The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Foods, Год журнала: 2022, Номер 11(20), С. 3297 - 3297

Опубликована: Окт. 21, 2022

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities health-promoting traits, maintaining microbiological safety foods. In this context, it is crucial to study these characterise production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable community studies through amplicon shotgun sequencing approaches. As field constantly develops, technologies becoming more accessible, affordable accurate with further shift from short read long being observed. Metagenomics enjoying wide-spread application in food recent years also employed concert synthetic biology techniques help tackle problems large amounts waste generated sector. This review presents an introduction current benefits their

Язык: Английский

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Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report)

Pure and Applied Chemistry, Год журнала: 2022, Номер 94(10), С. 1161 - 1194

Опубликована: Окт. 1, 2022

Abstract Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment aquatic toxicity pesticides is based range advanced tests. This does not apply to terrestrial ecosystems, where soil microorganisms, outdated and crude test (N mineralization). gap reinforced by recent methodological standardization advances in microbial ecology. The inclusion such standardized tools revised risk assessment will enable accurate estimation microorganisms associated ecosystem services. In review we (i) summarize work point ammonia-oxidizing (AOM) arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations experimental approaches used propose mitigation solutions, (iii) scientific gaps (iv) procedure assess microorganisms.

Язык: Английский

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Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Июнь 16, 2023

The study of microbiota has been revolutionized by the development DNA metabarcoding. This sequence-based approach enables direct detection microorganisms without need for culture and isolation, which significantly reduces analysis time offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there an accumulating number researches on bacteria, molecular fungi still remains challenging due to lack standardized tools incompleteness reference databases limiting accurate precise identification fungal taxa. Here, we present a metabarcoding workflow characterizing with high resolution. method involves amplifying longer stretches ribosomal RNA operons sequencing them using nanopore long-read technology. resulting reads were error-polished generate consensus sequences 99.5-100% accuracy, then aligned against genome assemblies. efficacy this was explored polymicrobial mock community patient-derived specimens, demonstrating marked potential combined calling classification. Our powerful tool rapid pathogenic promise improve our understanding role in health disease.

Язык: Английский

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A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Cell Reports, Год журнала: 2024, Номер 43(4), С. 114046 - 114046

Опубликована: Апрель 1, 2024

Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to health of Earth and its inhabitants. To identify bacteria fungi that are resistant susceptible habitat we analyze thousands genera detected 1,580 host, soil, aquatic samples. This large-scale analysis identifies 48 bacterial 4 fungal abundant across three biomes, demonstrating fitness diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These play a significant role shaping cross-kingdom community structure, boasting larger genomes more secondary metabolism antimicrobial resistance genes. Conversely, 30 19 only found single habitat, suggesting limited ability adapt different changing environments. findings contribute our understanding niche breadth consequences for global biodiversity loss.

Язык: Английский

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Frontiers in soil ecology—Insights from the World Biodiversity Forum 2022

Journal of Sustainable Agriculture and Environment, Год журнала: 2022, Номер 1(4), С. 245 - 261

Опубликована: Ноя. 11, 2022

Abstract Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much unknown about how function will in the future response to simultaneous alterations climate land use, as well other environmental drivers. It crucial understand direct, indirect interactive effects of global drivers on communities ecosystems contexts, not only today but also near future. This particularly relevant for international efforts tackle like Paris Agreement, considering failure achieve 2020 targets, especially target halting degradation. Here, we outline main frontiers related ecology that were presented discussed at thematic sessions World Biodiversity Forum 2022 Davos, Switzerland. We highlight multiple knowledge associated with data integration, causal inference, scenarios, critical facets, underrepresented drivers, collaboration, application transdisciplinarity, policy public communication. These identified research priorities are immediate interest scientific community may be considered priority programmes calls funding.

Язык: Английский

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