Current Opinion in Microbiology

Article	Citations
The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities	142
Synthetic microbial communities for studying and engineering the tree microbiome: challenges and opportunities	136
PhoU: a multifaceted regulator in microbial signaling and homeostasis	124
The mycobiome: interactions with host and implications in diseases	110
Citrobacter rodentium(ϕStx2dact), a murine infection model for enterohemorrhagic Escherichia coli	98
Genetic mechanisms governing sporulation initiation in Clostridioides difficile	87
Vertebrate and invertebrate animal infection models of Candida auris pathogenicity	85
Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration	84
Editorial overview: Antibiotics special issue	82
In vivo studies on Citrobacter rodentium and host cell death pathways	81
Genetic and environmental factors shape the host response to Helicobacter hepaticus: insights into IBD pathogenesis	80
Editorial overview: Fungal diversity: Now for something completely different	80
Renal implications of coronavirus disease 2019: insights into viral tropism and clinical outcomes	79
Seizing the moment: now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments	76
Innovative approaches in the discovery of terpenoid natural products	72
Editorial Board	69
Insights into Alphaproteobacterial regulators of cell envelope remodeling	68
The impact of the host microbiota on Candida albicans infection	66
Control of bacterial second messenger signaling and motility by heme-based direct oxygen-sensing proteins	65
Ca2+-calmodulin signalling at the host-pathogen interface	64
Manipulation of host cell plasma membranes by intracellular bacterial pathogens	62
Increasing the PACE of characterising novel transporters by functional genomics	62
Co-opting bacterial viruses for DNA exchange: structure and regulation of gene transfer agents	61
Crosstalk between (p)ppGpp and other nucleotide second messengers	61
Editorial overview: Unraveling microbiome complexity	61

Function of autophagy genes in innate immune defense against mucosal pathogens	57
Fungus–insect interactions beyond bilateral regimes: the importance and strategy to outcompete host ectomicrobiomes by fungal parasites	57
Coevolution of a generalist pathogen with many hosts: the case of the amphibian chytrid Batrachochytrium dendrobatidis	56
Advances in regulation of homeostasis through chromatin modifications by airway commensals	55
Fungal effectors: past, present, and future	55
Editorial overview: Human fungal pathogens: An increasing threat	54
Connecting microbial community assembly and function	54
Innovative and potential treatments for fungal central nervous system infections	53
Assembly of the exosporium layer in Clostridioides difficile spores	53
Bottlenecks and opportunities in antibiotic discovery against Mycobacterium tuberculosis	53
Neuroinvasion and neurotropism of severe acute respiratory syndrome coronavirus 2 infection	51
Defining the expanding mechanisms of phage-mediated activation of bacterial immunity	51
Soterobionts: disease-preventing microorganisms and proposed strategies to facilitate their discovery	51
Antifungal drug-resistance mechanisms in Candida biofilms	50
The maternal gut microbiome during pregnancy and its role in maternal and infant health	48
Host control by SPβ phage regulatory switch as potential manipulation strategy	48
Pain killers: the interplay between nonsteroidal anti-inflammatory drugs and Clostridioides difficile infection	45
Editorial overview: Bacterial microcompartments to the fore as metabolism is put in its place	45
Editorial Board	45
Activation of complement-like antiparasitic responses in Anopheles mosquitoes	44
Toward merging bottom–up and top–down model-based designing of synthetic microbial communities	43
Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species	43
How do interactions between mobile genetic elements affect horizontal gene transfer?	42
The power of the small: the underestimated role of small proteins in bacterial and archaeal physiology	40
Ready, STAT3, Go! Bacteria in the race for M2 macrophage polarisation	39
Cell cycle regulation in Escherichia coli: from governing principles, checkpoints, and control variables to molecular mechanisms	39
Environmental adaptation and diversification of bacterial two-component systems	38
Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease	36
Differences and similarities between innate immune evasion strategies of human coronaviruses	36
Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions	36
Dissecting skin microbiota and microenvironment for the development of therapeutic strategies	36
The human vaginal microbiota: from clinical medicine to models to mechanisms	36
A tale of two nitrous oxide reductases: a cautionary perspective	35
Editorial overview: There and back again: a phage’s tale	35
Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut	35
The intricate organizational strategy of nucleus-forming phages	34
Phage transmission strategies: are phages farming their host?	34
Editorial overview: Turtles all the way down: Bacterial cell regulation across scales	33
Cell cycle-regulated ApiAP2s and parasite development: the Toxoplasma paradigm	33
Editorial Board	33
Reservoirs of antimicrobial resistance in the context of One Health	33
Second messenger signaling in Clostridioides difficile	32
Antibiotic tolerance: targeting bacterial survival	31
Regulation of para-cresol production in Clostridioides difficile	31
Is Cryptococcus neoformans a pleomorphic fungus?	31
Investigating bacterial evolution in nature with metagenomics	31
SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function	30
Beyond resistance: antifungal heteroresistance and antifungal tolerance in fungal pathogens	30
Editorial overview: Recent advances in fundamental and translational research on parasitic protists	29
New targets for antimalarial drug discovery	29

Emergence and adaptation of the cellular machinery directing antigenic variation in the African trypanosome	29
Virulence-associated factors as targets for phage infection	29
The importance of persistence and dormancy in Trypanosoma cruzi infection and Chagas disease	29
Biological and bioinformatic tools for the discovery of unknown phage–host combinations	29
Chemical communication in plant–microbe beneficial interactions: a toolbox for precise management of beneficial microbes	28
Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease	28
Editorial overview: emerging avenues in antimicrobial research	28
PII-like signaling proteins: a new paradigm in orchestrating cellular homeostasis	28
Predicting the evolution of antibiotic resistance	27
Activation of the extracytoplasmic function σ factor σV by lysozyme in Clostridioides difficile	26
Surface-displayed glycopolymers of Clostridioides difficile	26
Gram-positive pathogens, inflammation, and the host lipid environment	26
Strains to go: interactions of the skin microbiome beyond its species	25
Editorial overview: Return of the phages — a new golden era of molecular discovery and synthetic biology	25
Clostridioides difficile peptidoglycan modifications	25
Temporospatial control of topoisomerases by essential cellular processes	25
Can a microbial community become an evolutionary individual?	24
Host genetics regulate the plant microbiome	24
Prokaryote pangenomes are dynamic entities	24
The promise of CRISPR-associated transposons for bacterial functional genomics	24
Deciphering mechanisms and implications of bacterial translocation in human health and disease	24
Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells	24
Host-directed therapies for malaria: possible applications and lessons from other indications	23
Editorial Board	23
Editorial Board	23
Innate immune response to Candida auris	22
Cooperative defenses during enteropathogenic infection	22
Microbiome rescue: directing resilience of environmental microbial communities	22
Plasmids of Clostridioides difficile	22
The ribosome as a small-molecule sensor	22
Role of pollution on the selection of antibiotic resistance and bacterial pathogens in the environment	21
Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology	21
Interplay of emerging and established technologies drives innovation in natural product antibiotic discovery	21
Phage defense origin of animal immunity	21
Encapsulins: catalysis inside a shell	21
The promise of copper ionophores as antimicrobials	21
Brownian ratchet mechanisms for carboxysome positioning in bacteria	21
Microbiomes for sustainable biomanufacturing	21
Molecular mechanisms of cellular quiescence in apicomplexan parasites	20
Flagellotropic phages: common yet diverse host interaction strategies	20
Editorial overview: current state and future of the microbiome field: why context matters	20
Editorial overview: Niche-specific and species-specific host-fungal interactions — how do they impact human health?	20
Recent advances in applying cell-free systems for high-value and complex natural product biosynthesis	19
Immunometabolism shapes chronic Staphylococcus aureus infection: insights from biofilm infection models	19
Aeromonas: the multifaceted middleman in the One Health world	19
The multifaceted roles of Myb domain–containing proteins in apicomplexan parasites	19
Listeriosis, a model infection to study host-pathogen interactions in vivo	19
Cell wall synthesizing complexes in Mycobacteriales	18
Dissecting S-itaconation at host–pathogen interactions with chemical proteomics tools	18
Antibiotics from rare actinomycetes, beyond the genus Streptomyces	18
Colonization resistance: metabolic warfare as a strategy against pathogenic Enterobacteriaceae	18
Within-host evolution of bacterial pathogens during persistent infection of humans	17
Targeting Helicobacter pylori for antibacterial drug discovery with novel therapeutics	17
Posttranslational modifications in bacteria during phage infection	17
Putting microbial interactions back into community contexts	17
Accessing nutrients as the primary benefit arising from chemotaxis	17
Yeast synthetic biology advances biofuel production	17
Drugging the microbiome: targeting small microbiome molecules	17
Climate change and plant pathogens	16
Editorial Board	16
Present and future outlooks on environmental DNA-based methods for antibiotic discovery	16
Hybrids unleashed: exploring the emergence and genomic insights of pathogenic yeast hybrids	16
Clostridioides difficile spore germination: initiation to DPA release	16
How pathogens drive adipose tissue loss in the host	16
Addressing antibiotic resistance: computational answers to a biological problem?	16
Yersinia interactions with regulated cell death pathways	16
Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin	16
Capers with caspases: Toxoplasma gondii tales of inflammation and survival	15
Argonaute proteins confer immunity in all domains of life	15
It's complicated: relationships between integrative and conjugative elements and their bacterial hosts	15
Cardiac damage and tropism of severe acute respiratory syndrome coronavirus 2	15
Functional ecology of bacteriophages in the environment	15
A brief guide to machine learning for antibiotic discovery	15
Archaea oxidizing alkanes through alkyl-coenzyme M reductases	15
Making sense of drug-efflux transporters in the physiological environment	15
Editorial Board	14
Use of pharmacokinetic/pharmacodynamic approaches for dose optimization: a case study of plazomicin	14
Histone code: a common language and multiple dialects to meet the different developmental requirements of apicomplexan parasites	14
From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory	14
Dividing lines: compartmentalisation and division in Streptomyces	14

Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints	14
The yin and yang of the universal transcription factor NusG	14
Interactions of Vibrio phages and their hosts in aquatic environments	14
Inflammasome activation by Salmonella	13
Editorial Board	13
What’s metal got to do with it? Transition metals in Clostridioides difficile infection	13
From dusty shelves toward the spotlight: growing evidence for Ap4A as an alarmone in maintaining RNA stability and proteostasis	13
Emergent CRISPR–Cas-based technologies for engineering non-model bacteria	13
The Lyme disease spirochete, Borrelia burgdorferi, as a model vector-borne pathogen: insights on regulation of gene and protein expression	13
Antibacterial particles and predatory bacteria as alternatives to antibacterial chemicals in the era of antibiotic resistance	13
Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products	13
Recent insights into type-3 secretion system injectisome structure and mechanism of human enteric pathogens	13
Synthesizing microbial biodiversity	13
Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity	13
Contributions of diverse models of the female reproductive tract to the study of Chlamydia trachomatis-host interactions	13
Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes	12
Engineering natural microbial communities: harnessing synthetic communities for bioremediation	12
Human and mouse NAIP/NLRC4 inflammasome responses to bacterial infection	12
Innate immune responses and monocyte-derived phagocyte recruitment in protective immunity to pathogenic bacteria: insights from Legionella pneumophila	12
Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses	12
CTP switches in ParABS-mediated bacterial chromosome segregation and beyond	12
Editorial Board	12
Pathogen adaptation to lung metabolites	12
Mechanisms and impact of antimicrobial resistance in Clostridioides difficile	12
Dirammox (direct ammonia oxidation) to nitrogen (N2): discovery, current status, and perspectives	12
Artificial selection of microbial communities: what have we learnt and how can we improve?	12
Immune evasion runs in the family: two surface protein families of Plasmodium falciparum–infected erythrocytes	12
Antibiotic persistence and tolerance: not just one and the same	12
Human milk oligosaccharides and the infant gut microbiome from an eco-evolutionary perspective	11
Multi-layered genome defences in bacteria	11
Evolution and synthetic biology	11
Toxin–antitoxin systems as mediators of phage defence and the implications for abortive infection	11
Editorial overview: AMR in the environment — too complex for surveillance?	11
Time to switch gears: how long noncoding RNAs function as epigenetic regulators in Apicomplexan parasites	11
Arginine sensing in intracellular parasitism of Leishmania	11
Sensing and responding to host-derived stress signals: lessons from fungal meningitis pathogen	11
Bioremediation of the herbicide glyphosate in polluted soils by plant-associated microbes	10
Co-ordinated assembly of the multilayered cell envelope of Gram-negative bacteria	10
The multifaceted lifestyle of enterococci: genetic diversity, ecology and risks for public health	10
Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion	10
Are microbes colimited by multiple resources?	10
Human microbiome variance is underestimated	10
Toll/interleukin-1 receptor domains in bacterial and plant immunity	10
Clostridioides difficile – phage relationship the RNA way	10
Glycan processing in gut microbiomes	10
Forgotten fungi: the importance of the skin mycobiome	10
Selective drivers of simple multicellularity	10
The mystery of persistent, asymptomatic Plasmodium falciparum infections	10
Nutritional control of bacterial DNA replication	9
Skin models for studying vector-borne kinetoplastid infections	9
Human intestinal organoids as models to study enteric bacteria and viruses	9
Editorial overview: Two to tango: The intricate communications between host and bacteria	9
Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?	9
Antimicrobial resistance acquisition via natural transformation: context is everything	9
The role of nucleoid-associated proteins in mediating responses to environmental changes	9
Nothing makes sense in drug resistance except in the light of evolution	9
Long-chain fatty acids as nutrients for Gram-negative bacteria: stress, proliferation, and virulence	9
Editorial Board	9
The emerging complexity of Chlamydia trachomatis interactions with host cells as revealed by molecular genetic approaches	9
Candida albicans natural diversity: a resource to dissect fungal commensalism and pathogenesis	9
Antibiotic resistance in the commensal human gut microbiota	9
Compartmentalization during bacterial spore formation	9
Lessons from arbuscular mycorrhizal fungal genomes	9
A cell–cell atlas approach for understanding symbiotic interactions between microbes	9
From genome structure to function: insights into structural variation in microbiology	9
The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment	9