metagenomics

FennoTraits: Dataset of plant functional traits and community composition in northern European flora

The paper introduces FennoTraits, a dataset of plant functional traits and community composition from northern European flora, highlighting trait patterns and species distribution across seven study areas.

Phylogenetic coherence in microbiome composition across environmental gradients

The paper investigates how environmental gradients shape microbial community composition by analyzing phylogenetic signals in response to environmental variables.

CULTURE AND ISOLATION OF BACTERIA ASSOCIATED WITH MEDITERRANEAN CORALS

The paper isolates and cultures bacteria from four Mediterranean corals, identifying 84 pure isolates, including novel species, to better understand their roles in the coral holobiont.

Bacterial fermentation dominates over respiration in upland soils during hypoxia

This study shows that bacterial fermentation, not respiration, dominates in upland soils during hypoxia, challenging the assumption that respiration is the primary metabolic strategy.

Ecological and metabolic signatures of biofilm viromes across a national river surveillance network

This study characterizes river biofilm viromes across a national network, revealing seasonal structure, host associations, and metabolic functions linked to environmental variables.

Pantoea ananatis-triggered systemic resistance requires root sensing through the LORE receptor kinase in Arabidopsis

This study shows that Pantoea ananatis triggers systemic resistance in Arabidopsis through root sensing via the LORE receptor kinase, using HAAs and 3-OH-C10 as MAMPs.

The global β-lactam resistome revealed by comprehensive sequence analysis

The paper maps the global distribution of β-lactamases across environments and microbes, revealing their abundance and potential origins in plant and wastewater ecosystems.

Integrated microbiome and metabolomic profiling reveals alterations across the adenoma-colorectal cancer sequence

This study identifies microbial and metabolic changes across the adenoma-carcinoma sequence in colorectal cancer using 16S rRNA sequencing and metabolomic profiling.

Nest Ecology-associated Impacts of Wastewater on Wild Bee Microbiomes

The paper compares gut microbiomes of ground-nesting and wood-nesting bees near wastewater, finding greater microbial disruption in ground-nesting bees.

A Pilot Study Investigating the Impact of Oral Probiotic Supplementation on the Vaginal Microbiota and Aspects of Well-being

This pilot study examines the effects of oral probiotic supplementation on vaginal microbiota and well-being in women with recurrent vaginal discomfort, finding increased detection of probiotic strains and reduced symptoms.

Viral host assignment across the tree of life with VHAMSTeR

VHAMSTeR predicts viral host associations across five categories using genomic language models and biological features, outperforming existing methods and uncovering new RNA bacteriophages.

Anaerobic methane oxidation by ANME-2a at 2 M chloride in the Orca Basin halocline

The paper investigates anaerobic methane oxidation in the Orca Basin, identifying ANME-2a's role at high salinity and revealing microbial communities involved in methane cycling.

Understanding cognitive function in post-COVID-19 condition with fatigue: an interdisciplinary multimodal investigation

This study investigates cognitive symptoms in post-COVID-19 condition with fatigue, finding subtle neurobiological changes not captured by standard assessments.

There are cores, indicators, and differences - a high-throughput and quantitative PCR study of the Ambrosia artemisiifolia L. leaf, root, and seed endophytic bacterial microbiomes within the European invasive range

The paper profiles endophytic bacterial microbiomes in Ambrosia artemisiifolia L. tissues across Europe, finding tissue type shapes community structure more than region or habitat.

Alternative management strategy influences litter microbiome dynamics in a commercial broiler rearing system

This study evaluates an alternative litter management strategy in broiler production, showing changes in microbiome structure and Enterococcus abundance without consistent antimicrobial effects.

RNA viruses that exploit self-cleaving ribozymes for translation initiation

This study identifies self-cleaving ribozymes in RNA viruses, showing their role in translation initiation across fungi and plants.

Most metagenomic vanT calls are not vancomycin resistance genes

The paper shows that most metagenomic vanTG gene calls are misannotations of alanine racemases, not vancomycin resistance genes.

Early-life core microbiota are associated with postlarval survival of Penaeus vannamei: A meta-analysis

This study identifies core microbiota associated with postlarval survival in shrimp through a meta-analysis of 16S rRNA gene datasets.

Once in a blue moon: an unexpected evolutionary route to blue floral pigmentation in orchids

The paper investigates the genetic basis of blue floral pigmentation in orchids, finding an unexpected pathway involving duplicated genes and regulatory changes rather than the expected CYP75A pathway.

Microbial priming controls terrestrial carbon burial in marine sediments

The paper uses sedimentary ancient DNA to show microbial priming influences terrestrial carbon burial in marine sediments by altering organic matter degradation pathways.

Strong habitat-associated differentiation of microbial communities across a fine-scale land-water interface

The paper examines microbial community differentiation across a land-water interface, finding strong habitat-associated differences between terrestrial and aquatic samples.

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

The paper maps subgingival microbiome states in 1,355 adults, identifying divergent dysbiosis trajectories linked to periodontitis and host factors.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

Dietary fiber-type-specific gut microbiome preconditioning drives differential susceptibility to sporadic colon cancer development

The paper shows that inulin supplementation increases colon tumor incidence in mice by altering gut microbiome and metabolome, creating a tumor-promoting environment when exposed to carcinogens.

Using Arabian Sea Coastal Water as a Model to Study Plasmid-mediated AMR Dissemination driven by Anthropogenic Impacts

The paper studies AMR dissemination in Arabian Sea coastal waters, identifying diverse plasmid replicons and clinically relevant antibiotic resistance genes linked to anthropogenic stressors.

Study on The Effect of a Propiconazole Based Fungicide on Plant Growth Promoting Properties of Isolates from Wheat Rhizosphere

This study examines how propiconazole affects six plant growth promoting properties of wheat rhizosphere isolates, finding that specific traits like siderophore and ammonia production are suppressed at high concentrations.

Longitudinal analysis of vaccine-associated alterations in the faecal microbiota of layer chickens using a vaccination schedule representative of commercial practice

This study examines how multiple vaccines affect the gut microbiota of layer chickens over time, finding stable microbial diversity and composition despite vaccination.

Unlocking the secrets of paired terminal genomic repeats utilised by the Burkholderia jumbo phage Matilda

This study identifies a novel jumbo phage with a tripartite genome architecture and describes its terminal elements' role in infection.

TRUEDA overturns replicated, decontaminated low-biomass disease-microbe associations and clinical decisions, recovers true pathogens and outperforms every decontamination method

TRUEDA identifies true pathogens in low-biomass disease-microbe associations by accounting for contamination, outperforming existing decontamination methods and correcting false associations.

Gut microbial interaction networks control autoimmunity to neuroretina

Akkermansia expansion reduces short-chain fatty acid-producing Firmicutes in human-flora uveitis mice, raising Th1 responses and disease; a Verrucomicrobia/Firmicutes ratio is elevated in uveitis, MS and Crohn's patients.