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Summary: Background: The involvement of Mediterranean fever (MEFV) gene mutations in patients with inflammatory bowel disease unclassified (IBDU) remains unclear. This study aimed to determine the clinical characteristics and responsiveness to colchicine in Japanese patients with IBDU carrying MEFV mutations. Methods: In this retrospective cohort study, we examined MEFV mutations using gene analysis, clinical information, and colchicine responsiveness. Furthermore, we examined cytokine production in exon 2-mutated THP-1 cells (a monocytic cell line) and microbiome analysis. Findings: Of the 396 patients diagnosed with IBDU, 60.1% had MEFV mutations. Exon 2 mutations were the most common (83.7%). Among patients with available clinical information, 43.3% of patients with IBDU had typical Familial Mediterranean fever (FMF). The efficacy of colchicine in patients with IBDU carrying MEFV mutations was 84.6%. Significant differences were noted in the production of inflammatory; cytokines between THP-1 cells with and without MEFV mutations. Microbial compositions differed between patients with IBDU carrying MEFV mutations and patients with IBD and healthy controls. Interpretation: Patients with IBDU carrying MEFV mutations responded well to colchicine treatment. A notable subset of patients met the criteria for typical FMF. Alterations in intestinal microbiota may contribute to disease pathogenesis. Funding: This work was supported by the Japan Agency for Medical Research and Development (21ek0410057h0003), a grant from the Uehara Memorial Foundation, and the Health and Labour Sciences Research Grants for research on intractable diseases from the Ministry of Health, Labour and Welfare (MHLW) of Japan (Investigation and Research for Intractable Inflammatory Bowel Disease; Grant Number 20316729).

The environment-mediated spread of antimicrobial resistance (AMR) has become a serious public health issue. Globally, indiscriminate waste discharges in marine environments are one of the key contributors to pathogenic bacteria, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). In this communication, we report the presence of 192 known bacterial pathogens at sites 3–40 km away from the coast of Kuwait. Pseudomonas aeruginosa was the most dominant species, recording a relative abundance of 88 % even at remote sites. Other pathogens, such as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Enterobacter cloacae, and Escherichia coli, prioritised by the World Health Organization (WHO) were also recorded. The raw sequencing reads matched with 667 ARGs, 1606 plasmids, 167 integrons and 2143 insertion sequences. The ARGs exhibited spatial variations and were distributed into three overlapping clusters (r2 = 0.277; p < 0.006). The observed Shannon and Simpson indices differed between the groups (ANOVA-p < 0.05). A positive correlation (R2–0.175, p < 0.065) between faecal sterols and ARGs was recorded. The presence of ARGs in non-polluted sites likely suggests that they are not restricted to waste outlets; it is quite probable that other emerging contaminants are also leading to AMR occurrence in the region. Hence, comprehensive screening and constant surveillance are warranted.

Plant growth-promoting bacteria (PGPB) are of increased interest as they offer sustainable alternatives to the more common chemical fertilisers. Research, however, has increased into the use of PGPB as bioinoculants to improve yields. Legumes are known to interact with diazotroph PGPB which increase nutrient uptake, prevent pathogenic infections, and actively fix nitrogen. This study aimed to comprehensively describe PGPB associated with legumes grown in Namibia through analysis of the site-specific bacterial microbiomes. In the present study, we used the 16S rRNA sequencing approach to determine the structure of rhizosphere, root, and seed endosphere microbiomes of five drought-tolerant legume species: Macrotyloma uniflorum, Vigna radiata, Vigna aconitifolia, Vigna unguiculata and Lablab purpureus. Several important phyla were identified including Actinobacteriota, Bacteroidota, Firmicutes, Proteobacteria and Verrucomicrobiota. Overall, Proteobacteria was the most abundant phylum followed by Actinobacteria. The most important genera identified were Bacillus, Mesorhizobium, Pseudomonas, Bradyrhizobium and the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group. The relative abundance of these genera varied across sample types and legume species. This study identified important diazotrophs across all the legume species. Bacillus, an important PGPB, was found to be the most abundant genus among all the niches analysed and legume species, while Rhizobium spp. was particularly enriched in roots. This study ultimately provides previously undescribed information on legume-associated bacterial communities in Namibia.

The possible influence of the continent on the microbiome of the Southwest Atlantic Ocean (SAO) is not yet fully known. The aim of the present study was to evaluate the metagenomic diversity of the SAO nearshore in different locations (e.g., rivers and upwellings) and offshore locations. The studied sites (n = 16) were clustered into four groups (G1-G4) according to the decadal sea surface temperature (SST) and levels of chlorophyll a (chl-a) (2007–2016). G1 (coastal upwelling) presented the highest chl-a values, G2 (shelf) had the highest SST, G3 (offshore north) had the lowest chl-a levels, and G4 (offshore south) was the coldest site. The higher nutrient levels may contribute to higher chl-a-based primary productivity and possibly higher bacterial productivity nearshore. The taxonomic and functional diversity of the total of 16 Illumina shotgun metagenomes were analysed (nearshore: 10, offshore: 6; mean ± standard deviation: 1.87 ± 0.41 million reads per sample). The SAO microbiomes were split into two groups: nearshore and offshore. The SAO coastal zone had higher abundance of picoplanktonic cyanobacteria (e.g., Prochlorococcus), copiotrophic bacteria (e.g., Alteromonas), chl-a photosynthesis, and metabolism of nitrogen and phosphorus. In clear contrast with offshore microbiomes, nearshore microbiomes were heterogenous as a possible effect of riverine runoff and the upwelling. G1 microbiomes had higher abundance of copiotrophic bacteria, while G2 had a higher abundance of Prochlorococcus, and G3 had a higher abundance of Pelagibacter. Offshore metagenomes (G3 and G4) had enrichment of proteorhodopsin light harvesting and sulfur metabolism, possible relevant processes in the SAO. Metagenome assembled genomes (MAGs) demonstrated significant novel microbiome diversity. The most abundant MAGs belong to Flavobacteria and Euryarchaeota. The discrimination of microbial populations and metabolisms in the four studied oceanographic groups provides a first glimpse on the microbial landscape in the SAO.

In this study, we investigated the change in microbiome composition of wild Sichuan takin (Budorcas tibetanus) during winter and spring and analyzed the physiological implications for such changes. Diversity analyses of the microbiome (average 15,091 high-quality reads per sample) in 24 fecal samples (15 from winter, 9 from spring) revealed that spring samples had higher species diversity and were compositionally different from winter samples (P

Background: Functional constipation is a common gastrointestinal disorder especially severely affecting the life quality of the aged. Jichuanjian (JCJ) has been widely used for aged functional constipation (AFC) in clinic. Yet, the mechanisms of JCJ merely scratch the surface with being studied at a single level, rather than from a systematic perspective of the whole. Aim: The purpose of this study was to explore the underlying mechanisms of JCJ in treating AFC from the perspectives of fecal metabolites and related pathways, gut microbiota, key gene targets and functional pathways, as well as “behaviors-microbiota-metabolites” relationships. Methods: 16S rRNA analysis and fecal metabolomics combined with network pharmacology were applied to investigate the abnormal performances of AFC rats, as well as the regulatory effects of JCJ. Results: JCJ significantly regulated the abnormalities of rats' behaviors, the microbial richness, and the metabolite profiles that were interrupted by AFC. 19 metabolites were found to be significantly associated with AFC involving in 15 metabolic pathways. Delightfully, JCJ significantly regulated 9 metabolites and 6 metabolic pathways. AFC significantly interrupted the levels of 4 differential bacteria while JCJ significantly regulated the level of SMB53. HSP90AA1 and TP53 were the key genes, and pathways in cancer was the most relevant signaling pathways involving in the mechanisms of JCJ. Conclusion: The current findings not only reveal that the occurrence of AFC is closely related to gut microbiota mediating amino acid and energy metabolism, but also demonstrate the effects and the underlying mechanisms of JCJ on AFC.

The Kuroshio Current structures environmental characteristics and biodiversity in the northwestern Pacific Ocean (NWPO), a region renowned for its dynamic oceanographic processes and rich marine ecosystems. However, the assembly and associations responses of prokaryotes and microeukaryotes to the Kuroshio Current remain largely unknown. Here, co-occurrence properties and stability of prokaryotic and eukaryotic microbiomes from three regions influenced by the Kuroshio: Kuroshio South of Japan (KSJ), Kuroshio Extension (KE), and the Kuroshio-Oyashio interfrontal zone (KOIZ) are systematically investigated. Microbiomes in the KE showed reduced phylogenetic distance and broader niche breadth than those in the KSJ and KOIZ. Microeukaryotic robustness was highest in the KE and lowest in the KOIZ, while prokaryotes showed the opposite pattern. Prokaryotic and microeukaryotic robustness and compositional stability formed complementary stabilizing and phylogenetic distance along vertical gradients in the KOIZ region, helping to maintain community and ecosystem stability. Prokaryotes and microeukaryotes formed complementary stabilizing under the influence of the Kuroshio Current. Overall, the network of prokaryotes was more stable than that of microeukaryotes, and microeukaryotes were more sensitive to environmental variations than prokaryotes. These results show how the Kuroshio Current influences the community organization and co-occurrence stability of prokaryotic and eukaryotic microbiomes, respectively, as well as their contrasting adaptability and survival strategies to environmental variation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier Ltd.)

A close relationship between the pathogenesis of chronic kidney disease (CKD) and abnormalities in the gut-kidney axis. Paotianxiong polysaccharides (PTXP) that have demonstrated therapeutic effects on CKD. However, the specific mechanism by which PTXP ameliorates CKD through the gut-kidney axis remains to be explored. In this study, the microbiomes and metabolomics were combined to investigate the impact of PTXP on intestinal flora structure and metabolism, further unveiling the relationship through correlation analysis. The results showed that PTXP intervention significantly modulated renal function abnormalities in CKD rats and significantly modulates gut microbial disorders, evidenced by an increased abundance of Lactobacillus murinus, Bacteroides fragilis, and a decreased abundance of Bifidobacterium pseudolongum. Furthermore, PTXP reversed the changes in intestinal metabolites, such as linoleic acid and docosahexaenoic acid, induced by CKD and identified unsaturated fatty acid metabolism as a key metabolic pathway. Correlation analyses also revealed associations among gut microorganisms, metabolites, and renal function indexes, confirming that PTXP alleviated CKD through the gut-kidney axis. Moreover, the above conclusions were verified by fecal bacteria transplantation experiments. These findings provide insights into the mechanism of PTXP for the treatment of CKD and provide new targets for the treatment of CKD., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The objective of this study was the isolation and enrichment of microbiomes capable of degrading the main hexachlorocyclohexane isomers quantified in environmental matrices, e.g.: the α, δ, β and γ-HCH isomers. Four microbiomes were isolated and enriched from an HCH-contaminated dumpsite in Italy, both in the presence of HCH isomers (1:1:1:1) as the sole carbon sources and under co-metabolic growth conditions in presence of glucose (0.1 % v/v). The microbiomes were assessed for their relevant metabolic capabilities. A quantitative metabarcoding approach was employed to analyze the compositional evolution of the four microbiomes during the enrichment phase and the phase of testing of the HCH isomers degradation kinetics. The use of a co-metabolic substrate during enrichment process was essential for selecting microbiomes with higher biodiversity. All microbiomes efficiently degraded the α, δ, and γ-HCH isomers. The highest efficiency in the β-HCH degradation capacity was positively correlated to the highest biodiversity of the microbiome, and the involvement of Chryseobacterium and Asinibacterium sps. have been proposed for a recorded increment in bacterial load during the HCH degradation process., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Giacomo Bernabei reports financial support was provided by Ministry of Education and Merit. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

As we stand on the brink of the post-antibiotic era, we are in dire need of novel antimicrobial compounds. Microorganisms produce a wealth of so-called secondary metabolites and have been our most prolific source of antibiotics so far. However, rediscovery of known antibiotics from well-studied cultured microorganisms, and the fact that the majority of microorganisms in the environment are out of reach by means of conventional cultivation techniques, have led to the exploration of the biosynthetic potential in natural microbial communities by novel approaches. In this mini review we discuss how sequence-based analyses have exposed an unprecedented wealth of potential for secondary metabolite production in soil, marine, and host-associated microbiomes, with a focus on the biosynthesis of non-ribosomal peptides and polyketides. Furthermore, we discuss how the complexity of natural microbiomes and the lack of standardized methodology has complicated comparisons across biomes. Yet, as even the most commonly sampled microbiomes hold promise of providing novel classes of natural products, we lastly discuss the development of approaches applied in the translation of the immense biosynthetic diversity of natural microbiomes to the procurement of novel antibiotics.

The studies on the composition of the human microbiomes in healthy individuals, its variability in the course of inflammation, infection, antibiotic therapy, diets and different pathological conditions have revealed their intra and inter-kingdom relationships. The lung microbiome comprises of major species members of the phylum Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Proteobacteria, which are distributed in ecological niches along nasal cavity, nasopharynx, oropharynx, trachea and in the lungs. Commensal and pathogenic species are maintained in equilibrium as they have strong relationships. Bacterial overgrowth after dysbiosis and/or imbalanced of CD4+ helper T cells, CD8+ cytotoxic T cells and regulatory T cells (Treg) populations can promote lung inflammatory reactions and distress, and consequently acute and chronic respiratory diseases. This review is aimed to summarize the latest advances in resident lung microbiome and its participation in most common pulmonary infections and pneumonia, community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), immunodeficiency associated pneumonia, SARS-CoV-2-associated pneumonia, acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). We briefly describe physiological and immunological mechanisms that selectively create advantages or disadvantages for relative growth of pathogenic bacterial species in the respiratory tract. At the end, we propose some directions and analytical methods that may facilitate the identification of key genera and species of resident and transient microbes involved in the respiratory diseases’ initiation and progression.

A marine aquaculture recycling system (RAS) for the production of post-smolt was monitored for microbial community structures during the first year of operation. Sample material was obtained monthly from the biofilter biofilm carriers, the production water (tank 3), the fish skin (tank 3) and the tank 3 wall biofilm. Additional samples were taken during outbreaks of fish skin wounds, washing of the plant, UV filtration of the inlet water and from various wall biofilms. Samples for depth profiles from all fish tanks were also collected. The sampling tools were a ladle for capturing biofilter biofilm carriers, toothbrushes for wall biofilm capture, filters for capture of water microbes and scalpels for skin tissue slicing. The sampling times were indicated by the production cycle number (cycle 2-5) and the week number within the cycle (W). Prior to bacterial community analysis, the stored samples were exposed to cell lysis and extraction of environmental DNA by commercial kits. All samples were subjected for PCR amplification of 16S rDNA sequences for library formations and prepared for Ion Torrent technology, which sequences 250 bp fragments. A total of 1.1 million reads were obtained from the 100 RAS samples analysed. The process from Ion Torren analysis to library involved bioinformatics steps with sorting, filtering, adjustment and taxonomic identification, and the final output was shown in a table as operational taxonomic units (OTUs) and relative abundance at different sampling sites and sampling time points. Of a total of 450 taxonomically assigned OTUs, 45% were classified at genus level. The 16S library raw data are deposited in the Mendeley data repository and cited in this Data in Brief article co-submitted with the article “Microbial colonization and stability in a marine post-smolt RAS inoculated with a commercial starter culture.” [1]. So far, the raw data are referenced in four more publications in progress. These cover microbial shifts and enrichments between sampling times, sulfur cycling, “in vivo biofilm” and identification of relatives of fish pathogens in RAS. All library sequences are available in GenBank with accession numbers MN890148-MN891672.

ABSTRACT: Pesticides are becoming a significant transnational pollutant in agricultural production environments. This review presents the interconnectedness and interaction effects of pesticides with the microbiomes in the environments of plant rhizosphere and animal (limited to insect and human) guts. The metabolic growth and functions of rhizosphere microbiomes are altered by complex mechanisms involving redox reactions and preferential substrate utilization. The rhizospheres of crop plants with the assemblies of microbiota and other biotic components are sensitive to the deliberate introduction of pesticides. Pesticides become one of the major drivers for the metabolic processes, which rely on the evolutionary mechanisms, including the genetic exchange events within the rhizosphere microbiomes. Pesticides, even at the below detection levels, in the rhizosphere enable the plant uptake which can be up to 1% of the dose applied and trophic transfers involving the animal gut environments. To overcome the metabolic constraints due to the nutrient-poor plant diets contaminated with pesticides, insects gain the resistance traits, mainly due to the pesticide-degrading members of the gut microbiomes. Such evolved microbiome members and their genes can increase their spread of resistance in the environment. Like the insect gut microbiomes, the human gut microbiomes get modulated by the pesticide-laden plant foods, leading to dysbiosis. The confounding effects of pesticides on the gut microbiomes which include mutational and genetic exchange events can upsurge many health disorders. The evolutionary and microbiome perspectives on the rhizosphere and animal guts as the hotspots of metabolic and horizontal gene transfer (HGT) events need careful considerations to mitigate the risks and health hazards due to extensive and intensive application of synthetic chemical pesticides in the modern agriculture.

ABSTRACT: Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and maintained in these types of production systems. Exposure to foodborne pathogens and potential for colonization in the gastrointestinal tract has to be considered with these types of production systems. The gastrointestinal tract microbial composition and function of birds grown and maintained in alternative poultry operations may differ depending on diets, breed, and age of bird. Dietary variety and foraging behavior are potential influential factors on bird nutrition. The gastrointestinal tract microbiomes of birds raised under alternative poultry production systems are now being characterized with next-generation sequencing to identify individual microbial members and assess the impact of different factors on the diversity of microbial populations. In this review, the gastrointestinal tract microbiota contributions to free-range or pasture-raised broiler and egg layer production systems, subsequent applications, and potential future directions will be discussed.

Long-term exposure to fine particulate matter (PM 2.5 ) posed injury for gastrointestinal and respiratory systems, ascribing with the lung-gut axis. However, the cross-talk mechanisms remain unclear. Here, we attempted to establish the response networks of lung-gut axis in mice exposed to PM 2.5 at environmental levels. Male Balb/c mice were exposed to PM 2.5 (dose of 0.1, 0.5, and 1.0 mg/kg) collected from Chengdu, China for 10 weeks, through intratracheally instillation, and examined the effect of PM 2.5 on lung functions of mice. The changes of lung and gut microbiota and metabolic profiles of mice in different groups were determined. Furthermore, the results of multi-omics were conjointly analyzed to elucidate the primary microbes and the associated metabolites in lung and gut responsible for PM 2.5 exposure. Accordingly, the cross-talk network and key pathways between lung-gut axis were established. The results indicated that exposed to PM 2.5 0.1 mg/kg induced obvious inflammations in mice lung, while emphysema was observed at 1.0 mg/kg. The levels of metabolites guanosine, hypoxanthine, and hepoxilin B3 increased in the lung might contribute to lung inflammations in exposure groups. For microbiotas in lung, PM 2.5 exposure significantly declined the proportions of Halomonas and Lactobacillus. Meanwhile, the metabolites in gut including L-tryptophan, serotonin, and spermidine were up-regulated in exposure groups, which were linked to the decreasing of Oscillospira and Helicobacter in gut. Via lung-gut axis, the activations of pathways including Tryptophan metabolism, ABC transporters, Serotonergic synapse, and Linoleic acid metabolism contributed to the cross-talk between lung and gut tissues of mice mediated by PM 2.5 . In summary, the microbes including Lactobacillus, Oscillospira, and Parabacteroides, and metabolites including hepoxilin B3, guanosine, hypoxanthine, L-tryptophan, and spermidine were the main drivers. In this lung-gut axis study, we elucidated some pro- and pre-biotics in lung and gut microenvironments contributed to the adverse effects on lung functions induced by PM 2.5 exposure., Competing Interests: Declaration of competing interest The authors have declared that no competing interests exist., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microorganisms inhabiting uranium (U)-rich environments have specific physiological and biochemical coping mechanisms to deal with U toxicity, and thereby play a crucial role in the U biogeochemical cycling as well as associated heavy metals. We investigated the diversity and functional capabilities of indigenous bacterial communities inhabiting historic U- and Rare-Earth-Elements-rich polymetallic tailings from the Mount Painter Inlier, Northern Flinders Ranges, South Australia. Bacterial diversity profiling identified Actinobacteria as the predominant phylum in all samples. GeoChip analyses revealed the presence of diverse functional genes associated with biogenic element cycling, metal homeostasis/resistance, stress response, and secondary metabolism. The high abundance of metal-resistance and stress-tolerance genes indicates the adaptation of bacterial communities to the "harsh" environmental (metal-rich and semi-arid) conditions of the Northern Flinders Ranges. Additionally, a viable bacterial consortium was enriched from polymetallic tailings. Laboratory experiments demonstrated that the consortium scrubbed uranyl from solution by precipitating a uranyl phosphate biomineral (chernikovite), thus contributing to U biogeochemical cycling. These specialised microbial communities reflect the high specificity of the mineralogy/geochemistry, and biogeography of these U-rich settings. This study provides the fundamental knowledge to develop future applications in securing long-term stability of polymetallic mine waste, and for reprocessing this "waste" to further extract critical minerals., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

The study investigated the effects of different silver nanoparticles (AgNPs) on the soil microbiome and wheat growth. For comparison purposes, a commercial fungicide and silver nitrate (AgNO 3 ) were used. The results revealed three distinct groups of nanoparticles based on their impacts. Small-size AgNPs (10 nm) with a negative charge, as well as fungicide had limited effects on the microbiome, similar to the no-treatment control. Bigger in size (30-60 nm) and a negative charge AgNPs showed the most beneficial effects on soil microbiota shifts. These AgNPs increased the abundance of bacteria with beneficial traits such as nitrogen-fixing, urease, protease, and lignin degradation bacteria. The third type of AgNPs had a positive charge of nanostructure and influenced specific microbial populations, increasing the abundance of anaerobic and autotrophic groups of microorganisms, which could be assessed as a harmful shift for plants growth promotions and was similar to the AgNO 3 treatment. Overall, the study emphasized the potential of AgNPs in agriculture not only as biocidal. The conducted study proved that AgNPs with bigger size/negative charge, used in low concentration can have a surprisingly stimulating effect on the positive characteristics of the rhizosphere microbiome. Moreover, the surface charge of AgNPs is a significant factor affecting microbial activity of wheat rhizosphere soil, which in this treatment is significantly similar to the AgNO 3 treatment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microbiomes play a key role in marine ecosystem functioning and sustainability. Their organization and stability in coastal areas, particularly in anthropogenic-influenced regions, however, remains unclear compared with an understanding of how microbial community shifts respond to marine environmental gradients. Here, the assembly and community associations across vertical and horizontal gradients in the East China Sea are systematically researched. The seawater microbial communities possessed higher robustness and lower fragmentation and vulnerability compared to the sediment microbiomes. Spatial gradients act as a deterministic filtering factor for microbiome organization. Microbial communities had lower phylogenetic distance and higher niche breadth in the nearshore and offshore areas compared to intermediate areas. The phylogenetic distance of microbiomes decreased from the surface to the bottom but the niche breadth was enhanced in surface and bottom environments. Vertical gradients destabilized microbial associations, while the community diversity was enhanced. Multivariate regression tree analysis and canonical correspondence analysis indicated that depth, distance from shore, nutrient availability, temperature, salinity, and chlorophyll a, affected the distribution and co-occurrence of microbial groups. Our results highlight the crucial roles of environmental gradients in determining microbiome association and stability. These results improve our understanding of the survival strategies/adaptive mechanisms of microbial communities in response to environmental variation and provide new insights for protecting the ecosystems and maintaining the sustainability of ecological functions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The process of forest range shift not only affects the vegetation aboveground but also influences the dynamics of belowground microbial communities. To investigate the changes in soil under forest range shift, we examined the natural forest soil microbiome along with its corresponding physicochemical properties, as well as the afforestation of natural forest by seedlings and sowing. By utilizing natural forests and employing different afforestation methods, we simulated the three stages of forest range shift: the staging stage, regeneration, and colonization. We employed network analysis and phylogenetic assemblages to examine the structure of soil microbial communities during these three stages in a macro-environmental change context. Ordination and regression analyses were also used to explore the correlation between microorganisms, environmental factors, and changes in their niches. The findings revealed that different afforestation (range shift) types led to distinct microbial compositions. Seedling afforestation exhibited similarities to mature forests, suggesting a significant influence on below-ground microorganisms. In contrast, sowing-based afforestation resulted in small changes in soil microbes, indicating a legacy effect on grassland soils. The impact of the rhizosphere on microbial composition remained consistent across the three forest types. Overall, this study underscores the significance of forest range shift in shaping soil microbial communities and emphasizes the need to consider these dynamics in forest management and restoration endeavours., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In order to help designing agricultural practices that minimize the spread of ARG, we fertilized, sown, and harvested lettuces and radish plants in experimental land plots for two consecutive agricultural cycles using four types of fertilizers: mineral fertilization, sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) identified a small, but significant overlap (<10%) between soil's and fertilizer microbiomes. Clinically relevant ARG were found in higher loads (up to 100 fold) in fertilized soils than in the initial soil, particularly in those treated with organic fertilizers, and their loads grossly correlated to the amount of antibiotic residues found in the corresponding fertilizer. Similarly, low, but measurable ARG loads were found in lettuce (tetM, sul1) and radish (sul1), corresponding the lowest values to samples collected from minerally fertilized fields. Comparison of soil samples collected along the total period of the experiment indicated a relatively year-round stability of soil microbiomes in amended soils, whereas ARG loads appeared as unstable and transient. The results indicate that ARG loads in soils and foodstuffs were likely linked to the contribution of bacteria from organic fertilizer to the soil microbiomes, suggesting that an adequate waste management and good pharmacological and veterinarian practices may significantly reduce the presence of these ARGs in agricultural soils and plant products., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Anti-tuberculosis (TB) drug-induced hepatotoxicity (ATDH) was related to metabolic and microbial dysregulation, but only limited data was available about the metabolomes and microbiomes in ATDH. We aimed at detecting the metabolic and microbial signatures of ATDH. Urine samples were obtained from ATDH (n = 33) and non-ATDH control (n = 41) and analyzed by untargeted gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). Metabolites were analyzed by orthogonal projections to latent structures-discriminate analysis (OPLS-DA) and pathway analysis. Eight ATDH and eight non-ATDH control were evaluated by sequencing of 16S rRNA genes, and the Clusters of Orthologous Groups of proteins (COG) database were used for function prediction. Linear discriminant analysis (LDA) effect size (LEfSe) was applied to detect the differential microbiotas between the two groups. The differential microbiotas were further validated by correlation analysis with differential metabolites. OPLS-DA analysis suggested 11 metabolites that differed ATDH from non-ATDH control. Pathway analysis demonstrated that metabolism of arginine and proline, metabolism of d-arginine and d-ornithine, glutathione glycine metabolism, galactose metabolism, niacin and nicotinamide metabolism, and glycine, serine and threonine metabolism were related to ATDH. LEfSe suggested significant differences in microbiotas between the two groups. The o&#95; Bacteroidales, f&#95;Prevotellaceae, and g&#95;Prevotella were significantly increased in ATDH. In contrast, the f&#95;Chitinophagaceae, c&#95;Gammaproteobacteria, and p&#95;Proteobacteria were significantly increased in non-ATDH group. The biological functions of the sequenced microbiota in this study were related to amino acid transport and metabolism and defense mechanisms. Finally, we detected strong association between urine metabolites and specific urine bacteria (|r| > 0.8). d-glucoheptose showed a strong relationship to Symbiobacterium. Creatine (r = -0.901; P < 0.001) and diglycerol were strongly associated with Alishewanella. Metabolomics and microbiomes indicate ATDH characterized by metabolic and microbial profiles may differ from non-ATDH control., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2021 Elsevier B.V. All rights reserved.)

This study aims to better understand the effects of heavy metal enrichment on microbiomes and resistomes and the source-specific ecological risks of metals in the sediments of an urban river. Geo-accumulation index and enrichment factor suggested the river sediments were contaminated by Cd, Cu, Pb, and Zn in varying degrees. High-throughput sequencing-based metagenomics analysis identified 430 types of antibiotic resistance genes (ARGs), dominated by the multidrug, MLS, bacitracin, quinolone, and aminoglycoside ARGs, and 52 metal resistance genes (MRGs) mainly conferring resistance to zinc, copper, cadmium, lead, mercury and multiple metals. Spearman correlation analysis and Mantel test showed the heavy metal enrichment exerted significant effects on the microbial community, ARGs and MRGs. Source apportionment using positive matrix factorization revealed that natural source (42.8%) was the largest contributor of metals in the river sediments, followed by urban activities (35.4%) and a mixed source (21.7%). However, when incorporating the apportionment results into a modified risk model to evaluate the source-specific ecological risks, results showed human activities dominated the risks of metals. Comparatively, the urban activities majorly caused moderate- and considerable- ecological risks, while the mixed source with respect to agricultural and industrial activities contributed higher percentages on high- and extremely high- ecological risks., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Pancreatic ductal adenocarcinoma is one of the most lethal malignancies and is known for its high resistance and low response to treatment. Cancer treatments can reshape the microbiota and in turn, the microbiota influences the therapeutic efficacy by regulating immune response and metabolism. This crosstalk is bidirectional, heterogeneous, and dynamic. In this review, we elaborated on the interactions between the microbiota and therapeutic resistance in pancreatic ductal adenocarcinoma. Regulating the microbiota in pancreatic tumor microenvironment may not only generate direct anti-cancer but also synergistic effects with other treatments, providing new directions in cancer therapy., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Objective: Microbiota comparisons between healthy and diseased dental tissues have accentuated the importance of cultivating and identifying bacterial species that play a role in the initiation and progression of dental caries. The objective of this study was to evaluate the bacterial community composition in caries-active and caries-free children., Methods: Supragingival plaque samples were collected from 64 caries-active and 64 caries-free Middle Eastern children. The hypervariable V3-V4 of the bacterial 16S rRNA gene was sequenced with Human Oral Microbe Identification using Next Generation Sequencing. Microbial community structure and composition analyses were performed by processing operational taxonomic units. Bioinformatic analyses, including analysis of similarity, alpha and beta diversities, and principal coordinate analysis, were carried out., Results: Diversity indices did not find differences between the caries-active and caries-free groups (p > 0.05). Similarity analysis demonstrated that the microbiota composition did not differ between the two groups. Comparative analysis at the species level revealed a significantly higher relative abundance of Leptotrichia shahii, Prevotella melaninogenica, Veillonella dispar, Leptotrichia HOT 498, and Streptococcus mutans in caries-active children (p < 0.05). Corynebacterium matruchotii, Lautropia mirabilis, Neisseria elongata, and Corynebacterium durum were relatively more abundant in the caries-free group (p < 0.05). Species belonging to the Leptotrichia, Prevotella, and Veillonella genera were significantly predominant in the caries-active subjects., Conclusion: In view of the lack of a clear association between Corynebacterium spp. and dental caries status in the literature, the predominance of these species in caries-free children warrants further research to understand their possible role in a health-associated microbial community., Clinical Significance: Understanding the relationship between specific bacteria present in dental biofilms and health and disease is essential for preventing and combating dental caries. Using advanced next generation sequencing techniques, the present study demonstrated the complexity of the caries microbiome and identified species/genera whose virulence or protective properties should be further explored., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Earthworms are widely known to impact soil health, having a key role in nutrient cycling and are often referred to as soil engineers. They are vital for soil microbial assemblages particularly through their feeding and burrowing activity in soil. Earthworms feed on soil organic matter and litter, and the resulting casts alter the soil microbial community. However, the gut microbiome of earthworms remains less known. In this study, we used amplicon sequencing of the 16S rRNA gene for bacteria and 18S rRNA gene for eukaryotes to assess the gut community assemblages of earthworm species within three genera Aporrectodea, Allolobophora and Lumbricus that represent different life forms sharing the same habitat. The objective was to compare the gut microbiome profiles of eukaryotic and prokaryotic organisms to assess significance of earthworm life forms, and to explore the cross kingdom networks in an attempt to identify keystone species. We found a high eukaryotic diversity with a dominance of the SAR supergroup along with fungi and metazoan in the earthworm gut. The bacterial community were dominated by members of Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. The eukaryotic and prokaryotic communities showed similar differences in alpha diversity, being lowest in Lumbricus herculeus. The beta diversity showed earthworm species as a key factor in shaping gut microbiomes with L. herculeus harboring distinct microbiomes compared to species of Aporrectodea caliginosa, A. longa, A. tuberculata and Allolobophora chlorotica. Cross kingdom networks showed high interactions between several protist and bacterial OTUs. In conclusion, this study suggested that the community assemblages of gut microbiomes were shaped by earthworm species and life form, and such assemblage consists of cross kingdom interactions among eukaryotes and prokaryotes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal., (Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.)

Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, bla CTX-M-32 , bla OXA-58 , mecA, and bla TEM , plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The One Health concept proposes that there is a connection between human, animal and environmental health. Plants and their health are not explicitly included. In this review, we broaden the One Health concept to include soil, plant, animal and ecosystem health. We argue that the health conditions of all organisms in an ecosystem are interconnected through the cycling of subsets of microbial communities from the environment (in particular the soil) to plants, animals and humans, and back into the environment. After an introduction on health concepts, we present examples of community stability and resilience, diversity and interconnectedness as affected by pollutants, and integrity of nutrient cycles and energy flows. Next, we explain our concept of microbial cycling in relation to ecosystem health, and end with examples of plant and animal disease outbreaks in relation to microbial community composition and diversity. We conclude that we need a better understanding of the role of interconnected microbiomes in promoting plant and animal health and possible ways to stimulate a healthy, diverse microbiome throughout human-dominated ecosystems. We suggest that it is essential to maintain ecosystem and soil health through diversification of plant communities and oligotrophication of managed ecosystems., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Social concern has raised during the last years due to the development of antibiotic resistance hotspots in different environmental compartments, including the edible parts of crops. To assess the influence of the water quality used for watering, we collected samples from soil, roots, leaves and beans from the legume plant Vicia faba (broad beans) in three agricultural peri-urban plots (Barcelona, NE Spain), irrigated with either groundwater, river water, or reclaimed water. Antibiotic resistance genes (ARGs) sul1, tetM, qnrS1, bla CTX-M-32, bla OXA-58 , mecA, and bla TEM were quantified by real-time PCR, along with 16S rDNA and intl1 sequences, as proxies for bacterial abundance and integron prevalence, respectively. Microbiome composition of all samples were analyzed by high-throughput DNA sequencing. Results show a gradient of bacterial species diversity and of ARG prevalence from highly diverse soil samples to microbially-poor beans and leaves, in which Rhizobiales essentially displaced all other groups, and that presented very small loads of ARGs and integron sequences. The data suggest that the microbiome and the associated resistome were likely influenced by agricultural practices and water quality, and that future irrigation water legal standards should consider the specific Physiology of the different crop plants., (Copyright © 2018 Elsevier Inc. All rights reserved.)

While the presence of antibiotic resistance genes (ARGs) in agricultural soils and products has been firmly established, their distribution among the different plant parts and the contribution of agricultural practices, including irrigation with reclaimed water, have not been adequately addressed yet. To this end, we analyzed the levels of seven ARGs (sul1, bla TEM , bla CTX-M-32 , mecA, qnrS1, tetM, bla OXA-58 ), plus the integrase gene intl1, in soils, roots, leaves, and fruits from two commercial tomato fields irrigated with either unpolluted groundwater or from a channel impacted by treated wastewater, using culture-independent, quantitative real-time PCR methods. ARGs and intl1 sequences were found in leaves and fruits at levels representing from 1 to 10% of those found in roots or soil. The relative abundance of intl1 sequences correlated with tetM, bla TEM , and sul1 levels, suggesting a high horizontal mobility potential for these ARGs. High-throughput 16S rDNA sequencing revealed microbiome differences both between sample types (soil plus roots versus leaves plus fruits) and sampling zones, and a correlation between the prevalence of Pseudomonadaceae and the levels of different ARGs, particularly in fruits and leaves. We concluded that both microbiome composition and ARGs levels in plants parts, including fruits, were likely influenced by agricultural practices., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Maritime ports are anthropogenic interventions capable of causing serious alterations in coastal ecosystems. In this study, we examined the benthic microbial diversity and community structure under the influence of two maritime ports, Mucuripe (MUC) and Pecém (PEC), at Equatorial Atlantic Ocean in Northeast Brazil. Those seaports differ in architecture, time of functioning, cargo handling and contamination. The microbiomes from MUC and PEC were also compared in silico to 11 other globally distributed marine microbiomes. The comparative analysis of operational taxonomic units (OTUs) retrieved by PCR-DGGE showed that MUC presents greater richness and β diversity of Bacteria and Archaea than PEC. In line with these results, metagenomic analysis showed that MUC and PEC benthic microbial communities share the main common bacterial phyla found in coastal environments, although can be distinguish by greater abundance of Cyanobacteria in MUC and Deltaproteobacteria in PEC. Both ports differed in Archaea composition, being PEC port sediments dominated by Thaumarchaeota. The microbiomes showed little divergence in their potential metabolic pathways, although shifts on the microbial taxonomic signatures involved in nitrogen and sulphur metabolic pathways were observed. The comparative analysis of different benthic marine metagenomes from Brazil, Australia and Mexico grouped them by the geographic location rather than by the type of ecosystem, although at phylum level seaport sediments share a core microbiome constituted by Proteobacteria, Cyanobacteria, Actinobacteria, Tenericuteres, Firmicutes, Bacteriodetes and Euryarchaeota. Our results suggest that multiple physical and chemical factors acting on sediments as a result of at least 60years of port operation play a role in shaping the benthic microbial communities at taxonomic level, but not at functional level., (Copyright © 2016 Elsevier B.V. All rights reserved.)