Hasil untuk "Microbial ecology"

Yutaka Yoshii, Stanislas Thiriet-Rupert, David Lebeaux et al.

Abstract The use of antibiotic lock therapy (ALT) to protect catheters from infection is still being debated due to its inconsistent effectiveness and the potential risk of promoting antibiotic resistance. Using an in vitro infection model of a pediatric venous access port, we demonstrated that 10 days of continuous therapy eradicates Escherichia coli biofilms in vitro without the emergence of antibiotic resistance. By contrast, an 8-h intermittent therapy used for infected parenteral nutrition patients rapidly selected low-level amikacin-resistant mutants both in vitro and in vivo in a clinically relevant rat model, primarily due to convergent fusA, sbmA, and cpxA mutations. Our findings indicate that intermittent dosing generates pulsed selective pressure, favoring the development of resistance mutants within spatially structured biofilm communities. This suggests that biofilms may act as evolutionary incubators, in which medical interventions could unintentionally influence adaptation outcomes. Furthermore, the low-level resistance developing in treated biofilms may be overlooked in clinical settings and contribute to the selection of high-level resistant mutants. Our study, therefore, underscores that, in addition to dosing, optimizing the timing of antimicrobial treatment could mitigate the emergence of resistance. These principles are applicable beyond catheters to any biofilm-related infections where short-term antibiotic exposure may impact microbial community adaptation.

Yongchao Zeng, Calum Brown, Ioannis Kyriakou et al.

Understanding socio-ecological systems requires insights from diverse stakeholder perspectives, which are often hard to access. To enable alternative, simulation-based exploration of different stakeholder perspectives, we develop the HoPeS (Human-Oriented Perspective Shifting) modelling framework. HoPeS employs agents powered by large language models (LLMs) to represent various stakeholders; users can step into the agent roles to experience perspectival differences. A simulation protocol serves as a "scaffold" to streamline multiple perspective-taking simulations, supporting users in reflecting on, transitioning between, and integrating across perspectives. A prototype system is developed to demonstrate HoPeS in the context of institutional dynamics and land use change, enabling both narrative-driven and numerical experiments. In an illustrative experiment, a user successively adopts the perspectives of a system observer and a researcher - a role that analyses data from the embedded land use model to inform evidence-based decision-making for other LLM agents representing various institutions. Despite the user's effort to recommend technically sound policies, discrepancies persist between the policy recommendation and implementation due to stakeholders' competing advocacies, mirroring real-world misalignment between researcher and policymaker perspectives. The user's reflection highlights the subjective feelings of frustration and disappointment as a researcher, especially due to the challenge of maintaining political neutrality while attempting to gain political influence. Despite this, the user exhibits high motivation to experiment with alternative narrative framing strategies, suggesting the system's potential in exploring different perspectives. Further system and protocol refinement are likely to enable new forms of interdisciplinary collaboration in socio-ecological simulations.

Ayana Ezoe, Makoto Katori, Tomoyuki Shirai

Random point configurations are said to be in hyperuniform states, if density fluctuations are anomalously suppressed in large-scale. Typical examples are found in Coulomb gas systems in two dimensions especially called log-gases in random matrix theory, in which points are repulsively correlated by long-range potentials. In infertile lands like deserts continuous survival competitions for water and nutrition will cause long-ranged repulsive interactions among plants. We have prepared digital data of spatial configurations of center-of-masses for bushes weighted by bush sizes which we call masses. Data analysis shows that such ecological point configurations do not show hyperuniformity as unmarked point processes, but are in hyperuniform states as marked point processes in which mass distributions are taken into account. We propose the non-equilibrium statistical-mechanics models to generate marked point processes having hyperuniformity, in which iterations of random thinning of points and coalescing of masses transform initial uncorrelated point processes into non-trivial point processes with hyperuniformity. Combination of data analysis and computer simulations shows the importance of strong correlations in probability law between spatial point configurations and mass distributions of individual points to realize hyperuniform marked point processes.

Amita Sekar, Fawaz Ben Malick, Shweta Uma Deepak et al.

Abstract While Staphylococcus aureus is the predominant pathogen in periprosthetic joint infections (PJI), polymicrobial infections involving Gram-negative organisms, such as Escherichia coli, complicate clinical outcomes. Little is known regarding implant-associated polymicrobial interactions; consequently, current PJI treatments are not optimized for their treatment. This study explored the dynamics of S. aureus-E. coli dual-species biofilms, focusing on biofilm properties, antibiotic susceptibility, and molecular interactions. Co-culture experiments revealed that E. coli significantly suppressed S. aureus biofilm viability, observed for methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). Microscopic analyses demonstrated enhanced E. coli attachment facilitated by S. aureus matrix proteins; however, over time, E. coli dominated the biofilm composition. In the presence of E. coli, MSSA biofilm exhibited improved gentamicin susceptibility while MRSA showed limited change, underscoring strain-specific interactions. Notably, E. coli biofilms exhibited enhanced resistance to gentamicin in dual-species settings. Gene expression profiling revealed molecular adaptation in S. aureus and E. coli, triggered by the differential regulation of stress, adhesion, virulence, and biofilm-associated genes within a dual-species implant-associated biofilm. The suppression of S. aureus by E. coli presents potential therapeutic avenues, and in vivo studies and mechanistic investigations are crucial for optimizing treatment strategies targeting polymicrobial PJIs.

Parker Smith, M. Schuster

Communication and cooperation are not restricted to complex, higher organisms. Microbes, too, perform a variety of collective, multicellular behaviors, including biofilm formation, quorum sensing, nutrient acquisition, and dispersal. The products of these microbial cooperative behaviors are generally referred to as public goods. Here we describe the nature of microbial public goods, the associated problem of cheating, and ways in which microbes maintain public goods in the face of cheating. We highlight work in a growing field at the interface of microbiology, evolution, and ecology that combines multiple approaches in experimental evolution, genetics, and mathematical modeling.

Christoffer Bugge Harder, Shingo Miyauchi, Máté Virágh et al.

Summary: Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2–8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants.Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

Jorien Favere, Fien Waegenaar, Mingsheng Jia et al.

Abstract Safeguarding the drinking water quality remains a challenge from the production site to the tap. Alternatively to chemical disinfection, biostable drinking water could serve as a more sustainable approach to produce microbially safe drinking water and to maintain the microbial quality in the drinking water distribution system (DWDS). In this study, the potential of hydrogen-oxidizing bacteria (HOB) to produce biostable drinking water was examined in a continuous trickling filter supplied with hydrogen gas. A biofilm was naturally enriched for 5 months and the bacterial regrowth, invasion potential, and nutrient composition of the water were determined. Treatment improved the biostability significantly, and it is hypothesized that nutrient limitation, especially phosphorous, was a driving force. As a result, the regrowth and invasion potential were lowered, as shown with specific biostability bioassays. Overall, this study demonstrates the proof-of-concept of HOB for producing biostable drinking water through nutrient limitation.

M. Rillig

Janelle R. Thompson, H. Rivera, Collin J. Closek et al.

In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.

Lindley R. Slipetz, Jeremy W. Eberle, Cheri A. Levinson et al.

Ecological momentary assessment (EMA) data have a broad base of application in the study of time trends and relations. In EMA studies, there are a number of design considerations which influence the analysis of the data. One general modeling framework is particularly well-suited for these analyses: state-space modeling. Here, we present the state-space modeling framework with recommendations for the considerations that go into modeling EMA data. These recommendations can account for the issues that come up in EMA data analysis such as idiographic versus nomothetic modeling, missing data, and stationary versus non-stationary data. In addition, we suggest R packages in order to implement these recommendations in practice. Overall, well-designed EMA studies offer opportunities for researchers to handle the momentary minutiae in their assessment of psychological phenomena.

Stav Marcus, Ari M Turner, Guy Bunin

Ecological communities with many species can be classified into dynamical phases. In systems with all-to-all interactions, a phase where a fixed point is always reached and a dynamically-fluctuating phase have been found. The dynamics when interactions are sparse, with each species interacting with only several others, has remained largely unexplored. Here we show that a new type of phase appears in the phase diagram, where for the same control parameters different communities may reach either a fixed point or a state where the abundances of a finite subset of species fluctuate, and calculate the probability for each outcome. These fluctuating species are organized around short cycles in the interaction graph, and their abundances undergo large non-linear fluctuations. We characterize the approach from this phase to a phase with extensively many fluctuating species, and show that the probability of fluctuations grows continuously to one as the transition is approached, and that the number of fluctuating species diverges. This is qualitatively distinct from the transition to extensive fluctuations coming from a fixed point phase, which is marked by a loss of linear stability. The differences are traced back to the emergent binary character of the dynamics when far away from short cycles in the local fluctuations phase.

Ece Polat, Hülya Ünver, Mahmut Altınbaş

Mucilage formation is a very complex phenomenon involving various biological and hydrological interactions. Mucilage is formed as a result of bacterial and phytoplankton-based activities in the environment. Oceanic shifts can provide an environment favorable for mucilage development; however, other factors also play a role in forming mucilage. Mucilage's microbiological structure and morphology, which have been studied in many waters and habitats since the 17th century, are also distinct. This is due to the fact that mucilage development is largely taxon-specific, and mucilage thickness and texture vary depending on environmental conditions. In mucilage studies, phytoplankton is the main component. A high level of organic matter and nutrients in the environment stimulates the formation of phytoplankton and the microenvironment. Furthermore, various water properties, such as temperature, fluidity, and so on, have an increasing effect on mucilage production. The purpose of this review is to describe how aggregates and mucilage are produced by dissolved organic matter (DOM) and microbial populations. Then, living groups discovered in the structure of mucilage during microbial ecology researches are discussed. Several examples of living organisms negatively affected by the development of mucilage were discussed following a detailed description of the dominant species observed in mucilage regions and case information.

Sarah Moraïs, I. Mizrahi

ABSTRACT The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.

Y. Dessaux, C. Grandclément, D. Faure

Zachary Jackson, BingKan Xue

Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among individual organisms even within the same species, causing heterogeneity in their interaction strengths with other species. The consequences of such heterogeneous interactions for the ecosystem have not been studied systematically. As a theoretical exploration, we analyze a simple ecosystem with trophic interactions between two predators and a shared prey, which would exhibit competitive exclusion in models with homogeneous interactions. We consider several scenarios where individuals of the prey species differentiate into subpopulations with different interaction strengths. We show that in all these cases, whether the heterogeneity is inherent, reversible, or adaptive, the ecosystem can stabilize at a new equilibrium where all three species coexist. Moreover, the prey population that has heterogeneous interactions with its predators reaches a higher density than it would without heterogeneity, and can even reach a higher density in the presence of two predators than with just one. Our results suggest that heterogeneity may be a naturally selected feature of ecological interactions that have important consequences for the stability and diversity of ecosystems.

Shengru Wu, Luisa Warchavchik Hugerth, Ina Schuppe-Koistinen et al.

Abstract Bacterial vaginosis (BV) is a condition in which the vaginal microbiome presents an overgrowth of obligate and facultative anaerobes, which disturbs the vaginal microbiome balance. BV is a common and recurring vaginal infection among women of reproductive age and is associated with adverse health outcomes and a decreased quality of life. The current recommended first-line treatment for BV is antibiotics, despite the high recurrence rate. Live biopharmaceutical products/probiotics and vaginal microbiome transplantation (VMT) have also been tested in clinical trials for BV. In this review, we discuss the advantages and challenges of current BV treatments and interventions. Furthermore, we provide our understanding of why current clinical trials with probiotics have had mixed results, which is mainly due to not administering the correct bacteria to the correct body site. Here, we propose a great opportunity for large clinical trials with probiotic strains isolated from the vaginal tract (e.g., Lactobacillus crispatus) and administered directly into the vagina after pretreatment.

Miguel Angel Alcalde, Maren Müller, Sergi Munné-Bosch et al.

Hairy roots are made after the integration of a small set of genes from Agrobacterium rhizogenes in the plant genome. Little is known about how this small set is linked to their hormone profile, which determines development, morphology, and levels of secondary metabolite production. We used C. asiatica hairy root line cultures to determine the putative links between the rol and aux gene expressions with morphological traits, a hormone profile, and centelloside production. The results obtained after 14 and 28 days of culture were processed via multivariate analysis and machine-learning processes such as random forest, supported vector machines, linear discriminant analysis, and neural networks. This allowed us to obtain models capable of discriminating highly productive root lines from their levels of genetic expression (rol and aux genes) or from their hormone profile. In total, 12 hormones were evaluated, resulting in 10 being satisfactorily detected. Within this set of hormones, abscisic acid (ABA) and cytokinin isopentenyl adenosine (IPA) were found to be critical in defining the morphological traits and centelloside content. The results showed that IPA brings more benefits to the biotechnological platform. Additionally, we determined the degree of influence of each of the evaluated genes on the individual hormone profile, finding that aux1 has a significant influence on the IPA profile, while the rol genes are closely linked to the ABA profile. Finally, we effectively verified the gene influence on these two specific hormones through feeding experiments that aimed to reverse the effect on root morphology and centelloside content.

Nicholas A. Bokulich, C. Bamforth

Jian Cheng, Jing Chen, Xiaonan Liu et al.

Diosgenin, mainly produced by Dioscorea species, is a traditional precursor of most hormonal drugs in the pharmaceutical industry. The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear. After sequencing the whole genome of Dioscorea zingiberensis, we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory. First, we found that P450 gene duplication and neo-functionalization, driven by positive selection, played important roles in the origin of the diosgenin biosynthetic pathway. Subsequently, we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands, which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch. Finally, by integrating genes from plants, animals, and yeast, we heterologously synthesized diosgenin to 10 mg/l in genetically-engineered yeast. Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea, but also introduces an alternative approach for the production of diosgenin through synthetic biology.

Franziska Tachtler, Toni Michel, Petr Slovák et al.

Unaccompanied migrant youth, fleeing to a new country without their parents, are exposed to mental health risks. Resilience interventions mitigate such risks, but access can be hindered by systemic and personal barriers. While much work has recently addressed designing technology to promote mental health, none has focused on the needs of these populations. This paper presents the results of interviews with 18 professional/ volunteer support workers and 5 unaccompanied migrant youths, followed by three design workshops. The results point to the diverse systems that can facilitate youths' resilience development. The relationship between the youth and volunteers acting as mentors is particularly important for increasing resilience but comes with challenges. This suggests the relevance of a social-ecological model of resilience with a focus on designing technology to support the mentors in order to help them better support the youth. We conclude by mapping out the design space for mentor support.