Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Temperature and wind speed help fermentation-sourced microbiota reconstruct the airborne microbiota in the Chinese baijiu fermentation region

Microorganisms are vital components of airborne particles and are closely linked to human health and industrial processes. As industrialization advances, factories are exacerbating their impact on environmental microbial communities, an area where our understanding remains limited. In this study, we investigated air microorganisms surrounding Chinese baijiu fermentation facilities, aiming to explore the dispersal mechanisms of fermentation-sourced microbiota and their potential impacts on local airborne microbial communities. The results revealed a significant overlap between microbial communities from fermentation processes and the surrounding air, with 14 genera commonly found in both habitats, suggesting widespread and substantial dispersal of factory microorganisms. Due to this dispersal, fermentation-sourced Saccharopolyspora and Streptomyces have become central nodes in the airborne microbial network. Environmental factors played a pivotal role in the microbiota dispersal process. Higher temperatures may facilitate microbial proliferation and increase the dispersal of fermentation microorganisms (r = 0.30, P < 0.01), while higher wind speeds may lead to a dilution effect and limit the uniform dispersal of microorganisms (r = -0.22, P < 0.05). Furthermore, air-resident microorganisms restricted the proliferation of fermentation microorganisms (r = -0.60, P < 0.001). These results confirm the modifying effect of fermentation facilities on environmental microbial communities and establish a theoretical foundation for optimizing factory site selection.

Exploring the Grapevine Microbiome: Insights into the Microbial Ecosystem of Grape Berries

Plant growth, health, and resilience to stress are intricately linked to their associated microbiomes. Grapevine, functioning as a holobiont, forms essential relationships with fungi and bacteria across both its belowground (roots) and aboveground (leaves and berries) compartments. The root microbiome exhibits a stable, site-specific structure, whereas the microbiomes of ephemeral tissues such as leaves and berries, which regenerate annually, display more stochastic assembly patterns across growing seasons. Among these, grape berries represent a critical component in viticulture due to their direct influence on wine quality and flavor complexity. Berries provide a unique ecological niche, hosting diverse microbial communities composed of yeasts, bacteria, and fungi that interact with the grapevine and its surrounding environment. These microorganisms are not only pivotal to berry development but also contribute significantly to the synthesis of secondary metabolites and fermentation processes, ultimately shaping the sensory and organoleptic properties of wine. This review consolidates current knowledge on the grapevine microbiome, with a particular emphasis on the microbial dynamics of grape berries.

Microbiome Literacy: Enhancing Public and Academic Understanding Through the 'Microbiome & Health' Online Course

Microorganisms are fundamental to life on Earth, influencing biogeochemical processes, soil fertility, and the health of humans, animals and plants. Human activities have left a remarkable footprint on the environment, including global microbiomes. Enhancing awareness and improving education about microbiome functions can contribute to a sustainable economy and resilient systems. However, public understanding of microbiome science is hindered by misinformation and limited accessible educational resources. To address this, we developed the massive open online course (MOOC) 'Microbiome & Health', available on iMooX.at and YouTube. The course, structured into six units, covers microbiome concepts, methodologies, human and plant microbiomes, antibiotic resistance, and environmental impacts, aligning with the One Health concept and the Sustainable Development Goals of the United Nations. Initial results show that the MOOC provides the means to increase microbiology literacy, with 73.2% external participation and above-average completion rates. Integration as a mandatory component in university courses has improved student performance, halting declining grades and pass rates. This highlights the MOOC's potential to enhance public and academic understanding of microbiome science, fostering informed decisions for sustainable health and environmental stewardship as well as paving the way for new microbiome-based solutions in biotechnology.

Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry

Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.

Deep learning in microbiome analysis: a comprehensive review of neural network models

Microbiome research, the study of microbial communities in diverse environments, has seen significant advances due to the integration of deep learning (DL) methods. These computational techniques have become essential for addressing the inherent complexity and high-dimensionality of microbiome data, which consist of different types of omics datasets. Deep learning algorithms have shown remarkable capabilities in pattern recognition, feature extraction, and predictive modeling, enabling researchers to uncover hidden relationships within microbial ecosystems. By automating the detection of functional genes, microbial interactions, and host-microbiome dynamics, DL methods offer unprecedented precision in understanding microbiome composition and its impact on health, disease, and the environment. However, despite their potential, deep learning approaches face significant challenges in microbiome research. Additionally, the biological variability in microbiome datasets requires tailored approaches to ensure robust and generalizable outcomes. As microbiome research continues to generate vast and complex datasets, addressing these challenges will be crucial for advancing microbiological insights and translating them into practical applications with DL. This review provides an overview of different deep learning models in microbiome research, discussing their strengths, practical uses, and implications for future studies. We examine how these models are being applied to solve key problems and highlight potential pathways to overcome current limitations, emphasizing the transformative impact DL could have on the field moving forward.

Tolerance to land-use changes through natural modulations of the plant microbiome

Land-use changes threaten ecosystems and are a major driver of species loss. Plants may adapt or migrate to resist global change, but this can lag behind rapid anthropogenic changes to the environment. Our data show that natural modulations of the microbiome of grassland plants in response to experimental land-use change in a common garden directly affect plant phenotype and performance, thus increasing plant tolerance. In contrast, direct effects of fertilizer application and mowing on plant phenotypes were less strong. Land-use intensity-specific microbiomes caused clearly distinguishable plant phenotypes also in a laboratory experiment using gnotobiotic strawberry plants in absence of environmental variation. Therefore, natural modulations of the plant microbiome may be key to species persistence and ecosystem stability. We argue that a prerequisite for this microbiome-mediated tolerance is the availability of diverse local sources of microorganisms facilitating rapid modulations in response to change. Thus, conservation efforts must protect microbial diversity, which can help mitigate the effects of global change and facilitate environmental and human health.

Harnessing the plant microbiome for sustainable crop production

Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.

Evidence driven indoor air quality improvement: An innovative and interdisciplinary approach to improving indoor air quality

Indoor air pollution is a recognized emerging threat, claiming millions of lives annually. People are constantly exposed to ambient and indoor air pollution. The latest research shows that people in developed countries spend up to 90% of their time indoors and almost 70% at home. Although impaired Indoor Air Quality (IAQ) represents a significant health risk, it affects people differently, and specific populations are more vulnerable: children, the elderly, and people with respiratory illnesses are more sensitive to these environmental risks. Despite rather extensive research on IAQ, most of the current understanding about the subject, which includes pollution sources, indoor-outdoor relationships, and ventilation/filtration, is still quite limited, mainly because air quality monitoring in the EU is primarily focused on ambient air quality and regulatory requirements are lacking for indoor environments. Therefore, the EDIAQI project aims to improve guidelines and awareness for advancing the IAQ in Europe and beyond by allowing user-friendly access to information about indoor air pollution exposures, sources, and related risk factors. The solution proposed with EDIAQI consists of conducting a characterization of sources and routes of exposure and dispersion of chemical, biological, and emerging indoor air pollution in multiple cities in the EU. The project will deploy cost-effective/user-friendly monitoring solutions to create new knowledge on sources, exposure routes, and indoor multipollutant body burdens. The EDIAQI project brings together 18 organizations from 11 different European countries that provide interdisciplinary skills and expertise in various fields, including environmental science and technology, medicine, and toxicology, as well as policy design and public engagement.

The microorganisms and metabolome of Pinus radiata Pollen

BACKGROUND

Pollen is a crucial source of nutrients and energy for pollinators. It also provides a unique habitat and resource for microbiota. Previous research on the microbiome of pollen has largely focused on angiosperm systems, with limited research into coniferous gymnosperms. This study characterises the pollen microbiome and metabolome associated with one of the world's most widely grown tree species, Pinus radiata. Trees were sampled from locations across Canterbury, New Zealand. Repeated collections were undertaken in 2020 and 2021.

RESULTS

Metabolomic analysis revealed the main compounds present on P. radiata pollen to be amino acids (principally proline), and carbohydrates (fructose, glucose, and sucrose). Although phenolic compounds such as ρ-coumaric acid and catechin, and terpenoids such as dehydroabietic acid, were present at low concentrations, their strong bioactive natures mean they may be important in ecological filtering of microbiome communities on pollen. The P. radiata pollen microbiome was richer in fungal taxa compared with bacteria, which differs from many angiosperm species. Geographic range and annual variation were evaluated as drivers of microbiome assembly. Neither sampling location (geographic range) nor annual variation significantly influenced the fungal community which exhibited remarkable conservation across samples. However, some bacterial taxa exhibited sensitivity to geographic distances and yearly variations, suggesting a secondary role of these factors for some taxa. A core microbiome was identified in P. radiata pollen, characterized by a consistent presence of specific fungal and bacterial taxa across samples. While the dominant phyla, Proteobacteria and Ascomycota, align with findings from other pollen microbiome studies, unique core members were unidentified at genus level.

CONCLUSION

This tree species-specific microbiome assembly emphasizes the crucial role of the host plant in shaping the pollen microbiome. These findings contribute to a deeper understanding of pollen microbiomes in gymnosperms, shedding light on the need to look further at their ecological and functional roles.

Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area

The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.

Urban air quality affects the apple microbiome assembly

Exposure to air pollution affects health of all organisms on earth but the impact on the plant microbiome is less understood. Here, we link the Air Quality Index with the dust and apple epiphytic and endophytic microbiome across the city of Graz (Austria). The microbiome of the apple episphere, peel endosphere and pulp endosphere, and surrounding dust was analyzed. Our results show that the fungal communities were more influenced by air quality than bacterial communities. Bacterial communities, instead, were more specific for the individual sample types, especially noticeable in the pulp endosphere. The microbiome of each sample type was comprised of distinct microbial communities. Overall, the bacterial communities were highly dominated by Proteobacteria followed by Bacteroidota and Actinobacteriota, and the fungal communities were dominated by Ascomycota followed by Basidiomycota. With lower air quality, the relative abundance of the fungal orders Hypocreales and Pleosporales decreased in the apple episphere and the peel endosphere, respectively. Interestingly, an unexpectedly high level of similarity was observed between the bacterial communities of dust and peel endosphere, while the epiphytic bacterial community was significantly different compared to the other samples. We suggested that dust served as a potential microbial colonization route for the fruit microbiome as most bacteria (55%) colonizing the peel endosphere originated from dust. In conclusion, air quality affects the microbiome of edible plants, which can cause health consequences in humans. Therefore, this knowledge should be considered in urban and horticultural farming strategies.

Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas

Contact with environmental microbial communities primes the human immune system. Factors determining the distribution of microorganisms, such as dispersal, are thus important for human health. Here, we used the relative number of bacteria shared between environmental and human samples as a measure of bacterial dispersal and studied these associations with living environment and lifestyles. We analyzed amplicon sequence variants (ASVs) of the V4 region of 16S rDNA gene from 347 samples of doormat dust as well as samples of saliva, skin swabs, and feces from 53 elderly people in urban and rural areas in Finland at three timepoints. We first enumerated the ASVs shared between doormat and one of the human sample types (i.e., saliva, skin swab, or feces) of each individual subject and calculated the shared ASVs as a proportion of all ASVs in the given sample type of that individual. We observed that the patterns for the proportions of shared ASVs differed among seasons and human sample type. In skin samples, there was a negative association between the proportion of shared ASVs and the coverage of built environment (a proxy for degree of urbanization), whereas in saliva data, this association was positive. We discuss these findings in the context of differing species pools in urban and rural environments.

IMPORTANCE

Understanding how environmental microorganisms reach and interact with humans is a key question when aiming to increase human contacts with natural microbiota. Few methods are suitable for studying microbial dispersal at relatively large spatial scales. Thus, we tested an indirect method and studied patterns of bacterial taxa that are shared between humans and their living environment.

The One Health approach in urban ecosystem rehabilitation: An evidence-based framework for designing sustainable cities

Rapid urbanization has led to negative, and sometimes unintended, consequences on biodiversity and human health. While cities offer numerous advantages in meeting the basic needs of a growing population, they also pose less apparent and longer-term health costs. To address the multifaceted impacts of urbanization, an evidence-based design framework for establishing mitigation and regeneration actions is essential. Via a "One Health" approach, this perspective provides recommendations and strategies for the urban ecosystem rehabilitation of future cities, placing biodiversity and ecosystem services at the core of designing healthy and sustainable urban spaces. The framework we propose is based on a Hub and Spoke model to integrate diverse perspectives from public and private sectors and declined in a six-building-blocks structure. This will ensure that efforts are sustainable, health-centered, socially inclusive, and grounded in high-quality data, reinforcing the essential connection between healthy environments and thriving communities.

Characterization of microbiome, resistome, mobilome, and virulome in anoxic and oxic wastewater treatment processes in Slovakia and Taiwan

This study presents a comprehensive analysis of samples from urban wastewater treatment plants using anoxic/oxic processes in Slovakia and Taiwan, focusing on microbiome, resistome, mobilome, and virulome, which were analyzed using a shotgun metagenomic approach. Distinct characteristics were observed; in Taiwan, a higher abundance and diversity of antibiotic resistance genes were found in both influent and effluent samples, while there was a higher prevalence of mobile genetic elements and virulence factor genes in Slovakia. Variations were noted in microbial community structures; influent samples in Taiwan were reflected from fecal and hospital sources, and those in Slovakia were derived from environmental elements. At the genus level, the samples from Taiwan's sewage treatment plants were dominated by Cloacibacterium and Bacteroides, while Acinetobacter was predominant in samples from Slovakia. Despite similar antibiotic usage patterns, distinct wastewater characteristics and operational disparities influenced microbiome, resistome, mobilome, and virulome compositions, with limited reduction of most resistance genes by the studied anoxic/oxic processes. These findings underscore the importance of region-specific insights into microbial communities for understanding the dynamics of antimicrobial resistance and pathogenicity in urban wastewater treatment systems. Such insights may lay the groundwork for optimizing treatment processes and reducing the dissemination of antibiotic resistance and pathogenicity genes for safeguarding public health.

Concepts and criteria defining emerging microbiome applications

In recent years, microbiomes and their potential applications for human, animal or plant health, food production and environmental management came into the spotlight of major national and international policies and strategies. This has been accompanied by substantial R&D investments in both public and private sectors, with an increasing number of products entering the market. Despite widespread agreement on the potential of microbiomes and their uses across disciplines, stakeholders and countries, there is no consensus on what defines a microbiome application. This often results in non-comprehensive communication or insufficient documentation making commercialisation and acceptance of the novel products challenging. To showcase the complexity of this issue we discuss two selected, well-established applications and propose criteria defining a microbiome application and their conditions of use for clear communication, facilitating suitable regulatory frameworks and building trust among stakeholders.

Regulation of immune responses to food by commensal microbes

The increasing prevalence of immune-mediated non-communicable chronic diseases, such as food allergies, has prompted a deeper investigation into the role of the gut microbiome in modulating immune responses. Here, we explore the complex interactions between commensal microbes and the host immune system, highlighting the critical role of gut bacteria in maintaining immune homeostasis. We examine how modern lifestyle practices and environmental factors have disrupted co-evolved host-microbe interactions and discuss how changes in microbiome composition impact epithelial barrier function, responses to food allergens, and susceptibility to allergic diseases. Finally, we examine the potential of bioengineered microbiome-based therapies, and live biotherapeutic products, for reestablishing immune homeostasis to prevent or treat food allergies.

From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture

Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Integrating research on bacterial pathogens and commensals to fight infections-an ecological perspective

The incidence of antibiotic-resistant bacterial infections is increasing, and development of new antibiotics has been deprioritised by the pharmaceutical industry. Interdisciplinary research approaches, based on the ecological principles of bacterial fitness, competition, and transmission, could open new avenues to combat antibiotic-resistant infections. Many facultative bacterial pathogens use human mucosal surfaces as their major reservoirs and induce infectious diseases to aid their lateral transmission to new host organisms under some pathological states of the microbiome and host. Beneficial bacterial commensals can outcompete specific pathogens, thereby lowering the capacity of the pathogens to spread and cause serious infections. Despite the clinical relevance, however, the understanding of commensal-pathogen interactions in their natural habitats remains poor. In this Personal View, we highlight directions to intensify research on the interactions between bacterial pathogens and commensals in the context of human microbiomes and host biology that can lead to the development of innovative and sustainable ways of preventing and treating infectious diseases.

Embracing complexity in plant-microbiome systems

Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.

Community context influences the conjugation efficiency of Escherichia coli

In urinary tract infections (UTIs), different bacteria can live in a polymicrobial community consisting of different species. It is unknown how community members affect the conjugation efficiency of uropathogenic Escherichia coli. We investigated the influence of individual species often coisolated from urinary infections (UTI) on the conjugation efficiency of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing the pOXA-48 plasmid and six uropathogenic E. coli isolates, in the presence and absence of five different species commonly coisolated in polymicrobial UTIs to elucidate their effect on the conjugation efficiency of E. coli. We found that the basal conjugation rates of pOXA-48, in the absence of other species, are dependent on the bacterial host genetic background. Additionally, we found that bacterial interactions have an overall positive effect on the conjugation rate of pOXA-48. Particularly, Gram-positive enterococcal species were found to enhance the conjugation rates towards uropathogenic E. coli isolates. We hypothesize that the nature of the coculture and physical interactions are important for these increased conjugation rates in an artificial urine medium environment.

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater

Introduction

Constructed wetlands (CWs) are nature-based solutions for wastewater treatment where the root system microbiome plays a key role in terms of nutrient and pollutant removal. Nonetheless, little is known on plant-microbe interactions and bacterial population selection in CWs, which are mostly characterized in terms of engineering aspects.

Methods

Here, cultivation-independent and cultivation-based analyses were applied to study the bacterial communities associated to the root systems of Phragmites australis and Typha domingensis co-occurring in the same cell of a CW receiving primary treated wastewaters.

Results and discussion

Two endophytic bacteria collections (n = 156) were established aiming to find novel strains for microbial-assisted phytodepuration, however basing on their taxonomy the possible use of these strains was limited by their low degrading potential and/or for risks related to the One-Health concept. A sharp differentiation arose between the P. australis and T. domingensis collections, mainly represented by lactic acid bacteria (98%) and Enterobacteriaceae (69%), respectively. Hence, 16S rRNA amplicon sequencing was used to disentangle the microbiome composition in the root system fractions collected at increasing distance from the root surface. Both the fraction type and the plant species were recognized as drivers of the bacterial community structure. Moreover, differential abundance analysis revealed that, in all fractions, several bacteria families were significantly and differentially enriched in P. australis or in T. domingensis. CWs have been also reported as interesting options for the removal of emerging contaminants (e.g, antibiotic resistance genes, ARGs). In this study, ARGs were mostly present in the rhizosphere of both plant species, compared to the other analyzed fractions. Notably, qPCR data showed that ARGs (i.e., ermB, bla TEM, tetA) and intl1 gene (integrase gene of the class 1 integrons) were significantly higher in Phragmites than Typha rhizospheres, suggesting that macrophyte species growing in CWs can display a different ability to remove ARGs from wastewater. Overall, the results suggest the importance to consider the plant-microbiome interactions, besides engineering aspects, to select the most suitable species when designing phytodepuration systems.

Urban sports fields support higher levels of soil butyrate and butyrate-producing bacteria than urban nature parks

Butyrate-producing bacteria colonise the gut of humans and non-human animals, where they produce butyrate, a short-chain fatty acid with known health benefits. Butyrate-producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important reservoirs of butyrate-producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate-producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r = .50), calcium (r = -.62), iron (ρ = .54), ammonium nitrogen (ρ = .58) and organic carbon (r = .45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ = .56) and calcium (ρ = -.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome-mediated human health benefits via butyrate.

Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations

Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.

Comparative analysis of the distribution and antifungal susceptibility of yeast species in cat facial hair and human nails

Zoonotic yeast species have been implicated in disease development in both humans and cats. This study analyzed the yeast mycobiota present in feline facial hair and human nails and explored potential interspecies associations. A total of 118 biological specimens were examined, including 59 feline facial hair and 59 human nail samples. DNA extraction and DNA sequencing were performed to identify the specific yeast species. The most predominant yeast species in humans and cats were selected for antifungal susceptibility testing (itraconazole, ketoconazole, miconazole, and terbinafine). The findings unveiled diverse yeast species in cats and humans. Malassezia pachydermatis (45.8%) and Malassezia furfur (30.5%) were the most common yeast species in cats and humans, respectively. However, no significant correlation was detected between the yeast species identified in cats and their owners residing in the same household (p > 0.05). Miconazole exhibited the highest minimum inhibitory concentrations (MICs) against Malassezia pachydermatis and Malassezia furfur in both cat and human isolates, whereas terbinafine showed the lowest MICs against most Malassezia pachydermatis and Malassezia furfur in both cat and human isolates. Diverse yeast species in cat facial hair and human nails suggest possible cross-contamination among humans, pets, and environments.

This is the Age of Microbial Technology: Crucial roles of learned societies and academies

Microbial technologies constitute a huge and unique potential for confronting major humanitarian and biosphere challenges, especially in the realms of sustainability and providing basic goods and services where they are needed and particularly in low-resource settings. These technologies are evolving rapidly. Powerful approaches are being developed to create novel products, processes, and circular economies, including new prophylactics and therapies in healthcare, bioelectric systems, and whole-cell understanding of metabolism that provides novel insights into mechanisms and how they can be utilised for applications. The modulation of microbiomes promises to create important applications and mitigate problems in a number of spheres. Collectively, microbial technologies save millions of lives each year and have the potential, through increased deployment, to save many more. They help restore environmental health, improve soil fertility, enable regenerative agriculture, reduce biodiversity losses, reduce pollution, and mitigate polluted environments. Many microbial technologies may be considered to be 'healing' technologies - healing of humans, of other members of the biosphere, and of the environment. This is the Age of Microbial Technology. However, the current exploitation of microbial technologies in the service of humanity and planetary health is woefully inadequate and this failing unnecessarily costs many lives and biosphere deterioration. Microbiologists - the practitioners of these healing technologies - have a special, preordained responsibility to promote and increase their deployment for the good of humanity and the planet. To do this effectively - to actually make a difference - microbiologists will need to partner with key enablers and gatekeepers, players such as other scientists with essential complementary skills like bioengineering and bioinformatics, politicians, financiers, and captains of industry, international organisations, and the general public. Orchestration and coordination of the establishment and functioning of effective partnerships will best be accomplished by learned societies, their academies, and the international umbrella organisations of learned societies. Effective dedication of players to the tasks at hand will require unstinting support from employers, particularly the heads of institutes of higher education and of research establishments. Humanity and the biosphere are currently facing challenges to their survival not experienced for millennia. Effectively confronting these challenges is existential, and microbiologists and their learned societies have pivotal roles to play: they must step up and act now.

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

EXECUTIVE SUMMARY

Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative-the IMiLI-is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators-learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators-learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships-a global societally relevant microbiology education ecosystem-in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient.

ABSTRACT

The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us-individuals/communities/nations/the human world-and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT: our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091-1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.

A comprehensive review on the utilization of probiotics in aquaculture towards sustainable shrimp farming

Probiotics in shrimp aquaculture have gained considerable attention as a potential solution to enhance production efficiency, disease management, and overall sustainability. Probiotics, beneficial microorganisms, have shown promising effects when administered to shrimp as dietary supplements or water additives. Their inclusion has been linked to improved gut health, nutrient absorption, and disease resistance in shrimp. Probiotics also play a crucial role in maintaining a balanced microbial community within the shrimp pond environment, enhancing water quality and reducing pathogen prevalence. This article briefly summarizes the many ways that probiotics are used in shrimp farming and the advantages that come with them. Despite the promising results, challenges such as strain selection, dosage optimization, and environmental conditions are carefully addressed for successful probiotic integration in shrimp aquaculture. The potential of probiotics as a sustainable and ecologically friendly method of promoting shrimp development and health while advancing environmentally friendly shrimp farming techniques is highlighted in this analysis. Further research is required to fully exploit probiotics' benefits and develop practical guidelines for their effective implementation in shrimp aquaculture.

Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations

Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations. We explored whether the effect of antimicrobial treatment is detectable with metagenomic sequencing, and whether AMR genes can be spread and established in unchallenged (not treated with antibiotics) individuals following contact with treated donors, and under various frequencies of interaction. Gut and soil substrate microbiomes were investigated by metagenomic sequencing for bacterial community composition and resistome profiling. We found that tetracycline treatment altered the treated gut microbiome by decreasing bacterial diversity and increasing the abundance of tetracycline resistance genes. Untreated cockroaches that interacted with treated donors also had elevated tetracycline resistance. The levels of resistance differed depending on the magnitude and frequency of donor transfer. Additionally, treated donors showed signs of microbiome recovery due to their interaction with the untreated ones. Similar patterns were also recorded in the soil substrate microbiomes. Our results shed light on how interacting microbiomes facilitate AMR gene transmission to previously unchallenged hosts, a dynamic influenced by the interaction frequencies, using an in vivo model to validate theoretical AMR transmission models.IMPORTANCEAntimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.

The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut

Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.

A targeted approach to enrich host-associated bacteria for metagenomic sequencing

Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the 'Endozoicomonas' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.

Rhizobiome Transplantation: A Novel Strategy beyond Single-Strain/Consortium Inoculation for Crop Improvement

The growing human population has a greater demand for food; however, the care and preservation of nature as well as its resources must be considered when fulfilling this demand. An alternative employed in recent decades is the use and application of microbial inoculants, either individually or in consortium. The transplantation of rhizospheric microbiomes (rhizobiome) recently emerged as an additional proposal to protect crops from pathogens. In this review, rhizobiome transplantation was analyzed as an ecological alternative for increasing plant protection and crop production. The differences between single-strain/species inoculation and dual or consortium application were compared. Furthermore, the feasibility of the transplantation of other associated micro-communities, including phyllosphere and endosphere microbiomes, were evaluated. The current and future challenges surrounding rhizobiome transplantation were additionally discussed. In conclusion, rhizobiome transplantation emerges as an attractive alternative that goes beyond single/group inoculation of microbial agents; however, there is still a long way ahead before it can be applied in large-scale agriculture.