Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing

Reply to: Bacterial DNA in Fetal Lung Samples May Be Explained by Sample Contamination

(2020) Denise Al Alam et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Viable bacterial colonization is highly limited in the human intestine in utero

(2020) E. Rackaityte et al.   NATURE MEDICINE

Lung Microbiota Contribute to Pulmonary Inflammation and Disease Progression in Pulmonary Fibrosis

(2019) David N O'Dwyer et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

(2019) Jason Lloyd-Price et al.   NATURE

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

(2019) Pirkka V. Kirjavainen et al.   NATURE MEDICINE

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health

(2019) Keylie M. Gibson et al.   Scientific Reports

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

(2019) Jeremiah J. Minich et al.   mSystems

A cluster-randomised controlled trial comparing school and community-based deworming for soil transmitted helminth control in school-age children: the CoDe-STH trial protocol

(2019) Naomi E. Clarke et al.   BMC INFECTIOUS DISEASES

Author Correction: Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

Author Correction: Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance

(2019) Sophia R. Levan et al.   Nature Microbiology

Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)

(2019) Pratima Chapagain et al.   BMC GENOMICS

The impact of vegan production on the kimchi microbiome

(2018) Michelle A. Zabat et al.   FOOD MICROBIOLOGY

The classroom microbiome and asthma morbidity in children attending 3 inner-city schools

(2018) Peggy S. Lai et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Early-life home environment and risk of asthma among inner-city children

(2018) George T. O'Connor et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Evaluation of DNA extraction methods to detect bacterial targets in aerosol samples

(2018) John Dunbar et al.   JOURNAL OF MICROBIOLOGICAL METHODS

How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis

(2018) Leonardo Terranova et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils

(2018) Philipp Wurm et al.   mSystems

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

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols

(2017) Yenkai Lim et al.   Scientific Reports

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

(2016) Timothy R. Sampson et al.   CELL

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material

(2016) Ali H.D. Janabi et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Extreme Dysbiosis of the Microbiome in Critical Illness

(2016) Daniel McDonald et al.   mSphere

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

(2016) Berith E. Knudsen et al.   mSystems

Testing the H56 Vaccine Delivered in 4 Different Adjuvants as a BCG-Booster in a Non-Human Primate Model of Tuberculosis

(2016) Rolf Billeskov et al.   PLoS One

Integrity of the Human Faecal Microbiota following Long-Term Sample Storage

(2016) Elahe Kia et al.   PLoS One

Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity

(2016) Albert M. Levin et al.   Scientific Reports

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges

(2014) Cole G. Easson et al.   Frontiers in Microbiology

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

(2014) Regina Lamendella et al.   Frontiers in Microbiology

Paramagnetic Cellulose DNA Isolation Improves DNA Yield and Quality Among Diverse Plant Taxa

(2014) Jackson R. Moeller et al.   Applications in Plant Sciences

A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples

(2013) Shantelle Claassen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection

(2013) K. E. Fujimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

The Lung Tissue Microbiome in Chronic Obstructive Pulmonary Disease

(2012) Marc A. Sze et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Clinical Outcomes in Household Contacts of Patients with Cholera in Bangladesh

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