Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among most important objectives in microbiology. In last decade, many studies have been devoted to characterizing diversity microbial populations address these issues. However, impact of extreme conditions, such as temperature salinity, on ecology evolution remains unclear so far. order better understand mechanisms adaptation, we studied (pan)genome Exiguobacterium, a poly-extremophile bacterium able grow wide range environments, from permafrost hot springs. To genome all known Exiguobacterium type strains, first sequenced those that were not yet available. Using reverse-ecology approach, showed how integration phylogenomic information, genomic features, gene pathway enrichment data, regulatory element analyses, protein amino acid composition, structure analyses entire pangenome allows sharply delineate consisting mesophilic, psychrophilic, halophilic-mesophilic, halophilic-thermophilic ecotypes. This in-depth study clarified defined ecotypes identified some key driving environments. Our points way organizing vast into meaningful ecologically units, which, turn, provides insight communities adapt respond different conditions changing world.

Language: Английский

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A phylogenetic approach to comparative genomics

Nature Reviews Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

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G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(3)

Published: Jan. 24, 2025

Abstract G-quadruplex (G4) structure is a nucleic acid secondary formed by guanine-rich sequences, playing essential roles in various biological processes such as gene regulation and environmental stress adaptation. Although prokaryotes growing at high temperatures have higher GC contents, the pattern of G4 associated with content variation thermal adaptation remains elusive. This study analyzed 681 bacterial genomes to explore role structures Our findings revealed strong positive correlation between patterns region encoding 16S rRNA genes optimal growth (Topt), whereas genomic did not show significant correlations Topt. Evolutionary analysis showed distinctive differences stability Thermotoga (Topt ≥ 80°C) Pseudothermotoga (60°C ≤ Topt < species, species exhibiting stability, indicating stronger selective pressure for structures. In vitro spectroscopy that base mutations key sites resulted absence structural integrity compared Pseudothermotoga. Collectively, this suggests regions emerged indicators contributes our understanding molecular basis evolutionary

Language: Английский

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Microbiome Analysis via OTU and ASV-Based Pipelines—A Comparative Interpretation of Ecological Data in WWTP Systems

Bioengineering, Journal Year: 2022, Volume and Issue: 9(4), P. 146 - 146

Published: March 29, 2022

Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., 16S rRNA gene, is a staple microbial ecology dependent disciplines. The certainty results, independent bioinformatic handling, imperative for any advances made within field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary waste-activated sludge prokaryotic were analyzed two pipelines that apply different principles when dealing technical, sequencing, PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while other (DADA2) based on sequencing error correction algorithms generates exact amplicon sequence variants (ASVs). outcomes both compared framework ecological-driven data analysis. Both provided comparable results would generally allow same interpretations. Yet, approaches also delivered compositions differed between 6.75% 10.81% pipelines. Inconsistencies observed linked to biologically driven variability in samples, which affected differently. These pipeline-dependent differences assignment could lead conclusions interfere downstream such mis- or not-identified species, network predictions their respective service.

Language: Английский

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Bioremediation strategies and mechanisms of bacteria for resistance against heavy metals: a review

Bioremediation Journal, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 33

Published: July 12, 2024

Language: Английский

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Purification, Characterization, and Assessment of Anticancer Activity of Iron Oxide Nanoparticles Biosynthesized by Novel Thermophilic Bacillus tequilensis ASFS1‏

Journal of Basic Microbiology, Journal Year: 2024, Volume and Issue: 64(9)

Published: June 23, 2024

ABSTRACT Magnetic nanoparticles (MNPs), particularly iron oxide (IONPs), are a fascinating group of that have been considerably investigated for biomedical applications because their superparamagnetic properties, biodegradable nature, and biocompatibility. A novel Gram‐positive moderately thermophilic bacterial strain, namely Bacillus tequilensis ASFS.1, was isolated identified. This strain is capable producing Fe 3 O 4 exhibiting magnetotaxis behavior. swimming behavior under static dynamic environments, where it behaved very much similar to the in magnetotactic bacteria. study first report bacterium from Bacillaceae family has potential intracellular biosynthesis IONPs. MNPs were separated by magnetic reproducible method which designed time this study. In addition, UV‐visible spectrophotometer, Fourier‐transform infrared spectroscopy, vibrating sample magnetometer, field emission scanning electron microscopy (FESEM), X‐ray diffraction, thermal gravimetric analysis utilized characterize bio‐fabricated magnetite nanoparticles. Analysis particle size distribution pattern biogenic FESEM imaging revealed range 10–100 nm with 10–40 being most frequent particles. VSM demonstrated displayed properties high saturation magnetization value 184 emu/g. After 24 h treatment 3T3, U87, A549, MCF‐7, HT‐29 cell lines MNPs, IC 50 values measured be 339, 641, 582, 149, μg mL −1 , respectively. presents ASFS.1 aid its paving information on isolation, characterization, vitro cytotoxicity MNPs. The showed promising applications, obviously subject additional studies.

Language: Английский

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Non-sporeforming thermoduric bacteria vary considerably in thermal resistance in milk media between strains from the same genus

Journal of Dairy Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Thermoduric bacteria, defined as those that survive temperatures considerably above their maximum growth temperature, are enumerated in milk using the Laboratory Pasteurization Count test. This test selects for bacteria show limited cell count reductions under vat pasteurization conditions (i.e., 63°C 30 min), however, this has limitations. One limitation of is a broad group thermoduric many which not reported to HTST pasteurization, most commonly used method United States. There 2 distinct groups can impact quality if implicated finished product: sporeforming and non-sporeforming. Contemporary studies have primarily focused on leaving gap research regarding non-sporeforming bacteria. Therefore, goals study were i) assemble set previously isolated from heat treated dairy matrices, ii) use identify one or more laboratory enumeration method(s) select relevant contemporary products. To end, 38 isolates inoculated into skim broth, independently subjected 4 different treatments (A: min, B: 65°C 15 C: 68°C 7 min D: 70°C 5 followed by plating media types (Standard Methods Agar Aerobic Petrifilms), each incubated at 32°C after 3 incubation periods (24h, 48h, 72h). Results unique compared with standard test). indicate Petrifilms over estimate some genera suggesting may be an appropriate enumerating these genera. Heat treatment D min) showed trend higher reduction counts A method) 48h allowed enough time bacterial recovery. we propose evaluation Standard future naturally contaminated milk. Our results also suggest there considerable variability thermal resistance between same genus. These phenotypic differences driven yet unknown genotypic features should further examined. Ultimately, provides update existing knowledge focus evaluating

Language: Английский

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Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 19, 2025

Regulatory sequences encode crucial gene expression signals, yet the sequence characteristics that determine their functionality across species remain obscure. Deep generative models have demonstrated considerable potential in various inverse design applications, especially engineering genetic elements. Here, we introduce DeepCROSS, a artificial intelligence framework for of cross-species and species-preferred 5' regulatory bacteria. DeepCROSS constructs meta-representation using 1.8 million from thousands bacterial genomes to depict general constraints sequences, employs intelligence-guided massively parallel reporter assay experiments E. coli P. aeruginosa explore space, performs multi-task optimization obtain de novo sequences. The optimized achieve similar or better performance functional natural with high success rates low similarities genome. Collectively, efficiently navigates sequence-function landscape enables but remains unclear. authors an AI-aided strategy utilises large-scale accurate predictor

Language: Английский

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Machine learning for optimal growth temperature prediction of prokaryotes using amino acid descriptors

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Abstract The optimal growth temperature of organisms is valuable in bioprospecting enzymes that work under extremophilic conditions. Existing prediction models achieve high accuracy, but they mainly capture the trends mesophiles (OGT = 15-45°C) and taxonomies are abundantly present training set. In this study, we investigated use a weighted root mean square deviation (RMSE) phylogenetic splits to improve generalizability trained on amino acid descriptors. To do this, first built new OGT database more than 10,000 species distributed over 51 phyla Bacteria, Archaea Eukaryota with special attention include extreme data. Then, machine learning 6,401 observations available genomes. best performance was from multi-layer perceptron an RMSE 5.05°C R 2 0.81. most important model descriptors were related charged residues, as well bulky, hydrophobic residues.

Language: Английский

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Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(12)

Published: March 18, 2025

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, the capabilities ecological roles these communities remain largely unknown. We observed widespread relatively abundant bacterial phylum (CSP1-3) in soils evaluated its phylogeny, ecology, metabolism, evolutionary history. Genome analysis indicated that members CSP1-3 were actively replicating situ widely involved carbon, nitrogen, sulfur cycles. identified potential adaptive traits for oligotrophic environments, including mixotrophic lifestyle, flexible energy metabolisms, conservation pathways. ancestor likely originated an aquatic environment, subsequently colonizing topsoil and, later, with major clades adapted to each distinct niches. transition into terrestrial environment was associated genome expansion, horizontal acquisition range genes carbohydrate metabolism one lineage, high-affinity terminal oxidases support microaerophilic lifestyle. Our results highlight ecology evolution microbes Critical Zone.

Language: Английский

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