Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review

Food Research International, Journal Year: 2024, Volume and Issue: 188, P. 114497 - 114497

Published: May 11, 2024

Language: Английский

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Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

EFSA Supporting Publications, Journal Year: 2024, Volume and Issue: 21(2)

Published: Feb. 1, 2024

Scientific interest in the use of environmental microbiomes for risk assessment is rapidly growing, as exemplified by various EFSA opinions. In absence official regulatory guidelines on how to integrate assessment, aims this report are therefore determine whether microbiome studies can be used such purposes, and propose a roadmap integration assessments under EFSA's remit. The identifies current gaps (in terms knowledge from technical point view) barriers that might delay implementation methods, offers recommendations standardised (multi-)omics techniques purposes. Our main findings identified five priorities: (i) defining core (what it encompasses what made of, including identification bioindicators) assess impact any type disturbance; (ii) standardising methodologies protocols, sampling interpretation, guarantee comparability analyses; (iii) developing tools facilitate interpretation; (iv) collecting microbiome-based data shared, curated maintained databases; (v) setting up European Network Microbiome Laboratories reach an agreement standardise studies, interactions between researchers access or samples, actively include multiple stakeholders discussions involving assessment. There both short- longer-term priorities, all which highlight need mobilise concurrently different agencies institutions, well research. also points out capacity building training, acceptance emerging technology, communication issues. These will hopefully contribute elaboration widely accepted framework dealing with.

Language: Английский

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Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter

Animal Microbiome, Journal Year: 2023, Volume and Issue: 5(1)

Published: Oct. 24, 2023

Microbiome in early life has long-term effects on the host's immunological and physiological development its disturbance is known to trigger various diseases host Deuterostome animals. The sea cucumber Apostichopus japonicus one of most valuable marine invertebrates Asia a model animal regeneration studies. To understand factors that impact holobiont maintenance, host-microbiome association been actively studied last decade. However, we currently lack knowledge core microbiome during ontogenesis how it benefits growth.We analyzed microbial community 28 samples from laboratory breeding system, designed replicate aquaculture environments, across six developmental stages (fertilized eggs juvenile stage) over three years-period examine microbiomes' dynamics stability. shifts occurred larval every case. Application sophisticated extraction methodology, hybrid approach with abundance-occupancy analyses (top 75% total reads > 70% occupation) index calculation, first revealed consisted Alteromonadaceae Rhodobacteraceae, as well stage consisting pioneer microbe Pseudoalteromonadaceae A. japonicus, suggesting stepwise establishment related feeding behavior japonicus. More interestingly, four ASVs affiliated Rhodobacteraceae were extracted microbiome. One ASV (ASV0007) was Sulfitobactor strain BL28 (Rhodobacteraceae), isolated blastula larvae 2019 raring batch. Unexpectedly, bioassay retains growth-promoting ability. Further meta-pangenomics genome abundant metagenomic sequence pool, particular, post-gut japonicus.Repeated rearing efforts using replicating environments particular growth promoting ability microbes, identified ASV0007. Genome which makes us consider effective probiotic uses those for resource production conservation. study also emphasizes importance influencing invertebrates. Understanding these could offer pathways improve growth, immunity, disease resistance

Language: Английский

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Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands

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

Published: Jan. 22, 2025

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from methane-emitting wetlands. Microorganisms drive cycling, but little is known about their conservation across To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual flux data 9 wetlands, creating Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource used link microbiome composition function emissions, focusing on methane-cycling microbes networks driving carbon decomposition. We identify eight genera shared wetlands show wetland-specific metabolic interactions marshes, revealing low connections between methanogens methanotrophs high-emitting Methanoregula emerged as a hub methanogen strong predictor flux. In these it also displays functional potential methylotrophic methanogenesis, highlighting importance this pathway ecosystems. Collectively, our findings illuminate trends microbial decomposition while providing an extensive publicly available database advance future research. The authors created multisite CH4 fluxes diverse differences cross-feeding dynamics that improve predictions

Language: Английский

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Tetrodotoxin, fungal pathogen infection, and bacterial microbiome associations are variable in the skin microecosystems of two Taricha newt species

Frontiers in Amphibian and Reptile Science, Journal Year: 2025, Volume and Issue: 2

Published: Jan. 28, 2025

A diverse metabolome exists on amphibian skin that mediates interactions between hosts and microbiomes. Tetrodotoxin is one such metabolite occurs across a variety of taxa, particularly well studied in newts the genus Taricha are susceptible to infection with chytrid fungi. The interaction tetrodotoxin microbiome, including pathogenic fungi, not understood, here we describe these patterns 12 populations granulosa T. torosa Washington, Oregon, California. We found no correlation TTX Batrachochytrium dendrobatidis (Bd) either or , pattern inconsistent previous study. In addition, TTX, but Bd, was significantly correlated microbiome composition . however, structure. relationship differed species, significant correlations observed only which exhibited higher concentrations. also detected abundances bacterial taxa (e.g., Pseudomonadaceae) associated production TTX. These (ASVs matching Aeromonas, Pseudomonas, Shewanella Sphingopyxis ) were all body sites previously sampled soil samples. Our results suggest toxins can shape newt may influence pathogen through indirect mechanisms, as showed direct inhibition Bd B. salamandrivorans growth.

Language: Английский

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A field survey: Distinctive composition of core and keystone taxa in root microbiota of Carex cepillacea on the Qinghai-Tibet Plateau

Soil Ecology Letters, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 12, 2025

Language: Английский

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The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 11, 2025

Abstract Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. grains can be reused to start new fermentations. Here we investigate the microbial composition function of 69 their ferments by shotgun metagenomics. A subset samples was subjected metabolomic, including volatilomic, analysis. The impact different fermentation practices on characteristics analysed it noted that, for example, common practice drying water significantly reduces diversity negatively impacts subsequent grain growth. Metagenomic analysis allowed detection 96 species within WK, definition core genera community states after 48 h fermentation. total 485 bacterial metagenome assembled genomes were obtained 18 putatively novel predicted. Metabolite volatile show associations between key with flavour compounds. We complex links practices, microbes product. results used as a foundation selection large scale production desired profiles guide regulatory framework commercial production.

Language: Английский

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Distinct Fecal Microbiome Communities and Functional Predictions in Spotted Seals: Age‐Dependent and Dietary Transformations

Marine Mammal Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 9, 2025

ABSTRACT The spotted seal ( Phoca largha ), which primarily inhabits the cold waters of Northwest Pacific Ocean, including China's northern Bohai and Yellow Seas, exhibits age‐related variations in its fecal microbiome that remain poorly understood. This study investigated composition predicted functional capabilities between adult juvenile seals. Firmicutes was dominant phylum both groups, with significant differences abundances Bacteroidota p < 0.05). Furthermore, higher taxonomic diversity found adults, six genera compared to three juveniles. Clostridium sensu stricto 1 UCG‐005 were identified as core genera, whereas Bacteroides Peptoclostridium specific adults Eubacterium fissicatena group Blautia Moreover, bacterial prediction revealed a enrichment 0.01) Transporters ABC transporters pathways juveniles, while Ribosome pathway abundant 0.01). adults’ displayed more complex stable interactions than Additionally, phylogenetic analysis perfringens distributed across marine terrestrial mammals, Faecalicatena juveniles demonstrated high host specificity. These findings help explain how age diet shape gut mammals.

Language: Английский

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Comparative analysis of deep dentinal caries microbiota in teeth with normal pulp, reversible pulpitis, symptomatic and asymptomatic irreversible pulpitis

International Endodontic Journal, Journal Year: 2025, Volume and Issue: unknown

Published: March 14, 2025

Abstract Aim To characterize the deep dentinal caries microbiota in teeth diagnosed with normal pulp (NP), reversible pulpitis (RP), symptomatic irreversible (SIP), and asymptomatic (AIP), to identify potential key pathogens associated progression, exploring their roles disease advancement. Methodology In this cross‐sectional study, we collected 108 samples, categorized into NP ( n = 27), RP SIP AIP according American Association of Endodontists' diagnostic criteria. 2 samples were excluded due contamination. Samples processed using Illumina MiSeq high‐throughput sequencing. Alpha beta diversity, taxa abundance differences, co‐occurrence network analysis, functional prediction evaluated. Correlation analysis between bacteria clinical diagnosis, signs, exposure status was performed Spearman Mantel test. Results The bacteriome exhibited statistically significant differences among NP, RP, SIP, groups. showed similar microbial community structures, comparable alpha bacterial phenotypes, functions, structures. contrast, displayed distinct profiles. characterized by higher diversity a greater gram‐negative bacteria, Propionibacterium Prevotella_7 identified as pathogenesis. On other hand, lower facultative anaerobes, Lactobacillus Limosilactobacillus Fusobacterium , Prevotella Treponema Selenomonas both SIP. Compared networks are more complex contain endodontic pathogens. These form positive correlations each numerous negative lactic acid bacteria. Conclusions differs significantly across AIP, exhibit communities, whereas display

Language: Английский

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Rare taxa in the core microbiome

Trends in Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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