Novel integrative elements and genomic plasticity in ocean ecosystems.

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.

Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.

Global Trends in Marine Plankton Diversity across Kingdoms of Life.

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT.

Biosynthetic potential of the global ocean microbiome.

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.

Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient.

Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth-related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon-degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long-term observations enhance our understanding of soil viruses in the context of climate-relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.

Genome-centric view of carbon processing in thawing permafrost.

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

Chemometric-based drug discovery approaches from natural origins using hyphenated chromatographic techniques.

INTRODUCTION: Isolation and characterization of bioactive components from complex matrices of marine or terrestrial biological origins are the most challenging issues for natural product chemists. Biochemometric is a new potential scope in natural product analytical science, and it is a methodology to find the compound's correlation to their bioactivity with the help of hyphenated chromatographic techniques and chemometric tools. OBJECTIVES: The present review aims to evaluate the application of chemometric tools coupled to chromatographic techniques for drug discovery from natural resources. METHODS: The searching keywords "biochemometric," "chemometric," "chromatography," "natural products bioassay," and "bioassay" were selected to search the published articles between 2010-2023 using different search engines including "Pubmed", "Web of Science," "ScienceDirect," and "Google scholar." RESULTS: An initial stage in natural product analysis is applying the chromatographic hyphenated techniques in conjunction with biochemometric approaches. Among the applied chromatographic techniques, liquid chromatography (LC) techniques, have taken up more than half (53%) and also, mass spectroscopy (MS)-based chromatographic techniques such as LC-MS are the most widely used techniques applied in combination with chemometric methods for natural products bioassay. Considering the complexity of dataset achieved from chromatographic hyphenated techniques, chemometric tools have been increasingly employed for phytochemical studies in the context of determining botanicals geographical origin, quality control, and detection of bioactive compounds. CONCLUSION: Biochemometric application is expected to be further improved with advancing in data acquisition methods, new efficient preprocessing, model validation and variable selection methods which would guarantee that the applied model to have good prediction ability in compound relation to its bioactivity.

Dissecting dietary and semisynthetic volatile phenylpropenes: A compile of their distribution, food properties, health effects, metabolism and toxicities.

Phenylpropenes represent a major subclass of plant volatiles, including eugenol, and (E)-anethole. They contribute to the flavor and aroma of many chief herbs and spices, to exert distinct notes in food, i.e., spicy anise- and clove-like to fruit. Asides from their culinary use, they appear to exert general health effects, whereas some effects are specific, e.g., eugenol being a natural local anesthetic. This review represents the most comprehensive overview of phenylpropenes with respect to their chemical structures, different health effects, and their food applications as flavor and food preservatives. Side effects and toxicities of these compounds represent the second main part of this review, as some were reported for certain metabolites generated inside the body. Several metabolic reactions mediating for phenylpropenes metabolism in rodents via cytochrome P450 (CYP450) and sulfotransferase (SULT) enzymes are presented being involved in their toxicities. Such effects can be lessened by influencing their pharmacokinetics through a matrix-derived combination effect via administration of herbal extracts containing SULT inhibitors, i.e., nevadensin in sweet basil. Moreover, structural modification of phenylpropanes appears to improve their effects and broaden their applications. Hence, such review capitalizing on phenylpropenes can help optimize their applications in nutraceuticals, cosmeceuticals, and food applications.

Red and white cabbages: An updated comparative review of bioactives, extraction methods, processing practices, and health benefits.

Red and white cabbages (Brassica oleracea var. capitata f. alba and rubra, respectively) are two of the most commercially valued vegetables in crucifers, well-recognized for their unique sensory and nutritive attributes in addition to a myriad of health-promoting benefits. The current review addressed the differential qualitative/quantitative phytochemical make-ups for the first time for better utilization as nutraceuticals and to identify potential uses based on the chemical makeup of both cultivars (cvs.). In addition, extraction methods are compared highlighting their advantages and/or limitations with regards to improving yield and stability of cabbage bioactives, especially glucosinolates. Besides, the review recapitulated detailed action mechanism and safety of cabbage bioactives, as well as processing technologies to further improve their effects are posed as future perspectives. White and red cabbage cvs. revealed different GLSs profile which affected by food processing, including enzymatic hydrolysis, thermal breakdown, and leaching. In addition, the red cultivar provides high quality pigment for industrial applications. Moreover, non-conventional modern extraction techniques showed promising techniques for the recovery of their bioactive constituents compared to solvent extraction. All these findings pose white and red cabbages as potential candidates for inclusion in nutraceuticals and/or to be commercialized as functional foods prepared in different culinary forms.

Metabolism of natural and synthetic bioactive compounds in Cunninghamella fungi and their applications in drug discovery.

Investigation of xenobiotic metabolism is a key step for drug discovery. Since the in vivo investigations may be associated with harmful effects attributed to production of toxic metabolites, it is deemed necessary to predict their structure especially at the preliminary clinical studies. Furthermore, the application of microorganisms that are capable of metabolizing drugs mimic human metabolism and consequently may predict possible metabolites. The genus Cunninghamella has been proven to be a potential candidate, which mimics xenobiotic metabolism occurring inside the human body, including phase I and II metabolic reactions. Moreover, biotransformation with Cunninghamella showed chemical diversity, where a lot of products were detected in relation to the initial substrates after being modified by oxidation, hydroxylation, and conjugation reactions. Some of these products are more bioactive than the parent compounds. The current review presents a comprehensive literature overview regarding the Cunninghamella organisms as biocatalysts, which simulate mammalian metabolism of natural secondary and synthetic compounds.

Fucoidan in Pharmaceutical Formulations: A Comprehensive Review for Smart Drug Delivery Systems.

Fucoidan is a heterogeneous group of polysaccharides isolated from marine organisms, including brown algae and marine invertebrates. The physicochemical characteristics and potential bioactivities of fucoidan have attracted substantial interest in pharmaceutical industries in the past few decades. These polysaccharides are characterized by possessing sulfate ester groups that impart negatively charged surfaces, low/high molecular weight, and water solubility. In addition, various promising bioactivities have been reported, such as antitumor, immunomodulatory, and antiviral effects. Hence, the formulation of fucoidan has been investigated in the past few years in diverse pharmaceutical dosage forms to be able to reach their site of action effectively. Moreover, they can act as carriers for various drugs in value-added drug delivery systems. The current work highlights the attractive biopharmaceutical properties of fucoidan being formulated in oral, inhalable, topical, injectable, and other advanced formulations treating life-quality-affecting diseases. Therefore, the present work points out the current status of fucoidan pharmaceutical formulations for future research transferring their application from in vitro and in vivo studies to clinical application and market availability.

Characterization and Cytotoxic Activity of Microwave-Assisted Extracted Crude Fucoidans from Different Brown Seaweeds.

Microwave-assisted extraction (MAE) is recognized as a green method for extraction of natural products. The current research aimed to explore the MAE for fucoidans extraction from different brown seaweeds, including Fucus vesiculosus, F. spiralis, and Laminaria saccharina. Following several solvent-extraction pre-treatment steps and MAE optimization, the algal biomasses were extracted in a ratio of 1:25 in 0.1 M HCl containing 2 M CaCl2 for 1.0 min. The results showed that L. saccharina's extract was different from the others, regarding the highest sugar content reached 0.47 mg glucose equivalent/mg extract being confirmed by monosaccharide composition analysis and the lowest fucoidan content and sulfation degree at 0.09 mg/mg extract and 0.13, respectively. Moreover, these findings were confirmed by tentative structural elucidation based on Fourier-transform infrared spectrometry which also showed a different spectrum. However, the MAE enhanced melanoidins formation in products, which was confirmed by the intense band at 1420 cm-1. Interestingly, the results of monomeric composition showed that fucoidan extract by MAE from F. vesiculosus belonged to sulfated galactofucans which are known for their potential bioactivities. Furthermore, the cytotoxic activity of the four fucoidans in concentrations ranging from 4.9 µg/mL to 2500 µg/mL was investigated and correlated with the chemical characterization showing that F. vesiculosus_MAE fucoidan was the most potent and safest. The current research revealed the chemical heterogeneity of fucoidans regarding taxonomical class and used greener extraction method of fucoidans toward the achievement of the UN sustainability goals.

Fucoidan's Molecular Targets: A Comprehensive Review of Its Unique and Multiple Targets Accounting for Promising Bioactivities Supported by In Silico Studies.

Fucoidan is a class of multifunctional polysaccharides derived from marine organisms. Its unique and diversified physicochemical and chemical properties have qualified them for potential and promising pharmacological uses in human diseases, including inflammation, tumors, immunity disorders, kidney diseases, and diabetes. Physicochemical and chemical properties are the main contributors to these bioactivities. The previous literature has attributed such activities to its ability to target key enzymes and receptors involved in potential disease pathways, either directly or indirectly, where the anionic sulfate ester groups are mainly involved in these interactions. These findings also confirm the advantageous pharmacological uses of sulfated versus non-sulfated polysaccharides. The current review shall highlight the molecular targets of fucoidans, especially enzymes, and the subsequent responses via either the upregulation or downregulation of mediators' expression in various tissue abnormalities. In addition, in silico studies will be applied to support the previous findings and show the significant contributors. The current review may help in understanding the molecular mechanisms of fucoidan. Also, the findings of this review may be utilized in the design of specific oligomers inspired by fucoidan with the purpose of treating life-threatening human diseases effectively.

Screening for oropharyngeal dysphagia in hospitalized COVID-19 patients: a prospective study.

PURPOSE: To screen for oropharyngeal dysphagia (OD) in hospitalized COVID-19 patients. METHODS: A descriptive longitudinal study was conducted on 500 adult patients with confirmed COVID-19 in the age range of 19-65 years who were admitted to the main university isolation hospital (whether admitted in the ward or the intensive care unit). Screening for OD was done using the Arabic version of the Eating Assessment Tool (EAT-10) and the Yale swallow protocol. RESULTS: 45.4% of the admitted and 40.97% of the discharged COVID-19 patients had a positive screen for OD. Several risk factors for OD could be detected. These include older age, longer duration of presenting symptoms of COVID-19, presence of ageusia and anosmia, presence of dysphonia, ICU admission, lower oxygen saturation, higher respiratory rate, presence of OD at admission, longer duration of hospital stay, and use of noninvasive ventilation (NIV) and/or invasive mechanical ventilation (IMV). CONCLUSIONS: Screening for OD in hospitalized COVID-19 patients is a mandatory procedure, whether for admitted or discharged patients.

efam: an expanded, metaproteome-supported HMM profile database of viral protein families.

MOTIVATION: Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. RESULTS: Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from 'conservative' to 'eXtremely Conservative' resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem. AVAILABILITY AND IMPLEMENTATION: The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Rediscovering bacterial exopolysaccharides of terrestrial and marine origins: novel insights on their distribution, biosynthesis, biotechnological production, and future perspectives.

Bacteria exist in colonies as aggregates or associated with surfaces forming biofilms rather than planktonic cells. Living in such a unique manner is always mediated via a matrix of extracellular polymeric substances, which are composed mainly of polysaccharides or specifically exopolysaccharides (EPS). Biofilm formation and hence EPS production are affected by biotic and abiotic factors inducing/inhibiting several involved genes and other molecules. In addition, various aspects of bacterial EPS regarding: physiological functions, molecular weight, and chemical composition were demonstrated. Recent investigations have revealed a wide spectrum of EPS chemical and physicochemical properties showing promising applications in different industrial sectors. For instance, lactic acid bacteria (LAB)- and marine-derived EPS exhibit: immunomodulatory, antioxidant, antitumor, bioremediation of heavy metals, as well as thickening and viscosity modifiers in the food industry. However, bacterial EPS have not yet been commercially implemented, in contrast to plant-derived analogues. The current review aims to rediscover the EPS structural and biosynthetic features derived from marine and terrestrial bacteria, and applications as well.

Gut homeostasis and microbiota under attack: impact of the different types of food contaminants on gut health.

Food contaminants represent food constituents that are accidentally introduced during food preparation cycle. In addition to their direct toxic effects on human health at different levels, they influence both gut microbiota composition and function. This often leads to metabolic disorders linked to many aspects of the human body. Foods are poisoned with physical, chemical, or biological factors either in agriculture or during processing steps. These include naturally occurring compounds such as mycotoxins, agricultural chemicals such as pesticides and antibiotics, persistent organic pollutants, thermal process contaminants (e.g., furans, aromatic compounds, and nitrosamines), or heavy metals. These xenobiotics cause a wide range of toxicities. They also disturb gut homeostasis by inducing intestinal damage and inflammation and gut microbiota dysbiosis. We present herein the first comprehensive review of how food contaminants can specifically influence gut microbiota and intestinal homeostasis, and likewise via gut microbiota-mediated contaminants metabolism. The first part summarizes the different classes of food contaminants and their impact on gut microbiota and its homeostasis, while, the second part discusses the promising role of the gut microbiota in the biodegradation of these xenobiotics and the possible unfortunate exaggerated toxicities in some cases. Finally, we summarize the novel strategies to minimize toxic effects of food contaminants and future directions needed to explore the interactions between food contaminants and the gut microbiota.

DRAM for distilling microbial metabolism to automate the curation of microbiome function.

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

Sulfated Galactofucans: An Outstanding Class of Fucoidans with Promising Bioactivities.

Fucoidans encompass versatile and heterogeneous sulfated biopolysaccharides of marine origin, specifically brown algae and marine invertebrates. Their chemistry and bioactivities have been extensively investigated in the last few decades. The reported studies revealed diverse chemical skeletons in which l-fucose is the main sugar monomer. However, other sugars, i.e., galactose, mannose, etc., have been identified to be interspersed, forming several heteropolymers, including galactofucans/fucogalactans (G-fucoidans). Particularly, sulfated galactofucans are associated with rich chemistry contributing to more promising bioactivities than fucans and other marine polysaccharides. The previous reports in the last 20 years showed that G-fucoidans derived from Undaria pinnatifida were the most studied; 21 bioactivities were investigated, especially antitumor and antiviral activities, and unique biomedical applications compared to other marine polysaccharides were demonstrated. Hence, the current article specifically reviews the biogenic sources, chemistry, and outstanding bioactivities of G-fucoidans providing the opportunity to discover novel drug candidates.