Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity
Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution
RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes
Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants
Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain)
Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean's Deepest Point
Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems
Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge
The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning
Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida
Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
ICGRM: integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
Beneficial microbial signals from alternative feed ingredients: a way to improve sustainability of broiler production?
Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station
MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches
Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities
GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes
Identifying Group-Specific Sequences for Microbial Communities Using Long k -mer Sequence Signatures
Getting back to the nature of the microbial world: from the description and inductive reasoning to deductive study after 'meta-omics'.
Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation
The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample.
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog.
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Alzheimer's Disease: MS4A
Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.
Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.
Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.
Genetic Screens in iPSC-derived Brain Cells
Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.
This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Pharmacology of Proteinopathies
This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.
Alignment-free Sequence Analysis Tools
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.