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The dynamic core microbiome: Structure, dynamics and stability

https://doi.org/10.1101/137885
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What this work says

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

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Trophic niche separation that facilitates co‐existence of high and low microbial abundance sponges is revealed by in situ study of carbon and nitrogen fluxes
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Microbial associations in sponges. III. Ultrastructure of the in situ associations in coral reef sponges
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Gametogenesis, embryogenesis, and larval features of the oviparous sponge Petrosia ficiformis (Haplosclerida, Demospongiae)
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Evidence of nitrification and denitrification in high and low microbial abundance sponges
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Bacterial Uptake by the Marine Sponge Aplysina aerophoba
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Do associated microbial abundances impact marine demosponge pumping rates and tissue densities?
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Dominant species, rather than diversity, regulates temporal stability of plant communities
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Deep sequencing reveals diversity and community structure of complex microbiota in five Mediterranean sponges
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Adaptation in a hybrid world with multiple interaction types: a new mechanism for species coexistence
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The effects of space and diversity of interaction types on the stability of complex ecological networks
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Sponge–Microbe Symbioses
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Compositional data analysis of the microbiome: fundamentals, tools, and challenges
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Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
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A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals
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The surprisingly complex immune gene repertoire of a simple sponge, exemplified by the NLR genes: A capacity for specificity?
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The role of Mediterranean sponges in benthic–pelagic coupling processes: Aplysina aerophoba and Axinella polypoides case studies
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Stability of competition–antagonism–mutualism hybrid community and the role of community network structure
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Temporal patterns of rarity provide a more complete view of microbial diversity
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Marine Bacterioplankton Seasonal Succession Dynamics
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Commonness, population depletion and conservation biology
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Resisting regime-shifts: the stabilising effect of compensatory processes
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So Many Variables: Joint Modeling in Community Ecology
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Aggregation, Variance and the Mean
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Weak trophic interactions and the balance of nature
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Variability in the abundance of animal and plant species
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The diversity–stability debate
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Food-web analysis through field measurement of per capita interaction strength
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Human gut microbes associated with obesity
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Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis
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Defining seasonal marine microbial community dynamics
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‘Sponge-specific’ bacteria are widespread (but rare) in diverse marine environments
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Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?
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The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts
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Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics
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Biodiversity as a barrier to ecological invasion
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Species interactions can explain Taylor's power law for ecological time series
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Explaining the excess of rare species in natural species abundance distributions
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The Human Microbiome Project
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A core gut microbiome in obese and lean twins
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Stability criteria for complex ecosystems
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A metagenome-wide association study of gut microbiota in type 2 diabetes
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Diversity, stability and resilience of the human gut microbiota
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Getting to the core of the gut microbiome
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Diversity, structure and convergent evolution of the global sponge microbiome
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Climate warming reduces the temporal stability of plant community biomass production
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Cooperative secretions facilitate host range expansion in bacteria
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The human microbiome: at the interface of health and disease
inferredcites →https://doi.org/10.1038/nrgastro.2017.173openalex-snapshot
Role of priority effects in the early-life assembly of the gut microbiota
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The gut microbiota shapes intestinal immune responses during health and disease
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Genomic insights into the marine sponge microbiome
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Marine microbial community dynamics and their ecological interpretation
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The winnowing: establishing the squid–vibrio symbiosis
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The microbiome and rheumatoid arthritis
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Self-regulation and the stability of large ecological networks
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Dominant species maintain ecosystem function with non‐random species loss
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Proceedings of the National Academy of Sciences
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Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life
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Human gut microbiome adopts an alternative state following small bowel transplantation
inferredcites →https://doi.org/10.1073/pnas.1000080107openalex-snapshot
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
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Animals in a bacterial world, a new imperative for the life sciences
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Commonness and rarity in the marine biosphere
inferredcites →https://doi.org/10.1073/pnas.1414577112openalex-snapshot
Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian
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The HMA-LMA Dichotomy Revisited: an Electron Microscopical Survey of 56 Sponge Species
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Toll-Like Receptors Are Part of the Innate Immune Defense System of Sponges (Demospongiae: Porifera)
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The Characterization of Sponge NLRs Provides Insight into the Origin and Evolution of This Innate Immune Gene Family in Animals
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Evaluating the Accuracy of Sampling-Based Approaches to the Calculation of Posterior Moments
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Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community
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Density dependence, regulation and variability in animal populations
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Resilience, Invariability, and Ecological Stability across Levels of Organization
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Testing the roles of competition, facilitation and stochasticity on community structure in a species‐rich assemblage
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Contrasting effects of spatial heterogeneity and environmental stochasticity on population dynamics of a perennial wildflower
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Measuring temporal turnover in ecological communities
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Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts
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Beyond the Venn diagram: the hunt for a core microbiome
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Sponge‐specific clusters revisited: a comprehensive phylogeny of sponge‐associated microorganisms
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Functional convergence of microbes associated with temperate marine sponges
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Structure–stability relationships in networks combining mutualistic and antagonistic interactions
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Morphology and ultrastructure of the swimming larvae of Crambe crambe (Demospongiae, Poecilosclerida)
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Differences in reproductive timing among sponges sharing habitat and thermal regime
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Dominant species constrain effects of species diversity on temporal variability in biomass production of tallgrass prairie
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Sponge heterotrophic capacity and bacterial community structure in high‐ and low‐microbial abundance sponges
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Signals from chloroplasts converge to regulate nuclear gene expression.
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Stochastic Community Assembly Causes Higher Biodiversity in More Productive Environments
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Diversity of Interaction Types and Ecological Community Stability
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The Long-Term Stability of the Human Gut Microbiota
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Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs
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The ecology of the microbiome: Networks, competition, and stability
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The fundamental advantages of temporal networks
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Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels
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Generalized Latent Variable Modeling
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Size-mediated non-trophic interactions and stochastic predation drive assembly and dynamics in a seabird community
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The strength of plant–pollinator interactions
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Specificity and temporal dynamics of complex bacteria–sponge symbiotic interactions
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The ultrastructure of the mature oocyte and the nurse cells of the ceractinomorpha Petrosia ficiformis
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Temporal dynamics in the ruminal microbiome of dairy cows during the transition period
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Microbiome Datasets Are Compositional: And This Is Not Optional
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Perturbation of the Human Microbiome as a Contributor to Inflammatory Bowel Disease
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Sponges as a source of dissolved inorganic nitrogen: Nitrification mediated by temperate sponges
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Complex interactions between marine sponges and their symbiotic microbial communities
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The geographic mosaic of coevolution
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The Geographic Mosaic of Coevolution
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Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras

What points at this work

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

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Native and invasive raccoon populations host distinct microbiomes that may facilitate invasion
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Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research
inferred← citeshttps://doi.org/10.1002/ece3.5949openalex-snapshot
Environmental influences on and antimicrobial activity of the skin microbiota of Proceratophrys boiei (Amphibia, Anura) across forest fragments
inferred← citeshttps://doi.org/10.1002/edn3.357openalex-snapshot
Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient‐impoverished ecosystem
inferred← citeshttps://doi.org/10.1007/s00248-022-02083-9openalex-snapshot
Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters
inferred← citeshttps://doi.org/10.1007/s00248-023-02262-2openalex-snapshot
Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru
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Host Species Mediate Distinct Seed Microbiome Responses to Restoration
inferred← citeshttps://doi.org/10.1016/j.algal.2024.103701openalex-snapshot
The microbiome of bioreactors containing mass-cultivated marine diatoms for industrial carbon capture and utilization
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Root rot induces a core assemblage of bacterial microbiome to prevent disease infection in Sanqi ginseng
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Periodic flooding alters ecological processes and carbon metabolism efficiency of riparian soil microbial communities in the three Gorges Reservoir area, China
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Six Decades of Taylor's Power Law: From Ecological and Statistical Regularity to Heterogeneity and Stability Across Complex Systems
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Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO2 vents
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Modularity and predicted functions of the global sponge-microbiome network
inferred← citeshttps://doi.org/10.1038/s41559-019-0935-xopenalex-snapshot
Vertical transmission of sponge microbiota is inconsistent and unfaithful
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Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges
inferred← citeshttps://doi.org/10.1038/s41598-019-42694-wopenalex-snapshot
Uncovering the hidden marine sponge microbiome by applying a multi-primer approach
inferred← citeshttps://doi.org/10.1038/s41598-020-80372-4openalex-snapshot
Parents with periodontitis impact the subgingival colonization of their offspring
inferred← citeshttps://doi.org/10.1038/s41598-025-28025-2openalex-snapshot
Respiratory bacteriome and its predicted functional profiles in blue whales (Balaenoptera musculus)
inferred← citeshttps://doi.org/10.1038/s42003-024-06109-5openalex-snapshot
High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits
inferred← citeshttps://doi.org/10.1039/d0en00442aopenalex-snapshot
The shape and speciation of Ag nanoparticles drive their impacts on organisms in a lotic ecosystem
inferred← citeshttps://doi.org/10.1071/mf20209openalex-snapshot
Shifts in the seagrass leaf microbiome associated with wasting disease in Zostera muelleri
inferred← citeshttps://doi.org/10.1073/pnas.2104429118openalex-snapshot
Defining and quantifying the core microbiome: Challenges and prospects
inferred← citeshttps://doi.org/10.1093/femsec/fiz127openalex-snapshot
Inevitable future: space colonization beyond Earth with microbes first
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Effects of past and present habitat on the gut microbiota of a wild rodent
inferred← citeshttps://doi.org/10.1099/mic.0.001088openalex-snapshot
Analysis of mouse faecal dysbiosis, during the development of cachexia, induced by transplantation with Lewis lung carcinoma cells
inferred← citeshttps://doi.org/10.1101/2022.12.29.522252openalex-snapshot
Common core respiratory bacteriome of the blue whale Balaenoptera musculus , in the Gulf of California
inferred← citeshttps://doi.org/10.1101/2023.12.13.571495openalex-snapshot
Exploring the impact of microbial manipulation on the early development of kelp ( Saccharina latissima ) using an ecological core microbiome framework
inferred← citeshttps://doi.org/10.1101/2024.01.08.574701openalex-snapshot
Hierarchical Ordination, A unifying framework for drivers of community processes
inferred← citeshttps://doi.org/10.1101/412213openalex-snapshot
Diversity and composition of methanotroph communities in caves
inferred← citeshttps://doi.org/10.1101/425009openalex-snapshot
Vertical transmission of sponge microbiota is inconsistent and unfaithful
inferred← citeshttps://doi.org/10.1111/1365-2656.13229openalex-snapshot
Applying the core microbiome to understand host–microbe systems
inferred← citeshttps://doi.org/10.1111/1462-2920.14932openalex-snapshot
Community assembly of the native C . elegans microbiome is influenced by time, substrate and individual bacterial taxa
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Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing
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Seed microbiota revealed by a large‐scale meta‐analysis including 50 plant species
inferred← citeshttps://doi.org/10.1128/aem.00301-25openalex-snapshot
An experimental test of the influence of microbial manipulation on sugar kelp ( Saccharina latissima ) supports the core influences host function hypothesis
inferred← citeshttps://doi.org/10.1128/aem.02237-23openalex-snapshot
Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes
inferred← citeshttps://doi.org/10.1128/msphere.00039-21openalex-snapshot
Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees
inferred← citeshttps://doi.org/10.1128/spectrum.01566-21openalex-snapshot
Diversity and Composition of Methanotroph Communities in Caves
inferred← citeshttps://doi.org/10.1186/s40168-026-02520-8openalex-snapshot
Phylogenetic measures of the core microbiome
inferred← citeshttps://doi.org/10.1186/s40793-022-00417-1openalex-snapshot
Long-term patterns of an interconnected core marine microbiota
inferred← citeshttps://doi.org/10.1186/s40793-022-00451-zopenalex-snapshot
Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity
inferred← citeshttps://doi.org/10.1186/s40793-024-00620-2openalex-snapshot
The interplay between host-specificity and habitat-filtering influences sea cucumber microbiota across an environmental gradient of pollution
inferred← citeshttps://doi.org/10.1201/9781003403319-3openalex-snapshot
Sponge Symbiosis: Microbes Make an Essential Part of What It Means to Be a Sponge
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008392openalex-snapshot
Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium
inferred← citeshttps://doi.org/10.21203/rs.3.rs-52941/v1openalex-snapshot
Compartmentalization Rather Than Host Tree Drives Truffle Microbiome
inferred← citeshttps://doi.org/10.21203/rs.3.rs-6485806/v1openalex-snapshot
Too hot for my bugs: Mediterranean heatwaves disrupt associated microbiomes in the sponge Petrosia ficiformis
inferred← citeshttps://doi.org/10.2460/ajvr.25.01.0014openalex-snapshot
A 5-month temporal, quantitative study investigating the core microbiome on the axilla, umbilical region, and groin of 15 healthy dogs in the UK
inferred← citeshttps://doi.org/10.3389/fevo.2022.967692openalex-snapshot
Wild Panax plants adapt to their thermal environment by harboring abundant beneficial seed endophytic bacteria
inferred← citeshttps://doi.org/10.3389/fmicb.2022.791079openalex-snapshot
Bacterial Recruitment to Carnivorous Pitcher Plant Communities: Identifying Sources Influencing Plant Microbiome Composition and Function
inferred← citeshttps://doi.org/10.3390/ani11113331openalex-snapshot
Core Microbiome of Slovak Holstein Friesian Breeding Bulls’ Semen
inferred← citeshttps://doi.org/10.3390/biology14040430openalex-snapshot
The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis
inferred← citeshttps://doi.org/10.3390/d18070399openalex-snapshot
Exploration of the Microbiota Associated with Body Regions Within the Host Sea Cucumber, Holothuria forskali (Echinodermata: Holothuroidea)
inferred← citeshttps://doi.org/10.3390/ijms21176307openalex-snapshot
Molecular Network and Culture Media Variation Reveal a Complex Metabolic Profile in Pantoea cf. eucrina D2 Associated with an Acidified Marine Sponge
inferred← citeshttps://doi.org/10.3390/jof6040364openalex-snapshot
Fungal Dysbiosis Correlates with the Development of Tumor-Induced Cachexia in Mice
inferred← citeshttps://doi.org/10.3390/nu14142872openalex-snapshot
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept
inferred← citeshttps://doi.org/10.3390/w11112422openalex-snapshot
New Pond—Indicator Bacteria to Complement Routine Monitoring in a Wet/Dry Tropical Wastewater Stabilization System
inferred← citeshttps://doi.org/10.4172/2572-4983.1000166openalex-snapshot
Neurodevelopment, Intestinal Function, and Autism
inferred← citeshttps://doi.org/10.70675/8723eba5z6f92z4a72z84dez1f21bbd2a07dopenalex-snapshot
Exploring temporal patterns of marine plankton communities in the Western English Channel through the analyses of morphological and metabarcoding time-series
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