Evaluating the Information Content of Shallow Shotgun Metagenomics

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Assessing the Human Gut Microbiota in Metabolic Diseases

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Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

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ConStrains identifies microbial strains in metagenomic datasets

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Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

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Library preparation methodology can influence genomic and functional predictions in human microbiome research

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Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

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Genome Differences That Distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis

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Estimating coverage in metagenomic data sets and why it matters

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How much metagenomic sequencing is enough to achieve a given goal?

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

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Daily sampling reveals personalized diet-microbiome associations in humans

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

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Consistent and correctable bias in metagenomic sequencing experiments

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The progress of gut microbiome research related to brain disorders

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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

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Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

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Host and gut microbial tryptophan metabolism and type 2 diabetes: an integrative analysis of host genetics, diet, gut microbiome and circulating metabolites in cohort studies

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Delivery Mode Affects Stability of Early Infant Gut Microbiota

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Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

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Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

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Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

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Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome

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Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches

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Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

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Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes

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Gut microbiota density influences host physiology and is shaped by host and microbial factors

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Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

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

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Syntrophy via Interspecies H ₂ Transfer between <i>Christensenella</i> and <i>Methanobrevibacter</i> Underlies Their Global Cooccurrence in the Human Gut

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A Guide to Diet-Microbiome Study Design

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Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

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Analysis of the gut microbiome in dogs and cats

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Developing standards for the microbiome field

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

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Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

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Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer

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The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

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Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes

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Benchmarking second and third-generation sequencing platforms for microbial metagenomics

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

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Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

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Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes

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

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What Is Metagenomics Teaching Us, and What Is Missed?

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Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

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Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

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The human milk microbiome: who, what, when, where, why, and how?

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In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls

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Associations of healthy food choices with gut microbiota profiles

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Sequencing-based analysis of microbiomes

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Differential gut microbiota and intestinal permeability between frail and healthy older adults: A systematic review

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Network analyses in microbiome based on high-throughput multi-omics data

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Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

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Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods

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Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

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Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations

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Comprehensive Evaluation of Shotgun Metagenomics, Amplicon Sequencing and Harmonization of Said Platforms for Epidemiological Studies Using the Large Multi-Center HCHS/SOL Cohort

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Generating amplicon reads for microbial community assessment with next‐generation sequencing

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Alteration of Gut Microbiome and Correlated Lipid Metabolism in Post-Stroke Depression

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A Comparison of DNA/RNA Extraction Protocols for High-Throughput Sequencing of Microbial Communities

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Shallow Shotgun Metagenomics as a cost-effective and accurate alternative to WGS for taxonomic profiling and clinical diagnosis

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