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At least 19 recordsLinked to original sources

PubMed2026

Metagenomic Insights into Microbial Assembly and Key Metabolic Genes Driving Flavor Formation in Spontaneously Fermented Zhejiang Rosy Vinegar.

The spontaneous fermentation of Zhejiang rosy vinegar (ZRV) is driven by environmental microbiota, but the processes underlying its flavor formation remain poorly understood. Using metagenomic sequencing, we investigated microbial community assembly, environmental drivers, and metabolic networks during industrial-scale ZRV fermentation. Acetic acid dominated the final organic acids. Community assembly shifted toward deterministic selection with rising acidity, with a slight rebound of stochastic processes in the late stage (R2 values of 0.442 and 0.346 for bacteria and fungi, respectively). Mantel tests confirmed that environmental factors significantly regulated microbial assembly. Co-occurrence networks grew more complex, with positive interactions accounting for 85.24% (bacteria) and 90.10% (fungi) in the late stage. Key genes (ldh, gapA, pgk) from Acetobacter pasteurianus and Lactobacillus acetotolerans dominated late-stage fermentation, while genes (adhP, SDH) from Aspergillus oryzae and Saccharomyces cerevisiae supported early- and mid-stage fermentation. These findings elucidate microbiota-driven metabolic pathways in ZRV, supporting the fermentation window optimization and industrial vinegar quality standardization.

Acetic Acid↗

PubMed2026

The genome sequence of a coronate scyphozoan jellyfish, Nausithoe racemosa (Komai, 1936) (Coronatae: Nausithoidae), and a metagenome-assembled genome of the associated cyanobacterium Moorena producens.

We present a genome assembly from a specimen of Nausithoe racemosa (coronate scyphozoan jellyfish; Cnidaria; Scyphozoa; Coronatae; Nausithoidae). The assembly contains two haplotypes with total lengths of 4 784.66 megabases and 4 868.20 megabases. Most of haplotype 1 (97.34%) is scaffolded into 20 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 13.97 kilobases. From the metagenome data, we recovered one high-quality metagenome-assembled genome.

Coronatae↗

PubMed2026

The chromosomal genome sequence of a staghorn coral, Acropora cf.  manni (Scleractinia: Acroporidae).

We present a genome assembly from a colony sample of Acropora cf. manni (staghorn coral; Cnidaria; Anthozoa; Scleractinia; Acroporidae). The assembly contains two haplotypes with total lengths of 459.26 megabases and 489.30 megabases. Most of haplotype 1 (94.39%) is scaffolded into 14 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 18.48 kilobases. Metagenome binning recovered one bacterial bin from the phylum Chlamydiota.

Acropora cf. manni↗

PubMed2026

De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.

Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.

DNA, Ancient↗

PubMed2026

The chromosomal genome sequence of the lesser starlet coral, Siderastrea radians (Pallas, 1766) (Scleractinia: Rhizangiidae) and its associated microbial metagenome sequences.

We present a genome assembly from a specimen of Siderastrea radians (lesser starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 807.19 megabases. Most of the assembly (94.17%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.38 kilobases. Gene annotation of this assembly by Ensembl identified 47 051 protein-coding genes. From the metagenome data, we recovered two binned metagenomes assigned to the bacterial phylum Bacteroidota and class Bacteroidia.

Scleractinia↗

PubMed2026

The chromosomal genome sequence of the spiny sea fan, Muricea muricata (Pallas, 1766) (Malacalcyonacea: Plexauridae) and its associated microbial metagenome sequences.

We present a genome assembly from a Muricea muricata specimen (spiny sea fan; Cnidaria; Anthozoa; Malacalcyonacea; Plexauridae). The genome sequence has a total length of 453.40 megabases. Most of the assembly (98.45%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.29 kilobases. Gene annotation of this assembly by Ensembl identified 52 164 protein-coding genes. From the metagenome data, we recovered five bins, of which three were high-quality MAGs.

Malacalcyonacea↗

PubMed2026

The chromosomal genome sequence of the maze coral, Meandrina meandrites (Linnaeus, 1758) (Scleractinia: Meandrinidae) and its associated microbial metagenome sequences.

We present a genome assembly from a specimen of Meandrina meandrites (maze coral; Cnidaria; Anthozoa; Scleractinia; Meandrinidae). The genome sequence has a total length of 551.16 megabases. Most of the assembly (99.25%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.2 kilobases. Gene annotation of this assembly by Ensembl identified 30 464 protein-coding genes. We recovered two bins from the metagenome data.

Meandrina meandrites↗

PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗

PubMed2026

Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.

BACKGROUND: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean. RESULTS: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses. CONCLUSIONS: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.

Membrane Transport Proteins↗

PubMed2026

Catalog of metagenome-assembled genomes of prokaryotic communities from the Red Sea hydrothermal vents.

This study presents medium- and high-quality prokaryotic metagenome-assembled genomes (MAGs) from microbial mats and sediments at Hatiba Mons, a Red Sea hydrothermal system. We recovered 1,217 bacterial and archaeal MAGs across 75 phyla, dominated by Planctomycetota and Thermoproteota. Approximately 70% of these genomes likely represent previously uncharacterized taxa.

extreme environment↗

PubMed2026

Minimizing decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea.

The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimizing pressure and temperature effects. When compared to samples collected under pressurized conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a >20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurized (e.g. members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g. Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.

Seawater↗

PubMed2026

Genomic and biosynthetic landscape of high-temperature Daqu microbiome.

As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82 % of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3 % are novel, and 17,031 biosynthetic gene clusters, of which 62.63 % are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.

Microbiota↗

PubMed2026

Metagenome-assembled genomes for N2-fixing cyanobacterium Nostoc sp. TISTR 8405 and co-occurring microorganisms from a long-term laboratory culture.

We report here metagenome-assembled genomes from a long-term laboratory culture of the nitrogen-fixing cyanobacterium Nostoc sp. TISTR 8405, originally sourced from a Thai freshwater lake. The community consists of two additional co-occurring microorganisms, Erythrobacter sp. THAI-01 and Allorhizobium sp. THAI-01, and contains putative plasmids associated with Nostoc and Allorhizobium, respectively.

co-culture↗

PubMed2025

The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.

Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.

Rumen↗

PubMed2026

Gut microbiota-driven indole-3-propionic acid and kynurenine production is associated with improved metabolic adaptation in periparturient dairy cows.

BACKGROUND: Gastrointestinal microbes convert tryptophan into various bioactive metabolites that influence host energy metabolism; however, these mechanisms are not well understood in periparturient dairy cows, which experience marked metabolic challenges during this period. RESULTS: In this study, we used periparturient dairy cows with rumen and ileal cannulas as in vivo models. Blood, rumen fluid, ileal digesta, and fecal samples were collected at four time points during the periparturient period. By combining metagenome-assembled genomes (MAGs) and targeted metabolite quantification, we characterized microbial tryptophan metabolism and associated metabolite profiles during the periparturient period. The results showed that postpartum cows exhibited significantly increased serum concentrations of triglyceride (TG), aspartate aminotransferase (AST), β-hydroxybutyrate (BHBA), and total bilirubin (T-Bil) compared with prepartum cows, together with decreased levels of several tryptophan metabolites, including indole-3-propionic acid (IPA) and kynurenine (KYN), indicating that tryptophan deficiency might aggravate metabolic disturbances. Metagenomic analysis identified 578 high-quality MAGs, of which 461 contained genes involved in microbial tryptophan metabolic pathways. Among these, the ruminal taxon CAG-791 harbors acdA and contributes to IPA production, whereas the hindgut taxon Treponema_D harbors kynB and promotes KYN formation. Decreases in both taxa were consistent with the reduced levels of these metabolites observed above. In a follow-up in vivo trial with tryptophan supplementation, the abundance of CAG-791 and Treponema_D increased, along with tryptophan-derived metabolites (IPA and KYN), which further partially mitigated metabolic disturbances. CONCLUSIONS: These findings characterize spatial and temporal changes in tryptophan metabolites and gut microbial features in periparturient dairy cows, and provide integrated evidence that alterations in tryptophan metabolism are associated with postpartum metabolic adaptation, thereby supporting the potential of tryptophan-targeted nutritional strategies to improve metabolic health in dairy cows.

Gastrointestinal microbiome↗

PubMed2025

Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.

The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ13C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.

Soil Pollutants↗

PubMed2026

Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.

Culture-independent techniques are playing a major role in exploring unique and novel microbial communities from complex ecosystems, leading to an outstanding impact on our basic understanding of the tree of life. Microbial communities are not extensively studied in layer chicken housing environments, particularly from the point of view of taxa carrying antimicrobial resistance genes, virulence genes and their functional potential. This study aimed to extract metagenomic-assembled genomes (MAGs) from the Illumina short-reads shotgun metagenomics sequenced data that originated from an Alberta poultry barn environment and then to study host tracking of antimicrobial resistance genes (ARGs) and the roles of genes involved in functions related to ammonia production, short-chain fatty acid (SCFA)-related pathways, sulfur metabolism, methane emission, stress and disinfectant-related pathways. A total of 251 high-quality MAGs were extracted, including 249 bacterial and two archaeal genomes from sequencing data of 30 metagenomic sequencing samples comprising 15 air and 15 manure samples collected from 15-layer farms. Interestingly 22 bacterial MAGs were not classified to species levels using GTDB-based classification. ARGs were mainly harbored by the genera Staphylococcus, Alistepes, Romboutsia, and Enterococcus. Bacteroides is a main taxon carrying ARGs in air samples. Ammonia production-related genes were mainly tracked in Staphylococcus, Ruminococcus and Corynebacterium genera. The assimilatory sulfate reduction genes responsible for sulfur metabolism and hydrogenase-related genes responsible for hydrogen cycling were traced from Staphylococcus originated from both air and manure. The current study provides characterizations of MAGs from a poultry housing environment by linking microbial taxa with virulence, resistance, and metabolic functions. The findings emphasize the role of microbiota in shaping gas emissions and AMR, with implications for poultry health and worker's safety and the ultimate aim of sustainable poultry production.

Animals↗

PubMed2026

Ecological Restoration of the Soil-Like Function in the Bauxite Residue: Natural Microbiomes Mediated Molecular Transformation of Dissolved Organic Matter.

Soilization of bauxite residues offers a scalable route for long-term carbon management and ecological restoration. However, the microbial processes that transform exogenous organic inputs into stable soil-like carbon pools remain poorly resolved. Here, we combined cross-ecosystem meta-analysis, machine-learning prediction, native synthetic community (SynCom) construction, 13C-labeled straw microcosms, field validation, Fourier transform ion cyclotron resonance mass spectrometry, and genome-resolved metagenomics to unravel microbiome-mediated carbon transformation at the dissolved organic matter (DOM) molecular scale. Our meta-analysis revealed that alkaline industrial wastes retained soil-like DOM signatures but were enriched in microbial humic- and protein-like components, indicating active yet incomplete carbon processing. Guided by these patterns, native SynCom inoculation increased 13C incorporation into total organic carbon (TOC) and dissolved organic carbon (DOC), enlarged biodegradable and adsorbable DOC fractions, and shifted DOM from recalcitrant aromatic pools toward oxygenated carbohydrate-, tannin-, and phenolic-like molecular classes. Genome-resolved analyses linked this transformation to complementary polymer degradation and nutrient-cycling functions across fungal and bacterial guilds, including enriched carbohydrate-active enzymes in straw-carbon-utilizing metagenome-assembled genomes. Null model and thermodynamic analyses further showed that microbial communities were constrained by homogeneous selection, whereas DOM molecules were diversified through variable selection and redox-dependent transformation. Field-scale validation confirmed that SynCom promoted TOC and DOC accumulation and humic-like, high-density DOM fractions under alkaline conditions. Together, these findings establish a mechanistic framework in which functional microbiomes couple plant carbon depolymerization, DOM molecular diversification, and mineral-interactive carbon stabilization, providing a microbiome-guided strategy for carbon sequestration and soilization in the bauxite residue.

Soil↗