scholarly journals Melatonin regulates the neurotransmitter secretion disorder induced by caffeine through the gut-brain axis in zebrafish (Danio rerio)

2020 ◽  
Author(s):  
Qiannan Peng ◽  
Zeng Zhang ◽  
Dongxue Huo ◽  
Shuaiming Jiang ◽  
Chenchen Ma ◽  
...  
Keyword(s):  
Microbial Interactions ◽  
Metagenomic Sequencing ◽  
Metabolic Pathway Analysis ◽  
Zebrafish Model ◽  
Germ Free ◽  
Neurotransmitter Secretion ◽  
Validation Experiment ◽  
Experiment Validation ◽  
Functional Features ◽  
Regulatory Effects

Abstract Background: Melatonin has been widely used as a "probiotic agent" capable of producing strong neurotransmitter secretion regulatory effects. The probiotics related researches also provide the evidence of microbial interactions with the gut-brain axis for mental health. In the present study, a zebrafish neural hyperactivity model was established using caffeine induction, and the regulation and mechanism of melatonin and probiotic on zebrafish neurotransmitter secretion disorder were explored. To further address the challenge that if the gut microbes play an essential role in the regulation of neurotransmitter secretion disorder via a process that involves melatonin, the Germ-free (GF) zebrafish model was used to verify the hypothesis. Results: Disorders of brain neurotransmitter secretion caused by caffeine, including that of dopamine (DA), γ-aminobutyric acid (γ-GABA), and 5-hydroxytryptamine (5-HT), were improved after interference treatment with melatonin or the probiotic. Metagenomic sequencing demonstrated that the melatonin-treated zebrafish gradually restored their normal intestinal microbial structure, while probiotic supplementation may restructure a new microbiome. Additionally, supplementation with melatonin significantly regulated intestinal microbial functional features, which indicated the gut microbiota plays the key role in the function of melatonin. Based on this activity, a Germ-free zebrafish model was applied to verified our hypothesis in the following validation experiment. Validation experiment results revealed that the effect on the zebrafish in the GF group could not achieve that on the zebrafish in the melatonin group after adding the same dose of melatonin, and subsequent real-time PCR and metabolic pathway analysis confirmed the conclusion. Meanwhile, the content of acetic acid and propionic acid in the gut of not-germ-free zebrafish decreased after caffeine induction and increased significantly after melatonin treatment. However, no acetic or propionic acids were found, detected, changed as there are germ-free zebrafish. Conclusions: In the present research, we identified the potential mechanism of melatonin regulation of neurotransmitter secretion disorder through the gut-brain axis, laying a foundation for exploring the prevention and treatment of some neuropsychiatric disorders by improving the intestinal microbiota.

scholarly journals Melatonin regulates the neurotransmitter secretion disorder induced by caffeine through the gut-brain axis in zebrafish (Danio rerio)

2019 ◽  
Author(s):  
Qiannan Peng ◽  
Zeng Zhang ◽  
Dongxue Huo ◽  
Shuaiming Jiang ◽  
Chenchen Ma ◽  
...  
Keyword(s):  
Metagenomic Sequencing ◽  
Microbial Structure ◽  
Metabolic Pathway Analysis ◽  
Melatonin Treatment ◽  
Probiotic Supplementation ◽  
Neurotransmitter Secretion ◽  
Validation Experiment ◽  
Brain Neurotransmitter ◽  
Functional Features ◽  
Regulatory Effects

Abstract Background : Melatonin has been widely used as a "probiotic agent" capable of producing strong neurotransmitter secretion regulatory effects. In the present study, a zebrafish neural hyperactivity model was established using caffeine induction, and the regulation and mechanism of melatonin and probiotic on zebrafish neurotransmitter secretion disorder were explored. Results : Disorders of brain neurotransmitter secretion caused by caffeine, including that of dopamine (DA), γ-aminobutyric acid (γ-GABA), and 5-hydroxytryptamine (5-HT), were improved after interference treatment with melatonin or the probiotic. Metagenomic sequencing demonstrated that the melatonin-treated zebrafish gradually restored their normal intestinal microbial structure, while probiotic supplementation may restructure a new microbiome. Additionally, supplementation with melatonin significantly regulated intestinal microbial functional features. Based on this activity, we supposed that gut microbes play an essential role in the regulation of neurotransmitter secretion disorder via a process that involves melatonin. Germ-free (GF) zebrafish were used to verify the hypotheses. Validation experiment results revealed that the effect on the zebrafish in the GF group could not achieve that on the zebrafish in the melatonin group after adding the same dose of melatonin, and subsequent real-time PCR and metabolic pathway analysis confirmed the conclusion. Meanwhile, the content of acetic acid and propionic acid in the zebrafish gut decreased after caffeine induction and increased significantly after melatonin treatment. Conclusions : In the present research, we identified the potential mechanism of melatonin regulation of neurotransmitter secretion disorder through the gut-brain axis, laying a foundation for exploring the prevention and treatment of some neuropsychiatric disorders by improving the intestinal microbiota.

scholarly journals Melatonin Regulates the Neurotransmitter Secretion Disorder Induced by Caffeine Through the Microbiota-Gut-Brain Axis in Zebrafish (Danio rerio)

2021 ◽  
Vol 9 ◽  
Author(s):  
Zeng Zhang ◽  
Qiannan Peng ◽  
Dongxue Huo ◽  
Shuaiming Jiang ◽  
Chenchen Ma ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Metabolic Pathways ◽  
Metagenomic Sequencing ◽  
Intestinal Microbes ◽  
Neurotransmitter Secretion ◽  
Shotgun Metagenomic Sequencing ◽  
Potential Mode ◽  
Brain Neurotransmitter ◽  
Regulatory Effects

Melatonin has been widely used as a “probiotic agent” capable of producing strong neurotransmitter secretion regulatory effects, and the microbiota-gut-brain axis-related studies have also highlighted the role of the gut microbiota in neuromodulation. In the present study, a zebrafish neural hyperactivity model was established using caffeine induction to explore the regulatory effects of melatonin and probiotic on neurotransmitter secretion disorder in zebrafish. Disorders of brain neurotransmitter secretion (dopamine, γ-aminobutyric acid, and 5-hydroxytryptamine) caused by caffeine were improved after interference treatment with melatonin or probiotic. Shotgun metagenomic sequencing demonstrated that the melatonin-treated zebrafish gradually restored their normal intestinal microbiota and metabolic pathways. Germ-free (GF) zebrafish were used to verify the essential role of intestinal microbes in the regulation of neurotransmitter secretion. The results of the neurotransmitter and short-chain fatty acid determination revealed that the effect on the zebrafish in the GF group could not achieve that on the zebrafish in the melatonin group after adding the same dose of melatonin. The present research revealed the potential mode of action of melatonin through the microbiota-gut-brain axis to regulate the disruption of neurotransmitter secretion, supporting the future development of psychotropic drugs targeting the intestinal microbiota.

scholarly journals Phyllosphere Microbiome in Response to Citrus Melanose

2020 ◽  
Author(s):  
Pudong Li ◽  
Jianping Xu ◽  
Zhengyi Wang ◽  
Hongye Li
Keyword(s):  
Microbial Community ◽  
Community Response ◽  
Microbial Interactions ◽  
Metagenomic Sequencing ◽  
Fungal Cell ◽  
Pathogen Invasion ◽  
Shotgun Metagenomic Sequencing ◽  
Dna Metabarcoding ◽  
Functional Features ◽  
Microbial Community Assembly

Abstract Background: Like microbiomes in the rhizosphere, phyllosphere microbiomes can have an important role in plant growth and health. However, whether and how the phyllosphere microbiomes respond to the invasion of pathogens is not well understood. In this study, we address this question using the citrus phyllosphere-associated microbiome as a model.Results: Through DNA metabarcoding (16S for bacteria and ITS for fungi) and shotgun metagenomic sequencing, we found that phyllosphere microbiomes in different ecological habitats (epiphytes and endophytes) responded differently to melanose disease caused by the fungal pathogen Diaporthe citri on citrus (Citrus unshiu) leaves. We observed that citrus phyllosphere-associated microbiome responded to the melanose disease in five ways: (1) increasing microbial richness; (2) reducing community evenness; (3) enriching selected microbes; (4) enhancing microbial interactions; and (5) enriching functional features involved in metabolism and fungal cell wall degrading.Conclusions: Our study revealed how phyllosphere microbiomes in the epiphytic and endophytic habitats differ between diseased and healthy leaves. Based on the differences at both the taxonomic and functional levels, we propose a general conceptual paradigm to describe the different microbial community assembly processes for the phyllosphere microbiome in response to leaf disease and how such processes impact plant health. Our results provide novel insights for understanding the contributions of the phyllosphere microbial community response during pathogen invasion.

Microbial community composition is linked to Sphagnum acclimation to warming

2021 ◽  
Author(s):  
Tatjana Živković ◽  
Alyssa A Carell ◽  
Gustaf Granath ◽  
Mats B Nilsson ◽  
Manuel Helbig ◽  
...  
Keyword(s):  
Growth Rate ◽  
Host Plant ◽  
Climate Warming ◽  
Elevated Temperatures ◽  
Critical Role ◽  
Temperature Acclimation ◽  
Microbial Interactions ◽  
Germ Free ◽  
Wide Range ◽  
Thermal Origin

<p>Peatlands store about third of the terrestrial carbon (C) and exert long-term climate cooling. Dominant plant genera in acidic peatlands, <em>Sphagnum</em> mosses, are main contributors to net primary productivity. Through associative relationships with diverse microbial organisms (microbiome), <em>Sphagnum</em> mosses control major biogeochemical processes, namely uptake, storage and potential release of carbon and nitrogen. Climate warming is expected to negatively impact C accumulation in peatlands and alter nutrient cycling, however <em>Sphagnum</em>-dominated peatland resilience to climate warming may depend on <em>Sphagnum</em>-microbiome associations. The ability of the microbiome to rapidly acclimatize to warming may aid <em>Sphagnum</em> exposed to elevated temperatures through host-microbiome acquired thermotolerance. We investigated the role of the microbiome on <em>Sphagnum</em>’s ability to acclimate to elevated temperatures using a microbiome-transfer approach to test: a) whether the thermal origin of the microbiome influences acclimation of <em>Sphagnum</em> growth and b) if microbial benefits to <em>Sphagnum</em> growth depend on donor <em>Sphagnum</em> species.</p><p>            Using a full-factorial design, microbiomes were separated from <em>Sphagnum</em> “donor” species from four different peatlands across a wide range of thermal environments (11.4-27°C). The microbiomes were transferred onto germ-free “recipient” <em>Sphagnum</em> species in the laboratory and exposed to a range of experimental temperatures (8.5 – 26.5°C) for growth analysis over 4 weeks.</p><p>            Normalized growth rates were maximized for plants that received a microbiome from a matched “donor” and with a similar origin temperature (ΔT<sub>treatment-origin</sub>: 0.3±0.9°C [±standard error], p = 0.73). For non-matched “donor-recipient” <em>Sphagnum</em> pairs, ΔT<sub>treatment-origin</sub> was slightly negative with -4.1±2.1°C (p = 0.06). The largest growth rate of the “recipient” was measured when grown with a microbiome from a matching “donor” <em>Sphagnum</em> species and was 252% and 48% larger than the maximum growth rate of the germ-free <em>Sphagnum</em> and the non-matched “donor-recipient” <em>Sphagnum</em> pairs, respectively.</p><p>            Our results suggest that the composition of the <em>Sphagnum</em> microbiome plays a critical role in host plant temperature acclimation. We found that microbially-provided benefits to the host plant were most pronounced when: 1) the thermal origin of the microbiome is similar to experimental temperatures, and 2) when donor and recipient <em>Sphagnum</em> species are the same. Together, these results suggest that <em>Sphagnum</em> temperature acclimation can be modulated, in part, by microbial interactions and may potentially play a role in peatland resilience to climate warming.</p>

scholarly journals BEEM-Static: Accurate inference of ecological interactions from cross-sectional metagenomic data

2020 ◽  
Author(s):  
Chenhao Li ◽  
Tamar V. Av-Shalom ◽  
Jun Wei Gerald Tan ◽  
Junmei Samantha Kwah ◽  
Kern Rei Chng ◽  
...  
Keyword(s):  
Ecological Model ◽  
Expectation Maximization Algorithm ◽  
Microbial Interactions ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Ecological Interactions ◽  
Cross Sectional ◽  
Key Species ◽  
Alternate Model ◽  
And Function

AbstractMotivationThe structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of metagenomic sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional metagenomic datasets for unravelling ecological structure in a scalable manner thus remains an open problem.MethodsWe present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples.ResultsBenchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n=4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species.ConclusionBEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of metagenomic data.

scholarly journals Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data

2018 ◽  
Author(s):  
Janko Tackmann ◽  
João Frederico Matias Rodrigues ◽  
Christian von Mering
Keyword(s):  
Graphical Models ◽  
Large Scale ◽  
Study Data ◽  
Microbial Interactions ◽  
Data Sets ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Data Set ◽  
Seamless Integration

AbstractThe recent explosion of metagenomic sequencing data opens the door towards the modeling of microbial ecosystems in unprecedented detail. In particular, co-occurrence based prediction of ecological interactions could strongly benefit from this development. However, current methods fall short on several fronts: univariate tools do not distinguish between direct and indirect interactions, resulting in excessive false positives, while approaches with better resolution are so far computationally highly limited. Furthermore, confounding variables typical for cross-study data sets are rarely addressed. We present FlashWeave, a new approach based on a flexible Probabilistic Graphical Models framework to infer highly resolved direct microbial interactions from massive heterogeneous microbial abundance data sets with seamless integration of metadata. On a variety of benchmarks, FlashWeave outperforms state-of-the-art methods by several orders of magnitude in terms of speed while generally providing increased accuracy. We apply FlashWeave to a cross-study data set of 69 818 publicly available human gut samples, resulting in one of the largest and most diverse models of microbial interactions in the human gut to date.

scholarly journals Microbial adaptation in vertical soil profiles contaminated by antimony smelting plant

2020 ◽  
Author(s):  
Rui Xu ◽  
Xiaoxu Sun ◽  
Feng Han ◽  
Enzong Xiao ◽  
Baoqin Li ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Soil Depth ◽  
Microbial Interactions ◽  
Individual Species ◽  
Soil Profiles ◽  
Metagenomic Sequencing ◽  
Deep Soil ◽  
Metabolic Potential ◽  
Microbial Adaptation ◽  
Shotgun Metagenomic Sequencing

Abstract BackgroundSoil microbes play critical roles in the biogeochemical cycling of antimony (Sb) and arsenic (As), and the effects of Sb and As contamination on soil microbiota have been well documented in surface soils (< 0.2 m). However, their effects in deep soils remain poorly understood. This study determined the depth-resolved effects of Sb and As contamination on the microbial adaptation throughout soil profiles (0–2 m) and compared contaminated soil samples to uncontaminated samples.Methods16S rRNA amplicon sequencing and shotgun metagenomic sequencing were employed to investigate the microbial community and their metabolism traits in soil profiles. Co-occurrence network analysis was used to present the pairwise interactions of microbes.ResultsAs soil depth increased, Acidobacteria (18.8%–44.7% from top to bottom, hereafter), Chloroflexi (8.7%–42.4%), Proteobacteria (11.4%–27.1%), and Thaumarchaeota (0.49%–20.17%) were the most variable phyla from surface to deep soil. A set of co-occurrence networks revealed an obvious changing pattern of microbial interactions as soil depth increased. The networks were loosely connected in the heavily contaminated surface soil but gradually recovered and were well connected in the less contaminated deep soil. Results suggested that individual species became more connected with other patterns to perform syntrophic functions in the less contaminated soil depth. Shotgun metagenomic sequencing results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with Sb and As concentrations. A set of arsenic-related genes was enriched by the high Sb and As contamination but reduced with soil depth. ConclusionsSoil depth-resolved characteristics are often many meters deep and their microbial diversity and community structures obviously change along their vertical soil profiles due to different nutrient contents and biomasses. The significance of this study is that it further reveals how the microbial communities and microbial physiological traits respond to different soil profiles contaminated by high concentrations of Sb and As.

scholarly journals Genome-Centered Metagenomics Analysis Reveals the Microbial Interactions of a Syntrophic Consortium during Methane Generation in a Decentralized Wastewater Treatment System

2019 ◽  
Vol 10 (1) ◽  
pp. 135 ◽  
Author(s):  
Kun Zhang ◽  
Yan-Ling Zhang ◽  
Xin Ouyang ◽  
Jun-Peng Li ◽  
Jun-Jie Liao ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Microbial Community ◽  
Anaerobic Digestion ◽  
Microbial Community Structure ◽  
High Efficiency ◽  
Microbial Interactions ◽  
Clear Understanding ◽  
Metagenomic Sequencing ◽  
Decentralized Wastewater Treatment

The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS.

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