List of works - Kyle Bittinger

QIIME allows analysis of high-throughput community sequencing data

scientific article

Linking long-term dietary patterns with gut microbial enterotypes

scientific article

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

scientific article (publication date: 15 January 2010)

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

scientific article published on 01 August 2019

Topographical continuity of bacterial populations in the healthy human respiratory tract

scientific article published on 16 June 2011

Normalization and microbial differential abundance strategies depend upon data characteristics

scientific article

Associating microbiome composition with environmental covariates using generalized UniFrac distances

scientific article

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

scientific article

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

scientific article

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

scientific article published on October 2015

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

scientific article

Disordered microbial communities in the upper respiratory tract of cigarette smokers

scientific article

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

scientific article published on 8 May 2017

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

scientific article

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

scientific article

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

scientific article

Optimizing methods and dodging pitfalls in microbiome research

scientific article (publication date: 5 May 2017)

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

scientific article

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

scientific article published on 29 March 2015

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

scientific article

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

scientific article published on August 2015

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

scientific article

Engineering the gut microbiota to treat hyperammonemia.

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

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

scientific article

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

scientific article published on 11 February 2016

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

scientific article published on 30 October 2018

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

scientific article

Switching between raltegravir resistance pathways analyzed by deep sequencing

scientific article

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

scientific article

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

scientific article published on 01 September 2019

Bidirectional interactions between indomethacin and the murine intestinal microbiota

scientific article published on 23 December 2015

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

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

scientific article published on 22 August 2017

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

scientific article

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

scientific article published on 22 February 2018

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

scientific article published on 18 December 2016

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

article

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

scientific article published on 2 April 2018

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

scientific article published on 23 August 2018

Alterations of the Subgingival Microbiota in Pediatric Crohnʼs Disease Studied Longitudinally in Discovery and Validation Cohorts

scientific article published on December 1, 2015

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

scientific article

A Pilot Characterization of the Human Chronobiome

scientific article published on 7 December 2017

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

scientific article published in 2019

Allometry and Ecology of the Bilaterian Gut Microbiome

scientific article published on 27 March 2018

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

scientific article published on 01 August 2017

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

scientific article published on 11 July 2018

Host mitochondria influence gut microbiome diversity: A role for ROS

scientific article published on 02 July 2019

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

scientific article

List of works by Kyle Bittinger

QIIME allows analysis of high-throughput community sequencing data

Linking long-term dietary patterns with gut microbial enterotypes

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

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

Topographical continuity of bacterial populations in the healthy human respiratory tract

Normalization and microbial differential abundance strategies depend upon data characteristics

Associating microbiome composition with environmental covariates using generalized UniFrac distances

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

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

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

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

Disordered microbial communities in the upper respiratory tract of cigarette smokers

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

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

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

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

Optimizing methods and dodging pitfalls in microbiome research

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

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

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

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

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

Engineering the gut microbiota to treat hyperammonemia.

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

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

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

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

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

Switching between raltegravir resistance pathways analyzed by deep sequencing

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

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

Bidirectional interactions between indomethacin and the murine intestinal microbiota

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

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

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

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

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

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

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

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

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

Alterations of the Subgingival Microbiota in Pediatric Crohnʼs Disease Studied Longitudinally in Discovery and Validation Cohorts

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

A Pilot Characterization of the Human Chronobiome

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

Allometry and Ecology of the Bilaterian Gut Microbiome

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

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

Host mitochondria influence gut microbiome diversity: A role for ROS

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