Associations of Childhood and Perinatal Blood Metals with Children’s Gut Microbiomes in a Canadian Gestation Cohort

Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure

(2021) Yike Shen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Multivariable association discovery in population-scale meta-omics studies

(2021) Himel Mallick et al.   PLoS Computational Biology

Oral Administration of Flavonifractor plautii Strongly Suppresses Th2 Immune Responses in Mice

(2020) Tasuku Ogita et al.   Frontiers in Immunology

Nutrient-toxic element mixtures and the early postnatal gut microbiome in a United States longitudinal birth cohort

(2020) Hannah E. Laue et al.   ENVIRONMENT INTERNATIONAL

Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area

(2020) Mengmeng Shao et al.   Scientific Reports

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood

(2020) Camille C. Cioffi et al.   PLoS One

Oral administration of Flavonifractor plautii attenuates inflammatory responses in obese adipose tissue

(2020) Ayane Mikami et al.   MOLECULAR BIOLOGY REPORTS

Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA

(2020) Sabrina Duranti et al.   Scientific Reports

Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years

(2020) Hannah E. Laue et al.   Scientific Reports

Human gut microbiota Agathobaculum butyriciproducens improves cognitive impairment in LPS-induced and APP/PS1 mouse models of Alzheimer's disease

(2020) Jun Go et al.   NUTRITION RESEARCH

Parabacteroides distasonis Alleviates Obesity and Metabolic Dysfunctions via Production of Succinate and Secondary Bile Acids

(2019) Kai Wang et al.   Cell Reports

Potential of Pectins to Beneficially Modulate the Gut Microbiota Depends on Their Structural Properties

(2019) Nadja Larsen et al.   Frontiers in Microbiology

Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites

(2019) Xuanji Li et al.   ENVIRONMENT INTERNATIONAL

Disturbance of trace element and gut microbiota profiles as indicators of autism spectrum disorder: A pilot study of Chinese children

(2019) Qixiao Zhai et al.   ENVIRONMENTAL RESEARCH

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Sex-specific association between gut microbiome and fat distribution

(2019) Yan Min et al.   Nature Communications

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

(2019) Yike Shen et al.   ENVIRONMENT INTERNATIONAL

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Structural and functional alterations of gut microbiome in mice induced by chronic cadmium exposure

(2019) Xiwei He et al.   CHEMOSPHERE

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

(2018) Morgane Sonia Thion et al.   CELL

Parabacteroides distasonis attenuates toll-like receptor 4 signaling and Akt activation and blocks colon tumor formation in high-fat diet-fed azoxymethane-treated mice

(2018) Gar Yee Koh et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2018) Joshua B. Richardson et al.   Scientific Reports

Butyrate: A Double-Edged Sword for Health?

(2018) Hu Liu et al.   Advances in Nutrition

Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population

(2018) Anne G. Hoen et al.   Scientific Reports

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

(2018) Tommi Vatanen et al.   NATURE

Species-level functional profiling of metagenomes and metatranscriptomes

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

Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics

(2017) Mireia Lopez-Siles et al.   ISME Journal

Manganese-induced sex-specific gut microbiome perturbations in C57BL/6 mice

(2017) Liang Chi et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Isolation of Human Intestinal Bacteria Capable of Producing the Bioactive Metabolite Isourolithin A from Ellagic Acid

(2017) María V. Selma et al.   Frontiers in Microbiology

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer

(2017) Daniela Börnigen et al.   Scientific Reports

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Sex-Specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome

(2016) Liang Chi et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Children with health impairments by heavy metals in an e-waste recycling area

(2016) Xiang Zeng et al.   CHEMOSPHERE

Maternal levels of endocrine disruptors, polybrominated diphenyl ethers, in early pregnancy are not associated with lower birth weight in the Canadian birth cohort GESTE

(2016) Yasmine K. Serme-Gbedo et al.   Environmental Health

Gut microbiome in health and disease: Linking the microbiome–gut–brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases

(2016) Shivani Ghaisas et al.   PHARMACOLOGY & THERAPEUTICS

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups

(2016) Deepak Yadav et al.   Gut Pathogens

Feed your gut with caution!

(2016) Vishal Singh et al.   Translational Cancer Research

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Proteobacteria: microbial signature of dysbiosis in gut microbiota

(2015) Na-Ri Shin et al.   TRENDS IN BIOTECHNOLOGY

Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders

(2015) John R. Kelly et al.   Frontiers in Cellular Neuroscience

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

(2015) Oscar Franzén et al.   Microbiome

Bifidobacterium pseudocatenulatum CECT 7765 Reduces Obesity-Associated Inflammation by Restoring the Lymphocyte-Macrophage Balance and Gut Microbiota Structure in High-Fat Diet-Fed Mice

(2015) Angela Moya-Pérez et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle et al.   SCIENCE

Health risks from the exposure of children to As, Se, Pb and other heavy metals near the largest coking plant in China

(2013) Suzhen Cao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Ecotoxicology inside the gut: impact of heavy metals on the mouse microbiome

(2013) Jérôme Breton et al.   BMC Pharmacology & Toxicology

Hypocholesterolaemic effect of yoghurt containing Bifidobacterium pseudocatenulatum G4 or Bifidobacterium longum BB536

(2012) Sadeq Hasan Al-Sheraji et al.   FOOD CHEMISTRY

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

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

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH