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Antarctic soil microbiomes encode structurally conserved and phylogenetically diverse beta‐lactamases

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/advs.202403563openalex-snapshot

Expanding the β‐Lactamase Family in the Human Microbiome

inferredcites →https://doi.org/10.1002/j.1460-2075.1994.tb06792.xopenalex-snapshot

Bacterial cell wall recycling provides cytosolic muropeptides as effectors for beta‐lactamase induction.

inferredcites →https://doi.org/10.1002/joc.6378openalex-snapshot

Antarctic temperature variability and change from station data

inferredcites →https://doi.org/10.1002/mbo3.1219openalex-snapshot

Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

inferredcites →https://doi.org/10.1007/978-981-16-9097-6openalex-snapshot

Beta-Lactam Resistance in Gram-Negative Bacteria

inferredcites →https://doi.org/10.1007/978-981-16-9097-6_3openalex-snapshot

Beta-Lactamases and Their Classification: An Overview

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Molecular analysis of the gene cluster involved in cephalosporin biosynthesis from Lysobacter lactamgenus YK90

inferredcites →https://doi.org/10.1007/s10096-025-05126-4openalex-snapshot

Emerging antibiotic resistance by various novel proteins/enzymes

inferredcites →https://doi.org/10.1007/s11033-021-06218-yopenalex-snapshot

Antimicrobial activity of Actinobacteria isolated from dry land soil in Yazd, Iran

inferredcites →https://doi.org/10.1007/s11356-015-5586-0openalex-snapshot

Urban riverine environment is a source of multidrug-resistant and ESBL-producing clinically important Acinetobacter spp.

inferredcites →https://doi.org/10.1007/s11783-019-1128-1openalex-snapshot

Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats

inferredcites →https://doi.org/10.1016/j.eng.2022.10.011openalex-snapshot

ARGs-OAP v3.0: Antibiotic-Resistance Gene Database Curation and Analysis Pipeline Optimization

inferredcites →https://doi.org/10.1016/j.envint.2020.105649openalex-snapshot

Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes

inferredcites →https://doi.org/10.1016/j.jhazmat.2020.124855openalex-snapshot

Foam shares antibiotic resistomes and bacterial pathogens with activated sludge in wastewater treatment plants

inferredcites →https://doi.org/10.1016/j.scitotenv.2021.152003openalex-snapshot

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes

inferredcites →https://doi.org/10.1016/j.scitotenv.2023.161505openalex-snapshot

Functional metagenomics reveals wildlife as natural reservoirs of novel β-lactamases

inferredcites →https://doi.org/10.1016/j.scitotenv.2024.172873openalex-snapshot

RATA: A novel class A carbapenemase with broad geographic distribution and potential for global spread

inferredcites →https://doi.org/10.1016/j.scitotenv.2024.177594openalex-snapshot

Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert

inferredcites →https://doi.org/10.1016/j.watres.2022.119018openalex-snapshot

Metagenomic insights into environmental risk of field microplastics in an urban river

inferredcites →https://doi.org/10.1016/s0140-6736(24)01867-1openalex-snapshot

Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050

inferredcites →https://doi.org/10.1021/acs.biochem.5c00044openalex-snapshot

Molecular Evolution and Origins of Antibiotic Resistance Genes

inferredcites →https://doi.org/10.1021/acs.est.3c00159openalex-snapshot

Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

inferredcites →https://doi.org/10.1038/ismej.2008.86openalex-snapshot

Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil

inferredcites →https://doi.org/10.1038/nature10388openalex-snapshot

Antibiotic resistance is ancient

inferredcites →https://doi.org/10.1038/nbt.3893openalex-snapshot

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

inferredcites →https://doi.org/10.1038/nbt.3988openalex-snapshot

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot

ModelFinder: fast model selection for accurate phylogenetic estimates

inferredcites →https://doi.org/10.1038/nrmicro2281openalex-snapshot

On the rocks: the microbiology of Antarctic Dry Valley soils

inferredcites →https://doi.org/10.1038/s41467-018-04964-5openalex-snapshot

Clustering huge protein sequence sets in linear time

inferredcites →https://doi.org/10.1038/s41467-019-11541-xopenalex-snapshot

Mesophilic microorganisms build terrestrial mats analogous to Precambrian microbial jungles

inferredcites →https://doi.org/10.1038/s41467-023-37896-wopenalex-snapshot

Sequence-structure-function relationships in the microbial protein universe

inferredcites →https://doi.org/10.1038/s41467-024-47155-1openalex-snapshot

Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

inferredcites →https://doi.org/10.1038/s41564-023-01351-9openalex-snapshot

AMR, One Health and the environment

inferredcites →https://doi.org/10.1038/s41579-021-00649-xopenalex-snapshot

Antibiotic resistance in the environment

inferredcites →https://doi.org/10.1038/s41587-021-01156-3openalex-snapshot

SignalP 6.0 predicts all five types of signal peptides using protein language models

inferredcites →https://doi.org/10.1038/s41587-023-01773-0openalex-snapshot

Fast and accurate protein structure search with Foldseek

inferredcites →https://doi.org/10.1038/s41587-025-02738-1openalex-snapshot

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper

inferredcites →https://doi.org/10.1038/s41592-019-0437-4openalex-snapshot

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

inferredcites →https://doi.org/10.1038/s41592-021-01101-xopenalex-snapshot

Sensitive protein alignments at tree-of-life scale using DIAMOND

inferredcites →https://doi.org/10.1038/s41592-022-01585-1openalex-snapshot

US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes

inferredcites →https://doi.org/10.1038/s41592-023-01940-wopenalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41598-020-68612-zopenalex-snapshot

Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms

inferredcites →https://doi.org/10.1038/s42003-020-01545-5openalex-snapshot

A framework for identifying the recent origins of mobile antibiotic resistance genes

inferredcites →https://doi.org/10.1039/d1md00200gopenalex-snapshot

β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates

inferredcites →https://doi.org/10.1073/pnas.2018269118openalex-snapshot

Microbial dynamics of elevated carbon flux in the open ocean’s abyss

inferredcites →https://doi.org/10.1080/14756366.2017.1344235openalex-snapshot

Beta-lactamase database (BLDB) – structure and function

inferredcites →https://doi.org/10.1080/14787210.2023.2194633openalex-snapshot

Classification for β-lactamases: historical perspectives

inferredcites →https://doi.org/10.1093/bioinformatics/btaa250openalex-snapshot

Phigaro: high-throughput prophage sequence annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btac672openalex-snapshot

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

inferredcites →https://doi.org/10.1093/bioinformatics/btaf147openalex-snapshot

CoverM: read alignment statistics for metagenomics

inferredcites →https://doi.org/10.1093/bioinformatics/btx433openalex-snapshot

ISEScan: automated identification of insertion sequence elements in prokaryotic genomes

inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot

fastp: an ultra-fast all-in-one FASTQ preprocessor

inferredcites →https://doi.org/10.1093/femsml/uqac003openalex-snapshot

Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols

inferredcites →https://doi.org/10.1093/gigascience/giab008openalex-snapshot

Twelve years of SAMtools and BCFtools

inferredcites →https://doi.org/10.1093/jac/dkaa392openalex-snapshot

An updated phylogeny of the metallo-β-lactamases

inferredcites →https://doi.org/10.1093/jac/dkz066openalex-snapshot

Identification of a novel metallo-β-lactamase, CAM-1, in clinical Pseudomonas aeruginosa isolates from Canada

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot

UFBoot2: Improving the Ultrafast Bootstrap Approximation

inferredcites →https://doi.org/10.1093/nar/gkab301openalex-snapshot

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

inferredcites →https://doi.org/10.1093/nar/gkad382openalex-snapshot

PHASTEST: faster than PHASTER, better than PHAST

inferredcites →https://doi.org/10.1093/nar/gky174openalex-snapshot

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

inferredcites →https://doi.org/10.1093/protein/gzab013openalex-snapshot

Evolution of β-lactamases and enzyme promiscuity

inferredcites →https://doi.org/10.1099/mgen.0.000685openalex-snapshot

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

inferredcites →https://doi.org/10.1099/mgen.0.001344openalex-snapshot

An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota

inferredcites →https://doi.org/10.1101/2024.03.01.583042openalex-snapshot

The global β-lactam resistome revealed by comprehensive sequence analysis

inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot

metaSPAdes: a new versatile metagenomic assembler

inferredcites →https://doi.org/10.1109/ipdps.2019.00041openalex-snapshot

Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems

inferredcites →https://doi.org/10.1111/j.1462-2920.2008.01644.xopenalex-snapshot

Responses of Antarctic soil microbial communities and associated functions to temperature and freeze–thaw cycle frequency

inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02422.xopenalex-snapshot

Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples

inferredcites →https://doi.org/10.1111/j.1574-6976.2007.00095.xopenalex-snapshot

Penicillin-binding proteins and β-lactam resistance

inferredcites →https://doi.org/10.1126/science.ade2574openalex-snapshot

Evolutionary-scale prediction of atomic-level protein structure with a language model

inferredcites →https://doi.org/10.1128/aac.00936-21openalex-snapshot

Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active-Site Glutamic Acid

inferredcites →https://doi.org/10.1128/aac.01009-09openalex-snapshot

Updated Functional Classification of β-Lactamases

inferredcites →https://doi.org/10.1128/aac.01076-18openalex-snapshot

Past and Present Perspectives on β-Lactamases

inferredcites →https://doi.org/10.1128/aac.42.1.1openalex-snapshot

Kinship and Diversification of Bacterial Penicillin-Binding Proteins and β-Lactamases

inferredcites →https://doi.org/10.1128/aac.44.6.1538-1543.2000openalex-snapshot

The Legionella ( Fluoribacter ) gormanii Metallo-β-Lactamase: a New Member of the Highly Divergent Lineage of Molecular-Subclass B3 β-Lactamases

inferredcites →https://doi.org/10.1128/aem.01746-17openalex-snapshot

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

inferredcites →https://doi.org/10.1128/aem.01968-19openalex-snapshot

Communication within East Antarctic Soil Bacteria

inferredcites →https://doi.org/10.1128/cmr.00115-20openalex-snapshot

New β-Lactam–β-Lactamase Inhibitor Combinations

inferredcites →https://doi.org/10.1128/jcm.42.7.2902-2906.2004openalex-snapshot

Molecular Characterization of Extended-Spectrum Beta-Lactamases Produced by Clinical Isolates of Klebsiella pneumoniae and Escherichia coli from a Korean Nationwide Survey

inferredcites →https://doi.org/10.1128/msystems.00039-18openalex-snapshot

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

inferredcites →https://doi.org/10.1128/msystems.01062-25openalex-snapshot

Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns

inferredcites →https://doi.org/10.1128/spectrum.00261-22openalex-snapshot

Detection of a Novel Metallo-β-Lactamase, CAM-2, in a Metagenome-Assembled Genome from China

inferredcites →https://doi.org/10.1128/spectrum.00315-22openalex-snapshot

An Extended Reservoir of Class-D Beta-Lactamases in Non-Clinical Bacterial Strains

inferredcites →https://doi.org/10.1146/annurev-biochem-030409-143718openalex-snapshot

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot

Prodigal: prokaryotic gene recognition and translation initiation site identification

inferredcites →https://doi.org/10.1186/s12859-021-04270-wopenalex-snapshot

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets

inferredcites →https://doi.org/10.1186/s12864-024-10410-2openalex-snapshot

Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

inferredcites →https://doi.org/10.1186/s12941-015-0113-1openalex-snapshot

Purification and characterization of a new β-lactamase OXA-205 from Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.1186/s13059-019-1817-xopenalex-snapshot

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

inferredcites →https://doi.org/10.1186/s13059-024-03166-1openalex-snapshot

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

inferredcites →https://doi.org/10.1186/s40168-017-0353-8openalex-snapshot

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

inferredcites →https://doi.org/10.1186/s40168-018-0424-5openalex-snapshot

A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils

inferredcites →https://doi.org/10.1186/s40168-023-01479-0openalex-snapshot

Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes

inferredcites →https://doi.org/10.1186/s40168-023-01719-3openalex-snapshot

Biogeographic survey of soil bacterial communities across Antarctica

inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot

Accelerated Profile HMM Searches

inferredcites →https://doi.org/10.1371/journal.pone.0034953openalex-snapshot

Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

inferredcites →https://doi.org/10.1371/journal.pone.0169339openalex-snapshot

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

inferredcites →https://doi.org/10.1371/journal.pone.0180121openalex-snapshot

Prevalence of ESBL-producing Pseudomonas aeruginosa isolates in Warsaw, Poland, detected by various phenotypic and genotypic methods

inferredcites →https://doi.org/10.1371/journal.pone.0182043openalex-snapshot

Crystal structure and kinetic analysis of the class B3 di-zinc metallo-β-lactamase LRA-12 from an Alaskan soil metagenome

inferredcites →https://doi.org/10.21105/joss.03167openalex-snapshot

Visualizations with statistical details: The 'ggstatsplot' approach

inferredcites →https://doi.org/10.3389/fchem.2023.1196073openalex-snapshot

Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance

inferredcites →https://doi.org/10.3389/fmicb.2013.00128openalex-snapshot

Beta-lactamase induction and cell wall metabolism in Gram-negative bacteria

inferredcites →https://doi.org/10.3389/fmicb.2016.01985openalex-snapshot

Expanding the Repertoire of Carbapenem-Hydrolyzing Metallo-ß-Lactamases by Functional Metagenomic Analysis of Soil Microbiota

inferredcites →https://doi.org/10.3389/fmicb.2019.00146openalex-snapshot

Comparative Metagenomics and Network Analyses Provide Novel Insights Into the Scope and Distribution of β-Lactamase Homologs in the Environment

inferredcites →https://doi.org/10.3389/fmicb.2024.1445155openalex-snapshot

Revealing antibiotic resistance’s ancient roots: insights from pristine ecosystems

inferredcites →https://doi.org/10.3390/antibiotics9030123openalex-snapshot

A Novel, Integron-Regulated, Class C β-Lactamase

inferredcites →https://doi.org/10.3390/md21020086openalex-snapshot

β-Lactams from the Ocean

inferredcites →https://doi.org/10.3390/microorganisms10040700openalex-snapshot

IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

inferredcites →https://doi.org/10.3390/microorganisms10071432openalex-snapshot

Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements

inferredcites →https://doi.org/10.48550/arxiv.1802.03426openalex-snapshot

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

inferredcites →https://doi.org/10.7717/peerj.16695openalex-snapshot

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

inferredcites →https://doi.org/10.7717/peerj.7359openalex-snapshot

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

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