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A genomic investigation of ecological differentiation between free‐living and Drosophila ‐associated bacteria

https://doi.org/10.1111/mec.14232
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Outgoing claims: the papers this work cites, builds on, or argues with.

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ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution
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New Insights into the Ecological Interaction Between Grape Berry Microorganisms and Drosophila Flies During the Development of Sour Rot
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Microbes Promote Amino Acid Harvest to Rescue Undernutrition in Drosophila
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Lessons from Studying Insect Symbioses
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Kin recognition inDrosophila: the importance of ecology and gut microbiota
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The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis
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A single regulatory gene is sufficient to alter bacterial host range
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Immunity in Drosophila melanogaster — from microbial recognition to whole-organism physiology
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Extreme genome reduction in symbiotic bacteria
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Symbiotic digestion of lignocellulose in termite guts
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Commensal bacteria play a role in mating preference of Drosophila melanogaster
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Animals in a bacterial world, a new imperative for the life sciences
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Uric acid provides an antioxidant defense in humans against oxidant- and radical-caused aging and cancer: a hypothesis.
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Uric acid, a natural scavenger of peroxynitrite, in experimental allergic encephalomyelitis and multiple sclerosis
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Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
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Uric Acid: The Oxidant-Antioxidant Paradox
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ProtTest 3: fast selection of best-fit models of protein evolution
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Acetic Acid Bacteria Genomes Reveal Functional Traits for Adaptation to Life in Insect Guts
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
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Microbial species delineation using whole genome sequences
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Invasive Drosophila suzukii facilitates Drosophila melanogaster infestation and sour rot outbreaks in the vineyards
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Chimpanzees recognize their own delayed self-image
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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Microbiology of sugar‐rich environments: diversity, ecology and system constraints
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Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats
inferredcites →https://doi.org/10.1111/1758-2229.12505openalex-snapshot
Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria
inferredcites →https://doi.org/10.1111/ele.12329openalex-snapshot
Gut microbes of mammalian herbivores facilitate intake of plant toxins
inferredcites →https://doi.org/10.1111/j.1462-2920.2011.02511.xopenalex-snapshot
Low‐diversity bacterial community in the gut of the fruitfly Drosophila melanogaster
inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01547.xopenalex-snapshot
EVOLUTIONARY PERSPECTIVES IN A MUTUALISM OF SEPIOLID SQUID AND BIOLUMINESCENT BACTERIA: COMBINED USAGE OF MICROBIAL EXPERIMENTAL EVOLUTION AND TEMPORAL POPULATION GENETICS
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Genome-wide phylogenetic analysis of Gluconobacter, Acetobacter, and Gluconacetobacter
inferredcites →https://doi.org/10.1111/mec.12421openalex-snapshot
The impact of microbial symbionts on host plant utilization by herbivorous insects
inferredcites →https://doi.org/10.1126/science.1188235openalex-snapshot
Adaptation via Symbiosis: Recent Spread of a Drosophila Defensive Symbiont
inferredcites →https://doi.org/10.1126/science.1212782openalex-snapshot
Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling
inferredcites →https://doi.org/10.1126/science.1216641openalex-snapshot
A Single Promoter Inversion Switches Photorhabdus Between Pathogenic and Mutualistic States
inferredcites →https://doi.org/10.1128/aem.01336-10openalex-snapshot
Acetic Acid Bacteria, Newly Emerging Symbionts of Insects
inferredcites →https://doi.org/10.1128/aem.01442-15openalex-snapshot
The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster
inferredcites →https://doi.org/10.1128/aem.02120-06openalex-snapshot
Geographical Distribution and Diversity of Bacteria Associated with Natural Populations of Drosophila melanogaster
inferredcites →https://doi.org/10.1128/aem.02742-13openalex-snapshot
Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster
inferredcites →https://doi.org/10.1128/iai.70.9.4851-4858.2002openalex-snapshot
In Vitro Culture of Borrelia garinii Results in Loss of Flagella and Decreased Invasiveness
inferredcites →https://doi.org/10.1128/mbio.00860-13openalex-snapshot
Frequent Replenishment Sustains the Beneficial Microbiome of Drosophila melanogaster
inferredcites →https://doi.org/10.1128/mbio.01631-14openalex-snapshot
Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster
inferredcites →https://doi.org/10.1128/mmbr.00011-16openalex-snapshot
Evolutionary Ecology of Prokaryotic Immune Mechanisms
inferredcites →https://doi.org/10.1152/physrev.00035.2002openalex-snapshot
Integrative Physiology and Functional Genomics of Epithelial Function in a Genetic Model Organism
inferredcites →https://doi.org/10.1186/1471-2164-15-654openalex-snapshot
Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
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The RAST Server: Rapid Annotations using Subsystems Technology
inferredcites →https://doi.org/10.1242/bio.017673openalex-snapshot
Comparative evaluation of the genomes of three common Drosophila -associated bacteria
inferredcites →https://doi.org/10.1371/journal.pgen.1002272openalex-snapshot
Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System
inferredcites →https://doi.org/10.1371/journal.pgen.1002787openalex-snapshot
Selection-Driven Gene Loss in Bacteria
inferredcites →https://doi.org/10.1371/journal.pone.0070749openalex-snapshot
Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment
inferredcites →https://doi.org/10.1371/journal.pone.0126210openalex-snapshot
A Comparison of Methods to Measure Fitness in Escherichia coli
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Drosophila on Oranges: Colonization, Competition, and Coexistence
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The symbiont side of symbiosis: do microbes really benefit?
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In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors
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Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions
inferredcites →https://doi.org/10.4161/gmic.19896openalex-snapshot
Gut-associated microbes of Drosophila melanogaster
inferredcites →https://doi.org/10.5281/zenodo.10755360openalex-snapshot
Genetic variations of Drosophila melanogaster.
inferredcites →https://doi.org/10.7554/elife.18855openalex-snapshot
Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Microbiome composition modulates the lethal outcome of Drosophila A virus infection
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Wolbachia improves the performance of an invasive fly after a diet shift
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Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity
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The Metabolome of Associations between Xylem-Feeding Insects and their Bacterial Symbionts
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Omics and the metabolic function of insect–microbial symbioses
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Metabolic Cooperation among Commensal Bacteria Supports Drosophila Juvenile Growth under Nutritional Stress
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Microbiota acquisition and transmission in Drosophila flies
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Leveraging microbial ecology for mosquito-borne disease control
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Beyond specialization: re-examining routes of host influence on symbiont evolution
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Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster
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Host determinants of among-species variation in microbiome composition in drosophilid flies
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An altered microbiome in a Parkinson’s disease model Drosophila melanogaster has a negative effect on development
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The Drosophila model for microbiome research
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Larval density affects phenotype and surrounding bacterial community without altering gut microbiota in Drosophila melanogaster
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Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome
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Functional traits of the gut microbiome correlated with host lipid content in a natural population of Drosophila melanogaster
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Microbial solutions to dietary stress: experimental evolution reveals host–microbiome interplay in Drosophila melanogaster
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Host evolutionary history and ecological context modulate the adaptive potential of the microbiome
inferred← citeshttps://doi.org/10.1101/2021.09.07.458894openalex-snapshot
Symbiotic bacterial community of Drosophila melanogaster changes with nutritional modifications of the diet but can alleviate negative effects on larval phenotypes
inferred← citeshttps://doi.org/10.1101/2022.11.09.515865openalex-snapshot
Flagellar genes are associated with the colonization persistence phenotype of the Drosophila melanogaster microbiota
inferred← citeshttps://doi.org/10.1101/2024.05.02.591907openalex-snapshot
Humidity determines penetrance of a latitudinal gradient in genetic selection on the microbiota by Drosophila melanogaster
inferred← citeshttps://doi.org/10.1101/471540openalex-snapshot
The microbiota influences the Drosophila melanogaster life history strategy
inferred← citeshttps://doi.org/10.1101/546838openalex-snapshot
Environmental specificity and evolution in Drosophila -bacteria symbiosis
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Nutrient factories: metabolic function of beneficial microorganisms associated with insects
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The microbiota influences the Drosophila melanogaster life history strategy
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Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection
inferred← citeshttps://doi.org/10.1128/aem.00883-25openalex-snapshot
Environment and diet shape the geography-specific Drosophila melanogaster microbiota composition
inferred← citeshttps://doi.org/10.1128/aem.01882-18openalex-snapshot
Metabolic Basis for Mutualism between Gut Bacteria and Its Impact on the Drosophila melanogaster Host
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A Functional Analysis of the Purine Salvage Pathway in Acetobacter fabarum
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Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback
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How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts
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Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota
inferred← citeshttps://doi.org/10.1186/s12915-021-01124-yopenalex-snapshot
Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.1186/s42523-021-00133-0openalex-snapshot
Influence of bacteria on the maintenance of a yeast during Drosophila melanogaster metamorphosis
inferred← citeshttps://doi.org/10.1186/s42523-023-00248-6openalex-snapshot
A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont
inferred← citeshttps://doi.org/10.1242/dmm.049965openalex-snapshot
Antimicrobial peptides do not directly contribute to aging in Drosophila , but improve lifespan by preventing dysbiosis
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How gut microbiome interactions affect nutritional traits of Drosophila melanogaster
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Which experimental systems should we use for human microbiome science?
inferred← citeshttps://doi.org/10.1371/journal.pbio.2005710openalex-snapshot
Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000681openalex-snapshot
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002897openalex-snapshot
MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies
inferred← citeshttps://doi.org/10.1371/journal.ppat.1008398openalex-snapshot
Drosophila as a model for the gut microbiome
inferred← citeshttps://doi.org/10.1534/g3.117.300530openalex-snapshot
A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster
inferred← citeshttps://doi.org/10.1534/genetics.118.300224openalex-snapshot
Anatomy and Physiology of the Digestive Tract of Drosophila melanogaster
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1433155openalex-snapshot
The impact of altered dietary adenine concentrations on the gut microbiota in Drosophila
inferred← citeshttps://doi.org/10.3390/cells9112401openalex-snapshot
The Microbiota and Gut-Related Disorders: Insights from Animal Models
inferred← citeshttps://doi.org/10.3390/insects13010084openalex-snapshot
Nitrogen Acquisition Strategies Mediated by Insect Symbionts: A Review of Their Mechanisms, Methodologies, and Case Studies
inferred← citeshttps://doi.org/10.3390/microorganisms11122867openalex-snapshot
Effect of Ciprofloxacin on the Composition of Intestinal Microbiota in Sarcophaga peregrina (Diptera: Sarcophagidae)
inferred← citeshttps://doi.org/10.4039/tce.2021.45openalex-snapshot
Analyses of the gut bacteriomes of four important Drosophila pests
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682754openalex-snapshot
Additional file 1 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682757openalex-snapshot
Additional file 2 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682760openalex-snapshot
Additional file 3 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682763openalex-snapshot
Additional file 4 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682766openalex-snapshot
Additional file 5 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682769openalex-snapshot
Additional file 6 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682772openalex-snapshot
Additional file 7 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16682775openalex-snapshot
Additional file 8 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.16727553openalex-snapshot
Additional file 1 of Influence of bacteria on the maintenance of a yeast during Drosophila melanogaster metamorphosis
inferred← citeshttps://doi.org/10.70675/cb338438z608dz437ezb427z8f850ef4cca4openalex-snapshot
Influence des facteurs alimentaires et du microbiote intestinal sur la tolérance au stress chez Drosophila melanogaster
inferred← citeshttps://doi.org/10.70675/f8169d85zba6cz4618za651z46b4396bf483openalex-snapshot
Drosophila-Lactobacillus plantarum as a model of facultative nutritional mutualism
inferred← citeshttps://doi.org/10.7287/peerj.8097v0.1/reviews/1openalex-snapshot
Peer Review #1 of "The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8097v0.1/reviews/2openalex-snapshot
Peer Review #2 of "The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8097v0.1/reviews/3openalex-snapshot
Peer Review #3 of "The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster (v0.1)"
inferred← citeshttps://doi.org/10.7554/elife.110808openalex-snapshot
Environmental temperature is a strong driver of subspecies competition in the Drosophila microbiome
inferred← citeshttps://doi.org/10.7554/elife.110808.1openalex-snapshot
Environmental temperature is a strong driver of subspecies competition in the Drosophila microbiome
inferred← citeshttps://doi.org/10.7717/peerj.8097openalex-snapshot
The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster
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