Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life

Bacterial colonization reprograms the neonatal gut metabolome

(2020) Kyle Bittinger et al.   Nature Microbiology

Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2′-O-Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat

(2019) Manuela Centanni et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

(2019) Abigail J. Johnson et al.   Cell Host & Microbe

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

(2019) Marc A. Sze et al.   mBio

Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

(2019) Yan Shao et al.   NATURE

The Role of Iron and Siderophores in Infection, and the Development of Siderophore Antibiotics

(2019) Malcom G P Page   CLINICAL INFECTIOUS DISEASES

Lactoferrin in Human Milk of Prolonged Lactation

(2019) Czosnykowska-Łukacka et al.   Nutrients

Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal

(2019) Kieran James et al.   Scientific Reports

Individuality and convergence of the infant gut microbiota during the first year of life

(2018) Eric J. de Muinck et al.   Nature Communications

Maturation of the gut microbiome and risk of asthma in childhood

(2018) Jakob Stokholm et al.   Nature Communications

Modifying and reacting to the environmental pH can drive bacterial interactions

(2018) Christoph Ratzke et al.   PLOS BIOLOGY

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

(2018) Nicholas A. Bokulich et al.   Microbiome

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

(2018) Tommi Vatanen et al.   NATURE

Temporal development of the gut microbiome in early childhood from the TEDDY study

(2018) Christopher J. Stewart et al.   NATURE

Identification of genes involved in galactooligosaccharide utilization in Bifidobacterium breve strain YIT 4014T

(2017) Hidetsugu Sotoya et al.   MICROBIOLOGY-SGM

Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens

(2017) Yun-Gi Kim et al.   SCIENCE

Fucosyllactose and L-fucose utilization of infant Bifidobacterium longum and Bifidobacterium kashiwanohense

(2016) Vera Bunesova et al.   BMC MICROBIOLOGY

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Signals from the gut microbiota to distant organs in physiology and disease

(2016) Bjoern O Schroeder et al.   NATURE MEDICINE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

How colonization by microbiota in early life shapes the immune system

(2016) Thomas Gensollen et al.   SCIENCE

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development

(2016) Takahiro Matsuki et al.   Nature Communications

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

Differences in acid tolerance between Bifidobacterium breve BB8 and its acid-resistant derivative B. breve BB8dpH, revealed by RNA-sequencing and physiological analysis

(2015) Xu Yang et al.   ANAEROBE

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro

(2015) A. Dostal et al.   mBio

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity

(2015) Shaillay Dogra et al.   mBio

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape

(2014) Meredith M. Curtis et al.   Cell Host & Microbe

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

(2014) Erica D. Sonnenburg et al.   Cell Metabolism

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism

(2014) Gary Frost et al.   Nature Communications

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43

(2013) Ikuo Kimura et al.   Nature Communications

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Low iron availability in continuousin vitrocolonic fermentations induces strong dysbiosis of the child gut microbial consortium and a decrease in main metabolites

(2012) Alexandra Dostal et al.   FEMS MICROBIOLOGY ECOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

(2011) Tingting Wang et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Propionate as a health-promoting microbial metabolite in the human gut

(2011) Elham Hosseini et al.   NUTRITION REVIEWS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Succession of microbial consortia in the developing infant gut microbiome

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

Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides

(2010) David A. Sela et al.   TRENDS IN MICROBIOLOGY

Two distinct  -L-fucosidases from Bifidobacterium bifidum are essential for the utilization of fucosylated milk oligosaccharides and glycoconjugates

(2009) H. Ashida et al.   GLYCOBIOLOGY

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA