metagenomics

Impaired Fermentation in the Absence of Gut Microbiota Promotes Inulin-Induced Intestinal Inflammation

The paper shows that impaired gut microbiota fermentation of inulin leads to intestinal inflammation in mice, highlighting the importance of microbial metabolism in fiber tolerance.

Symbiotic and commensal root microbes are key determinants of plant responses to rising CO2

The paper shows that root-associated microbial communities, including symbiotic and commensal microbes, significantly influence plant responses to elevated CO2 by altering carbon allocation and growth.

Integrating Microbial Ecology and Sustainability: Linking Agricultural Waste Gas Streams to Microbial Community Shifts in a Photobioreactor

This study examines microbial community dynamics in a photobioreactor using agricultural waste gas streams, showing spatially structured communities and partial nitrogen recovery.

Engineered DNA materials shape microbial physiology and ecological selection

This study shows engineered DNA materials influence microbial physiology and community dynamics by altering stress responses and shaping genetic interactions in wastewater microbiomes.

Environmental Frass Remodels the Larval Gut Microbiome to Enable Black Soldier Fly (Hermetia illucens) Bioconversion of Livestock Manure

This study shows that wild frass enhances BSFL growth on rabbit manure by introducing lignocellulose-degrading microbes, which are lost in captive-reared frass.

Programmable interphyla communication for Staphylococcus aureus by transferability of homoserine lactone sensors between Bacillales bacteria

This study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

GeneEmbedLLM: Harnessing Large Language Models for Gene Functional Embedding and Association Prediction

This paper introduces GeneEmbedLLM, a framework using large language models to generate gene embeddings from multi-source textual annotations, achieving competitive performance in various downstream tasks.

AOPTK: Open-Source Software for AI-Assisted Toxicological Literature Analysis

AOPTK automates toxicological literature analysis using AI, achieving high accuracy in identifying chemical-biological effect relationships.

Rapid environmental DNA detection with isothermal amplification methods: a comparison with the real-time quantitative PCR in the natterjack toad (Epidalea calamita).

This paper compares isothermal amplification methods (LAMP and RPA) with qPCR for detecting natterjack toad eDNA, finding RPA matches qPCR sensitivity while LAMP is less sensitive.

Impact of iron-enriched diets on the nutritional composition and microbiome diversity of house crickets (Acheta domesticus)

This study investigates how varying iron levels in diets affect the nutritional profile and microbiome of house crickets, finding that high iron increases their iron content without altering microbial diversity.

Two decades of EU pesticide substitution have not reduced impacts on stream invertebrates

This study shows that two decades of EU pesticide substitution have not reduced environmental harm to stream invertebrates, as toxic pressure and impairment remained stable over time.

Assembly of host-specific bacterial and fungal communities from soil by diverse subaerial green algae

This study shows subaerial green algae from Chlorophyta and Streptophyta assemble distinct phycosphere communities from soil, with host identity driving bacterial composition more strongly than fungal.

TestNet-PA: Sampling-Zero-Aware Inference of Microbial Presence-Absence Networks

TestNet-PA addresses sampling zeros in microbial presence-absence networks by modeling them as structural or sampling zeros, improving FDR control and sensitivity compared to Fisher's exact test.

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

Material context and TGF-β blockade timing determine retained matrix in patient-derived bioprinted keratoconus stroma

This study shows that timing of TGF-β blockade and material context affect matrix retention in bioprinted keratoconus stroma, with optimal regimens improving collagen retention and reducing contractile gene expression.

Interspecific social contacts spread gut microbiota in wild rodent communities

This study shows that social interactions between different rodent species can spread gut microbiota, with stronger transmission from wood mice to yellow-necked mice.

Continental scale genetic diversity supports geo-clustered ecoregions connectivity

The paper examines genetic diversity and connectivity between ecoregions, finding a divide between eastern and western regions with restricted gene flow in the west.

Global homeostatic forces shape the composition of a hyperdiverse tropical insect fauna

The paper estimates Madagascar's insect fauna contains at least 250,000 species, most unrecorded, and finds global homeostatic forces, not lineage composition, shape its ecological similarity to temperate forests.

A Minimal Synthetic Cleavage Module Enables Selective Degradation of Pathogenic r(CUG) Repeats in Cells

This study develops a synthetic cleavage module that selectively degrades pathogenic r(CUG) repeats in cells, reducing DM1-associated pathology without DNA damage.

Application of metagenomic sequencing to improve sessile serrated lesion detection using the faecal immunochemical test

This study investigates whether FIT samples can reveal a microbial signature of sessile serrated lesions, finding no significant differences in community structure but suggesting potential functional differences.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

Sexing carnivores from faecal metagenomes: calibrating Rx for stone marten and red fox

The paper evaluates the use of the X-to-autosome ratio (Rx) for sexing carnivores from faecal metagenomes, finding it effective above a certain read depth.

Integrative identification of Tetratostichococcus sp. CCAH0201 (Trebouxiophyceae, Chlorophyta) from Rhizophora leaves in the Can Gio Mangrove Forest, Vietnam

The paper identifies a microalgal strain from mangrove leaves using molecular markers and phylogenetic analysis, placing it closely related to Tetratostichococcus jenerensis.

Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

The paper uses metatranscriptomics to analyze viral diversity in freshwater and marine environments, identifying new RNA viruses associated with microalgae and proposing a new genus within Marnaviridae.

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

RoDPAA integrates multi-view microbiome data using dissimilarity-based principal angle analysis, recovering shared structure in IBD cohorts where log-ratio methods failed.

High reproducibility demonstrated in a direct-to-consumer microbiome testing workflow under real-world conditions using fecal reference material

This study demonstrates high reproducibility in a DTC microbiome testing workflow using NIST fecal reference material across multiple processing steps and real-world conditions.

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.