Oral administration of Brevibacterium linens from washed cheese increases the proportions of short‐chain fatty acid‐producing bacteria and lactobacilli in the gut microbiota of mice DOI Creative Commons

Aito Murakami,

Koharu Toyomoto,

Fu Namai

и другие.

Animal Science Journal, Год журнала: 2023, Номер 94(1)

Опубликована: Янв. 1, 2023

Abstract Brevibacterium linens ( B. ) is a dairy microorganism used in the production of washed cheese. However, there has been little research on , especially regarding its effects vivo. Herein, we report morphological characteristics such as two‐phase growth and V‐ Y‐shaped bodies. We also that oral administration increased diversity gut microbiota promoted lactobacilli short‐chain fatty acid‐producing bacteria, Lachnospiraceae Muribaculaceae. These findings suggest ingestion may have beneficial humans animals.

Язык: Английский

Recent advances in model-assisted metabolic engineering DOI
Steinn Guðmundsson, Juan Nogales

Current Opinion in Systems Biology, Год журнала: 2021, Номер 28, С. 100392 - 100392

Опубликована: Окт. 13, 2021

Язык: Английский

Процитировано

23
De novo evolution of antibiotic resistance to Oct-TriA1 DOI Creative Commons
Farhan Rahman Chowdhury, Laura Domínguez Mercado,

Katya Kharitonov

и другие.

Microbiological Research, Год журнала: 2025, Номер 293, С. 128056 - 128056

Опубликована: Янв. 14, 2025

Язык: Английский

Процитировано

0
Actionable Forecasting as a Determinant of Biological Adaptation DOI Creative Commons
José M. G. Vilar, Leonor Saiz

Advanced Science, Год журнала: 2025, Номер unknown

Опубликована: Фев. 27, 2025

Abstract Organisms continuously adapt to changing environments survive. Here, contrary the prevailing view that predictive strategies are essential for perfect adaptation, it is shown biological systems can precisely track their optimal state by adapting a non‐anticipatory actionable target integrates current optimum with its rate of change. Predictive mechanisms, such as circadian rhythms, beneficial accurately inferring when environmental sensing slow or unreliable. A new mathematical framework developed, showing dynamics‐informed neural networks embodying these principles efficiently capture adaptation even in noisy environments. These results provide fundamental insights into interplay between forecasting, control, and inference systems, redefining guiding design advanced adaptive biomolecular circuits.

Язык: Английский

Процитировано

0
Geometrically balanced model of cell growth DOI
Alexei Vázquez, Tomáš Gedeon

Journal of Theoretical Biology, Год журнала: 2025, Номер unknown, С. 112085 - 112085

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Differential anaerobic oxidation of benzoate in Geotalea daltonii FRC-32 DOI Creative Commons
Christina M. Kiessling,

Sujay F. Greenlund,

James E. Bullows

и другие.

Microbiology Spectrum, Год журнала: 2025, Номер unknown

Опубликована: Март 5, 2025

The efficient carbon source utilization in dynamic environments, including anoxic subsurface contaminated by aromatic compounds, is a challenge for anaerobic bacteria such as Geotalea daltonii strain FRC-32. aim of this study was to elucidate the metabolic pathways employed G. FRC-32 during benzoate oxidation presence acetate, key intermediate organic matter degradation, predict transport and strategies. Simultaneous monoauxic growth were observed cultures grown on 1 mM + 5 2 acetate spiked with benzoate. Sequential diauxic only Benzoate accumulation whole cell lysates indicated that intracellular occurred acetate. Expression analyses putative transporter BenK protein-ligand binding affinity prediction suggested BenK's specificity transporting Relative expression levels gene benK, encoding BenK, genes bamNOPQ, involved benzoyl-CoA pathway, significantly higher both than sole source, indicating facilitated regulation bamNOPQ. Our results demonstrated can perform differential either simultaneous or sequential oxidation, which plasticity response varying availability.IMPORTANCEThe contamination environments crude oil derivatives compounds global concern due persistence toxicity these pollutants. Anaerobic play crucial role degradation hydrocarbons under conditions; however, potential mechanisms are not well understood. This contributed elucidating how efficiently utilizes Findings associated understanding FRC-32's pathways, provided significant insights into modulate energetically favorable strategies environmental conditions.

Язык: Английский

Процитировано

0
New insights in metabolism modelling to decipher plant–microbe interactions DOI Creative Commons

Clara Blonde,

Amélie Caddeo,

William Nasser

и другие.

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 21, 2025

Summary Plant disease outbreaks, exacerbated by climate change, threaten food security and environmental sustainability world‐wide. Plants interact with a wide range of microorganisms. The quest for resilient agriculture requires deep insight into the molecular ecological interplays between plants their associated microbial communities. Omics methods, profiling entire sets, have shed light on these complex interactions. Nonetheless, deciphering relationships among thousands components remains formidable challenge, studies that integrate cohesive biological networks involving microbes are still limited. Systems biology has potential to predict effects biotic abiotic perturbations networks. It is therefore promising framework addressing full complexity plant–microbiome

Язык: Английский

Процитировано

0
The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions DOI Creative Commons

Ilias Toumpe,

Subham Choudhury, Vassily Hatzimanikatis

и другие.

ACS Synthetic Biology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 22, 2025

Researchers have invested much effort into developing kinetic models due to their ability capture dynamic behaviors, transient states, and regulatory mechanisms of metabolism, providing a detailed realistic representation cellular processes. Historically, the requirements for parametrization significant computational resources created barriers development adoption high-throughput studies. However, recent advancements, including integration machine learning with mechanistic metabolic models, novel parameter databases, use tailor-made strategies, are reshaping field modeling. In this Review, we discuss these developments offer future directions, highlighting potential advances drive progress in systems synthetic biology, engineering, medical research at an unprecedented scale pace.

Язык: Английский

Процитировано

0
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches DOI Creative Commons
Blox Bloxham, Hyunseok Lee, Jeff Gore

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Фев. 21, 2023

Abstract How natural communities maintain their remarkable biodiversity and which species survive in complex are central questions ecology. Resource competition models successfully explain many phenomena but typically predict only as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles support more than resources. We explore how modify own environments by sequentially depleting to form sequences of temporal niches, intermediately depleted environments. Biodiversity is enhanced when community-driven environmental fluctuations modulate the depletion order produce different niches on each cycle. Community-driven under constant conditions rare, exploring them illuminates niche structure emerges from utilization. With fluctuations, find most have stably coexisting survivors accurately predicted same following a distinct optimal strategy. Our results thus present new niche-based approach understanding highly diverse fluctuating communities.

Язык: Английский

Процитировано

8
The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies DOI Creative Commons

Sotaro Takano,

Jean C. C. Vila, Ryo Miyazaki

и другие.

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(9)

Опубликована: Авг. 23, 2023

Microbial strategies for resource use are an essential determinant of their fitness in complex habitats. When facing environments with multiple nutrients, microbes often them sequentially according to a preference hierarchy, resulting well-known patterns diauxic growth. In theory, the evolutionary diversification metabolic hierarchies could represent mechanism supporting coexistence and biodiversity by enabling temporal segregation niches. Despite this ecologically critical role, extent which substrate can evolve diversify remains largely unexplored. Here, we used genome-scale modeling systematically explore evolution across vast space network genotypes. We find that only limited number readily evolve, corresponding most commonly observed genome-derived models. further show how novel is constrained architecture central metabolism, determines both propensity change ranks between pairs substrates effect specific reactions on hierarchy evolution. Our analysis sheds light genetic mechanistic determinants microbial hierarchies, opening new research avenues understand evolution, evolvability, ecology.

Язык: Английский

Процитировано

6
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale DOI Creative Commons
Daniel C. Zielinski, Arjun Patel, Bernhard Ø. Palsson

и другие.

Microorganisms, Год журнала: 2020, Номер 8(12), С. 2050 - 2050

Опубликована: Дек. 21, 2020

Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines driven by predictive design tools, these tools have been difficult build biological due the complexity systems and many unknowns their quantitative behavior. However, recent advances, gap between in biology other fields is closing. In this work, we discuss promising areas development computational microbial strains. We define five frontiers active research: (1) Constraint-based modeling metabolic network reconstruction, (2) Kinetics thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence (5) Regulatory analysis. Experimental machine learning drivers enabled methods improve leaps bounds both scope accuracy. Modern strain projects will require be comprehensively applied entire cell efficiently integrated within a single workflow. expect that frontiers, ongoing revolution big data science, drive forward more advanced powerful strategies.

Язык: Английский

Процитировано

13