CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

QUAST: quality assessment tool for genome assemblies

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Pfam: the protein families database

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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.

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Community structure and metabolism through reconstruction of microbial genomes from the environment

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Insights into the phylogeny and coding potential of microbial dark matter

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DendroPy: a Python library for phylogenetic computing

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Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

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Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

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The minimum information about a genome sequence (MIGS) specification

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Towards a Genome-Based Taxonomy for Prokaryotes

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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

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The TIGRFAMs database of protein families

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PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

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Improving the coverage of the cyanobacterial phylum using diversity driven genome sequencing

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GAGE: A critical evaluation of genome assemblies and assembly algorithmsPreprint

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Gene and translation initiation site prediction in metagenomic sequences

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Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

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PhyloSift: phylogenetic analysis of genomes and metagenomes

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PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

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A genomic update on clostridial phylogeny: G ram‐negative spore formers and other misplaced clostridia

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IMG 4 version of the integrated microbial genomes comparative analysis system

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Community-wide analysis of microbial genome sequence signatures

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Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

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Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

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Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonizationPreprint

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Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

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Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

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Genome Project Standards in a New Era of Sequencing

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Accurate and universal delineation of prokaryotic species

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GroopM: an automated tool for the recovery of population genomes from related metagenomes

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An Expanded Genomic Representation of the Phylum Cyanobacteria

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Detecting genomic islands using bioinformatics approaches

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Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME‐1 group

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Genomes from Metagenomics

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Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

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Taxonomic metagenome sequence assignment with structured output models

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Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

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Classifying short genomic fragments from novel lineages using composition and homology

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First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

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What is Finished, and Why Does it Matter: Figure 1.Preprint

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Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading N , N -Dimethylformamide

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TreeOTU: Operational Taxonomic Unit Classification Based on Phylogenetic TreesPreprint

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dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

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GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

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MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

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Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

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

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CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

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Single-cell genome sequencing: current state of the science

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A unified catalog of 204,938 reference genomes from the human gut microbiome

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Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

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Asgard archaea illuminate the origin of eukaryotic cellular complexity

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A new genomic blueprint of the human gut microbiota

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Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

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Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

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New insights from uncultivated genomes of the global human gut microbiome

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Prevotella Diversity, Niches and Interactions with the Human Host

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MetaQUAST: evaluation of metagenome assemblies

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Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

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Current challenges and best-practice protocols for microbiome analysis

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Sequence modeling and design from molecular to genome scale with Evo

Nguyen, E., Poli, M., Durrant, M. G., Kang, B., Katrekar, D., Li, D. B., Bartie, L. J., Thomas, A. W., King, S. H., Brixi, G., et al. (2024) · Science · doi:10.1126/science.ado9336 · Cited by 580 · see citing works

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

Narunsky-Haziza, L., Sepich-Poore, G. D., Livyatan, I., Asraf, O., Martino, C., Nejman, D., Gavert, N., Stajich, J. E., Amit, G., González, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.005 · Cited by 538 · see citing works

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

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Profiling the human intestinal environment under physiological conditions

Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., et al. (2023) · Nature · doi:10.1038/s41586-023-05989-7 · Cited by 484 · see citing works

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future

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The person-to-person transmission landscape of the gut and oral microbiomes

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Microbial abundance, activity and population genomic profiling with mOTUs2

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Accurate and complete genomes from metagenomes

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The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

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Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

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Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

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The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

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High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

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The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

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Mobile genes in the human microbiome are structured from global to individual scales

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A rooted phylogeny resolves early bacterial evolution

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High-throughput microbial culturomics using automation and machine learning

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