Microbial Genomics

Article	Citations
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification	160
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes	127
Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank	95
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores	75
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses	68
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history	60
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance	58
Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid	54
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands	53
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex	50
Recovery of small plasmid sequences via Oxford Nanopore sequencing	35
Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland	33
A comprehensive and high-quality collection of Escherichia coli genomes and their genes	33
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis	31
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors	29
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12	28
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones	28
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning	27
Genomic characterization of Salmonella Uzaramo for human invasive infection	27
Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes	25
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex	24
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery	24
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains	23
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants	22
From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment	22

Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles	21
A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage	21
Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients	21
Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147	20
Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae	20
Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens	20
Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence	20
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands	20
ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data	20
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici	19
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates	19
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm	19
Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.	19
Genomic comparisons of Escherichia coli ST131 from Australia	19
Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital	19
Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli	19
A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics	18
Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care	18
Microbial genomics amidst the Arctic crisis	18
Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species	18
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences	17
Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction	17
Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes	17
Bacterial genomic epidemiology with mixed samples	17
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation	17
Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology	17
Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants	17
Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses	16
Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence	16
Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim	16
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction	16
Genomic epidemiology and population structure of Neisseria gonorrhoeae in Norway, 2016–2017	16
The promiscuous and highly mobile resistome of Acinetobacter baumannii	16
Phylogenomics and antimicrobial resistance of Salmonella Typhi and Paratyphi A, B and C in England, 2016–2019	16
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data	16
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods	16
Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii	15
Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population	15
The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites	15
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria	14
Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study	14
Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea	14
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management	14
Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone	14
Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales	14
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data	14
Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure	14
Plasmids encode niche-specific traits in Lactobacillaceae	14
Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections	14
Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs	14

Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage	14
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak	13
Different evolutionary trends form the twilight zone of the bacterial pan-genome	13
Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital	13
Insertion sequences drive the emergence of a highly adapted human pathogen	13
An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus	13
Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex	13
Optimized use of Oxford Nanopore flowcells for hybrid assemblies	13
Introduction and adaptation of an emerging pathogen to olive trees in Italy	13
Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species	12
Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina	12
Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes	12
Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection	12
Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance	12
The past, present and future of ancient bacterial DNA	12
Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins	12
Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types	11
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	11
Genomic epidemiology of Escherichia coli isolates from a tertiary referral center in Lilongwe, Malawi	11
Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates	11
Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA	11
Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia	11
Rapid molecular evolution of Spiroplasma symbionts of Drosophila	11
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes	11
Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species	11
A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome	11
Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12	11
Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds	11
Insights into evolution and coexistence of the colibactin- and yersiniabactin secondary metabolite determinants in enterobacterial populations	11
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis	11
Flanker: a tool for comparative genomics of gene flanking regions	11
Antibiotic resistance in Pseudomonas aeruginosa and adaptation to complex dynamic environments	11
Forensic genomics of a novel Klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology	11
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin	11
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access	11
Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis	11
The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large	11
A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages	11
Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa	11
Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains	11
The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?	10
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients	10
The open pan-genome architecture and virulence landscape of Mycobacterium bovis	10
socru: typing of genome-level order and orientation around ribosomal operons in bacteria	10
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases	10
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia	10
The structure and diversity of strain-level variation in vaginal bacteria	10
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain	10
Hogwash: three methods for genome-wide association studies in bacteria	10
Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA	10
Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks	10
Emerging carbapenem-resistant Klebsiella pneumoniae sequence type 16 causing multiple outbreaks in a tertiary hospital in southern Vietnam	10
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L as	10
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations	10
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium	10
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1	10
Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective	10
Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales	9
Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates	9
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection	9
Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire	9
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex	9
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials	9
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae	9
Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage	9
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019	9
Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity	9
Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite	9
Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad	9
Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase	9
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps	9
Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals	9
Dual transcriptome analysis reveals differential gene expression modulation influenced by Leishmania arginase and host genetic background	9
Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia	9
Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing	9
Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli	9
Association between metabolic status and gut microbiome in obese populations	9
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae	8
Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium	8
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom	8

Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach	8
Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping	8
Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase	8
Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium	8
Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms	8
Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity	8
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes	8
Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy	8
Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of bla CTX-M-harbouring pESI plasmids	8
Differential nasopharyngeal microbiota composition in children according to respiratory health status	8
Evaluation of methods for detecting human reads in microbial sequencing datasets	8
Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway	8
Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities	8
Colonization with Staphylococcus aureus and Klebsiella pneumoniae causes infections in a Vietnamese intensive care unit	8
Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phen	8
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility	8
Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon	8
Population structure and transmission of Mycobacterium bovis in Ethiopia	8
Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility	8
Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing	8
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients	8
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts	8
Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance	8
Comprehensive and accurate genetic variant identification from contaminated and low-coverage Mycobacterium tuberculosis whole genome sequencing data	8
Exploring the evolution and epidemiology of European CC1-MRSA-IV: tracking a multidrug-resistant community-associated meticillin-resistant Staphylococcus aureus clone	8
Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand	8
Phenotypic and genomic characterization of a Vibrio parahaemolyticus strain causing disease in Penaeus vannamei provides insights into its niche adaptation and pathogenic mechanism	8
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing	8
Monomorphic Trypanozoon: towards reconciling phylogeny and pathologies	8
Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes	8
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes	7
Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail	7
Bilateral symmetry of linear streptomycete chromosomes	7
A panel of diverse Klebsiella pneumoniae clinical isolates for research and development	7
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections	7
Caution regarding the specificities of pan-cancer microbial structure	7
Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels	7
Generalizable characteristics of false-positive bacterial variant calls	7
Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data	7
Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition	7
prewas: data pre-processing for more informative bacterial GWAS	7
Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2	7
The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors	7
Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases	7
Complete microbial genomes for public health in Australia and the Southwest Pacific	7
The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19	7
Comparative genomic insights into culturable symbiotic cyanobacteria from the water fern Azolla	7
Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment	7
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes	7
Long read genome assemblers struggle with small plasmids	7
Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome	7
Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina	7
Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes	7
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)	7
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signalling-molecule diversity	7
In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes	7
Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria	7
Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC	7
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen	7
The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach	7
Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam	7
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications	7
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster	7
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK	7
Genomic and temporal analyses of Mycobacterium bovis in southern Brazil	7
Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity	7
Curation of the AMRFinderPlus databases: applications, functionality and impact	7
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance	7
Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)	7
Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution	7