List of works - Jose C Clemente

A dietary intervention to improve the microbiome composition of pregnant women with Crohn's disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design

scientific article published on 04 May 2020

Advancing the microbiome research community

scientific article

Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer

scientific article published on 01 November 2018

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients.

scientific article published on 22 March 2017

Biphasic assembly of the murine intestinal microbiota during early development

scientific article

Can inflammatory bowel disease be permanently treated with short-term interventions on the microbiome?

scientific article published on 10 February 2015

Changes in vaginal microbiota following antimicrobial and probiotic therapy

scientific article

Cohabiting family members share microbiota with one another and with their dogs

scientific article

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

scientific article (publication date: October 2011)

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

scientific article published on 19 June 2014

Correction: Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation.

scientific article published on 2 July 2014

Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

scientific article published on 01 April 2019

Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

scientific article published on 18 August 2020

Detecting and phasing minor single-nucleotide variants from long-read sequencing data

scientific article published on 24 May 2021

Diet Modifies Colonic Microbiota and CD4+ T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23

scientific article published on 15 June 2018

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans

scientific article (publication date: 20 May 2011)

Disease-modifying therapies alter gut microbial composition in MS

scientific article published on 26 October 2018

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents

scientific article

Early-life gut microbiome composition and milk allergy resolution

scientific article published on 10 May 2016

Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases

scientific article published on July 2015

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

scientific article published on July 2013

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

scientific article published on 04 April 2016

Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary Th17 Response that Mitigates Susceptibility to Streptococcus pneumoniae

scientific article published on 09 November 2020

Evaluation of the airway microbiome in nontuberculous mycobacteria disease

scientific article published on 25 October 2018

Evidence for environmental-human microbiota transfer at a manufacturing facility with novel work-related respiratory disease

journal article published in 2020

Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis

scientific article published on 09 April 2020

Global biogeography of highly diverse protistan communities in soil

scientific article published on 13 December 2012

Gut Microbiota Perturbations in Reactive Arthritis and Post-Infectious Spondyloarthritis.

scientific article published on 26 October 2017

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus

scientific article published on 25 October 2017

Gut microbiota density influences host physiology and is shaped by host and microbial factors

scientific article published on 22 January 2019

Gut microbiota from twins discordant for obesity modulate metabolism in mice

scientific article (publication date: 6 September 2013)

Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome.

scientific article

Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice

scientific article published on 29 April 2019

Inflammatory bowel disease microbiotas alter gut CD4 T-cell homeostasis and drive colitis in mice

Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice.

scientific article published on 23 November 2017

Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation

scientific article published on 12 March 2020

Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice

scientific article

Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity

scientific article published on 10 June 2019

Lower airway dysbiosis affects lung cancer progression

scientific article published on 11 November 2020

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

scientific article

Methods in Lung Microbiome Research

scientific article published on 01 March 2020

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease

scientific article published on 01 May 2019

Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior.

scientific article published on 20 April 2016

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.

scientific article

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

scientific article

Our microbial selves: what ecology can teach us

scientific article

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

scientific article

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

scientific article published on 27 September 2021

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

scientific article (publication date: September 2013)

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung

scientific article

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

scientific article

Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes

scientific article published on 31 March 2016

Severe obstructive sleep apnea is associated with alterations in the nasal microbiome and an increase in inflammation

journal article published in 2019

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

scientific article (publication date: 2013)

Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis

scientific article published on 06 December 2018

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

scientific article

Subsistence strategies in traditional societies distinguish gut microbiomes

scientific article

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

2012 scientific article

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

scientific article published in May 2012

The long-term stability of the human gut microbiota

scientific article

The lung microbiota in early rheumatoid arthritis and autoimmunity

scientific article

The microbiome in early life: implications for health outcomes

scientific article

The microbiome of uncontacted Amerindians

scientific article published in April 2015

The role of the gut microbiome in systemic inflammatory disease.

scientific article published on 8 January 2018

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice

scientific article

List of works by Jose C Clemente

A dietary intervention to improve the microbiome composition of pregnant women with Crohn's disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design

Advancing the microbiome research community

Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients.

Biphasic assembly of the murine intestinal microbiota during early development

Can inflammatory bowel disease be permanently treated with short-term interventions on the microbiome?

Changes in vaginal microbiota following antimicrobial and probiotic therapy

Cohabiting family members share microbiota with one another and with their dogs

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

Correction: Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation.

Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Diet Modifies Colonic Microbiota and CD4+ T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans

Disease-modifying therapies alter gut microbial composition in MS

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents

Early-life gut microbiome composition and milk allergy resolution

Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary Th17 Response that Mitigates Susceptibility to Streptococcus pneumoniae

Evaluation of the airway microbiome in nontuberculous mycobacteria disease

Evidence for environmental-human microbiota transfer at a manufacturing facility with novel work-related respiratory disease

Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis

Global biogeography of highly diverse protistan communities in soil

Gut Microbiota Perturbations in Reactive Arthritis and Post-Infectious Spondyloarthritis.

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus

Gut microbiota density influences host physiology and is shaped by host and microbial factors

Gut microbiota from twins discordant for obesity modulate metabolism in mice

Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome.

Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice

Inflammatory bowel disease microbiotas alter gut CD4 T-cell homeostasis and drive colitis in mice

Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice.

Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation

Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice

Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity

Lower airway dysbiosis affects lung cancer progression

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Methods in Lung Microbiome Research

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease

Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior.

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

Our microbial selves: what ecology can teach us

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

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

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

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes

Severe obstructive sleep apnea is associated with alterations in the nasal microbiome and an increase in inflammation

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

Subsistence strategies in traditional societies distinguish gut microbiomes

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

The long-term stability of the human gut microbiota

The lung microbiota in early rheumatoid arthritis and autoimmunity

The microbiome in early life: implications for health outcomes

The microbiome of uncontacted Amerindians

The role of the gut microbiome in systemic inflammatory disease.

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice