Hasil untuk "Microbial ecology"

V. Torsvik, L. Øvreås

A. Douglas

Lucia Žifčáková, T. Větrovský, A. Howe et al.

Johnny M. Souza, Pedro H. C. Ribeiro, Danilo D. Millen

Ruminants play an essential role in food production due to their ability to utilize forages through fermentation in the rumen. This fermentative chamber hosts a diverse microbial community capable of degrading fiber and non-fiber carbohydrates, producing short-chain fatty acids (SCFAs) and microbial protein, which are essential for the animal’s metabolism. Throughout their evolution, ruminants developed a symbiotic relationship with microorganisms specialized in the degradation of plant fibers, enabling the use of forages as a dietary foundation. However, modern intensive production systems have introduced concentrate ingredients to their diets (such as grains and industrial by-products), which represent a significant departure from ancestral diets based exclusively on forages. Dietary composition is the primary factor driving changes in the ruminal microbiota and can significantly alter its composition. Variations in the forage-to-concentrate ratio can drastically alter microbial activity, affecting the stability of the ruminal ecosystem. Sequencing technologies and omics approaches have enhanced the understanding of this ecology, allowing for more effective nutritional interventions. The objective of this review is to assess how contemporary diets in intensive production systems differ from ancestral, forage-only diets and how these differences reshape the ruminal microbiota. To this end, we characterized the variations in the ruminal microbiota composition of animals fed high-concentrate and high-forage diets, describing the specific microbial profiles of each condition and identifying beneficial and potentially detrimental microorganisms. This review synthesizes current evidence on how dietary transitions reshape ruminal microbial cross-feeding networks and proposes an integrative framework linking microbial symbiotic balance, rumen health, and production efficiency. By emphasizing the dynamic regulation of microbial interactions rather than isolated taxa, this work highlights cross-feeding stability as a central target for nutritional, microbial, and genetic interventions in intensive ruminant production systems.

Giulio Valentino Dalla Riva

We study language models as evolving model organisms and ask when autoregressive next-token learning selects for world-tracking representations. For any encoding of latent world states, the Bayes-optimal next-token cross-entropy decomposes into the irreducible conditional entropy plus a Jensen--Shannon excess term. That excess vanishes if and only if the encoding preserves the training ecology's equivalence classes. This yields a precise notion of ecological veridicality for language models and identifies the minimum-complexity zero-excess solution as the quotient partition by training equivalence. We then determine when this fixed-encoding analysis applies to transformer families: frozen dense and frozen Mixture-of-Experts transformers satisfy it, in-context learning does not enlarge the model's separation set, and per-task adaptation breaks the premise. The framework predicts two characteristic failure modes: simplicity pressure preferentially removes low-gain distinctions, and training-optimal models can still incur positive excess on deployment ecologies that refine the training ecology. A conditional dynamic extension shows how inter-model selection and post-training can recover such gap distinctions under explicit heredity, variation, and selection assumptions. Exact finite-ecology checks and controlled microgpt experiments validate the static decomposition, split-merge threshold, off-ecology failure pattern, and two-ecology rescue mechanism in a regime where the relevant quantities are directly observable. The goal is not to model frontier systems at scale, but to use small language models as laboratory organisms for theory about representational selection.

H. Marcotte, M. Lavoie

Daniel R. Kollath, Daniel R. Kollath, Kathrine McAulay et al.

IntroductionThe function of the respiratory microbiome during an active infection is not well characterized. Studies from the gut microbiome suggest a diverse community can aid in modulating the immune system to control infectious pathogens. MethodsTo determine if there are microbial community compositional changes in the human lung during an infection, we conducted an analysis of both the 16S rDNA and the Internal Transcribed Spacer (ITS) region of DNA from bronchoalveolar lavage fluid (BALF) of patients from Mayo Clinic Arizona. In addition to general classification, we assessed differences in the lung microbiome of patients with different infections including coccidioidomycosis, a common fungal pneumonia in Arizona.ResultsWe observed patterns of dysbiosis in the lung microbiome during active fungal infection. Patients with active coccidioidomycosis infections had an overabundance of Malassezia, Epicoccum, and Penicillium species in the fungal communities and bacteria in the classes Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria. Patients with disseminated coccidioidomycosis showed evidence of extreme dysbiosis in the lung microbiome with a significant overabundance of Malassezia and Bacilli. We also observed differences in the fungal communities of patients with an active Candida albicans infection, with an overabundance of the genera Candida and Nakaseomyces. Additionally, we observed a decrease in diversity in the lung fungal communities in patients with an active Coccidioides or Candida infection but no difference in the bacterial community.DiscussionThese compositional changes in the lung microbiome during an active Coccidioides spp. infection associated with shifts in the fungal community. This is the first study to examine how these fungal pathogens affect the lung microbial community of humans.

Mengmeng Yu, Hao He, Liyang Cheng et al.

The application of bio-organic fertilizers (BOFs) represents a promising strategy for mitigating soil degradation in continuous monoculture systems, yet their long-term mechanistic impacts in aged cotton fields remain poorly elucidated. This study aims to uncover how BOFs enhance soil health, reshape microbial communities, and sustain cotton productivity under decades-long continuous cropping in Xinjiang, China. A two-year field experiment compared conventional chemical fertilization (CK, N−P−K: 300–180–150 kg·ha⁻¹) with combined chemical and BOF treatment (BOF, N−P−K: 300−180−150 kg·ha⁻¹, BOFs: 4159 kg·ha⁻¹ in 2023 and 4545 kg·ha⁻¹ in 2024). The BOFs used in this study contained ≥40.0% organic matter and ≥0.20 × 10⁸ CFU·g⁻¹ of <i>Bacillus amyloliquefaciens</i>. The results demonstrated that BOF application significantly increased seed cotton yield by 19.82–28.17% and total plant biomass by 56.66–61.97%, with the latter reflecting improved root development and nutrient acquisition—key factors contributing to yield gains. Soil analysis indicated substantial elevations in organic matter (12.05–17.72%) and available nutrients without altering pH. Metagenomic sequencing revealed that the BOF treatment enriched beneficial taxa (e.g., <i>Lysobacter</i> increased by 50.53%), suppressed <i>Fusarium</i> (decreased by 36.08%), enhanced microbial network complexity, and reinforced disease-suppressive functions. These findings provide mechanistic insights into the role of BOFs in restoring rhizosphere ecology and promoting soil resilience. This study supports the practical integration of BOFs as a sustainable measure for rejuvenating degraded cotton monoculture systems and optimizing fertilizer management in arid agroecosystems.

Laura Bonillo-Lopez, Noelia Carmona-Vicente, Ferran Tarrés-Freixas et al.

Abstract Background Interactions between the nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. Currently, there is a lack of experimental models to study such interactions under defined in vitro conditions. Here, we developed a porcine nasal organoid (PNO) system from nasal tissue of pigs as well as from cytological brushes. Results PNOs exhibited similar structure and cell types to the nasal mucosa, as evaluated by immunostaining. PNOs were inoculated with porcine commensal strains of Moraxella pluranimalium, Rothia nasimurium, and the pathobiont Glaesserella parasuis for examining host-commensal-pathogen interactions. All strains adhered to the PNOs, although at different levels. M. pluranimalium and G. parasuis strains stimulated the production of proinflammatory cytokines, whereas R. nasimurium induced the production of IFNγ and diminished the proinflammatory effect of the other strains. Conclusions Overall, PNOs mimic the in vivo nasal mucosa and can be useful to perform host-microbe interaction studies. Video Abstract

Marius Bredon, Pierre Hausfater, Loubna Khalki et al.

Abstract Although COVID-19 primarily affects the respiratory system, many patients experience gastrointestinal symptoms, suggesting a role for the gut microbiota in disease pathogenesis. To explore this, we performed shotgun metagenomic sequencing on stool samples from 200 COVID-19 patients and 102 healthy controls in Morocco and France. Despite geographic differences in microbiota composition, patients with COVID-19 in both continents exhibited significant gut microbiota alterations, which were more pronounced in severe cases, with similar features compared with controls. Functional pathways, including L-Tryptophan biosynthesis, were disrupted, particularly in patients with severe disease. Machine learning models accurately predicted disease severity based on gut microbial profiles in the Moroccan cohort, though not in the French cohort. These results highlight consistent microbiota changes associated with COVID-19 and support a potential link between gut dysbiosis and disease severity.

Tingyu Zhang, Jian Feng, Xia Gao et al.

Jinhong tablet (JHT), a traditional Chinese medicine made from four herbs, effectively treats chronic superficial gastritis (CSG) by soothing the liver, relieving depression, regulating qi, and promoting blood circulation. However, its pharmacokinetics are underexplored. This study investigates JHT's pharmacokinetics in normal rats and its differences in normal, CSG, and intestinal microbial disorder rats. A quantitative method for seven active ingredients in rat plasma was established using UPLC-TQ-MS/MS. After administering various JHT doses, plasma concentrations were measured to assess pharmacokinetics in normal rats. The pharmacokinetics of four main ingredients were compared in normal, CSG, and fecal microbiota transplantation (FMT) rats. Intestinal microbial changes were evaluated by high-throughput sequencing. Spearman correlation analysis linked ingredient exposure to gut microbiota disturbances. The method showed good linearity, precision, accuracy, extraction recovery, and stability. In normal rats, all seven ingredients were rapidly absorbed. Tetrahydropalmatine, corydaline, costunolide, and rhamnosylvitexin had good exposure, while dehydrocorydaline, allocryptopine, and palmatine hydrochloride had low exposure. Tetrahydropalmatine, corydaline, and costunolide followed linear pharmacokinetics (AUC0-t, Cmax) at doses of 0.7-5.6 g/kg, while rhamnosylvitexin and dehydrocorydaline showed linearity at 0.7-2.8 g/kg. In CSG and FMT rats, pharmacokinetic differences were observed. CSG enhanced costunolide exposure and Cmax, and increased rhamnosylvitexin exposure. FMT raised corydaline exposure and rhamnosylvitexin Cmax, linked to 20 bacterial genera.

Joseph Bejjani, Chase Van Amburg, Chengrui Wang et al.

We explore how physical scale and population size shape the emergence of complex behaviors in open-ended ecological environments. In our setting, agents are unsupervised and have no explicit rewards or learning objectives but instead evolve over time according to reproduction, mutation, and selection. As they act, agents also shape their environment and the population around them in an ongoing dynamic ecology. Our goal is not to optimize a single high-performance policy, but instead to examine how behaviors emerge and evolve across large populations due to natural competition and environmental pressures. We use modern hardware along with a new multi-agent simulator to scale the environment and population to sizes much larger than previously attempted, reaching populations of over 60,000 agents, each with their own evolved neural network policy. We identify various emergent behaviors such as long-range resource extraction, vision-based foraging, and predation that arise under competitive and survival pressures. We examine how sensing modalities and environmental scale affect the emergence of these behaviors and find that some of them appear only in sufficiently large environments and populations, and that larger scales increase the stability and consistency of these emergent behaviors. While there is a rich history of research in evolutionary settings, our scaling results on modern hardware provide promising new directions to explore ecology as an instrument of machine learning in an era of increasingly abundant computational resources and efficient machine frameworks. Experimental code is available at https://github.com/jbejjani2022/ecological-emergent-behavior.

P. L. Stark, A. Lee

Alsayed Alfiky, Eliane Abou-Mansour, Mout De Vrieze et al.

Potato growers worldwide have been at war for more than 150 years with an enemy whose lifecycle, genome size and architecture, infection rate, and economic impacts are the epitome of a plant pathogen. Phytophthora infestans is an oomycete that causes the notorious late blight infection in potato and tomato fields. This study explored the benefits of the multitalented plant symbiotic fungi Trichoderma spp. and their metabolites as potential biopesticides against P. infestans. Eleven strains of Trichoderma spp. were obtained from soil and tree barks and were identified using DNA sequence analysis of three molecular markers. The antagonistic potential of the strains against P. infestans was first evaluated in vitro. In dual-culture assays, P. infestans growth was significantly inhibited (53 to 95%) by different Trichoderma spp. through direct mycoparasitism, competition for space and nutrients, or antibiosis. The cell-free filtrates (CFFs) of different Trichoderma strains were obtained and characterized for anti-Phytophthora activities as well as biochemical stability. The obtained results indicated that Trichoderma CFFs were chemically stable and strongly decreased P. infestans’ mycelial growth and zoospore motility and viability. Similarly, in leaf-disk assays, Trichoderma CFFs showed significant protection against P. infestans infection. Ultraperformance liquid chromatography analysis revealed the presence of harzianic acid, iso-harzianic acid, and 6-pentyl-2H-pyran-2-one as major compounds in different Trichoderma CFFs. Furthermore, selected Trichoderma strains significantly protected potato plants against soil-mediated late blight infection. Finally, Trichoderma spp. showed high compatibility with a copper-based fungicide, especially at lower concentrations, suggesting that both protective agents could be combined in integrated pest management programs. [Graphic: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Kai Luo, Alkis Taryn, Eun-Hye Moon et al.

Abstract Background Left ventricular diastolic dysfunction (LVDD) is an important precursor of heart failure (HF), but little is known about its relationship with gut dysbiosis and microbial-related metabolites. By leveraging the multi-omics data from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a study with population at high burden of LVDD, we aimed to characterize gut microbiota associated with LVDD and identify metabolite signatures of gut dysbiosis and incident LVDD. Results We included up to 1996 Hispanic/Latino adults (mean age: 59.4 years; 67.1% female) with comprehensive echocardiography assessments, gut microbiome, and blood metabolome data. LVDD was defined through a composite criterion involving tissue Doppler assessment and left atrial volume index measurements. Among 1996 participants, 916 (45.9%) had prevalent LVDD, and 212 out of 594 participants without LVDD at baseline developed incident LVDD over a median 4.3 years of follow-up. Using multivariable-adjusted analysis of compositions of microbiomes (ANCOM-II) method, we identified 7 out of 512 dominant gut bacterial species (prevalence > 20%) associated with prevalent LVDD (FDR-q < 0.1), with inverse associations being found for Intestinimonas_massiliensis, Clostridium_phoceensis, and Bacteroide_coprocola and positive associations for Gardnerella_vaginali, Acidaminococcus_fermentans, Pseudomonas_aeruginosa, and Necropsobacter_massiliensis. Using multivariable adjusted linear regression, 220 out of 669 circulating metabolites with detection rate > 75% were associated with the identified LVDD-related bacterial species (FDR-q < 0.1), with the majority being linked to Intestinimonas_massiliensis, Clostridium_phoceensis, and Acidaminococcus_fermentans. Furthermore, 46 of these bacteria-associated metabolites, mostly glycerophospholipids, secondary bile acids, and amino acids, were associated with prevalent LVDD (FDR-q < 0.1), 21 of which were associated with incident LVDD (relative risk ranging from 0.81 [p = 0.001, for guanidinoacetate] to 1.25 [p = 9 × 10−5, for 1-stearoyl-2-arachidonoyl-GPE (18:0/20:4)]). The inclusion of these 21 bacterial-related metabolites significantly improved the prediction of incident LVDD compared with a traditional risk factor model (the area under the receiver operating characteristic curve [AUC] = 0.73 vs 0.70, p = 0.001). Metabolite-based proxy association analyses revealed the inverse associations of Intestinimonas_massilliensis and Clostridium_phoceensis and the positive association of Acidaminococcus_fermentans with incident LVDD. Conclusion In this study of US Hispanics/Latinos, we identified multiple gut bacteria and related metabolites linked to LVDD, suggesting their potential roles in this preclinical HF entity. Video Abstract

Julius Eyiuche Nweze, Vladimír Šustr, Andreas Brune et al.

Abstract Background Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics. Results The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet. Conclusions Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract

Tom Verbeelen, Celia Alvarez Fernandez, Thanh Huy Nguyen et al.

Summary: The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.

Gunter Bombaerts, Tom Hannes, Martin Adam et al.

As the signatories of this manifesto, we denounce the attention economy as inhumane and a threat to our sociopolitical and ecological well-being. We endorse policymakers' efforts to address the negative consequences of the attention economy's technology, but add that these approaches are often limited in their criticism of the systemic context of human attention. Starting from Buddhist philosophy, we advocate a broader approach: an ecology of attending, that centers on conceptualizing, designing, and using attention (1) in an embedded way and (2) focused on the alleviating of suffering. With 'embedded' we mean that attention is not a neutral, isolated mechanism but a meaning-engendering part of an 'ecology' of bodily, sociotechnical and moral frameworks. With 'focused on the alleviation of suffering' we explicitly move away from the (often implicit) conception of attention as a tool for gratifying desires.

Richard D. Paul, Johannes Seiffarth, Hanno Scharr et al.

Live-cell microscopy allows to go beyond measuring average features of cellular populations to observe, quantify and explain biological heterogeneity. Deep Learning-based instance segmentation and cell tracking form the gold standard analysis tools to process the microscopy data collected, but tracking in particular suffers severely from low temporal resolution. In this work, we show that approximating cell cycle time distributions in microbial colonies of C. glutamicum is possible without performing tracking, even at low temporal resolution. To this end, we infer the parameters of a stochastic multi-stage birth process model using the Bayesian Synthetic Likelihood method at varying temporal resolutions by subsampling microscopy sequences, for which ground truth tracking is available. Our results indicate, that the proposed approach yields high quality approximations even at very low temporal resolution, where tracking fails to yield reasonable results.

R. Logares, Sylvie V. M. Tesson, Björn Canbäck et al.

Whether or not communities of microbial eukaryotes are structured in the same way as bacteria is a general and poorly explored question in ecology. Here, we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted selection driven by the salinity gradient in bacterial communities (explaining ∼ 72% of taxa turnover), while microeukaryotic counterparts were predominantly structured by ecological drift (∼72% of the turnover). Nevertheless, we also detected a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, selection has had a role in the structuring of specific members of their communities. In sum, we conclude that microeukaryotes and bacteria inhabiting the same communities can be structured predominantly by different processes. This should be considered in future studies aiming to understand the mechanisms that shape microbial assemblages.