microbiome

7 April 2017

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A human gut microbial gene catalogue established by metagenomic sequencing

7 April 2017

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Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

7 April 2017

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A core gut microbiome in obese and lean twins

7 April 2017

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Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

7 April 2017

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Metagenomic analysis of the human distal gut microbiome

7 April 2017

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Diversity of the human intestinal microbial flora

7 April 2017

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Phylogenetic structure of the prokaryotic domain: The primary kingdoms

7 April 2017

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Obesity and cancer: a gut microbial connection

7 April 2017

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Microbiota impact on the epigenetic regulation of colorectal cancer

7 April 2017

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Liver ischemic preconditioning (IPC) improves intestinal microbiota following liver transplantation in rats through 16s rDNA-based analysis of microbial structure shift

7 April 2017

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The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea

7 April 2017

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Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

7 April 2017

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Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

7 April 2017

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Microbial ecology: human gut microbes associated with obesity

7 April 2017

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Environmental genome shotgun sequencing of the Sargasso Sea

7 April 2017

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Minireview: Gut microbiota: the neglected endocrine organ

7 April 2017

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The gut microbiota--masters of host development and physiology

7 April 2017

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A metagenomic insight into our gut's microbiome

7 April 2017

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Low diversity of the gut microbiota in infants with atopic eczema

7 April 2017

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Functional characterization of the antibiotic resistance reservoir in the human microflora

7 April 2017

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Human intestinal bacteria as reservoirs for antibiotic resistance genes

7 April 2017

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High-throughput system for the presentation of secreted and surface-exposed proteins from Gram-positive bacteria in functional metagenomics studies

7 April 2017

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Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Diet rapidly and reproducibly alters the human gut microbiome

7 April 2017

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A metagenome-wide association study of gut microbiota in type 2 diabetes

7 April 2017

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Next-generation DNA sequencing

7 April 2017

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Comparative metagenomics of microbial communities

7 April 2017

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Community structure and metabolism through reconstruction of microbial genomes from the environment

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders

7 April 2017

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Richness of human gut microbiome correlates with metabolic markers

7 April 2017

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Functional interactions between the gut microbiota and host metabolism

7 April 2017

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Gut microbiota composition correlates with diet and health in the elderly

7 April 2017

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The impact of the gut microbiota on human health: an integrative view

7 April 2017

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The human microbiome: at the interface of health and disease

7 April 2017

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Bifidobacteria can protect from enteropathogenic infection through production of acetate

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Succession of microbial consortia in the developing infant gut microbiome

7 April 2017

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Antibiotics for emerging pathogens

7 April 2017

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Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Metagenomics: application of genomics to uncultured microorganisms

7 April 2017

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Alterations of the human gut microbiome in liver cirrhosis

7 April 2017

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Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

28 September 2017

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An integrated catalog of reference genes in the human gut microbiome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Combination of metagenomics and culture-based methods to study the interaction between ochratoxin a and gut microbiota

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Role of gut microbiota and Toll-like receptors in nonalcoholic fatty liver disease

28 September 2017

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Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Aberrant gut microbiota composition at the onset of type 1 diabetes in young children

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Persistent gut microbiota immaturity in malnourished Bangladeshi children

28 September 2017

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Relating the metatranscriptome and metagenome of the human gut.

28 September 2017

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Microbiota and diabetes: an evolving relationship.

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome

28 September 2017

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Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data

28 September 2017

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Dynamics and associations of microbial community types across the human body

28 September 2017

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IBD. Understanding gut microbiota in new-onset Crohn's disease

28 September 2017

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Overgrowth of the indigenous gut microbiome and irritable bowel syndrome

28 September 2017

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The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

28 September 2017

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Inflammation and colorectal cancer, when microbiota-host mutualism breaks

28 September 2017

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Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing

28 September 2017

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Geographical variation of human gut microbial composition

28 September 2017

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Metagenomic analysis of the stool microbiome in patients receiving allogeneic stem cell transplantation: loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal graft-versus-host disease.

28 September 2017

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Non-invasive fecal metabonomic detection of colorectal cancer

28 September 2017

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Microbiome analysis of stool samples from African Americans with colon polyps.

28 September 2017

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Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach

28 September 2017

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Your gut microbiota are what you eat.

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Low gut microbiota diversity in early infancy precedes asthma at school age.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Metabolism in 2013: The gut microbiota manages host metabolism

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Human gut microbiome and risk for colorectal cancer

28 September 2017

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Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity.

28 September 2017

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Metagenomic Analysis of the Dynamic Changes in the Gut Microbiome of the Participants of the MARS-500 Experiment, Simulating Long Term Space Flight

28 September 2017

1 reference

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The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide

28 September 2017

1 reference

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The gut microbiome, kidney disease, and targeted interventions

28 September 2017

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Rifaximin alters intestinal bacteria and prevents stress-induced gut inflammation and visceral hyperalgesia in rats.

28 September 2017

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Metagenomic species profiling using universal phylogenetic marker genes

28 September 2017

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Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Human gut microbiota community structures in urban and rural populations in Russia

28 September 2017

1 reference

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Bacterial colonization factors control specificity and stability of the gut microbiota

28 September 2017

1 reference

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Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Human intestinal metagenomics: state of the art and future

28 September 2017

1 reference

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The long-term stability of the human gut microbiota

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans

28 September 2017

1 reference

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Gut metagenome in European women with normal, impaired and diabetic glucose control

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Country-specific antibiotic use practices impact the human gut resistome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Symptomatic atherosclerosis is associated with an altered gut metagenome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Ageing and gut microbes: perspectives for health maintenance and longevity

28 September 2017

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Genomic approaches to studying the human microbiota

28 September 2017

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Reciprocal interactions of the intestinal microbiota and immune system.

28 September 2017

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The Human Microbiome Project: a community resource for the healthy human microbiome

28 September 2017

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Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions

28 September 2017

1 reference

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Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Metatranscriptomic approach to analyze the functional human gut microbiota

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Metagenomic analyses: past and future trends

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Viruses in the faecal microbiota of monozygotic twins and their mothers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

The intestinal microbiota in inflammatory bowel diseases: time to connect with the host

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

The challenges of sequencing by synthesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Metabolomics reveals metabolic biomarkers of Crohn's disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Molecular mechanisms of antibacterial multidrug resistance

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

The worldwide emergence of plasmid-mediated quinolone resistance

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Sampling the antibiotic resistome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Gut microorganisms, mammalian metabolism and personalized health care

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Quantifying the accessibility of the metagenome by random expression cloning techniques.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Molecular assessment of intestinal microflora

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Identification of NF-κB modulation capabilities within human intestinal commensal bacteria

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4299332

The gut microbiome in health and disease

31 May 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

The microbiome explored: recent insights and future challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

The core gut microbiome, energy balance and obesity

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Characterization of fecal microbial communities in patients with liver cirrhosis

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH.

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Neurodevelopmental disorders: the gut-microbiome-brain connection.

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Ecology drives a global network of gene exchange connecting the human microbiome

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Prediction of effective genome size in metagenomic samples

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Shotgun metaproteomics of the human distal gut microbiota

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Metabolomics of Fecal Extracts Detects Altered Metabolic Activity of Gut Microbiota in Ulcerative Colitis and Irritable Bowel Syndrome

21 January 2018

1 reference

https://api.crossref.org/works/10.3748%2FWJG.V21.I3.803

Rapid and Noninvasive Metabonomic Characterization of Inflammatory Bowel Disease

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25624713

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Gut microbiome, obesity-related comorbidities, and low-grade chronic inflammation

1 reference

https://pubmed.ncbi.nlm.nih.gov/25624713

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3748/WJG.V21.I3.803

0 references

1 reference

PubMed publication ID

25624713

1 reference