Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits - Environmental Microbiome Background In recent years, there has been increasing concerns about antibiotic resistance. Although studies have investigated resistance in food-associated bacteria, fresh produce microbes remain underexplored as potential hub of resistance genes capable for horizontal transfer to human via consumption. To this end, we tested the antibiotic resistance profiles of bacterial isolates recovered from Golden Reinders and Mandy apple cultivars. We aimed to investigate the effects of orchard-cultivar combinations and microbial lifestyle on the antibiotic resistance profiles. The apples (Golden Reinders and Mandy) were sampled from four separate orchards (EEL-Lleida, Esterri, Fruits-de-Ponent and Gotarta) in Spain. We used combination of culture-dependent and whole genome sequencing approaches to analyse the antibiotic resistance profiles. Results A total of 516 bacterial isolates were screened for susceptibility against seven different classes of antibiotics. Results showed that 272 isolates were resistant to at least one antibiotic. From those, 203 were epiphytes and 95 classified as endophytes (isolated from surface-sterilized apple peels), whereas 26 isolates were shared between the groups. The resistance profiles varied across the antibiotics, with over 50% of the isolates exhibiting resistance to tetracycline, quinolones and cephalosporins. In contrast, none of the isolates showed resistance to imipenem. Whole genome sequencing (WGS) was performed on 18 isolates, however, only 10 genomes passed quality-control thresholds and were included in subsequent resistome analyses. We found ARGs encoding resistance to 14 main antibiotic classes, with the majority of the confirmed resistances attributed to multidrug resistance (MDR). Only few target-specific ARGs were annotated, including (Rif)iri (rifampicin), lnu(A) (lincomycin) and FosD (Fosfomycin). Pantoea agglomerans possessed higher number of ARGs, while Staphylococcus arlettae exhibited notable prevalence of plasmid-encoded ARGs. Conclusion Overall, the study highlights the prevalence of antibiotic resistance in apple microbiomes. The presence of multidrug-resistance (MDR) genes further underscores the persistent threat of ‘antibiotic resistance’, underlining the necessity for deeper insight into antibiotic resistance within food chain.

In #EnvironmentalMicrobiome

Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits🍎

Read more 👉 doi.org/q3dr #OpenAccess #Fruit #Bacteria

In #Microbiome

🚨Scale reliant mixed effects models enhance microbiome data analysis

🦠Introducing Scale-Reliant Mixed-Effects Models (SR-MEM): a general framework for mixed-effects modeling of microbiome sequence count data.

👉 doi.org/q3c5 #OpenAccess

In #AnimalMicrobiome

Lactobacillus plantarum (LPsca12) enhances growth phenotype and muscle nutrition in abalone (Haliotis discus hannai) by modulating microbial function and metabolism through the Amino Acid-Driven Gut-Muscle Axis🦠

Read more👉 doi.org/qz6x #OpenAccess

In #Microbiome

🚨Ethical models are needed to resolve the imbalances in microbiome research

🦠Outlining structural requirements needed to ensure the implementation of new frameworks & advance both scientific integrity & global health equity

👉 doi.org/qz52 #OpenAccess

In #EnvironmentalMicrobiome

🔍Exploring the eelgrass microbiome & disease dynamics under field and lab heat stress

🚨Advancing our understanding of how environmental change shapes disease ecology in seagrass ecosystems

👉 doi.org/qz6v #OpenAccess

In #Microbiome

🦠What do we know about the seed microbiome?

🚨Optimizing the composition of seed endophytes through microbiome engineering holds significant implications for sustainable agriculture

Read more👉 doi.org/qz5z #OpenAccess

In #AnimalMicrobiome

🔍Decoding the dynamics of calves’ respiratory & gut microbiota: exploring stability, resistance & individual patterns

🚨The first month of life is a critical window for interventions targeting the fecal microbiota

Read more➡️ doi.org/qm7t #OpenAccess #Microbiome #Microbiota

In #Microbiome

🚨Introducing RamEx: A powerful new tool for microbial Ramanome analyses

🦠Providing a toolkit for exploring microbial ecology, metabolic interactions & antibiotic susceptibility at the single-cell resolution

👉 doi.org/qzkd #OpenAccess

In #EnvironmentalMicrobiome

Examining the microbial community dynamics across diel & seasonal scales in the coastal South China sea🦠

Viral communities maintained high similarity between seasons, indicating a persistent viral reservoir in this region

👉 doi.org/qzj8 #OpenAccess

In #Microbiome

🚨Uncommon bacteria may be a new source of treatments for drug-resistant infection

🔍Employing enrichment cultivation to access antimicrobial peptides encoded by low-abundance bacteria within a marine biofilm community

👉 doi.org/qzkc #OpenAccess

Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows - Animal Microbiome Animal Microbiome - Lipopolysaccharides (LPS) from pathogenic Gram-negative bacteria play a key role in the pathophysiology of mastitis. Subacute ruminal acidosis (SARA) induces rumen dysbiosis,...

In #AnimalMicrobiome

🔍Investigating the effects of a high-grain diet & intramammary LPS challenge on the milk microbiome of dairy cows

🚨High-grain feeding reduced microbial abundance over 30 days

👉 doi.org/qtt7 #OpenAccess

In #EnvironmentalMicrobiome

🦠Developing microbe-based strategies for enhancing drought stress tolerance in spruce seedlings

🚨Caballeronia sp. Ke431 and Paraburkholderia sp. Ke296 showed positive effects on spruce growth under drought conditions

👉 doi.org/qxb9 #OpenAccess

In #Microbiome

🚨Introduction of forest soil changes household dust microbiomes

🦠Airborne dust near entrances had an increase in microbes associated with lower asthma risk

Read more👉 doi.org/qxcb #OpenAccess

New paper out today in @microbiomej.bsky.social: “Environmental microbiota transfer from forest soil into urban homes: a proof-of-principle study.” We show that a simple soil-on-rug intervention can shift bacterial microbiota in house dust in urban homes. link.springer.com/article/10.1...

In #AnimalMicrobiome

🔍Investigating supplementation fucosidase in pig feed as a tool to reduce enteric methane production & improve growth performance in pigs

🚨In-feed fucosidase may lead to lower methane emission at later pig production stages

👉 doi.org/qwcs #OpenAccess

In #Microbiome

🚨A link between a plant gene, a xylem sap microbe and growth in cucumber

🥒Investigating the composition and functional significance of the cucumber xylem microbiome

👉 doi.org/qwcr #OpenAccess

In #EnvironmentalMicrobiome

🔍Investigating the structure & distribution of marine viral communities in subantarctic Chilean Patagonia fjords

🚨Temperature emerged as the strongest driver structuring viral communities

👉 doi.org/qwct #OpenAccess

In #Microbiome

🚨MHC-I effects on the gut microbiome of wild Seychelles warbler

🔍Using shotgun metagenomics to explore how variation in MHC genes shapes the taxonomy & function of the gut microbiome

👉 doi.org/qwcp #OpenAccess

In #AnimalMicrobiome

🔍Investigating how the leptin receptor gene affects gut microbiota composition & nutrient utilization in pigs🐷

🚨Underscoring the importance of feed intake as a microbiota-altering factor

👉 doi.org/qvdc #OpenAccess

In #Microbiome

🚨Introducing quantile thresholding (QuanT): a novel tool for comprehensive identification of unmeasured heterogeneity in microbiome data

🦠Valuable for data integration & comprehensive analysis in microbiome research

👉 doi.org/qvdk #OpenAccess

Identifying unmeasured heterogeneity in microbiome data via quantile thresholding (QuanT) - Microbiome Background Microbiome data, like other high-throughput data, suffer from technical heterogeneity stemming from differential experimental designs and processing. In addition to measured artifacts such ...

In #Microbiome

🚨Introducing quantile thresholding (QuanT): a novel tool for comprehensive identification of unmeasured heterogeneity in microbiome data

🦠Valuable for data integration & comprehensive analysis in microbiome research

👉 doi.org/qvdk #OpenAccess

In #EnvironmentalMicrobiome

🔍Exploring how the bark microbiome of bald cypress trees responds to hydrochemical dynamics

🚨Wet bark was more diverse & had higher relative abundances of bacteria linked to key ecosystem services

👉 doi.org/qvdg #OpenAccess #Bark #Bacteria #Ecosystem

I’m grateful to @microbiomej.bsky.social for publishing this work. Many thanks to the editors and reviewers for their thoughtful feedback.

In #Microbiome

🚨The path to sustainable crop growth is through the root microbes

🌾Comparing the root microbiomes of 17 wild rice species & one cultivated species across the genus Oryza, spanning nearly 15 million years of evolution

👉 doi.org/qvdh #OpenAccess #Rice #Microbes #Roots

In #AnimalMicrobiome

🔍Investigating the effects of a high-grain diet and intramammary LPS challenge on the milk microbiome or dairy cows🐄

🚨A roughage-rich diet promoted higher microbial abundance, whereas high-grain feeding reduced abundance

👉 doi.org/qtt7 #OpenAccess

In #Microbiome

🔍Investigating the association between the gut microbiota & temperament plasticity in Merino sheep

🦠The first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock

👉 doi.org/qtvb #OpenAccess

In #EnvironmentalMicrobiome

🔍Investigating the performance & microbial dynamics of UASB reactor subjected to gradual temperature reduction from 35 to 20 °C

🚨Enhancing our understanding of temperature effects on anaerobic systems

👉 doi.org/qtt8 #OpenAccess

In #Microbiome

🔍Exploring the conserved and indispensable roles of intestinal T cells in teleost fish🐟

🚨Highlighting their dual function in pathogen defense and mucosal homeostasis

👉 doi.org/qtt9 #OpenAccess

In #AnimalMicrobiome

🚨Lawsonia intracellularis infection induces changes in microbial community function and composition associated with reduced pig growth and feed efficiency

Read more👉 doi.org/qszr #OpenAccess #Microbes

In #Microbiome

🔍Exploring the spatial & temporal patterns in the species diversity of public transit aerobiomes🦠

🏙️Cities were the strongest driver of diversity & community structure, each exhibiting its own distinct microbial signature

👉 doi.org/qr6s #OpenAccess #Aerobiomes