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List of works by Rob Knight

47.2 EARLY-LIFE PREBIOTICS, PROBIOTICS, AND A STRESS ROBUST PHENOTYPE ⬇️

scholarly article

846 TIME RESTRICTED FEEDING PROTECTS AGAINST ATHEROSCLEROSIS BY MODULATING LUMINAL GUT MICROBIOME RHYTHMS

scientific article published in 2021

A Distinct Microbiome Signature in Posttreatment Lyme Disease Patients

scientific article published on 29 September 2020

A Lightweight, Scalable Grid Computing Framework for Parallel Bioinformatics Applications

A Microbiome Foundation for the Study of Crohn's Disease

scientific article published on March 2017

A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children

scientific article published on 20 August 2019

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

scientific article published on 06 January 2021

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

article

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition

scientific article published on 14 July 2021

A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats

scientific article published on 01 January 2022

A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats

scientific article published on 24 May 2022

A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats

scientific article published on 6 June 2024

A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity

scientific article published on 13 July 2021

A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2

scientific article published on 20 October 2020

A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis

scientific article published on 24 June 2020

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

scientific article published on 14 November 2020

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

scientific article published on 8 January 2009

A core gut microbiome in obese and lean twins

scientific article

A data analysis and coordination center for the human microbiome project.

scientific article

A distinct immunogenic region of glutamic acid decarboxylase 65 is naturally processed and presented by human islet cells to cytotoxic CD8 T cells.

scientific article published on January 2015

A framework for human microbiome research

scientific article

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets

scientific article

A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice

scientific article published on 11 February 2020

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease

scientific article published on 29 March 2019

A gut-derived metabolite alters brain activity and anxiety behaviour in mice

scientific article

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

scientific article

A meta-analysis of changes in bacterial and archaeal communities with time

scientific article published on 11 April 2013

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system ⬇️

scientific article

A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease

scientific article

A preliminary survey of lichen associated eukaryotes using pyrosequencing

scientific article published on 12 December 2011

A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins

scientific article

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids

scientific article

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

scientific article published on 22 August 2008

Activating and inhibiting connections in biological network dynamics

scientific article

Advancing analytical algorithms and pipelines for billions of microbial sequences

scientific article

Advancing our understanding of the human microbiome using QIIME

scientific article

Advancing the microbiome research community

scientific article

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults

scientific article published on 14 May 2019

Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing

scientific article published on 02 March 2020

Alterations in the gut microbiota associated with HIV-1 infection

scientific article

Altered Gut Microbiota and Host Metabolite Profiles in HIV-infected Women

scientific article published on 21 November 2019

American Gut: an Open Platform for Citizen Science Microbiome Research

article

An Elegan(t) Screen for Drug-Microbe Interactions

scientific article published in May 2017

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

scientific article (publication date: March 2012)

Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet

scientific article

Analysis of composition of microbiomes: a novel method for studying microbial composition

scientific article published on 29 May 2015

Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MS.

scientific article published on March 2006

Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.

scientific article

Analytic Strategies for Understanding Host-Associated Microbial Communities

scientific article published in 2011

Analyzing partially randomized nucleic acid pools: straight dope on doping

scientific article

Ancient Thali Diet: Gut Microbiota, Immunity, and Health.

scientific article

Ancient human oral plaque preserves a wealth of biological data

scientific article

Animal Models for Microbiome Research and Drug Discovery ⬇️

scholarly article

Antibiotic discovery is a walk in the park

scientific article published on 09 December 2016

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism

scientific article published in Nature Communications

Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens

scientific article published in 2015

Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns

scientific article published on January 2008

Are microbiome studies ready for hypothesis-driven research?

scientific article published on 27 July 2018

Artificial Selection: Finding Function amongst Randomized Sequences

article

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection

scientific article published in 2021

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium.

scientific article

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

scientific article published on 21 July 2020

Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort

scientific article published on 27 August 2020

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life

scientific article published on 28 October 2015

Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study

scientific article published on 26 February 2021

Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity

scientific article published on 01 July 2019

Author Correction: Farm-like indoor microbiota in non-farm homes protects children from asthma development

scientific article published on 01 August 2019

Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

scientific article published on 25 February 2020

Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

scientific article published in Nature

Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models

scientific article published on 01 December 2018

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

scientific article published on 01 September 2019

Authors' reply to Mawer and Wilcox and Mullish and Williams

scientific article

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

scientific article published on 09 November 2020

Bacteria from diverse habitats colonize and compete in the mouse gut.

scientific article

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.

scientific article

Bacterial colonization and succession in a newly opened hospital.

scientific article

Bacterial communities associated with the lichen symbiosis

scientific article published on 17 December 2010

Bacterial communities of disease vectors sampled across time, space, and species

scientific article

Bacterial community changes in an industrial algae production system

article

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

article

Bacterial community structures are unique and resilient in full-scale bioenergy systems

scientific article

Bacterial community variation in human body habitats across space and time

scientific article (publication date: 18 December 2009)

Bacterial density rather than diversity correlates with hatching success across different avian species.

scientific article published on 9 February 2018

Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

scientific article

Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations

scientific article published on 24 February 2022

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

scientific article published on 18 August 2020

Bacterial phylogeny structures soil resistomes across habitats

scientific article published on 21 May 2014

Balance Trees Reveal Microbial Niche Differentiation.

scientific article published on 17 January 2017

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).

scientific article

BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences

scientific article

Bayesian community-wide culture-independent microbial source tracking

scientific article published on 17 July 2011

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome

scientific article published on 16 September 2019

Best practices for analysing microbiomes

scientific article published on 01 July 2018

Biogeography and habitat modelling of high-alpine bacteria

scientific article

Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations

scientific article published on May 2008

Biphasic assembly of the murine intestinal microbiota during early development

scientific article

Boulder ALignment Editor (ALE): a web-based RNA alignment tool

scientific article

Bringing the Dynamic Microbiome to Life with Animations

scientific article published in January 2017

CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection

scientific article published on 21 September 2020

Calour: an Interactive, Microbe-Centric Analysis Tool

Can Your Microbiome Tell You What to Eat?

scientific article

Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process

scientific article published on 6 March 2022

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

scientific article published on 30 June 2021

Carcass mass has little influence on the structure of gravesoil microbial communities

scientific article

Cell Tracking Profiler: a user-driven analysis framework for evaluating 4D live cell imaging data

scientific article published on 22 October 2020

Challenges in the construction of knowledge bases for human microbiome-disease associations

scientific article published on 05 September 2019

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water

scientific article published on 13 November 2014

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

scientific article

Changes in vaginal microbiota following antimicrobial and probiotic therapy

scientific article

Changes through time: integrating microorganisms into the study of succession

scientific article published on 22 June 2010

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

scientific article published on 26 April 2019

Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei

scientific article

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

scientific article published on 08 April 2019

Characterizing microbial communities through space and time

scientific article published on 7 December 2011

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

scientific article published on 16 November 2020

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

scientific article published on 5 May 2020

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

scientific article (publication date: March 2011)

Clean room microbiome complexity impacts planetary protection bioburden

scientific article published on 04 December 2021

Closure of the NCBI SRA and implications for the long-term future of genomics data storage

scientific article

Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere

scientific article

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

scientific article published on 29 September 2011

CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition

scientific article

CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes

scientific article published on 11 March 2009

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

scientific article

Colitis in TLR5-deficiency Mice: Role of the Microbiota

Collaborative cloud-enabled tools allow rapid, reproducible biological insights ⬇️

scientific article published on October 25, 2012

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies

scientific article published on 24 November 2015

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

scientific article published on 13 September 2020

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

scientific article published in February 2022

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

scientific article (publication date: October 2011)

Commensal bacteria and MAMPs are necessary for stress-induced increases in IL-1β and IL-18 but not IL-6, IL-10 or MCP-1.

scientific article

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

scientific article published on 19 June 2014

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

scientific article published on 07 January 2020

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

scientific article published in December 2011

Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies

scientific article published on 19 August 2016

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

scientific article published on 16 December 2016

Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh.

scientific article published on 3 March 2017

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

scientific article

Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts

scientific article published on 22 November 2021

Comparison of methods for estimating the nucleotide substitution matrix

scientific article

Comparison of oral collection methods for studies of microbiota

scientific article published on 27 September 2018

Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings

scientific article

Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice

scientific article published on February 2013

Composition of human skin microbiota affects attractiveness to malaria mosquitoes

scientific article published in 2011

Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers

scientific article published on 02 June 2021

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

scientific article published in 2022

ConStrains identifies microbial strains in metagenomic datasets

scientific article

Conceptualizing a Genomics Software Institute (GSI)

scientific article (publication date: 19 March 2012)

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

scientific article

Conducting a microbiome study

scientific article

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems

scientific article published in December 2010

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

scientific article published on 17 March 2020

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

scientific article published on 26 November 2018

Context and the human microbiome

scientific article

Context-aware deconvolution of cell–cell communication with Tensor-cell2cell

scientific article published in 2022

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

scientific article published on 31 August 2020

Convergence of gut microbiomes in myrmecophagous mammals

scientific article

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

scientific article published on 08 October 2019

Coprolites reveal ecological interactions lost with the extinction of New Zealand birds.

scientific article published on 12 February 2018

Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

scientific article published on 07 March 2017

Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort".

scientific article published on March 2017

Correction for Morton et al., "Uncovering the Horseshoe Effect in Microbial Analyses".

scientific article published in January 2018

Correction: Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1.

scientific article published on 21 August 2013

Correction: The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

scientific article published on 20 December 2013

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

scientific article

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples

scientific article published on 19 June 2017

Creating a 3D microbial and chemical snapshot of a human habitat

scientific article published on 27 February 2018

Cross-biome comparison of microbial association networks

scientific article

Crystal ball - 2013

Culturing: Looking it up in our gut

article

Current understanding of the human microbiome.

scientific article published in April 2018

DNA extraction for streamlined metagenomics of diverse environmental samples

scientific article published on June 2017

Database-Driven Grid Computing and Distributed Web Applications: A Comparison

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

scientific article published on 07 March 2017

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

scientific article published on 25 November 2020

Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas.

scientific article

Defining seasonal marine microbial community dynamics

scientific article

Defining the human microbiome

scientific article

Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

scientific article published on 29 September 2020

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

scientific article

Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2

scholarly article

Development of the human gastrointestinal microbiota and insights from high-throughput sequencing

scientific article published on May 2011

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

scientific article

Diet and the Gut Microbiome in 10–18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19)

scientific article published on 13 June 2019

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

scientific article (publication date: 20 May 2011)

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity

scientific article published on January 2016

Dietary effects on human gut microbiome diversity

scientific article published on 11 December 2014

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

scientific article published on 24 April 2015

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects

scientific article published on 26 September 2018

Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis

scientific article published on 15 October 2018

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults

scientific article published on 14 February 2020

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

scientific article

Direct sequencing of the human microbiome readily reveals community differences

scientific article

Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes

scientific article

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

DivergentSet, a tool for picking non-redundant sequences from large sequence collections

scientific article published on 11 June 2006

Diversity of Rickettsiales in the microbiome of the lone star tick, Amblyomma americanum

scientific article

Diversity, distribution and sources of bacteria in residential kitchens

scientific article published on 22 November 2012

Diversity, stability and resilience of the human gut microbiota

scientific article

Diversity, structure and convergent evolution of the global sponge microbiome

scientific article

Do universal codon-usage patterns minimize the effects of mutation and translation error?

scientific article

Does protein structure influence trypsin miscleavage? Using structural properties to predict the behavior of related proteins.

scientific article

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks

scientific article

Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants

scientific article

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

scholarly article published 7 March 2017

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

scientific article published on 30 March 2015

Dynamics of the human gut microbiome in inflammatory bowel disease.

scientific article published on 13 February 2017

EMP Sample Submission Guide v1 (protocols.io.pfqdjmw)

EMPeror: a tool for visualizing high-throughput microbial community data

scientific article

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

scientific article published on 15 March 2021

Early-Career Scientists Shaping the World

scientific article published on 07 May 2019

Early-life gut dysbiosis linked to juvenile mortality in ostriches

scientific article published on 12 October 2020

Earth Microbiome Project and Global Systems Biology

scientific article published on 10 April 2018

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

scientific article published on 04 June 2020

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks

scientific article published on 27 March 2015

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

scientific article

Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes

scientific article published on 01 August 2020

Effects of Immunization With the Soil-Derived Bacterium <i>Mycobacterium vaccae</i> on Stress Coping Behaviors and Cognitive Performance in a "Two Hit" Stressor Model

scientific article published on 01 January 2020

Effects of field conditions on fecal microbiota

scientific article published on 26 September 2016

Eggshell bacterial load is related to antimicrobial properties of feathers lining barn swallow nests.

scientific article published on 7 December 2013

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

scientific article

Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data

Engineered bacteria detect tumor DNA

scientific article published on 10 August 2023

Engineering the microbiome for animal health and conservation

scientific article published on 18 February 2019

Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study

scientific article published on 26 March 2020

Enhancing untargeted metabolomics using metadata-based source annotation

scientific article published in 2022

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment

article

Enterotypes in the landscape of gut microbial community composition.

scientific article published on 18 December 2017

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

scientific article

Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus

scientific article published on 09 July 2018

Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape

scientific article

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month

article

Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes".

scientific article published on 19 July 2017

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

scientific article published on 11 September 2017

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

scientific article published on 31 July 2015

Erratum to: The sponge microbiome project

scientific article published on 01 December 2018

Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

scientific article published on 22 November 2017

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project

scientific article published on 12 October 2017

Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

scientific article published on 10 February 2008

Establishing microbial composition measurement standards with reference frames.

scientific article

Estimate of the abundance of cardiomyopathic mutations in the β-myosin gene

scientific article

Euphorbia plant latex is inhabited by diverse microbial communities

scientific article published on 11 December 2015

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic

scientific article published in 2020

Evaluating the Information Content of Shallow Shotgun Metagenomics

scientific article published on 13 November 2018

Evaluating the impact of domestication and captivity on the horse gut microbiome.

scientific article published on 14 November 2017

Evidence for a persistent microbial seed bank throughout the global ocean

scientific article (publication date: 19 March 2013)

Evolution of mammals and their gut microbes

scientific article (publication date: 20 June 2008)

Evolutionary rates vary among rRNA structural elements

scientific article

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

scientific article published on 11 July 2018

Examining the global distribution of dominant archaeal populations in soil

scientific article published on 18 November 2010

Exercise is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats

scientific article published on 27 May 2015

Expanding magnetic organelle biogenesis in the domain Bacteria

scientific article published on 30 October 2020

Expanding our Understanding of the Role of the Microbiome in Health and Disease

scientific article published on 8 February 2018

Expanding the scope and scale of microbiome research

scientific article published on 05 September 2019

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

scientific article published on 24 June 2021

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome

scientific article published on 12 March 2018

Experimental and analytical tools for studying the human microbiome

scientific article

Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics).

scientific article published on 9 January 2018

Exposure to toxic metals triggers unique responses from the rat gut microbiota.

scientific article published on 26 April 2018

Extreme Dysbiosis of the Microbiome in Critical Illness

scientific article published on July 2016

FXR Regulates Intestinal Cancer Stem Cell Proliferation

scientific article published on 01 February 2019

Faecal transplants

scientific article published on 20 October 2015

Farm-like indoor microbiota in non-farm homes protects children from asthma development

scientific article published on 17 June 2019

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

scientific article

Fast-Find: a novel computational approach to analyzing combinatorial motifs

scientific article

Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake

scientific article published on 19 October 2016

Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs

scientific article published on 18 May 2020

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

scientific article published on 18 August 2020

Fecal Microbiome in Epidemiologic Studies-Response

scientific article published on 9 March 2016

Fecal Microbiota Transplant is Highly Effective in Real-World Practice: Initial Results from the FMT National Registry

scientific article published on 30 September 2020

Finding specific RNA motifs: function in a zeptomole world?

scientific article published in February 2003

Finding the missing links among metabolites, microbes, and the host

scientific article

Forensic identification using skin bacterial communities

scientific article published on 15 March 2010

From Sample to Multi-Omics Conclusions in under 48 Hours

scientific article (publication date: 26 April 2016)

From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal

scientific article published on 29 January 2008

From molecules to dynamic biological communities

scientific article

Fructose stimulated de novo lipogenesis is promoted by inflammation

scientific article published on 24 August 2020

GABA-modulating bacteria of the human gut microbiota

scientific article published on 10 December 2018

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity

scientific article published on 07 October 2020

Genetic Determinants of the Gut Microbiome in UK Twins

scientific article published on May 2016

Genetic and environmental control of host-gut microbiota interactions

scientific article published on 10 August 2015

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice

scientific article

Genetic determinants of risk and survival in pulmonary arterial hypertension

article

Genetic influences on the human oral microbiome

scientific article

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

scientific article

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits

scientific article published on 19 October 2015

Genomic Standards Consortium Projects

article

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota

scientific article published in Nature Communications

Genomic standards consortium projects

scientific article

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

scientific article

Geography and Location Are the Primary Drivers of Office Microbiome Composition

scientific article published on March 2016

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

scientific article

Global biogeography of highly diverse protistan communities in soil

scientific article published on 13 December 2012

Global chemical analysis of biology by mass spectrometry

scientific article published on 05 July 2017

Global chemical effects of the microbiome include new bile-acid conjugations

scientific article published on 26 February 2020

Global patterns in bacterial diversity

scientific article

Global patterns in the biogeography of bacterial taxa

scientific article published in January 2011

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

scientific article published on 3 June 2010

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations

scientific article

Ground beef microbiome changes with antimicrobial decontamination interventions and product storage

scientific article published on 05 June 2019

Guiding longitudinal sampling in IBD cohorts

scientific article published on 21 October 2017

Guilt by association: the arginine case revisited

scientific article

Gut Instinct

scientific article published in 2017

Gut Microbiome in Schizophrenia: Altered Functional Pathways Related to Immune Modulation and Atherosclerotic Risk

scientific article published on 21 October 2020

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction

scientific article published on 30 January 2018

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease

scientific article

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort

scientific article published on 23 October 2018

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

scientific article published on 11 September 2017

Gut microbes and the brain: paradigm shift in neuroscience

scientific article

Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis

scientific article published on 02 June 2018

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

scientific article published on 01 November 2019

Gut microbiome in serious mental illnesses: A systematic review and critical evaluation

scientific article published on 05 September 2019

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 microbiomes of Malawian twin pairs discordant for kwashiorkor

scientific article published on 30 January 2013

Gut microbiota from twins discordant for obesity modulate metabolism in mice

scientific article (publication date: 6 September 2013)

Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi

scientific article published on 20 May 2019

Gut microbiota utilize immunoglobulin A for mucosal colonization

scientific article published in Science

HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats

scientific article

Heritable components of the human fecal microbiome are associated with visceral fat.

scientific article published on 26 September 2016

High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county

scientific article published on 18 November 2020

High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy

scientific article published on 23 June 2020

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity

High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County

scientific article published on 2 March 2021

High-fat diet determines the composition of the murine gut microbiome independently of obesity

scientific article published on 23 August 2009

Home chemical and microbial transitions across urbanization

scientific article published on 04 November 2019

Hopanoid-producing bacteria in the Red Sea include the major marine nitrite-oxidizers.

scientific article published on 12 April 2018

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta).

scientific article

Host remodeling of the gut microbiome and metabolic changes during pregnancy

scientific article

Host variables confound gut microbiota studies of human disease

scientific article published on 04 November 2020

Host-associated and free-living phage communities differ profoundly in phylogenetic composition

scientific article

Host-bacterial coevolution and the search for new drug targets

scientific article published on February 2008

How biologists conceptualize genes: an empirical study

article

How delivery mode and feeding can shape the bacterial community in the infant gut

scientific article published on 11 February 2013

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

scientific article published on 01 May 2019

Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension

scientific article

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

scientific article published on 11 February 2020

Human genetics shape the gut microbiome.

scientific article

Human gut microbiome viewed across age and geography

scientific article

Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013

scientific article

Human oral, gut, and plaque microbiota in patients with atherosclerosis

scientific article

Human-associated microbial signatures: examining their predictive value

scientific article

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis

scientific article published on 25 June 2019

Identifying and Predicting Novelty in Microbiome Studies

scientific article published in 2018

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

scientific article

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

scientific article

Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment

scientific article

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice

scientific article published on 16 May 2016

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome

scientific article published on 17 October 2017

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.

scientific article

Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon

scientific article

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

scientific article

Impacts of the Human Gut Microbiome on Therapeutics.

scientific article published on 2 October 2017

Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

scientific article published on 13 May 2021

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys ⬇️

scientific article

Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples

scientific article

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

scientific article published on July 2004

Improving saliva shotgun metagenomics by chemical host DNA depletion

scientific article published on 27 February 2018

Individual diet has sex-dependent effects on vertebrate gut microbiota

scientific article

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).

scientific article published on 22 May 2014

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

scientific article

Information, probability, and the abundance of the simplest RNA active sites

scientific article published in May 2008

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas).

scientific article published on 13 November 2015

Insights and inferences about integron evolution from genomic data

scientific article

Insights from characterizing extinct human gut microbiomes

scientific article

Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness

scientific article

Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis.

scientific article published on 5 June 2011

Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-Oxide

scientific article published on 5 July 2017

Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome

scientific article published in 2021

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome.

scientific article published in May 2018

Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separation

scientific article

Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes

scientific article published in 2022

Is the Genetic Code Really a Frozen Accident? New Evidence from in Vitro Selection

article

Is there convergence of gut microbes in blood-feeding vertebrates?

scientific article published on 03 June 2019

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

scientific article published on 13 March 2018

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

scientific article published on 13 June 2016

Key challenges in proteomics and proteoinformatics. Progress in proteins

scientific article

Lake microbial communities are resilient after a whole-ecosystem disturbance

scientific article published on 28 June 2012

Large-scale replicated field study of maize rhizosphere identifies heritable microbes.

scientific article published on 25 June 2018

Learning representations of microbe-metabolite interactions

scientific article published on 04 November 2019

Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players

scientific article published on 05 July 2024

Let researchers try new paths

scientific article published on 26 October 2016

Leveling up citizen science

scientific article published on 24 September 2020

Life Through A Microbial Lens

Lifestyle chemistries from phones for individual profiling

scientific article (publication date: 29 November 2016)

Limited microbiome differences in captive and semi-wild primate populations consuming similar diets

scientific article published in 2022

Linking long-term dietary patterns with gut microbial enterotypes

scientific article

Links between environment, diet, and the hunter-gatherer microbiome

scholarly article by Gabriela K. Fragiadakis et al published 17 August 2018 in Gut microbes

Longitudinal analysis of microbial interaction between humans and the indoor environment

scientific article

Longitudinal survey of microbiome associated with particulate matter in a megacity

scientific article published on 03 March 2020

METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection

scholarly article by Na Li published in May 2021

MICROBIOME. A unified initiative to harness Earth's microbiomes

scientific article published on 28 October 2015

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

scientific article

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

scientific article

Major shifts in gut microbiota during development and its relationship to growth in ostriches

scientific article published on 11 May 2019

Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites

scientific article

Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection.

scientific article published on 11 September 2017

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

scientific article published on 12 October 2016

Mass spectrometry searches using MASST

scientific article published on 01 January 2020

Mathematical Approaches for Describing Microbial Populations: Practice and Theory for Extrapolation of Rich Environments

scholarly article published 2 August 2013

Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012.

scientific article

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

scientific article

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010

scientific article (publication date: 15 December 2010)

Meeting report: fungal its workshop (october 2012).

scientific article published on 15 April 2013

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

Meta-analyses of human gut microbes associated with obesity and IBD

scientific article published on 13 October 2014

Meta-analyses of studies of the human microbiota

scientific article

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

scientific article published on 16 October 2019

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

scientific article published on 3 December 2017

Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5

scientific article (publication date: 9 April 2010)

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs

scientific article published on 10 March 2020

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil

scientific article published on 7 September 2007

Metagenomic covariation along densely sampled environmental gradients in the Red Sea.

scientific article

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

scientific article (publication date: July 2014)

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

scientific article published on 30 October 2018

Methods for phylogenetic analysis of microbiome data

scientific article published on 24 May 2018

Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium

scientific article published on 18 August 2020

Microbes do not follow the elevational diversity patterns of plants and animals

scientific article published in April 2011

Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations

scientific article published on 10 January 2020

Microbial Skin Inhabitants: Friends Forever

scientific article published on May 2016

Microbial biogeography and ecology of the mouth and implications for periodontal diseases

scientific article published on 01 February 2020

Microbial biogeography of public restroom surfaces

scientific article published on 23 November 2011

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

scientific article published on 10 December 2021

Microbial community assembly and metabolic function during mammalian corpse decomposition.

scientific article published on 10 December 2015

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).

scientific article

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

scientific article

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

scientific article published on 5 September 2010

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

scientific article published on 22 November 2020

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

scientific article published on 17 April 2020

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus)

scientific article published on 31 August 2018

Microbial endocrinology: the interplay between the microbiota and the endocrine system

scientific article

Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions

scientific article

Microbiology of death

scientific article

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

scientific article published on 18 September 2018

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models

scientific article published on 16 February 2018

Microbiome Tools for Forensic Science

scientific article

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

scientific article published on 11 March 2020

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

scientific article published on 28 July 2020

Microbiome-wide association studies link dynamic microbial consortia to disease

scientific article

Microbiota and Host Nutrition across Plant and Animal Kingdoms

scientific article

Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt

scientific article published on 15 May 2015

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish

scientific article

Microbiota restoration: natural and supplemented recovery of human microbial communities

scientific article

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort

scientific article published on September 2016

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis

scientific article published on 24 September 2019

Molecular cartography of the human skin surface in 3D

scientific article published on 30 March 2015

Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures

scientific article published on 01 September 2020

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus.

scientific article published on 04 April 2017

MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs

scientific article published on 15 August 2008

Moving pictures of the human microbiome

scientific article published in 2011

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

scientific article published in 2022

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

scientific article published on 29 May 2019

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

scientific article published on 6 June 2021

Multilevel Research Strategies and Biological Systems

article

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention

scientific article published in 2022

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria

article

Multiple pattern matching: a Markov chain approach.

scientific article published on August 2007

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search

scientific article published on 17 March 2020

Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli

scientific article published on 14 November 2016

Natural and artificial RNAs occupy the same restricted region of sequence space

scientific article

Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories

scientific article

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

article

New Insight into the Diversity of Life's Building Blocks: Evenness, Not Variance

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017

article

Niche partitioning of a pathogenic microbiome driven by chemical gradients

scientific article published on 26 September 2018

Nonalcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet

scientific article published on 29 May 2021

Normalization and microbial differential abundance strategies depend upon data characteristics

scientific article

Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch

scientific article

Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.

scientific article

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

scientific article

Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India

scientific article published on 23 September 2020

Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids

scientific article

Open-Source Sequence Clustering Methods Improve the State Of the Art.

scientific article

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

scientific article published on 31 October 2019

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

scientific article

Organ-level protein networks as a reference for the host effects of the microbiome

scientific article published on 28 January 2020

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

scientific article

Origin of microbial biomineralization and magnetotaxis during the Archean

scientific article published on 13 February 2017

Origins of the genetic code: the escaped triplet theory.

scientific article

Our microbial selves: what ecology can teach us

scientific article

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder

scientific article

Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression

scientific article published on 29 August 2023

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

scientific article

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli

scientific article

Parallel evolution of the genetic code in arthropod mitochondrial genomes.

scientific article

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

scientific article published on 14 February 2017

Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice

scientific article published on 04 June 2020

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

scientific article

Pathological rate matrices: from primates to pathogens

scientific article

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate

scientific article published on 26 January 2017

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study

scientific article published on 07 February 2020

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites

scientific article published on September 2017

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.

scientific article published on 17 April 2018

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species

scientific article published on 24 November 2015

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

scientific article

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

scientific article published on 02 December 2019

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

scientific article published on 04 April 2022

Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance

scientific article published on 2 June 2017

Postprandial remodeling of the gut microbiota in Burmese pythons

scientific article

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.

scientific article published on 19 May 2020

Precision medicine in alcoholic and nonalcoholic fatty liver disease via modulating the gut microbiota

scientific article

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota

scientific article published on September 2015

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

scientific article (publication date: September 2013)

Predictive modeling of gingivitis severity and susceptibility via oral microbiota

scientific article

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

scientific article published on 03 May 2016

Preserving microbial diversity

scientific article published in Science

Preserving microbial diversity

scientific article

Prevalence and genetic diversity of Blastocystis in family units living in the United States

scientific article

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

scientific article

Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity.

scientific article published in September 2016

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

scientific article published on 17 December 2019

Publisher Correction: Enterotypes in the landscape of gut microbial community composition

scientific article published on 13 February 2018

Publisher Correction: The gut-liver axis and the intersection with the microbiome

scientific article published on 01 December 2018

PyCogent: a toolkit for making sense from sequence

scientific article published in January 2007

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

scientific article (publication date: 15 January 2010)

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

scientific article published on 01 June 2020

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

scientific article

Qiita: rapid, web-enabled microbiome meta-analysis

scientific article published on 01 October 2018

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

scientific article

Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load

scientific article published on 15 February 2021

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

scientific article published on 25 June 2019

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

scientific article

RNA structure prediction from evolutionary patterns of nucleotide composition

scientific article published on 7 January 2009

RNA-amino acid binding: a stereochemical era for the genetic code

scientific article

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

scientific article

Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus

scientific article published on 10 August 2021

Rapid, large-scale wastewater surveillance and automated reporting system enabled early detection of nearly 85% of COVID-19 cases on a University campus

preprint

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

scientific article

ReDU: a framework to find and reanalyze public mass spectrometry data

scientific article published on 17 August 2020

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

scientific article

Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes

scientific article published on 17 June 2019

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV

scientific article published in 2020

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

scientific article published on 27 August 2018

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation

scholarly article

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome

scientific article published on 20 February 2020

Replenishing our defensive microbes

scientific article

Reply to Moossavi and Azad, "Quantifying and Interpreting the Association between Early-Life Gut Microbiota Composition and Childhood Obesity"

article

Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newborn.

scientific article

Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy"

scientific article published on 06 August 2019

Reply to Wang and Chen: An ancient origin of magnetotactic bacteria.

scientific article published on 12 June 2017

Reports of the death of the gene are greatly exaggerated

article

Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations

scientific article published on 18 November 2019

Reproducibility: In praise of open research measures

scientific article published in June 2013

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

scientific article published on 01 August 2019

Research priorities for the management of freshwater fish habitat in Canada

scientific article

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

scientific article

Responses of gut microbiota to diet composition and weight loss in lean and obese mice

scientific article published on 19 May 2011

Rethinking "enterotypes".

scientific article

Reverse metabolomics for the discovery of chemical structures from humans

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

scientific article

Ribosomal RNA, the lens into life

scientific article published in April 2015

Rob Knight: How our microbes make us who we are

TED2014

Role of the microbiome in human development

scientific article published on 22 January 2019

Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness

scientific article published on 18 June 2016

Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms

scientific article published in 2021

SARS-CoV-2 Infection Among Symptom-Free Healthcare Workers

scientific article published on 05 August 2020

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

scientific article published on 08 June 2021

SHOGUN: a modular, accurate, and scalable framework for microbiome quantification

scientific article published on 04 May 2020

Sa1915 – Altered Circadian Rhythm Cycling of Microbes and Metabolites in a Murine Model of Sleep Apnea

scholarly article

Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides

scientific article published on 14 March 2022

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

scientific article

Satellite remote sensing data can be used to model marine microbial metabolite turnover.

scientific article

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania.

scientific article

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

scientific article

Seasonal variation of postmortem microbial communities

scientific article published on 4 March 2015

Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences

scientific article

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

scientific article

Selection, history and chemistry: the three faces of the genetic code.

scientific article

Sequencing our way towards understanding global eukaryotic biodiversity

scientific article (publication date: April 2012)

Sharing and archiving nucleic acid structure mapping data

scientific article (publication date: July 2011)

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

scientific article (publication date: 9 August 2016)

Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil

scientific article published in June 2010

Short Course in the Microbiome

scientific article published in January 2015

Short pyrosequencing reads suffice for accurate microbial community analysis

scientific article published on 18 September 2007

Short-term temporal variability in airborne bacterial and fungal populations

scientific article published on 2 November 2007

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.

scientific article

Simple, recurring RNA binding sites for L-arginine

scientific article (publication date: April 2010)

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

scientific article (publication date: 2013)

Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

scientific article published on 24 December 2019

SitePainter: a tool for exploring biogeographical patterns

scientific article published on 9 December 2011

Size, constant sequences, and optimal selection

scientific article

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis

article by Whitney M. Holden et al published July 2015 in Biological Conservation

SnapShot: the human microbiome

scientific article

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality

scientific article published on 5 December 2017

Soil bacterial and fungal communities across a pH gradient in an arable soil

scientific article published on 6 May 2010

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

scientific article published in November 2010

Sources of bacteria in outdoor air across cities in the midwestern United States.

scientific article published on 29 July 2011

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

scientific article

Spatial and temporal variability of the human microbiota

scientific article

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments

scientific article published on 4 November 2010

Specialized metabolites from the microbiome in health and disease

scientific article

Species abundance information improves sequence taxonomy classification accuracy

scientific article published on 11 October 2019

Species divergence and the measurement of microbial diversity

scientific article

Species-level functional profiling of metagenomes and metatranscriptomes

scholarly article by Eric A Franzosa published in October 2018

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

scientific article published on 20 May 2015

Stable tRNA-based phylogenies using only 76 nucleotides

scientific article published on 17 June 2010

Strains, functions and dynamics in the expanded Human Microbiome Project

scientific article

Stress response, gut microbial diversity and sexual signals correlate with social interactions.

scientific article published on June 2016

Striped UniFrac: enabling microbiome analysis at unprecedented scale

scientific article published on 01 November 2018

Structural basis for diversity in the SAM clan of riboswitches

scientific article

Structure, function and diversity of the healthy human microbiome

scientific article

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

Succession of microbial consortia in the developing infant gut microbiome

scientific article

Supervised classification of human microbiota

scientific article

Supervised classification of microbiota mitigates mislabeling errors

scientific article

Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice

scientific article published on 27 February 2019

TaskSpaces: A Software Framework for Parallel Bioinformatics on Computational Grids

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm.

scientific article

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

scientific article published on 11 May 2021

Technology and techniques for microbial ecology via DNA sequencing

scientific article

Temporal variability is a personalized feature of the human microbiome

scientific article

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

scientific article published on 20 May 2020

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

scientific article published on 25 July 2019

Testing GitHub projects on custom resources using unprivileged Kubernetes runners

scientific article published on 10 September 2023

The 'rare biosphere': a reality check

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

2012 scientific article

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

scientific article

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011.

scientific article published on 22 November 2011

The Earth Microbiome project: successes and aspirations

scientific article

The Ecology of Microbial Communities Associated with Macrocystis pyrifera

scientific article

The Effects of Captivity on the Mammalian Gut Microbiome

scientific article published in October 2017

The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder

scientific article published in 2021

The Genomic Standards Consortium

scientific article (publication date: June 2011)

The Gut Microbiome, Aging, and Longevity: A Systematic Review

scientific article published on 07 December 2020

The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

scientific article published on 15 April 2013

The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients

scientific article published on 01 April 2022

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

scientific article

The Impact of the Gut Microbiota on Human Health: An Integrative View ⬇️

scientific article (publication date: 16 March 2012)

The Microbiome and Human Biology.

scientific article published on 20 March 2017

The Microbiome and Its Potential for Pharmacology

scientific article published on 01 January 2019

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study

scientific article published on 11 July 2017

The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health

scientific article

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat

scientific article published on July 2016

The RNA structure alignment ontology

scientific article published on 21 July 2009

The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment

scientific article published on 24 August 2020

The UniFrac significance test is sensitive to tree topology

scientific article published on 7 July 2015

The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction

scientific article published on 24 March 2022

The Western English Channel contains a persistent microbial seed bank

scientific article

The amphibian skin-associated microbiome across species, space and life history stages

scientific article

The bacterial microbiota in the oral mucosa of rural Amerindians

scientific article

The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework

scientific article

The convergence of carbohydrate active gene repertoires in human gut microbes

scholarly article

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves

scientific article published in November 2010

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months

scientific article published on 11 February 2020

The emergence of microbiome centres

scientific article published on 01 January 2020

The founding charter of the Genomic Observatories Network

scientific article published on 7 March 2014

The genetic basis for adaptation of model-designed syntrophic co-cultures

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The genomic standards consortium: bringing standards to life for microbial ecology

scientific article (publication date: October 2011)

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

scientific article published on 04 June 2018

The gut microbiota in human energy homeostasis and obesity

scientific article published on 6 August 2015

The gut-liver axis and the intersection with the microbiome

scientific article published on 01 July 2018

The human microbiome in evolution.

scientific article published on 27 December 2017

The human microbiome project

scientific article (publication date: 18 October 2007)

The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology

scientific article

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins

scientific article published in October 2011

The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study)

scientific article published in 2022

The impact of skin care products on skin chemistry and microbiome dynamics

scientific article published on 12 June 2019

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

scholarly article

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

scientific article published in May 2012

The intestinal metabolome: an intersection between microbiota and host

scientific article

The long-term stability of the human gut microbiota

scientific article

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis

scientific article

The microbiome explored: recent insights and future challenges

scientific article published on 4 February 2013

The microbiome of uncontacted Amerindians

scientific article published in April 2015

The microbiome quality control project: baseline study design and future directions

scientific article published on 9 December 2015

The mind-body-microbial continuum

scientific article

The molecular basis of nuclear genetic code change in ciliates.

scientific article

The molecular impact of life in an indoor environment

scientific article published in 2022

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus

scientific article published on 26 November 2018

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease

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The sponge microbiome project

scientific article published on October 2017

The treatment-naive microbiome in new-onset Crohn's disease

scientific article

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

scientific article published in July 2011

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Three Dimensional Cartography of Microbiome and Metabolome Data onto Radiological Images of the Human Lung

scientific article published in 2018

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

scientific article published on 17 October 2017

Tiny microbes, enormous impacts: what matters in gut microbiome studies?

scientific article

Tools for the Microbiome: Nano and Beyond

scientific article published on 22 December 2015

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

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Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

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Toward anthropomimetic robotics: development, simulation, and control of a musculoskeletal torso

scientific article published on 27 November 2012

Toward effective probiotics for autism and other neurodevelopmental disorders

scientific article

Toward unrestricted use of public genomic data:

scientific article

Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients

scientific article

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

scientific article published on 08 November 2018

Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy

scientific article published on 01 January 2017

Tracking down the sources of experimental contamination in microbiome studies

scientific article published on 17 December 2014

Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment

scientific article published on 01 August 2019

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes

scientific article published on 2 February 2017

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

scientific article

Translating the human microbiome

scientific article published in April 2013

Translational medicine and the human microbiome

scientific article published on 11 October 2010

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

scientific article published on 22 September 2020

Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease

scientific article published on 23 November 2020

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary

scientific article published on 24 May 2019

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project

scientific article

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics.

scientific article published in August 2018

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota

scientific article published on 23 September 2020

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection

scientific article published on 01 December 2020

UCHIME improves sensitivity and speed of chimera detection ⬇️

scientific article (publication date: 15 August 2011)

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms ⬇️

scientific article (publication date: August 2012)

Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely

scientific article published on 15 June 2020

Uncovering the Horseshoe Effect in Microbial Analyses

scientific article published on January 2017

UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context

scientific article (publication date: 7 August 2006)

UniFrac: a new phylogenetic method for comparing microbial communities

scientific article

UniFrac: an effective distance metric for microbial community comparison

scientific article

Unique Strain of Rickettsia parkeri Associated with the Hard Tick Dermacentor parumapertus Neumann in the Western United States

scientific article published on 17 February 2017

Unlocking capacities of genomics for the COVID-19 response and future pandemics

scientific article published on 08 April 2022

Unlocking the potential of metagenomics through replicated experimental design

scientific article published on 7 June 2012

Using QIIME to analyze 16S rRNA gene sequences from microbial communities

scientific article

Using QIIME to analyze 16S rRNA gene sequences from microbial communities

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Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease

scholarly article published December 2016

Using the gut microbiota as a novel tool for examining colobine primate GI health

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Using the nucleotide substitution rate matrix to detect horizontal gene transfer

scientific article

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data

scientific article published on 29 April 2021

Variable responses of human and non-human primate gut microbiomes to a Western diet

scientific article published on 16 November 2015

Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex

scientific article

Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin

scientific article published on 16 March 2016

Vertebrate decomposition is accelerated by soil microbes

scientific article

Visualizing 'omic feature rankings and log-ratios using Qurro

scientific article published on 28 April 2020

Vitamin D metabolites and the gut microbiome in older men

scientific article published on 26 November 2020

Voices in methods development

scientific article published on 01 October 2019

Walls talk: Microbial biogeography of homes spanning urbanization.

scientific article published on 12 February 2016

Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project

scientific article published on 20 October 2021

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

scientific article published in September 2022

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

preprint

Wastewater surveillance for public health

scientific article published on 6 January 2023

What is the value of a food and drug administration investigational new drug application for fecal microbiota transplantation to treat Clostridium difficile Infection?

scientific article published on 20 October 2013

Which is more important for classifying microbial communities: who's there or what they can do?

scientific article

Why Microbiome Treatments Could Pay Off Soon

Why microbiome treatments could pay off soon

scientific article published on February 2015

Widespread colonization of the lung by Tropheryma whipplei in HIV infection

scientific article published on May 2013

Worlds within worlds: evolution of the vertebrate gut microbiota

scientific article (publication date: October 2008)

Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players

scientific article published on March 2013

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data ⬇️

scientific article published in 2024

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

scientific article published on September 2016

pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils

scholarly article by Youzhi Feng et al published July 2014 in Soil Biology and Biochemistry

redbiom: a Rapid Sample Discovery and Feature Characterization System

scientific article published on 25 June 2019

tRNA Creation by Hairpin Duplication

Špína je dobrá: význam bakterií pro vývoj imunitního systému vašeho dítěte

book edition published in 2018

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