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Pollution can negatively impact aquatic ecosystems, aquaculture operations, and recreational water quality. Many aquatic microbes can sequester or degrade pollutants and have been utilized for bioremediation. While planktonic and benthic microbes are well-studied, host-associated microbes likely play an important role in mitigating the negative impacts of aquatic pollution and represent an unrealized source of microbial potential. For example, aquatic organisms that thrive in highly polluted environments or concentrate pollutants may have microbiomes adapted to these selective pressures. Understanding microbe-pollutant interactions in sensitive and valuable species could help protect human well-being and improve ecosystem resilience. Investigating these interactions using appropriate experimental systems and overcoming methodological challenges will present novel opportunities to protect and improve aquatic systems. In this perspective, we review examples of how microbes could mitigate negative impacts of aquatic pollution, outline target study systems, discuss challenges of advancing this field, and outline implications in the face of global changes.

Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.

Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4-40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.

In this work, a conceptual framework is proposed for translating microbial research into usable design tools in an urban built environment. This study on Microbiomes of the Built Environment (MoBE), specifically the cultivable microbial count, incorporates building code and built environment design factors applied in the Philippine setting. The National Building Code of the Philippines with focus on minimum habitable room specifications was used to provide basis for the framework process. Human presence and ventilation were used as parameters to produce data that can be used as design tools. Using passive air sampling, the three experiments were conducted within Metro Manila according to the proposed framework. The first experiment using settle plates of culture media in the morning and afternoon seeks to understand how bacterial and fungal counts are affected in a naturally ventilated and in a non-ventilated room. The second and third experiments were done to test the effects of different window sizes and the number of humans on bacterial count, respectively. Results showed higher bacterial count in the room with natural ventilation compared to the room with no ventilation. The use of different window sizes did not show significant difference in counts with the number replicates used but as the number of humans in the area increased, the bacterial counts also increased. Data produced in the preliminary experiments were used to conceptually design a space in this paper. The authors suggest that this building-code inspired framework be used as a guide for MoBE studies as a starting point and be further developed to understand and eventually produce healthier built environments. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer initiation is not precisely defined yet. It should be the point of shift from normal/benign to malignant. However, it is still controversial in spite of the abundant accumulation of data on carcinogenesis. Cancer initiation is overviewed here from different viewpoints of genetics, epigenetics, viral/microbial infections, and chronic inflammation. The advent of cancer stem cells is discussed as the point at which a normal cell acquires malignancy. Exposure to radiation and chemicals, oncogenic viruses, microbiomes, and inflammation are the major events of cancer initiation. DNA damage and chromosomal aberrations are classically considered the main causes of cancer. The recent idea of epigenetics is broadening the concept, including the suggestion that oncogenic virus infection disrupts various intracellular signaling cascades. Chronic inflammation was proposed as the origin of cancer in the 19th century, and the molecular level of events has been made clear with scientific development. Much knowledge of cancer initiation has become available for integration into research. Simultaneously, the presence of cancer stem cells has been identified and characterized. However, the point of shift from normal to malignant still appears obscure even when taking cancer stem cells into consideration. From these points of view, the advent of cancer stem cells and cancer initiation are briefly discussed as the points of shift from normal to malignant in this paper. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognized reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilized opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems. [ABSTRACT FROM AUTHOR]

Wound healing in the oral mucosa is superior to that in the skin, with faster wound closure accompanied by reduced inflammation, less angiogenesis, and minimal scar formation. A well-characterized oral wound model is critical to investigating the mechanisms of oral wound closure and the efficacy of various clinical interventions. Currently, there are a few human oral wound models, although none of them are well characterized. In the present study, we describe and characterize a human hard palate wound healing model. A 3.5-mm circular and two 1 × 5-mm rectangular full-thickness wounds were made in the first and second molar region, 5 mm from the gingival margin, on the hard palate of human subjects. The circular wound was used to monitor wound closure and collect swabs for a microbiome analysis via 16s rRNA sequencing. The rectangular wounds were biopsied and the tissue was used to evaluate the gene expression of wound healing-related mediators by real-time polymerase chain reaction. Saliva was also collected to examine the protein levels of similar molecules by enzyme-linked immunosorbent assays. Circular wounds were nearly closed on day 7 after wounding. Significant changes in the gene expression of inflammatory cytokines, growth factors, antimicrobial peptides, and extracellular matrix-related molecules were identified in day 1 and day 3 wound tissue and compared with unwounded tissue on day 0. Changes in the protein levels of various mediators were limited in the saliva. In addition, alpha diversity, beta diversity, and differential microbiome analysis demonstrated significant changes in bacterial colonization of the wound surface over time compared with unwounded mucosa. In summary, we comprehensively characterize a human hard palate wound-healing model that details the dynamic changes of wound closure, levels of wound healing-related mediators in the wound and saliva, and the oral wound microbiome. [ABSTRACT FROM AUTHOR]

Objective: This study investigated the differences in oral saliva microbiota composition and metabolic products among Han Chinese populations living at different altitudes, as well as their correlations. Method: The analysis was conducted using the 16S rRNA gene sequencing method and untargeted metabolomics. Results: 16S gene sequencing results showed significant differences in bacterial diversity and composition between HH (High altitude Han) group and LH (Low altitude Han) group. LEfSe analysis showed that Selenomonas, Leptotrichia, Veillonella, Prevotella relatively abundant are higher in HH group, Haemophilus, Neisseria, Actinobacillus, Aggregatibacter are higher in LH group (p <0.05). Furthermore, as depicted in the phylogenetic tree, there are differences observed between the two groups at all taxonomic levels: 4 phyla, 6 classes, 6 orders, 9 families, 9 genera and 8 species (p <0.05). After conducting PICRUSt functional prediction analysis, we identified 11 significantly different KEGG categories (level 2) between the two groups. These categories primarily encompass energy metabolism, amino acid metabolism, and carbohydrate metabolism. Furthermore, non-targeted metabolomics analysis revealed a total of 997 distinct metabolites in the two groups. These differentiated metabolites can be classified into 13 Class I categories including amino acids and their metabolites, benzene and its derivatives, organic acids and their derivatives, heterocyclic compounds, aldehydes, ketones and esters, nucleotides and their metabolites among others. Additionally, fatty acyl compounds, alcohols and amines as well as glycerophospholipids are present along with carbohydrates and other physiologically active components such as hormones. Finally, Pearson correlation analysis of the top 20 differential metabolites with microorganisms demonstrated an interaction between them; however further experimental verification is required to elucidate the specific mechanism of action. Conclusion: Therefore, this study revealed the effect of altitude on oral saliva microbes and metabolites, as well as their correlations. [ABSTRACT FROM AUTHOR]

This study explores the diversity and functions of microbiomes in ancient agroecosystems of the Mixteca Alta Geopark (MAG). Microbiome analysis could provide insights into soil bacterial communities and their role in enhancing soil fertility, nutrient cycling, and plant growth. We used 16S rRNA gene amplicon sequencing to identify key features in the composition of the microbiota of the Lama-bordo, Valley, and Terrace agroecosystems in MAG. Analysis of agroecosystem soils revealed 21 bacterial phyla, with Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi dominating. These microbial communities contribute to soil health, carbon cycling, and disease suppression. The study identified specific phylogroups and metabolic pathways associated with nutrient-rich environments like Lama-bordo and Valley, and nutrient-poor, sandy soils like Terrace. Soils from Lama-bordo and Valley were grouped due to microbiome similarity despite geographic separation, whereas Terrace soils differed. Nutrient-rich Lama-bordo and Valley soils host copiotrophic bacteria, while nutrient-poor Terrace soils favor oligotrophic species like Acidobacteria. Functional analysis of microbiomes reveals distinct metabolic pathways, including antibiotic biosynthesis (streptomycin, vancomycin) suggesting a role in plant disease resistance, amino acid pathways indicating active nitrogen cycling, and vitamin B5 and lipoic acid pathways contributing to energy metabolism and antioxidant functions. [ABSTRACT FROM AUTHOR]

Microbial communities serve as reservoirs of antibiotic resistance genes (ARGs) and facilitate the dissemination of these genes to bacteria that infect humans. Relatively little is known about the taxonomic distribution of bacteria harboring ARGs in these reservoirs and the avenues of transmission due to the technical hurdles associated with characterizing the contents of complex microbial populations and the assignment of genes to particular genomes. Focusing on the array of tetracycline resistance (Tcr) genes in the primary and secondary phases of wastewater treatment, 17 of the 22 assayed Tcr genes were detected in at least one sample. We then applied emulsion, paired isolation, and concatenation PCR (epicPCR) to link tetracycline resistance genes to specific bacterial hosts. Whereas Tcr genes tend to vary in their distributions among bacterial taxa according to their modes of action, there were numerous instances in which a particular Tcr gene was associated with a host that was distantly related to all other bacteria bearing the same gene, including several hosts not previously identified. Tcr genes are far less host-restricted than previously assumed, indicating that complex microbial communities serve as settings where ARGs are spread among divergent bacterial phyla.

Abstract Background Permafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales. Results Permafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes. Conclusion We have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.

The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies. [ABSTRACT FROM AUTHOR]

Background: Permafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales. Results: Permafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes. Conclusion: We have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads. [ABSTRACT FROM AUTHOR]

This study investigated the combined effects of novel plant growth-promoting rhizobacteria (PGPR)—Agrobacterium pusense NC2, Kosakonia oryzae WN104, and Phytobacter sp. WL65—and Ascophyllum nodosum seaweed extract (ANE) as biostimulants (PGPR-ANE) on rice growth, yield, and rhizosphere bacterial communities using the RD79 cultivar. The biostimulants significantly enhanced plant growth, shoot and root length, and seedling vigour; however, seed germination was not affected. In pot experiments, biostimulant application significantly increased the richness and evenness of bacterial communities in the rhizosphere, resulting in improvements in rice growth and yield, with increases in plant height (9.6–17.7%), panicle length (14.3–17.9%), and seeds per panicle (48.0–53.0%). Notably, biostimulant treatments also increased post-harvest soil nutrient levels, with nitrogen increasing by 7.7–19.2%, phosphorus by 43.4–161.4%, and potassium by 16.9–70.4% compared to the control. Principal coordinate analysis revealed distinct differences in bacterial composition between the tillering and harvesting stages, as well as between biostimulant treatments and the control. Beneficial bacterial families, including Xanthobacteraceae, Beijerinckiaceae, Acetobacteraceae, Acidobacteriaceae, and Hyphomicrobiaceae, increased in number from the tillering to harvesting stages, likely contributing to soil health improvements. Conversely, methanogenic bacterial families, such as Methanobacteriaceae and Methanosarcinaceae, decreased in number compared to the control. These findings highlight the dynamic responses of the rhizosphere microbiome to biostimulant treatments and underscore their potential benefits for promoting sustainable and productive agriculture. [ABSTRACT FROM AUTHOR]

There are sparse data on the role of the vaginal microbiome (VMB) in pregnancy among pregnant women living with HIV (PWLWH) and its association with spontaneous preterm birth (sPTB). We conducted a scoping review to assess associations between vaginal microbiota and sPTB among PWLWH. Three studies were included, representing a total of 180 PWLWH out of 652 total pregnancies. All studies used modern DNA sequencing methods (16S rRNA amplification, metagenomics, or metatranscriptomics). PWLWH had higher VMB richness and diversity compared to HIV‐uninfected pregnant women and higher sPTB rates in two of three studies. A higher proportion of sPTB among PWLWH was observed in those with Lactobacillus‐deficient, anaerobe‐dominant vaginal microbiota. In two of three studies, higher concentrations of vaginal inflammation markers were associated with increased VMB richness and diversity. HIV status was independently associated with sPTB. It is unclear if increased vaginal microbial diversity among PWLWH or increased vaginal inflammation contributes more to PTB, but HIV does appear to alter the VMB in pregnant individuals and may also affect PTB rates in microbiome‐independent pathways. Given the limited number of studies, heterogeneity in sample size, sample collection methods, and inconsistent results it is difficult to causally link HIV, VMB, inflammatory cytokines, and sPTB. [ABSTRACT FROM AUTHOR]

This review paper attempts to interpret the various role of phyllosphere microbiome, survival, resistant mechanisms to confront the adverse environmental conditions, production of pigment, extracellular polysaccharides, biosurfactants to promote surface attachment desiccation protection, volatile organic compounds, phytoalexins, as a defensive role to compete for space and nutrients. The beneficial phyllosphere microbes contributing to promotion of plant growth by facilitating nutrient acquisition, modulating hormonal signaling, biocontrol for plant pathogens in multi-various crops is discussed in detail. Phyllobacteria show encouraging interactions with host plants in improving plant health and biometric traits by regulating nutrient acquisition, phytohormones production, biotic and abiotic stress management. The members of genera Bacillus, Enterobacter, Microbacterium, Methylobacterium, Stenotrophomonas, Pseudomonas, Pseudarthrobacter, and Kocuria were the most dominant plant growth promoting bacteria reported in phyllosphere. The beneficial phyllosphere microorganism enhances crop yield while reducing the environmental footprint associated with synthetic fertilizers and pesticides. The review focuses and thrust on the development as well as commercialization of biostimulants derived from phyllosphere microbiomes. These biostimulants, and their metabolites, can be tapped to enhance plant growth, nutrient uptake, and overall crop performance in organic farming. Furthermore, this review paper focus on certain drawbacks that there have been few researches on phyllosphere yeast and its symbiotic association with bacteria, thereby emphasizing subsequent research in this area. [ABSTRACT FROM AUTHOR]

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The influential rare biosphere concept in microbial ecology focuses on taxonomic scarcity and treats functional rarity implicitly. Microbes can possess functions distinct from other taxa in a community and can be present at high or low abundances. We define functionally rare microbes as possessing distinct functions and being numerically scarce. Functionally rare microbes can contribute disproportionately to ecosystem multifunctionality. The functional rarity concept helps to mechanistically connect microbial functional diversity, ecosystem functioning, and evolutionary processes. It also highlights the need for conservation of rare functions in microbial communities. The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions. [ABSTRACT FROM AUTHOR]

Microbial products are becoming common alternatives for pesticides and fertilizers in light of the unsustainability of chemical products. What the microbes in these products are, though--that is, how they are enacted--varies across regulatory, research and development, and growing spaces, and that variation matters to how they are regulated. From document analyses, interviews, and ethnographic work with scientists, growers, and policy actors, we find that these microbes are epistemically uneven, sometimes with pinned-down identities, and sometimes with loosely woven textures with holes. Amid calls to tailor regulations specifically for these products, we suggest that regulations predicated on discrete identities and predictable and controllable functions will fail to account for all users' experiences, and that regulation may need to learn to live with the lacy texture of microbes across contexts. [ABSTRACT FROM AUTHOR]

Aims: The accumulation of organic acids in soil can trigger autotoxicity, resulting in the continuous cropping obstacles (CCOs) for Panax notoginseng under conventional management systems. However, limited information is available about the threshold value of organic acids representing the CCOs in the soil of P. notoginseng from the forest understorey. Methods: In this study, mixed organic acids at different concentrations were exogenously applied to simulate the P. notoginseng CCO. The plant growth, edaphic factors, soil extracellular enzyme activity, and bacterial/fungal abundances and diversity in the rhizospheric soil were assessed in the P. notoginseng from the forest understorey. Results: High concentrations (>150 mg/kg) rather than low concentrations (<150 mg/kg) of organic acid decreased the dry and fresh weight of plants (1.99%-1.98%), edaphic properties (2.75%-1.03%) and soil extracellular enzyme activities (3.38%-1.05%). Under high organic acid concentrations, the fungal abundance increased by 2.37%, whereas the bacterial abundance decreased by 4.56%. Moreover, the abundance of Pseudomonadales, Xanthomonadales, and Ilyonectria as pathogenic bacteria tended to increase. Compared to bacteria, the fungal community structure varied significantly, and the fungal core flora was more abundant. The SEM results showed that the direct and indirect factors affecting the α-diversity in the rhizosphere of P. notoginseng were increased under the high organic acid concentrations. Conclusion: Organic acid concentrations greater than 150 mg/kg in P. notoginseng soils are detrimental to the relationships among plant growth, soil environment, and microbiomes, which implies the occurrence of the CCOs in P. notoginseng; and therefore, we recommend that P. notoginseng should not be planted again. [ABSTRACT FROM AUTHOR]

In this work, a conceptual framework is proposed for translating microbial research into usable design tools in an urban built environment. This study on Microbiomes of the Built Environment (MoBE), specifically the cultivable microbial count, incorporates building code and built environment design factors applied in the Philippine setting. The National Building Code of the Philippines with focus on minimum habitable room specifications was used to provide basis for the framework process. Human presence and ventilation were used as parameters to produce data that can be used as design tools. Using passive air sampling, the three experiments were conducted within Metro Manila according to the proposed framework. The first experiment using settle plates of culture media in the morning and afternoon seeks to understand how bacterial and fungal counts are affected in a naturally ventilated and in a non-ventilated room. The second and third experiments were done to test the effects of different window sizes and the number of humans on bacterial count, respectively. Results showed higher bacterial count in the room with natural ventilation compared to the room with no ventilation. The use of different window sizes did not show significant difference in counts with the number replicates used but as the number of humans in the area increased, the bacterial counts also increased. Data produced in the preliminary experiments were used to conceptually design a space in this paper. The authors suggest that this building-code inspired framework be used as a guide for MoBE studies as a starting point and be further developed to understand and eventually produce healthier built environments.

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).

Abstract Background Salvia miltiorrhiza Bunge, a significant and widely used medicinal herb, is also recognized in the US Pharmacopoeia as a dietary supplement. However, the decline in yield and quality limits its further development as a traditional herbal medicine. Therefore, a deeper understanding of how synthetic communities (SynCom) affect the quality and yield of S. miltiorrhiza and the underlying mechanisms is necessary. Results In this study, we selected S. miltiorrhiza as the research subject and designed two synthetic communities (SynCom 1 and SynCom 2) using five endophytic fungi without significantly growth-promoting effect. We conducted both greenhouse and field experiments to investigate their impact on the yield and quality of the herbal plants. Greenhouse experiments confirmed that SynCom 1 significantly increased the biomass of S. miltiorrhiza, whereas SynCom 2 had the opposite effect. Field experiments further demonstrated that the application of SynCom 1 promoted photosynthesis and enhanced carbon and nitrogen metabolism, steady and markedly promoted plant growth, and thus increased S. miltiorrhiza yield compared to the uninoculated. In contrast, SynCom 2 inhibited yield but increased the content of the main active components. Un-targeted metabolomics analysis showed that SynCom 1 mainly promoted tricarboxylic acid cycle and nitrogen assimilation process to increase yield, and SynCom 2 mainly increase substrate content in the salvianolic acid and tanshinone synthesis pathways to improve quality. Conclusion These beneficial qualities exhibited by SynComs composed of fungi without apparent growth-promoting abilities represent an untapped resource that can be leveraged to enhance crop productivity. This opens up new research avenues for precision manipulation of plant microbiomes. Graphical abstract

Background: Salvia miltiorrhiza Bunge, a significant and widely used medicinal herb, is also recognized in the US Pharmacopoeia as a dietary supplement. However, the decline in yield and quality limits its further development as a traditional herbal medicine. Therefore, a deeper understanding of how synthetic communities (SynCom) affect the quality and yield of S. miltiorrhiza and the underlying mechanisms is necessary. Results: In this study, we selected S. miltiorrhiza as the research subject and designed two synthetic communities (SynCom 1 and SynCom 2) using five endophytic fungi without significantly growth-promoting effect. We conducted both greenhouse and field experiments to investigate their impact on the yield and quality of the herbal plants. Greenhouse experiments confirmed that SynCom 1 significantly increased the biomass of S. miltiorrhiza, whereas SynCom 2 had the opposite effect. Field experiments further demonstrated that the application of SynCom 1 promoted photosynthesis and enhanced carbon and nitrogen metabolism, steady and markedly promoted plant growth, and thus increased S. miltiorrhiza yield compared to the uninoculated. In contrast, SynCom 2 inhibited yield but increased the content of the main active components. Un-targeted metabolomics analysis showed that SynCom 1 mainly promoted tricarboxylic acid cycle and nitrogen assimilation process to increase yield, and SynCom 2 mainly increase substrate content in the salvianolic acid and tanshinone synthesis pathways to improve quality. Conclusion: These beneficial qualities exhibited by SynComs composed of fungi without apparent growth-promoting abilities represent an untapped resource that can be leveraged to enhance crop productivity. This opens up new research avenues for precision manipulation of plant microbiomes. Highlights: The Synthetic communities with non-growth promoting fungi promote the growth and quality of Salvia miltiorrhiza Bge. SynCom 1 promoted tricarboxylic acid cycle and nitrogen assimilation process to increase yield. SynCom 2 increase substrate content in the salvianolic acid and tanshinone synthesis pathways to improve quality. The SynComs possess the potential to be applied to field planting and promote medicine food homology plant development as well. The addition of distant species changes the interaction pattern among closely related species. [ABSTRACT FROM AUTHOR]

The intensive applications of nanomaterials in the agroecosystem led to the creation of several environmental problems. More efforts are needed to discover new insights in the nanomaterial–microbe–plant nexus. This relationship has several dimensions, which may include the transport of nanomaterials to different plant organs, the nanotoxicity to soil microbes and plants, and different possible regulations. This review focuses on the challenges and prospects of the nanomaterial–microbe–plant nexus under agroecosystem conditions. The previous nano-forms were selected in this study because of the rare, published articles on such nanomaterials. Under the study's nexus, more insights on the carbon nanodot–microbe–plant nexus were discussed along with the role of the new frontier in nano-tellurium–microbe nexus. Transport of nanomaterials to different plant organs under possible applications, and translocation of these nanoparticles besides their expected nanotoxicity to soil microbes will be also reported in the current study. Nanotoxicity to soil microbes and plants was investigated by taking account of morpho-physiological, molecular, and biochemical concerns. This study highlights the regulations of nanotoxicity with a focus on risk and challenges at the ecological level and their risks to human health, along with the scientific and organizational levels. This study opens many windows in such studies nexus which are needed in the near future. [ABSTRACT FROM AUTHOR]

Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin‐degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin‐degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter‐connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes. [ABSTRACT FROM AUTHOR]

Microbial communities have been documented as playing many pivotal roles, and contributing to the growth or health performance of animal hosts. Thus, many studies are currently looking for potential beneficial bacteria "probiotics" from diverse environments, including wild species. The present study aimed to investigate the diversity and potential metabolic functions of bacterial communities in the gastrointestinal tract of wild spiny lobsters. The gastrointestinal (GI) tracts of two wild lobster species (Panulirus ornatus and Panulirus homarus) were dissected aseptically and analyzed through high-throughput sequencing, followed by PICRUSt analysis. The results exposed that the most dominant phyla inhabiting both lobster species at the post-puerulus and juvenile stages were Proteobacteria, Firmicutes, Bacteriodota, Patescibacteria, and Verrucomicrobiota, while at the genus level, the GI tracts were mostly dominated by Photobacterium, Candidatus Bacillopora, Vibrio, and Catenococcus at the post-peurulus stage, and Vibrio, Catenococcus, Acanthopleuribacter, Acinetobacter, Pseudoalteromonas, Grimontia, and Photobacterium at the juvenile stage. Further metagenomic prediction analysis discovers many potential probiont properties indicated by the detection of marker genes corresponding to many important metabolic activities, such as antimicrobial compounds (streptomycin, vancomycin, carbapenem, tetracycline, novobiocin, penicillin, cephalosporin, ansamycines, butirosin, and neomycin), antioxidants (e.g., flavonoids and carotenoids), and several important digestive enzymes (e.g., lipase, protease, and amylase). These results suggest that GI tracts of wild spiny lobsters are potential sources to discover novel probionts for aquaculture purposes. Further studies, such as the isolation of the natural product-producing bacteria, or cloning of the beneficial compound-identified genes, are highly recommended to develop novel probiotic strains for aquaculture purposes. [ABSTRACT FROM AUTHOR]

Background: Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs). Methods: This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes. Results: Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed. [ABSTRACT FROM AUTHOR]

Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the everincreasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities. [ABSTRACT FROM AUTHOR]

ABSTRACT Multiple factors explain the proper development of sourdough starters. Although the role of raw ingredients and geography, among other things, have been widely studied recently, the possible effect of air quality and water chlorination on the overall bacterial communities associated with sourdough remains to be explored. Here, using 16S rRNA amplicon sequencing, we show that clean, filtered-air severely limited the presence of lactic acid bacteria in sourdough starters, suggesting that surrounding air is an important source of microorganisms necessary for the development of sourdough starters. We also show that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, using targeted sequencing, which offers a higher resolution, we found that the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic-resistance genes in spoilage and pathogenic bacteria, increased significantly with the level of water chlorination. Although our results suggest that water chlorination might not impact sourdough starters at a deep phylogenetic level, they indicate that it can favor the spread of genetic elements associated with spoilage bacteria.IMPORTANCEProper development of sourdough starters is critical for making tasty and healthy bread. Although many factors contributing to sourdough development have been studied, the effect of water chlorination on the bacterial communities in sourdough has been largely ignored. Researchers used sequencing techniques to investigate this effect and found that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, they discovered that water chlorination could increase the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic resistance genes in spoilage and pathogenic bacteria. This suggests that water chlorination could favor the growth of key spoilage bacteria and compromise the quality and safety of the bread. These findings emphasize the importance of considering water quality when developing sourdough starters for the best possible bread.

ObjectiveThis study investigated the differences in oral saliva microbiota composition and metabolic products among Han Chinese populations living at different altitudes, as well as their correlations.MethodThe analysis was conducted using the 16S rRNA gene sequencing method and untargeted metabolomics.Results16S gene sequencing results showed significant differences in bacterial diversity and composition between HH (High altitude Han) group and LH (Low altitude Han) group. LEfSe analysis showed that Selenomonas, Leptotrichia, Veillonella, Prevotella relatively abundant are higher in HH group, Haemophilus, Neisseria, Actinobacillus, Aggregatibacter are higher in LH group (p

ABSTRACT Pollution can negatively impact aquatic ecosystems, aquaculture operations, and recreational water quality. Many aquatic microbes can sequester or degrade pollutants and have been utilized for bioremediation. While planktonic and benthic microbes are well-studied, host-associated microbes likely play an important role in mitigating the negative impacts of aquatic pollution and represent an unrealized source of microbial potential. For example, aquatic organisms that thrive in highly polluted environments or concentrate pollutants may have microbiomes adapted to these selective pressures. Understanding microbe–pollutant interactions in sensitive and valuable species could help protect human well-being and improve ecosystem resilience. Investigating these interactions using appropriate experimental systems and overcoming methodological challenges will present novel opportunities to protect and improve aquatic systems. In this perspective, we review examples of how microbes could mitigate negative impacts of aquatic pollution, outline target study systems, discuss challenges of advancing this field, and outline implications in the face of global changes.

At high latitudes, lake whitefish (Coregonus clupeaformis) and others in the closely related Coregonus species complex (CSC) including cisco (C. autumnalis and C. sardinella) can be diadromous, seasonally transitioning between freshwater lakes and the Arctic Ocean. CSC skin- and intestine microbiomes were collected, facilitated by Inuit fishers at sites on and around King William Island, Nunavut, at the northern range limits of lake whitefish. Community composition was explored using 16S rRNA gene sequencing and microbiota distinctly grouped depending on fishing site salinity. Overall, lake whitefish intestine communities were more variable than those of the two cisco with higher Shannon diversity, suggesting that lake whitefish and their microbiomes could be susceptible to environmental stress possibly leading to dysbiosis. Lake whitefish showed lower condition (K) in the ocean than in freshwater rivers, whereas cisco condition was similar among distinct seasonal habitats. Taken together, the impact of changing habitats on fish condition and microbial composition may inform approaches to CSC health in fisheries and aquaculture, in addition to being relevant for northern Indigenous peoples with subsistence and economic interests in these resources.

As most life-forms exist as holobionts, reduction of host-level biodiversity drives parallel habitat losses to their host-adapted microorganisms. The holobiont concept helps us to understand how species are habitats for – often ignored – coevolved microorganisms also worthy of conservation. Indeed, loss of host-associated microbial biodiversity may accelerate the extinction risks of their host. [ABSTRACT FROM AUTHOR]

Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'. [ABSTRACT FROM AUTHOR]