Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(28)

Published: July 5, 2022

The genetic composition of the gut microbiota is constantly reshaped by ecological and evolutionary forces. These strain-level dynamics are challenging to understand because they depend on complex spatial growth processes that take place within a host. Here we introduce population framework predict how stochastic forces emerge from simple models microbial in spatially extended environments like intestinal lumen. Our shows fluid flow longitudinal variation rate combine shape frequencies variants simulated fecal samples, yielding analytical expressions for effective generation times, selection coefficients, rates drift. We find over longer timescales, emergent can often be captured well-mixed lack explicit structure, even when there substantial species-level composition. By applying these results human colon, continuous forms wall alone unlikely create sufficient bottlenecks allow large fluctuations mutant also times may significantly shorter than expected traditional average estimates. provide starting point quantifying turnover settings relevant other ecosystems where unidirectional plays an important role.

Language: Английский

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From worms to humans: Understanding intestinal lipid metabolism via model organisms

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Journal Year: 2023, Volume and Issue: 1868(4), P. 159290 - 159290

Published: Feb. 3, 2023

Language: Английский

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Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: July 16, 2021

The genetic composition of the gut microbiota is constantly reshaped by ecological and evolutionary forces. These strain-level dynamics can be challenging to understand because they emerge from complex spatial growth processes that take place within a host. Here we introduce general population framework predict how stochastic forces simple models microbial in spatially extended environments like intestinal lumen. Our shows fluid flow longitudinal variation rate combine shape frequencies variants sequenced fecal samples, yielding analytical expressions for effective generation times, selection coefficients, rates drift. We find emergent often captured well-mixed lack explicit structure, even when there substantial species-level composition. By applying these results human colon, continuous forms wall are unlikely create sufficient bottlenecks allow large fluctuations mutant also gener-ation times may significantly shorter than expected traditional average estimates. provide starting point qua ntifying turnover settings microbiota, relevant other ecosystems where unidirectional plays an important role.

Language: Английский

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Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the <em>Drosophila</em> Microbiome

Journal of Visualized Experiments, Journal Year: 2023, Volume and Issue: 191

Published: Jan. 13, 2023

The intestines of animals are colonized by commensal microbes, which impact host development, health, and behavior. Precise quantification colonization is essential for studying the complex interactions between microbe both to validate microbial composition study its effects. Drosophila melanogaster, has a low native diversity economical rear with defined composition, emerged as model organism gut microbiome. Analyzing microbiome an individual requires identification species present their absolute abundance. This article presents method analysis large number fly microbiomes. flies prepared in 96-well plates, enabling handling samples at once. Microbial abundance quantified plating up 96 whole homogenates on single agar plate array spots then counting colony forming units (CFUs) that grow each spot. system paired automated CFU platform, incorporates photography differentiation fluorescent colonies, colonies using ImageJ plugin. Advantages (i) this sensitive enough detect differences treatments, (ii) spot accurate traditional methods, (iii) process faster than manual counting. workflow presented here enables high-throughput CFUs replicates can be applied other microbiology systems including vitro small animal models.

Language: Английский

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Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the <em>Drosophila</em> Microbiome

Journal of Visualized Experiments, Journal Year: 2023, Volume and Issue: 191

Published: Jan. 13, 2023

The intestines of animals are colonized by commensal microbes, which impact host development, health, and behavior. Precise quantification colonization is essential for studying the complex interactions between microbe both to validate microbial composition study its effects. Drosophila melanogaster, has a low native diversity economical rear with defined composition, emerged as model organism gut microbiome. Analyzing microbiome an individual requires identification species present their absolute abundance. This article presents method analysis large number fly microbiomes. flies prepared in 96-well plates, enabling handling samples at once. Microbial abundance quantified plating up 96 whole homogenates on single agar plate array spots then counting colony forming units (CFUs) that grow each spot. system paired automated CFU platform, incorporates photography differentiation fluorescent colonies, colonies using ImageJ plugin. Advantages (i) this sensitive enough detect differences treatments, (ii) spot accurate traditional methods, (iii) process faster than manual counting. workflow presented here enables high-throughput CFUs replicates can be applied other microbiology systems including vitro small animal models.

Language: Английский

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Computer Fluid Design Models of Thermal Performance of Heat Sink with Various Geometries of Notches

Published: Dec. 15, 2023

Various shapes of system are designed in reducing the loss vital energy through wasteful use and improving exchange context heat. This is done due to increased demand for vitality worldwide. Increasing cooling capacity maximizing heat sink efficacy two most significant aims developing contemporary thermal systems. In this current work, an attempt has been made take into account different geometries fins improve dissipation electronic numerically experimentally. study performance interrupted when compared that continuous fins, analyzing by using a range rectangular arrays covers arrangements orientations, and, construction mathematical equation correlating temperature difference (i.e., base minus environment) duration shutdowns. The former ratio per time unit divided fin length. CFD paved way deriving model NASYS FLUENT numerical simulation particular. validation process was carried out showed good agreement with average differences less than 9 % experimental three types sinks. results show increases input increases, as relationship between them positive. A shows highest second long interruption lowest fifth model. reduction rate 35%. also percentage increase Nussle number stag. 5-30 2.24% int.-5-30 higher cont. corresponds 17.9%. Furthermore, findings reveal differential ambient rises power consumption 20, 40, 60, 80, 100, 120 W types. seen Stag rib. Another overlapping finding 22% improvement transfer coefficient third first

Language: Английский

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Intestinal Microflora Vs Protozoan Parasites: From Interaction to Competition

South Asian Journal of Research in Microbiology, Journal Year: 2022, Volume and Issue: unknown, P. 36 - 46

Published: July 25, 2022

Aims: To reveal the interaction between intestinal microflora and protozoan parasite organisms how it affect their host’s performance. Discussion: The vertebrate gastro-intestinal system contain wide array of diverse but dynamic bacterial microbiota population that has ubiquitous consequences on its well-being including physiology, nutrition, metabolism, immunity, locally systematically. Naturally, these bacteria share milleu with a more or less similar parasitic eukaryotes (e.g., protozoan, helminths, fungi). Both parasites in combination prokaryotic microorganisms as inhabitant normal can dynamically shift bio-physics immune intestine (locally) even host whole (systematically), creating abundant chances for them to interact each other; where ideally, both side is equilibrium state. Beside function, (commensal) mainly contribute several activities control survival determines outcome several, if not many, parasite-base disease. Normal actively limiting pathogenicity many parasites. steadiness among number composition seems vital perpetuation. But unfortunately, this further shifted into competition leads dominance one party probably also strength. Those spectrum interactions may critically modify infection outcomes (active dormant/carrier) turn overall condition. Active invasion hosts resident microflora, either supporting preventing against condition dysbiosis inflammatory Conversely, controls parasite's settlement, multiplication, virulency; properties modulate along parasitism-mutualism sphere. Conclusion: Intestinal pathogenesis infections.

Language: Английский

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Scale-dependent tipping points of bacterial colonization resistance

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: May 15, 2021

ABSTRACT Bacteria are efficient colonizers of a wide range secluded micro-habitats, such as soil pores, skin follicles, or intestinal crypts. How the structural diversity these habitats modulates microbial self-organization remains poorly understood, in part because challenge to specifically manipulate physical structure environments. Using microfluidic device grow bacteria crypt-like incubation chambers systematically varied lengths, we show that small variations micro-habitat can drastically alter bacterial colonization success and resistance against invaders. Small crypts un-colonizable, intermediately sized stably support dilute populations, while beyond second critical lengthscale, populations phase-separate into jammed region. The state is characterized by extreme resistance, even if resident strain suppressed an antibiotic. Combined with flexible biophysical model, demonstrate associated priority effects be explained crowding-induced phase transition, which results from competition between proliferation density-dependent cell leakage. emerging sensitivity scale underscores need control for ecology experiments. Systematic flow-adjustable lengthscale may serve promising strategy elucidate further scale-sensitive tipping points rationally modulate stability resilience colonizers.

Language: Английский

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The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study ofDrosophila-colonizingOrbaceae

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 16, 2023

ABSTRACT Toolkits of plasmids and genetic parts streamline the process assembling DNA constructs engineering microbes. Many these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested non-model microbial systems, it is often unclear which tools techniques will function newly isolated strains. To address this challenge, we Pathfinder toolkit for quickly determining compatibility a bacterium different plasmid components. combine three broad-host-range origins replication multiple antibiotic resistance cassettes reporters, so that sets can be rapidly screened through multiplex conjugation. We first tested Escherichia coli , strain Sodalis praecaptivus colonizes insects, Rosenbergiella isolate from leafhoppers. Then, used to engineer previously unstudied bacteria family Orbaceae several fly species. Engineered strains able colonize Drosophila melanogaster could visualized guts. are common abundant guts wild-caught flies but have not been included studies how microbiome affects health. Thus, work provides foundational studying new host-associated microbes, including key constituent gut model insect IMPORTANCE fully understand evolved interact their environments, one must modify genomes. However, difficult laborious discover approaches isolate. Bacteria recently described microbiomes insects. developed testing cultured bacteria. demonstrate its utility by express fluorescent proteins characterizing they gut. widespread wild examining nutrition, health, longevity. Our establishes path aimed at understanding altering interactions between other hosts.

Language: Английский

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Using Silver Nanoparticles to Increase Some Glycosidic Compounds of Stevia Rebaudiana in Vitro

Published: Dec. 15, 2023

This experiment was objected to increase some Glycosides active compounds production in Stevia rebaudiana seedlings through plant seeds treatment with different concentrations of silver nanoparticles that diagnosed and characterized using AFM technique. research implemented at tissue culture laboratory College biotechnology - Al Nahrain University, throughout the period 2022 2023. The designed factorial within CRD three expermentse ten replicates. Sodium hypochlorite concentration (S1, S2, S3, S4) (0.0, 1, 2, 3%) represented first experment, duration time (T1, T2, T3) (5, 10, 15min) (C1, C2, C3, C4) (0, 20, 30 mg.l-1) MS media, 3. Results showed contamination rate selected S. explant reduced registered 10 15min 3% sodium hypochlorite. results also there were a significant shoots numbers mg.l-1 AgNPs reach highest terms numbers, increasing shoot length the10 enrolment 14.5cm then decreased both , dry weight significantly raised up 20 while droped AgNPs., all analyzed HPLC device as Rubsoside Dulcoside ,Stevioside increased AgNPs, comparsion control

Language: Английский

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