Hasil untuk "Microbial ecology"

D. Gevers, F. Cohan, J. Lawrence et al.

M. Blaser, J. Atherton

E. Grice, J. Segre

G. Muyzer

Catherine M. Burke, P. Steinberg, Doug Rusch et al.

R. M. D. Orduña

L. Gram, P. Dalgaard

A. Richardson

Masaru Tanaka, J. Nakayama

Gut microbial ecology and function are dynamic in infancy, but are stabilized in childhood. The 'new friends' have a great impact on the development of the digestive tract and host immune system. In the first year of life, especially, the gut microbiota dramatically changes through interactions with the developing immune system in the gut. The process of establishing the gut microbiota is affected by various environmental factors, with the potential to be a main determinant of life-long health. In this review, we summarize recent findings regarding gut microbiota establishment, including the importance of various factors related to the development of the immune system and allergic diseases later in life.

Hailiang Dong, Liuqin Huang, Linduo Zhao et al.

Abstract Mineral–microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization. Through these interactions, minerals and microbes co-evolve through Earth history. Mineral–microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral–microbe interactions for the benefit of humankind.

Richard R. Stein, V. Bucci, Nora C. Toussaint et al.

The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka–Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli.

A. M. Eren, Hilary G. Morrison, Pamela J Lescault et al.

Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing technologies enable extensive surveys of marker gene libraries that sometimes include nearly identical sequences. Computational approaches that rely on pairwise sequence alignments for similarity assessment and de novo clustering with de facto similarity thresholds to partition high-throughput sequencing datasets constrain fine-scale resolution descriptions of microbial communities. Minimum Entropy Decomposition (MED) provides a computationally efficient means to partition marker gene datasets into ‘MED nodes’, which represent homogeneous operational taxonomic units. By employing Shannon entropy, MED uses only the information-rich nucleotide positions across reads and iteratively partitions large datasets while omitting stochastic variation. When applied to analyses of microbiomes from two deep-sea cryptic sponges Hexadella dedritifera and Hexadella cf. dedritifera, MED resolved a key Gammaproteobacteria cluster into multiple MED nodes that are specific to different sponges, and revealed that these closely related sympatric sponge species maintain distinct microbial communities. MED analysis of a previously published human oral microbiome dataset also revealed that taxa separated by less than 1% sequence variation distributed to distinct niches in the oral cavity. The information theory-guided decomposition process behind the MED algorithm enables sensitive discrimination of closely related organisms in marker gene amplicon datasets without relying on extensive computational heuristics and user supervision.

Jose A Navas-Molina, J. Peralta‐Sánchez, Antonio Gonzalez et al.

J. Jansson, Ryan McClure, R. Egbert

Jeremy Wertheim Co Chen, Rendell Christian Ngo, Cedric Matthew Yu et al.

Extended reality (XR) enables new music-mixing workflows by moving beyond 2D faders toward embodied, spatial interaction. However, it remains unclear which six-degree-of-freedom (6DoF) gestures align with real-world mixing practices and whether such interactions support manageable cognitive load and positive user experience. We conducted a design workshop with experienced mixers to elicit gesture concepts for core audio tasks gain, compression, equalization, and automation, and implemented these in an XR prototype. A user study (n=12) evaluated the ecological validity of the gestures using cognitive load measures, user-experience ratings, and interviews. Participants generally found 6DoF gestures intuitive and well-mapped to mixing tasks, reporting strong immersion and a sense of connection with the audio environment. Cognitive load differences across gestures were minimal, though participants expressed preferences shaped by workflow familiarity and perceived control. We discuss implications for designing XR mixing tools that balance expressiveness, precision, and ecological validity.

Aline Ovalle, Estefanía López, Jimena Sierralta et al.

Abstract The gut-brain axis enables communication between the central nervous system and the gut, with certain microbial metabolites influencing neurodegeneration. Using genome-scale metabolic modeling, we designed and tested a synthetic microbial consortium with predicted capacity to produce GABA and other neurometabolites in a Drosophila melanogaster model of neurodegeneration of Parkinson’s Disease (PD). The consortium (Levilactobacillus brevis, Lacticaseibacillus paracasei, Bacteroides thetaiotaomicron) produced GABA in bioreactors. Female PD flies receiving the consortium exhibited protection from locomotor impairment at 10 and 25 days upon consortium administration. Head metabolomics revealed partial restoration of PD-associated alterations in energy balance, amino acid and neurotransmitter metabolism, and disease-related biomarkers. Early administration increased microbiome diversity and Lactobacillus abundance. These findings suggest that rationally designed microbial consortia targeting neurometabolite production can modulate brain physiology and confer neuroprotection, supporting their potential for microbiome-based interventions in neurodegenerative disease.

Ishraq Tashdid, Dewan Saiham, Nafisa Anjum et al.

Traditional hardware platforms - ASICs and FPGAs - offer competing trade-offs among performance, flexibility, and sustainability. ASICs provide high efficiency but are inflexible post-fabrication, require costly re-spins for updates, and expose IPs to piracy risks. FPGAs offer reconfigurability and reuse, yet suffer from substantial area, power, and performance overheads, resulting in higher carbon footprints. We present ECOLogic, a hybrid design paradigm that embeds lightweight eFPGA fabric within ASICs to enable secure, updatable, and resource-aware computation. Central to this architecture is ECOScore, a quantitative scoring framework that evaluates IPs based on adaptability, piracy threat, performance tolerance, and resource fit to guide RTL partitioning. Evaluated across six diverse SoC modules, ECOLogic retains an average of 90 percent ASIC-level performance (up to 2 GHz), achieves 9.8 ns timing slack (versus 5.1 ns in FPGA), and reduces power by 480 times on average. Moreover, sustainability analysis shows a 99.7 percent reduction in deployment carbon footprint and 300 to 500 times lower emissions relative to FPGA-only implementations. These results position ECOLogic as a high-performance, secure, and environmentally sustainable solution for next-generation reconfigurable systems.

Francesco Ferraro, Christian Grilletta, Emanuele Pigani et al.

Explaining the wide range of dynamics observed in ecological communities is challenging due to the large number of species involved, the complex network of interactions among them, and the influence of multiple environmental variables. Here, we consider a general framework to model the dynamics of species-rich communities under the effects of external environmental factors, showing that it naturally leads to delayed interactions between species, and analyze the impact of such memory effects on population dynamics. Employing the generalized Lotka-Volterra equations with time delays and random interactions, we characterize the resulting dynamical phases in terms of the statistical properties of community interactions. Our findings reveal that memory effects can generate persistent and synchronized oscillations in species abundances in sufficiently competitive communities. This provides an additional explanation for synchronization in large communities, complementing known mechanisms such as predator-prey cycles and environmental periodic variability. Furthermore, we show that when reciprocal interactions are negatively correlated, time delays alone can induce chaotic behavior. This suggests that ecological complexity is not a prerequisite for unpredictable population dynamics, as intrinsic memory effects are sufficient to generate long-term fluctuations in species abundances. The techniques developed in this work are applicable to any high-dimensional random dynamical system with time delays.

Pulak Kundu, Uzzwal Kumar Mallick

The introduction of mongooses from Indian subcontinent to Amami Oshima Island, Japan, aimed at controlling the population of venomous Habu snakes, has led to significant ecological disruptions, raising concerns about the long-term sustainability of the islands biodiversity. To highlight the unintended consequences of such interventions and the necessity of understanding predator-prey dynamics in preserving ecological balance, a mathematical model incorporating snake, mongooses, mouse and natural resources has been proposed to explore their role in the ongoing ecological disaster and analysis the other scenarios if the authorities applied different approaches in place of already implemented strategy. Determining the model's existence and uniqueness, stability at equilibrium points, and state variable characteristics are some of the parts of the analytical analysis of the model. Additionally, sensitivity analysis is conducted to identify sensitive factors. In addition, the Runge-Kutta 4th order has been used to execute the numerical simulations. Our research reveals that although the government began killing and trapping mongooses almost 20 years after their introduction, but if trapping had started just 10 years after their introduction, the outcome could have been drastically different. This time, mongooses would not have been extinct, and their coexistence with other native species would have helped to preserve the ecological balance and prevent the severe ecological damage that is presently being seen. Thus, It is recommended to use mathematical modeling to explore alternatives before decision-making, ensuring sustainable ecosystem management while preventing irreversible impacts of invasive species.

Perla Abigail Figueroa-Gonzalez, Till L. V. Bornemann, Tjorven Hinzke et al.

Abstract Background Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany. Results We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level. Conclusions We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract