List of works - Kyle Bittinger

A Pilot Characterization of the Human Chronobiome

scientific article published on 7 December 2017

A role for bacterial urease in gut dysbiosis and Crohn's disease.

scientific article

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

scientific article

Allometry and Ecology of the Bilaterian Gut Microbiome

scientific article published on 27 March 2018

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts

scientific article published on 17 August 2015

Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria

article

Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota

scientific article published on 15 February 2019

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts

scientific article

Associating microbiome composition with environmental covariates using generalized UniFrac distances

scientific article

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome.

scientific article published on 8 May 2017

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

Bacterial colonization reprograms the neonatal gut metabolome

scientific article published on 13 April 2020

Bidirectional interactions between indomethacin and the murine intestinal microbiota

scientific article published on 23 December 2015

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

scientific article published on 11 July 2018

Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation

scientific article

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

scientific article

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

scientific article

Composition and dynamics of the respiratory tract microbiome in intubated patients.

scientific article published on 11 February 2016

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

scientific article

Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance

scientific article published on 20 June 2013

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium

scientific article

Disordered microbial communities in the upper respiratory tract of cigarette smokers

scientific article

Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation

scientific article published on 01 November 2019

Effect of topical swallowed steroids on the bacterial and fungal esophageal microbiota in eosinophilic esophagitis

scientific article published on 29 September 2020

Engineering the gut microbiota to treat hyperammonemia.

scientific article

Establishing a mucosal gut microbial community in vitro using an artificial simulator

scientific article published on 17 July 2018

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid

scientific article published on 23 August 2018

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

scientific article published on August 2015

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment

scientific article

Gut microbiota modulate dendritic cell antigen presentation and radiotherapy-induced antitumor immune response

scientific article published on 01 January 2020

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12.

scientific article published on 22 February 2018

Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection

scientific article published on 02 February 2021

Host mitochondria influence gut microbiome diversity: A role for ROS

scientific article published on 02 July 2019

INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes

scientific article

INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.

scientific article published on 18 December 2016

Impact of Steviol Glycosides and Erythritol on the Human and Cebus apella Gut Microbiome

scientific article published on 07 January 2020

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing

scientific article

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

scientific article published on October 2015

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

scientific article published on 01 August 2017

Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly

scientific article published on 09 November 2020

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

scientific article published on 30 October 2018

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians

scientific article published on 25 May 2020

Linking long-term dietary patterns with gut microbial enterotypes

scientific article

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

scientific article

Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform

scientific article published on 18 November 2019

Metagenomic assessment of the Cebus apella gut microbiota

scientific article published on 26 June 2019

Microbes vs. chemistry in the origin of the anaerobic gut lumen.

scientific article published on 2 April 2018

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples.

scientific article

Microbiota-dependent signals are required to sustain TLR-mediated immune responses

article

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit

scientific article published on 18 December 2018

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

scientific article published on 11 August 2020

Normalization and microbial differential abundance strategies depend upon data characteristics

scientific article

Optimizing methods and dodging pitfalls in microbiome research

scientific article (publication date: 5 May 2017)

Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma

scientific article published on 27 May 2020

Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria

scientific article

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

scientific article published on 29 March 2015

Protective major histocompatibility complex allele prevents type 1 diabetes by shaping the intestinal microbiota early in ontogeny.

scientific article published on 22 August 2017

PyNAST: a flexible tool for aligning sequences to a template alignment

scientific article (publication date: 15 January 2010)

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME allows analysis of high-throughput community sequencing data

scientific article

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

scientific article

Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection

scientific article published on 09 March 2020

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

scientific article published in 2019

Switching between raltegravir resistance pathways analyzed by deep sequencing

scientific article

The dynamics of the stool virome in very early onset inflammatory bowel disease

scientific article published on 14 May 2020

The stepwise assembly of the neonatal virome is modulated by breastfeeding

scientific article published on 15 April 2020

Topographical continuity of bacterial populations in the healthy human respiratory tract

scientific article published on 16 June 2011

Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro

scientific article published on 25 June 2020

Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant

scientific article published on 01 November 2019

List of works by Kyle Bittinger

A Pilot Characterization of the Human Chronobiome

A role for bacterial urease in gut dysbiosis and Crohn's disease.

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

Allometry and Ecology of the Bilaterian Gut Microbiome

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts

Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria

Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bacterial colonization reprograms the neonatal gut metabolome

Bidirectional interactions between indomethacin and the murine intestinal microbiota

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

Composition and dynamics of the respiratory tract microbiome in intubated patients.

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

Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium

Disordered microbial communities in the upper respiratory tract of cigarette smokers

Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation

Effect of topical swallowed steroids on the bacterial and fungal esophageal microbiota in eosinophilic esophagitis

Engineering the gut microbiota to treat hyperammonemia.

Establishing a mucosal gut microbial community in vitro using an artificial simulator

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment

Gut microbiota modulate dendritic cell antigen presentation and radiotherapy-induced antitumor immune response

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12.

Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection

Host mitochondria influence gut microbiome diversity: A role for ROS

INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes

INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.

Impact of Steviol Glycosides and Erythritol on the Human and Cebus apella Gut Microbiome

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians

Linking long-term dietary patterns with gut microbial enterotypes

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform

Metagenomic assessment of the Cebus apella gut microbiota

Microbes vs. chemistry in the origin of the anaerobic gut lumen.

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples.

Microbiota-dependent signals are required to sustain TLR-mediated immune responses

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

Normalization and microbial differential abundance strategies depend upon data characteristics

Optimizing methods and dodging pitfalls in microbiome research

Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma

Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

Protective major histocompatibility complex allele prevents type 1 diabetes by shaping the intestinal microbiota early in ontogeny.

PyNAST: a flexible tool for aligning sequences to a template alignment

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME allows analysis of high-throughput community sequencing data

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

Switching between raltegravir resistance pathways analyzed by deep sequencing

The dynamics of the stool virome in very early onset inflammatory bowel disease

The stepwise assembly of the neonatal virome is modulated by breastfeeding

Topographical continuity of bacterial populations in the healthy human respiratory tract

Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro

Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant