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Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.
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http://dx.doi.org/10.1007/s12275-023-00085-x | DOI Listing |
J Am Chem Soc
September 2025
Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn,Gerhard-Domagk-Straße 1,Bonn 53121,Germany.
Terpene synthases produce a remarkable structural diversity from acyclic precursors through complex carbocation cascades. Here, we report the crystal structure of the bacterial sesterterpene synthase StvirS bound to geranylfarnesyl thiopyrophosphate (GFSPP), revealing a preorganized active site that enforces a defined folding of the C25 backbone. Guided by this structure, active-site engineering at 11 positions yielded 23 enzyme variants and 13 new sesterterpenes.
View Article and Find Full Text PDFAllergy
September 2025
Institute of Allergology, Charité Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität Zu Berlin, Berlin, Germany.
SYN-53, a multi-strain probiotic food supplement, was recently shown to significantly alleviate allergic rhinoconjunctivitis (ARC) and its symptoms. The diversity and dosage of bacterial strains administered via SYN-53 have been proposed as key drivers of its efficacy. The aim of this study was to assess the role of bacterial diversity and dosage by comparing SYN-53 to a low dose variant (SYN-53-LD), a low diversity variant (SYN-4), and a placebo in the management of ARC.
View Article and Find Full Text PDFGenes Genet Syst
September 2025
Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University.
In most eubacteria the initiator protein DnaA triggers chromosomal replication by forming an initiation complex at the origin of replication and also functions as a transcriptional regulator, coordinating gene expression with cell cycle progression. While DnaA-regulated genes are relatively well characterized in exponentially growing cells, its role in gene regulation during stationary phase remains insufficiently explored. Here, using an aquatic bacterium Caulobacter crescentus as a model, we show that C.
View Article and Find Full Text PDFNucleic Acids Res
September 2025
Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States.
Glycine is an important metabolite and cell signal in diverse organisms, yet tools to visualize intracellular glycine dynamics have not been developed. In this study, diverse and bright RNA-based glycine biosensors were developed by fusing the architecturally complex glycine riboswitch with Broccoli class fluorogenic aptamers. The brightest sensor with the highest activation, glyS, and its two-dye ratiometric counterpart, Pepper-glyS, allowed for visualization of a drug-induced accumulation of endogenous glycine in live Escherichia colicells.
View Article and Find Full Text PDFCell
September 2025
Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Fleming Initiative, Imperial College London, London W2 1NY, UK; Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address:
Artificial intelligence (AI) models have been proposed for hypothesis generation, but testing their ability to drive high-impact research is challenging since an AI-generated hypothesis can take decades to validate. Here, we challenge the ability of a recently developed large language model (LLM)-based platform, AI co-scientist, to generate high-level hypotheses by posing a question that took years to resolve experimentally but remained unpublished: how could capsid-forming phage-inducible chromosomal islands (cf-PICIs) spread across bacterial species? Remarkably, the AI co-scientist's top-ranked hypothesis matched our experimentally confirmed mechanism: cf-PICIs hijack diverse phage tails to expand their host range. We critically assess its five highest-ranked hypotheses, showing that some opened new research avenues in our laboratories.
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