Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Авг. 23, 2024

Microbes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host–microbe interactions across vertical compartments in plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized. Here, we investigated microbial communities associated with CSR-resistant and CSR-susceptible cultivars using multi-omics analysis coupled experimental verification. Maize resistant to CSR reshaped microbiota recruited Bacillus species three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion antimicrobial compounds, no inhibition alleviate pathogen stress. By inducing expression Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes production tyramine dopamine, isolates do not directly suppress infection induced synthesis berberine, isoquinoline alkaloid inhibits growth. These beneficial bacteria were from rhizosphere transferred stems but grains plants. The current study offers insight into how respond interact their microbiome lays foundation preventing treating soil-borne pathogens.

Язык: Английский

---

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

PLoS ONE, Год журнала: 2024, Номер 19(1), С. e0296672 - e0296672

Опубликована: Янв. 19, 2024

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, three species representing important plankton groups different cell structures; ciliate Tetrahymena thermophila , diatom Phaeodactylum tricornutum dinoflagellate Heterocapsa sp. Both fixation permeabilization steps were adjusted. For dinoflagellate, number transcripts spots single significantly higher than for background spots, overall expression patterns correlated bulk RNA, while much smaller it was not possible separate from background. The MASC-seq method holds promise investigating "microbial dark matter”, although further optimizations necessary increase signal-to-noise ratio.

Язык: Английский

---

Comprehensive profiling of antibiotic resistance genes in diverse environments and novel function discovery

The Innovation Life, Год журнала: 2024, Номер 2(1), С. 100054 - 100054

Опубликована: Янв. 1, 2024

<p>Antibiotic resistance genes (ARGs) have emerged in pathogens and are arousing worldwide concern, accurately identifying unknown ARGs is a formidable challenge studying the generation spread of antibiotic diverse environments. Current methods can identify known but limited utility for discovery novel ARGs, thus rendering profiling incomprehensive. Here, we developed ONN4ARG, an ontology-aware deep learning approach comprehensive ARG discovery. Systematic evaluation revealed that ONN4ARG outperforms previous terms efficiency, accuracy, comprehensiveness. Experiments using 200 million microbial collected from 815 metagenomic samples environments or hosts resulted 120,726 candidate which more than 20% not yet present public databases. The set environment-specific host-specific patterns. wet-lab functional validation together with structural investigation validated streptomycin gene oral microbiome samples, confirming ONN4ARG’s ability to discover functions. In summary, enables toward grand view worldwide.</p>

Язык: Английский

---

Artificial Intelligence in Omics

Genomics Proteomics & Bioinformatics, Год журнала: 2022, Номер 20(5), С. 811 - 813

Опубликована: Окт. 1, 2022

---

Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities

Critical Reviews in Microbiology, Год журнала: 2024, Номер unknown, С. 1 - 21

Опубликована: Фев. 22, 2024

Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in environment can undergo cultivation for study under laboratory conditions, and rest enigmatic, world remains mysterious, constituting a kind “microbial dark matter” (MDM). In last two decades, remarkable progress has been made culture-dependent culture-independent techniques. More recently, studies MDM have relied techniques to recover genetic material through either unicellular genomics or shotgun metagenomics construct single-amplified genomes (SAGs) metagenome-assembled (MAGs), respectively, which provide information about evolution metabolism. Despite past functional diversity still uncharacterized. This review comprehensively summarizes recently developed characterizing MDM, discussing major challenges, opportunities, potential applications. These activities contribute expanding our knowledge implications various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary Planetary biology. Overall, this aims peel off layers from shed light recent advancements, identify future illuminate exciting opportunities that lie ahead unraveling secrets intriguing realm.

Язык: Английский

---

Modelling of microbial interactions in anaerobic digestion: from black to glass box

Current Opinion in Microbiology, Год журнала: 2023, Номер 75, С. 102363 - 102363

Опубликована: Авг. 3, 2023

Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles Earth's climate. These ecological niches characterised by low free oxygen oxidants, or lack thereof. Under these conditions, interactions between species for supporting growth syntrophic maintaining thermodynamic feasibility anaerobic fermentation. Kinetic models provide a simplified view complex metabolic networks, while genome-scale flux-balance analysis (FBA) aim unravel systems as whole. The target this review is outline main similarities, differences challenges associated with kinetic modelling, describe state-of-the-art modelling practices studying syntrophies digestion (AD) case study.

Язык: Английский

---

Coalescence characteristics of free-living and particle-attached bacteria in a cascade river-reservoir system: A case study of the Jinsha River

Journal of Environmental Management, Год журнала: 2025, Номер 374, С. 124088 - 124088

Опубликована: Янв. 13, 2025

Язык: Английский

---

Biology’s Dark Matter: From Galaxies to Microbes

Theory Culture & Society, Год журнала: 2025, Номер unknown

Опубликована: Янв. 16, 2025

Emergent research in metagenomics has unveiled large quantities of previously unknown and unclassified prokaryotic DNA. As these prokaryotes constitute the vast majority microbial life environmental samples, some microbiologists commentators scientific media have referred to this expansive as ‘biological dark matter’, translating rhetorical power matter from physical sciences. Engaging literatues approaches across philosophy, history, social studies science, we explore cultural significance theory sciences examine implications its conceptual reworking biology, through critically engaging political narratives folded within matter’s genealogies. ‘Dark matter’ designates both zones importance turbulence, simultaneously emphasizing microbiologists’ creativity whilst constructing new ways relating microbiota. Such a situation, propose, also invites theoretical analysis it calls for reconsideration gene fundamental role

Язык: Английский

---

Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers

Microbiome, Год журнала: 2025, Номер 13(1)

Опубликована: Март 4, 2025

As the first line of defense against external pathogens, skin and its resident microbiota are responsible for protection eubiosis. Innovations in DNA sequencing have significantly increased our knowledge microbiome. However, current characterizations do not discriminate between from live cells remnant dead organisms (relic DNA), resulting a combined readout all microorganisms that were currently present on rather than actual living population Additionally, most methods lack capability absolute quantification microbial load skin, complicating extrapolation clinically relevant information. Here, we integrated relic-DNA depletion with shotgun metagenomics bacterial determination to quantify cell abundances across different sites. Though discovered up 90% be relic DNA, saw no significant effect this relative taxa determined by sequencing. Relic-DNA prior strengthened underlying patterns microbiomes volunteers reduced intraindividual similarity. We abundance fraction alive several common body sites found taxa-specific differential bacteria regions estimates generated total (live + dead) Our results reveal bias has low biomass samples like skin. The similarity following highlights introduced traditional (total DNA) diversity comparisons samples. divergent levels viability measured sites, along inconsistencies vs sequencing, suggest an important hypothesis certain being susceptible pathogen infection. Overall, study demonstrates characterization microbiome overcomes provide baseline will further improve mechanistic studies infection, disease progression, design therapies Video Abstract.

Язык: Английский

---

A novel culture method with filter paper for isolating aerial microalgae under aerial-phase conditions

Algal Research, Год журнала: 2025, Номер unknown, С. 104019 - 104019

Опубликована: Март 1, 2025

Язык: Английский

---