Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Numerous cultivated and uncultivated viruses encode ribosomal proteins

(2019) Carolina M. Mizuno et al.   Nature Communications

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model

(2019) Bryan B. Hsu et al.   Cell Host & Microbe

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes

(2019) Nachiket P. Marathe et al.   Microbiome

Diarrhoeal disease and subsequent risk of death in infants and children residing in low-income and middle-income countries: analysis of the GEMS case-control study and 12-month GEMS-1A follow-on study

(2019) Myron M Levine et al.   Lancet Global Health

Mining the Core Gut Microbiome from a Sample Indian Population

(2018) Abhijit S. Kulkarni et al.   INDIAN JOURNAL OF MICROBIOLOGY

Global increase and geographic convergence in antibiotic consumption between 2000 and 2015

(2018) Eili Y. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

(2018) Jina Rajkumari et al.   3 Biotech

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

(2018) Jina Rajkumari et al.   3 Biotech

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

(2018) Norman Goodacre et al.   mSphere

The influence of ethnicity and geography on human gut microbiome composition

(2018) Christopher A. Gaulke et al.   NATURE MEDICINE

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

(2018) Yan He et al.   NATURE MEDICINE

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas

(2018) Bhabatosh Das et al.   Scientific Reports

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

Dietary Amino Acids and the Gut-Microbiome-Immune Axis: Physiological Metabolism and Therapeutic Prospects

(2018) Ning Ma et al.   COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin

(2017) Simone Rampelli et al.   ENVIRONMENTAL MICROBIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Clostridium difficile infection in low- and middle-human development index countries: a systematic review

(2017) Joseph D. Forrester et al.   TROPICAL MEDICINE & INTERNATIONAL HEALTH

The Inuit gut microbiome is dynamic over time and shaped by traditional foods

(2017) Geneviève Dubois et al.   Microbiome

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

MEGARes: an antimicrobial resistance database for high throughput sequencing

(2016) Steven M. Lakin et al.   NUCLEIC ACIDS RESEARCH

Xenobiotic Metabolism and Gut Microbiomes

(2016) Anubhav Das et al.   PLoS One

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Prevalence and molecular types of Clostridium difficile isolates from faecal specimens of patients in a tertiary care centre

(2015) Chetana Vaishnavi et al.   JOURNAL OF MEDICAL MICROBIOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Subsistence strategies in traditional societies distinguish gut microbiomes

(2015) Alexandra J. Obregon-Tito et al.   Nature Communications

Gut bacterial diversity of the tribes of India and comparison with the worldwide data

(2015) Madhusmita Dehingia et al.   Scientific Reports

The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

(2015) Inés Martínez et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study

(2013) Karen L Kotloff et al.   LANCET

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS