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When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought-providing a time series of short-term transcriptional response during rewetting.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237402 | PMC |
http://dx.doi.org/10.1128/mra.00322-24 | DOI Listing |
Nucleic Acids Res
September 2025
Institute for Fundamental Biomedical Resea rch, BSRC "Alexander Fleming," 16672 Vari, Greece.
The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences.
View Article and Find Full Text PDFCell Host Microbe
July 2025
Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF).
View Article and Find Full Text PDFmSystems
August 2025
State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China.
Saltwater intrusion and sea level rise (SWISLR) threaten coastal agroecosystems, yet their impact on the methanogenic food web in rice paddies remains virtually unknown. Using "double-RNA" metatranscriptomics (rRNA, mRNA), we investigated salinity effects on the methanogenic community in straw-amended slurries following different preincubation periods. Our results demonstrate that salt stress significantly inhibits methane (CH) production, with the degree of inhibition varying by the community's successional stage.
View Article and Find Full Text PDFVirology
September 2025
Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand.
The New Zealand sea lion (pakake; Phocarctos hookeri) is the largest and only endemic otariid species in Aotearoa (New Zealand), classified as 'nationally critical' due to low population numbers and limited distribution. Infectious disease is a significant factor contributing to sea lion population instability; however, we know almost nothing about viral organisms harboured by these species. To this end, we conducted a metatranscriptomic analysis of faecal samples from healthy New Zealand sea lions collected along the Otago coastline over twelve months.
View Article and Find Full Text PDFAzithromycin is often prescribed unnecessarily for respiratory infections, many of which are viral. During the COVID-19 pandemic, its use was widespread, in part due to alleged therapeutic benefits, which have since been disproven. Here, we sought to understand the impact of azithromycin exposure on the respiratory microbiome, antimicrobial resistome, and host immune response in a prospective multicenter cohort of 1164 patients hospitalized for SARS-CoV-2 infection.
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