Resolution of MALDI-TOF compared to whole genome sequencing for identification of Bacillus species isolated from cleanrooms at NASA Johnson Space Center

Frontiers in Microbiology, Год журнала: 2025, Номер 16

Опубликована: Апрель 9, 2025

Introduction Bacteria are frequently isolated from surfaces in cleanrooms, where astromaterials curated, at NASA’s Lyndon B. Johnson Space Center (JSC). Bacillus species of particular interest because endospores can endure extreme conditions. Current monitoring programs JSC rely on culturing microbes swabs followed by identification 16S rRNA sequencing and the VITEK 2 Compact bacterial system. These methods have limited power to resolve species. Whole genome (WGS) is current standard for but expensive time-consuming. Matrix-assisted laser desorption - time flight mass spectrometry (MALDI-TOF MS), provides a rapid, low-cost, method identifying isolates has higher resolution than sequencing, particularly species; however, few studies compared this WGS cleanrooms. Methods To address this, we selected 15 analysis with MALDI-TOF MS. Hybrid next-generation (Illumina) 3rd-generation (nanopore) were used draft genomes. Mass spectra, generated MS, processed custom scripts identify clusters closely related isolates. Results MS identified 13/15 9/14 level, respectively, showed good agreement, terms congruence partitioning, phylotypes WGS. Pairs strains that > 94% similar each other, average amino acid identity (AAI) predicted WGS, consistently cosine similarities spectra >0.8. The only discordance was pair classified as Paenibacillus This relatively high similarity (0.85) 85% AAI. In addition, some cleanrooms appeared spacecraft assembly Discussion Since costs less whole offers throughput hundreds per hour, approach appears offer cost-efficient option species, microbes, during routine built environments.

Язык: Английский

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Exploring phylogenetic diversity of antibiotic resistance genes in activated sludge: A host and genomic location perspective

Environmental Research, Год журнала: 2025, Номер unknown, С. 121588 - 121588

Опубликована: Апрель 1, 2025

Язык: Английский

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Linking Fungal Genomics to Thermal Growth Limits: A Dataset of 730 Sequenced Species

Data, Год журнала: 2025, Номер 10(4), С. 42 - 42

Опубликована: Март 25, 2025

The response of fungal species to changes in temperature is theoretical and practical importance a world changing temperatures, ecologies populations. Genomic sequencing identify their potential metabolic capabilities well established, but linking this growth conditions has been limited. To that end, I describe dataset brings together the maximum minimum limits for 730 Fungi Oomycetes which genome sequences are available, with supporting proteome taxonomic data literature references. set will provide an entry studies into how genomic structure sequence can be used predict at low or high hence industrial use pathogenic liability existing new species.

Язык: Английский

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PRODIGIOSIN PIGMENT-PRODUCING STREPTOMYCES DIASTATICUS ON SEMI-SOLID MEDIA AND ANTICANCER ACTIVITY AGAINST COLORECTAL (COLO-205) CELL LINE

Microbial Pathogenesis, Год журнала: 2025, Номер unknown, С. 107579 - 107579

Опубликована: Апрель 1, 2025

Язык: Английский

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Marine viruses disperse bidirectionally along the natural water cycle

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 10, 2023

Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards atmosphere remains a knowledge gap. Here, we show that 6.2% of studied virus population were shared between and rainwater. Virus enrichment 1-mm thin surface microlayer sea foams happened selectively, variant analysis proved transfer to aerosols collected ~2 m height above level rain. Viruses detected rain these showed significantly higher percent G/C base content compared marine viruses. CRISPR spacer matches prokaryotes foreign rainwater prove regular virus-host encounters interface. Our findings on aerosolization, adaptations, support transmission along natural water cycle.

Язык: Английский

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Genome-scale phylogeny and comparative genomics of the fungal order Sordariales

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 189, С. 107938 - 107938

Опубликована: Окт. 10, 2023

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles large economic importance. Despite its importance, a robust genome-scale phylogeny, associated comparative genomic analysis of the lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, seven outgroup taxa. We inferred comprehensive phylogeny that resolved several contentious relationships amongst families in order, cleared-up intrafamily within Podosporaceae. Extensive genomics showed genomes three largest dataset (Chaetomiaceae, Podosporaceae Sordariaceae) differ greatly GC content, genome size, gene number, repeat percentage, evolutionary rate, content affected by repeat-induced point mutations (RIP). All traits phylogenetic signal, ancestral state reconstruction revealed variation properties stems primarily within-family evolution. Together, results provide thorough framework for understanding evolution important group fungi.

Язык: Английский

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Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea

Frontiers in Microbiology, Год журнала: 2024, Номер 15

Опубликована: Фев. 29, 2024

This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within Chloroflexota phylum. Employing multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration adaptive features, research unveils novel insights family’s taxonomy dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, mesophilic lineage, tentatively named Mesolinea , emerges showcasing distinctive profile apparent adaptation to lifestyle. comprehensive analyses shed light on complex patterns, conservation key operons thermophiles, providing foundation for understanding ecological roles strategies Anaerolineaceae members.

Язык: Английский

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Ecological versatility and biotechnological promise: Comprehensive characterization of the isolated thermophilic Bacillus strains

PLoS ONE, Год журнала: 2024, Номер 19(4), С. e0297217 - e0297217

Опубликована: Апрель 18, 2024

This study focuses on isolated thermophilic Bacillus species' adaptability and physiological diversity, highlighting their ecological roles potential industrial applications. We specifically investigated capacity to thrive in extreme conditions by examining environmental tolerances adaptations at the metabolic genetic levels. The primary objective is evaluate suitability of these species for biotechnological applications, considering resilience harsh environments. conducted a comparative analysis parameters various species. included growth temperature ranges, pH tolerance, oxygen requirements, carbohydrate fermentation patterns, colony morphology, enzymatic activities, properties. Controlled laboratory experiments provided data, which were then analyzed determine patterns diversity. research revealed that could endure temperatures as high 73°C, with generally lower limit 43°C. However, strains TBS35 TBS40 exceptions, growing 37°C. Most preferred slightly alkaline (optimal 8), but TBS34, TBS35, exhibited highly environments (pH 11). Oxygen requirement tests classified into aerobic, anaerobic, facultative aerobic categories. Genetic highlighted variations DNA concentrations, 16s rRNA gene lengths, G+C content across Although glucose was substrate fermentation, exceptions indicated flexibility. profiles varied, universal absence urease differences catalase oxidase production. Our findings underscore significant diversity under conditions. Their temperatures, levels, varied conditions, diverse features emphasize These insights deepen our understanding highlight

Язык: Английский

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Unexpected functional diversity of stream biofilms within and across proglacial floodplains despite close spatial proximity

Limnology and Oceanography, Год журнала: 2023, Номер 68(9), С. 2183 - 2194

Опубликована: Авг. 18, 2023

Abstract High‐mountain streams are particularly vulnerable to climate change because they intimately interface with the cryosphere. As glaciers shrink and snowpack diminishes, proglacial will eventually shift from being glacier‐fed fed by groundwater, snowmelt precipitation. This affect both flow regime physico‐chemical characteristics of streams, possibly also structure function their benthic microbiome. Here, we applied genome‐resolved metagenomics biofilms groundwater‐fed tributaries within three floodplains in Swiss Alps. Despite close spatial proximity between stream types, microbiome differed consistently for prokaryotes eukaryotes. The was taxonomically functionally less diverse than its counterpart, had smaller genomes, but conservation central metabolic functions primarily related nitrogen sulfur cycling. Consequently, much higher functional variability associated tributary mainly due abundant genes involved transport degradation organic matter. Our findings suggest that glacier shrinkage cause shifts functioning microbiomes yet unknown consequences downstream biogeochemistry.

Язык: Английский

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Lineage-specific evolution of Aquibium , a close relative of Mesorhizobium , during habitat adaptation

Applied and Environmental Microbiology, Год журнала: 2024, Номер unknown

Опубликована: Фев. 27, 2024

ABSTRACT The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. genomes of species isolated water were smaller and had higher GC contents than those species. Six lacking found to exhibit low similarity in average nucleotide identity values other 24 Therefore, they classified as non-N 2 -fixing lineage (N-ML), an evolutionary intermediate results our phylogenomic analyses loss Rhizobiales-specific fur/mur indicated may have evolved through ecological transition. Halotolerant alkali-resistant microcysteis belonging N-ML possessed many tripartite ATP-independent periplasmic transporter sodium/proton antiporter subunits composed seven genes ( mrpABCDEFG ). These not present N (ML), suggesting acquired for adaptation highly saline alkaline environments lost during evolution ML habitat changed soil. Land-to-water changes species, close relatives could influenced their genomic by gain genes. Our study lineage-specific played a significant role shaping genome architecture conferring ability thrive different habitats. IMPORTANCE Phylogenetic revealed (AL) (N-ML) monophyletically grouped into distinct clusters separate (ML). N-ML, having characteristics both ancestral descendant provide snapshot genetic occur adaptation. Genomic AL, levels related transporters, chemotaxis, nitrogen fixation likely reflect adaptations environmental conditions. sheds light on complex dynamic nature rhizobia response environment highlights crucial analysis understanding these processes.

Язык: Английский

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